@article{https://authors.library.caltech.edu/records/4bdzc-r3y87,
    authors = "Gorin, Gennady and Pachter, Lior",
    title = {New and notable: Revisiting the "two cultures" through extrinsic noise},
    journal = "Biophysical Journal",
    publisher = "Cell Press",
    year = "2024",
    url = "https://authors.library.caltech.edu/records/4bdzc-r3y87",
    id = "https://authors.library.caltech.edu/records/4bdzc-r3y87",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2023.11.3400",
    volume = "123",
    number = "1",
    pages = "1-3"
}


@article{https://authors.library.caltech.edu/records/axtf4-cb576,
    authors = "Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph) and Gehring, Jase and Pachter, Lior",
    title = "Quantifying orthogonal barcodes for sequence census assays",
    journal = "Bioinformatics Advances",
    publisher = "Oxford University Press",
    year = "2024",
    url = "https://authors.library.caltech.edu/records/axtf4-cb576",
    id = "https://authors.library.caltech.edu/records/axtf4-cb576",
    issn = "2635-0041",
    doi = "10.1093/bioadv/vbad181",
    volume = "4",
    pmcid = "PMC10783946",
    pages = "vbad181"
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@article{https://authors.library.caltech.edu/records/ntw84-7bx60,
    authors = "Xiong, Lingyun and Liu, Jing and Han, Seung Yub and Koppitch, Kari and Guo, Jin-Jin and Rommelfanger, Megan and Miao, Zhen and Gao, Fan and Hallgrimsdottir, Ingileif B. and Pachter, Lior and Kim, Junhyong and MacLean, Adam L. and McMahon, Andrew P.",
    title = "Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney",
    journal = "Developmental Cell",
    publisher = "Cell Press",
    year = "2023",
    url = "https://authors.library.caltech.edu/records/ntw84-7bx60",
    id = "https://authors.library.caltech.edu/records/ntw84-7bx60",
    issn = "1878-1551",
    doi = "10.1016/j.devcel.2023.08.010",
    volume = "58",
    number = "21",
    pages = "2338-2358.e5"
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@article{https://authors.library.caltech.edu/records/5z5v2-jjy66,
    authors = "Gorin, Gennady and Yoshida, Shawn and Pachter, Lior",
    title = "Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing",
    journal = "Bulletin of Mathematical Biology",
    publisher = "Springer Nature",
    year = "2023",
    url = "https://authors.library.caltech.edu/records/5z5v2-jjy66",
    id = "https://authors.library.caltech.edu/records/5z5v2-jjy66",
    issn = "0092-8240",
    doi = "10.1007/s11538-023-01213-9",
    volume = "85",
    number = "11",
    pages = "114"
}


@article{https://authors.library.caltech.edu/records/x9gbd-0gk44,
    authors = "Gorin, Gennady and Vastola, John J. and Pachter, Lior",
    title = "Studying stochastic systems biology of the cell with single-cell genomics data",
    journal = "Cell Systems",
    publisher = "Cell Press",
    year = "2023",
    url = "https://authors.library.caltech.edu/records/x9gbd-0gk44",
    id = "https://authors.library.caltech.edu/records/x9gbd-0gk44",
    issn = "2405-4712",
    doi = "10.1016/j.cels.2023.08.004",
    volume = "14",
    number = "10",
    pmcid = "PMC10725240",
    pages = "822-843.e22"
}


@article{https://authors.library.caltech.edu/records/hs9mc-jb762,
    authors = "Booeshaghi, A. Sina and Beltrame, Eduardo da Veiga and Bannon, Dylan and Gehring, Jase and Pachter, Lior",
    title = "Author Correction: Principles of open source bioinstrumentation applied to the poseidon syringe pump system",
    journal = "Scientific Reports",
    publisher = "Nature Publishing Group",
    year = "2023",
    url = "https://authors.library.caltech.edu/records/hs9mc-jb762",
    id = "https://authors.library.caltech.edu/records/hs9mc-jb762",
    issn = "2045-2322",
    doi = "10.1038/s41598-023-42035-y",
    volume = "13",
    pmcid = "PMC10491597",
    pages = "14834"
}


@article{https://authors.library.caltech.edu/records/ewrjt-pbk58,
    authors = "Jackson, Kayla C. and Pachter, Lior",
    title = "A standard for sharing spatial transcriptomics data",
    journal = "Cell Genomics",
    publisher = "Cell Press",
    year = "2023",
    url = "https://authors.library.caltech.edu/records/ewrjt-pbk58",
    id = "https://authors.library.caltech.edu/records/ewrjt-pbk58",
    issn = "2666-979X",
    doi = "10.1016/j.xgen.2023.100374",
    volume = "3",
    number = "8",
    pmcid = "PMC10435375",
    pages = "100374"
}


@article{https://authors.library.caltech.edu/records/fzh9v-hjh15,
    authors = "Chari, Tara and Pachter, Lior",
    title = "The specious art of single-cell genomics",
    journal = "PLOS Computational Biology",
    publisher = "Public Library of Science",
    year = "2023",
    url = "https://authors.library.caltech.edu/records/fzh9v-hjh15",
    id = "https://authors.library.caltech.edu/records/fzh9v-hjh15",
    issn = "1553-7358",
    doi = "10.1371/journal.pcbi.1011288",
    volume = "19",
    number = "8",
    pmcid = "PMC10434946",
    pages = "e1011288"
}


@article{https://authors.library.caltech.edu/records/nvj6h-bzw14,
    authors = "Fenelon, Kelli D. and Gao, Fan and Borad, Priyanshi and Abbasi, Shiva and Pachter, Lior and Koromila, Theodora",
    title = "Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliless/OTX regulate early head development in embryos",
    journal = "Frontiers in Cell and Developmental Biology",
    publisher = "Frontiers Media",
    year = "2023",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230502-708586900.1",
    id = "https://authors.library.caltech.edu/records/nvj6h-bzw14",
    issn = "2296-634X",
    doi = "10.3389/fcell.2023.1126507",
    volume = "11",
    pmcid = "PMC10083704",
    pages = "Art. No. 1126507"
}


@article{https://authors.library.caltech.edu/records/nz49t-npq98,
    authors = "Luebbert, Laura and Pachter, Lior",
    title = "Efficient querying of genomic reference databases with gget",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2023",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230725-706344000.34",
    id = "https://authors.library.caltech.edu/records/nz49t-npq98",
    issn = "1367-4811",
    doi = "10.1093/bioinformatics/btac836",
    volume = "39",
    number = "1",
    pmcid = "PMC9835474",
    pages = "Art. No. btac836"
}


@article{https://authors.library.caltech.edu/records/ryza3-50d52,
    authors = "Gálvez-Merchán, Ángel and Min, Kyung Hoi (Joseph) and Pachter, Lior and Booeshaghi, A. Sina",
    title = "Metadata retrieval from sequence databases with ffq",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2023",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230411-694477200.2",
    id = "https://authors.library.caltech.edu/records/ryza3-50d52",
    issn = "1367-4811",
    doi = "10.1093/bioinformatics/btac667",
    volume = "39",
    number = "1",
    pmcid = "PMC9883619",
    pages = "Art. No. btac667"
}


@article{https://authors.library.caltech.edu/records/d6ppt-egs07,
    authors = "Gorin, Gennady and Vastola, John J. and Fang, Meichen and Pachter, Lior",
    title = "Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments",
    journal = "Nature Communications",
    publisher = "Nature Publishing Group",
    year = "2022",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20230622-883274000.1",
    id = "https://authors.library.caltech.edu/records/d6ppt-egs07",
    issn = "2041-1723",
    doi = "10.1038/s41467-022-34857-7",
    volume = "13",
    pmcid = "PMC9734650",
    pages = "Art. No. 7620"
}


@article{https://authors.library.caltech.edu/records/sgfnt-bab08,
    authors = "Gorin, Gennady and Fang, Meichen and Chari, Tara and Pachter, Lior",
    title = "RNA velocity unraveled",
    journal = "PLOS Computational Biology",
    publisher = "Public Library of Science",
    year = "2022",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20220916-665804000.785",
    id = "https://authors.library.caltech.edu/records/sgfnt-bab08",
    issn = "1553-7358",
    doi = "10.1371/journal.pcbi.1010492",
    volume = "18",
    number = "9",
    pmcid = "PMC9499228",
    pages = "Art. No. e1010492"
}


@article{https://authors.library.caltech.edu/records/m4wef-4m072,
    authors = "Moses, Lambda and Pachter, Lior",
    title = "Museum of spatial transcriptomics",
    journal = "Nature Methods",
    publisher = "Nature Publishing Group",
    year = "2022",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210513-122736659",
    id = "https://authors.library.caltech.edu/records/m4wef-4m072",
    issn = "1548-7091",
    doi = "10.1038/s41592-022-01409-2",
    volume = "19",
    number = "5",
    pages = "534-546"
}


@article{https://authors.library.caltech.edu/records/myke3-zsv09,
    authors = "Gorin, Gennady and Pachter, Lior",
    title = "Modeling bursty transcription and splicing with the chemical master equation",
    journal = "Biophysical Journal",
    publisher = "Cell Press",
    year = "2022",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210325-075042340",
    id = "https://authors.library.caltech.edu/records/myke3-zsv09",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2022.02.004",
    volume = "121",
    number = "6",
    pages = "1056-1069"
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@article{https://authors.library.caltech.edu/records/jy3nx-j5b58,
    authors = "Gayoso, Adam and Lopez, Romain and Xing, Galen and Boyeau, Pierre and Amiri, Valeh Valiollah Pour and Hong, Justin and Wu, Katherine and Jayasuriya, Michael and Mehlman, Edouard and Langevin, Maxime and Liu, Yining and Samaran, Jules and Misrachi, Gabriel and Nazaret, Achille and Clivio, Oscar and Xu, Chenling and Ashuach, Tal and Gabitto, Mariano and Lotfollahi, Mohammad and Svensson, Valentine and da Veiga Beltrame, Eduardo and Kleshchevnikov, Vitalii and Talavera-López, Carlos and Pachter, Lior and Theis, Fabian J. and Streets, Aaron and Jordan, Michael I. and Regier, Jeffrey and Yosef, Nir",
    title = "A Python library for probabilistic analysis of single-cell omics data",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2022",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210503-142332959",
    id = "https://authors.library.caltech.edu/records/jy3nx-j5b58",
    issn = "1087-0156",
    doi = "10.1038/s41587-021-01206-w",
    volume = "40",
    number = "2",
    pages = "163-166"
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@article{https://authors.library.caltech.edu/records/5afgq-qgg51,
    authors = "Chari, Tara and Weissbourd, Brandon and Gehring, Jase and Ferraioli, Anna and Leclère, Lucas and Herl, Makenna and Gao, Fan and Chevalier, Sandra and Copley, Richard R. and Houliston, Evelyn and Anderson, David J. and Pachter, Lior",
    title = "Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types",
    journal = "Science Advances",
    publisher = "American Association for the Advancement of Science",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210126-133110736",
    id = "https://authors.library.caltech.edu/records/5afgq-qgg51",
    issn = "2375-2548",
    doi = "10.1126/sciadv.abh1683",
    volume = "7",
    number = "48",
    pmcid = "PMC8626072",
    pages = "Art. No. eabh1683"
}


@article{https://authors.library.caltech.edu/records/mn91e-p6r12,
    authors = "Rahman, Atif and Pachter, Lior",
    title = "SWALO: scaffolding with assembly likelihood optimization",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210930-221100053",
    id = "https://authors.library.caltech.edu/records/mn91e-p6r12",
    issn = "0305-1048",
    doi = "10.1093/nar/gkab717",
    volume = "49",
    number = "20",
    pages = "Art. No. e117"
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@article{https://authors.library.caltech.edu/records/6zspp-xxk39,
    authors = "Adkins, Ricky S. and Aldridge, Andrew I. and Allen, Shona and Ament, Seth A. and An, Xu and Armand, Ethan and Ascoli, Giorgio A. and Bakken, Trygve E. and Bandrowski, Anita and Banerjee, Samik and Barkas, Nikolaos and Bartlett, Anna and Bateup, Helen S. and Behrens, M. Margarita and Berens, Philipp and Berg, Jim and Bernabucci, Matteo and Bernaerts, Yves and Bertagnolli, Darren and Biancalani, Tommaso and Boggeman, Lara and Booeshaghi, A. Sina and Bowman, Ian and Bravo, Héctor Corrada and Cadwell, Cathryn René and Callaway, Edward M. and Carlin, Benjamin and O'Connor, Carolyn and Carter, Robert and Casper, Tamara and Castanon, Rosa G. and Castro, Jesus Ramon and Chance, Rebecca K. and Chatterjee, Apaala and Chen, Huaming and Chun, Jerold and Colantuoni, Carlo and Crabtree, Jonathan and Creasy, Heather and Crichton, Kirsten and Crow, Megan and D'Orazi, Florence D. and Daigle, Tanya L. and Dalley, Rachel and Dee, Nick and Degatano, Kylee and Dichter, Benjamin and Diep, Dinh and Ding, Liya and Ding, Song-Lin and Dominguez, Bertha and Dong, Hong-Wei and Dong, Weixiu and Dougherty, Elizabeth L. and Dudoit, Sandrine and Ecker, Joseph R. and Eichhorn, Stephen W. and Fang, Rongxin and Felix, Victor and Feng, Guoping and Feng, Zhao and Fischer, Stephan and Fitzpatrick, Conor and Fong, Olivia and Foster, Nicholas N. and Galbavy, William and Gee, James C. and Ghosh, Satrajit S. and Giglio, Michelle and Gillespie, Thomas H. and Gillis, Jesse and Goldman, Melissa and Goldy, Jeff and Gong, Hui and Gou, Lin and Grauer, Michael and Halchenko, Yaroslav O. and Harris, Julie A. and Hartmanis, Leonard and Hatfield, Joshua T. and Hawrylycz, Mike and Helba, Brian and Herb, Brian R. and Hertzano, Ronna and Hintiryan, Houri and Hirokawa, Karla E. and Hockemeyer, Dirk and Hodge, Rebecca D. and Hood, Greg and Horwitz, Gregory D. and Hou, Xiaomeng and Hu, Lijuan and Hu, Qiwen and Huang, Z. Josh and Huo, Bingxing and Ito-Cole, Tony and Jacobs, Matthew and Jia, Xueyan and Jiang, Shengdian and Jiang, Tao and Jiang, Xiaolong and Jin, Xin and Jorstad, Nikolas L. and Kalmbach, Brian E. and Kancherla, Jayaram and Keene, C. Dirk and Kelly, Kathleen and Khajouei, Farzaneh and Kharchenko, Peter V. and Kim, Gukhan and Ko, Andrew L. and Kobak, Dmitry and Konwar, Kishori and Kramer, Daniel J. and Krienen, Fenna M. and Kroll, Matthew and Kuang, Xiuli and Kuo, Hsien-Chi and Lake, Blue B. and Larsen, Rachael and Lathia, Kanan and Laturnus, Sophie and Lee, Angus Y. and Lee, Cheng-Ta and Lee, Kuo-Fen and Lein, Ed S. and Lesnar, Phil and Li, Anan and Li, Xiangning and Li, Xu and Li, Yang Eric and Li, Yaoyao and Li, Yuanyuan and Lim, Byungkook and Linnarsson, Sten and Liu, Christine S. and Liu, Hanqing and Liu, Lijuan and Lucero, Jacinta D. and Luo, Chongyuan and Luo, Qingming and Macosko, Evan Z. and Mahurkar, Anup and Martone, Maryann E. and Matho, Katherine S. and McCarroll, Steven A. and McCracken, Carrie and McMillen, Delissa and Miranda, Elanine and Mitra, Partha P and Miyazaki, Paula Assakura and Mizrachi, Judith and Mok, Stephanie and Mukamel, Eran A. and Mulherkar, Shalaka and Nadaf, Naeem M. and Naeemi, Maitham and Narasimhan, Arun and Nery, Joseph R. and Ng, Lydia and Ngai, John and Nguyen, Thuc Nghi and Nickel, Lance and Nicovich, Philip R. and Niu, Sheng-Yong and Ntranos, Vasilis and Nunn, Michael and Olley, Dustin and Orvis, Joshua and Osteen, Julia K. and Osten, Pavel and Owen, Scott F. and Pachter, Lior and Palaniswamy, Ramesh and Palmer, Carter R. and Pang, Yan and Peng, Hanchuan and Pham, Thanh and Pinto-Duarte, Antonio and Plongthongkum, Nongluk and Poirion, Olivier and Preissl, Sebastian and Purdom, Elizabeth and Qu, Lei and Rashid, Mohammad and Reed, Nora M. and Regev, Aviv and Ren, Bing and Ren, Miao and Rimorin, Christine and Risso, Davide and Rivkin, Angeline C. and Muñoz-Castañeda, Rodrigo and Romanow, William J. and Ropelewski, Alexander J. and Roux de Bézieux, Hector and Ruan, Zongcai and Sandberg, Rickard and Savoia, Steven and Scala, Federico and Schor, Michael and Shen, Elise and Siletti, Kimberly and Smith, Jared B. and Smith, Kimberly and Somasundaram, Saroja and Song, Yuanyuan and Sorensen, Staci A. and Stafford, David A. and Street, Kelly and Sulc, Josef and Sunkin, Susan and Svensson, Valentine and Tan, Pengcheng and Tan, Zheng Huan and Tasic, Bosiljka and Thompson, Carol and Tian, Wei and Tickle, Timothy L. and Tieu, Michael and Ting, Jonathan T. and Tolias, Andreas Savas and Torkelson, Amy and Tung, Herman and Vaishnav, Eeshit Dhaval and Van den Berge, Koen and van Velthoven, Cindy T.J. and Vanderburg, Charles R. and Veldman, Matthew B. and Vu, Minh and Wakeman, Wayne and Wang, Peng and Wang, Quanxin and Wang, Xinxin and Wang, Yimin and Wang, Yun and Welch, Joshua D. and White, Owen and Williams, Elora and Xie, Fangming and Xie, Peng and Xiong, Feng and Yang, X. William and Yanny, Anna Marie and Yao, Zizhen and Yin, Lulu and Yu, Yang and Yuan, Jing and Zeng, Hongkui and Zhang, Kun and Zhang, Meng and Zhang, Zhuzhu and Zhao, Sujun and Zhao, Xuan and Zhou, Jingtian and Zhuang, Xiaowei and Zingg, Brian",
    title = "A multimodal cell census and atlas of the mammalian primary motor cortex",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20201027-075126222",
    id = "https://authors.library.caltech.edu/records/6zspp-xxk39",
    issn = "0028-0836",
    doi = "10.1038/s41586-021-03950-0",
    volume = "598",
    number = "7879",
    pages = "86-102"
}


@article{https://authors.library.caltech.edu/records/13dbk-bh430,
    authors = "Yao, Zizhen and Liu, Hanqing and Xie, Fangming and Fischer, Stephan and Adkins, Ricky S. and Aldrige, Andrew I. and Ament, Seth A. and Bartlett, Anna and Behrens, M. Margarita and Van den Berge, Koen and Bertagnolli, Darren and de Bezieux, Hector Roux and Biancalani, Tommaso and Booeshaghi, A. Sina and Corrada Bravo, Hector and Casper, Tamara and Colantuoni, Carlo and Crabtree, Jonathan and Creasy, Heather and Crichton, Kirsten and Crow, Megan and Dee, Nick and Dougherty, Elizabeth L. and Doyle, Wayne I. and Dudoit, Sandrine and Fang, Rongxin and Felix, Victor and Fong, Olivia and Giglio, Michelle and Goldy, Jeff and Hawrylycz, Michael and Herb, Brian R. and Hertzano, Ronna and Hou, Xiaomeng and Hu, Qiwen and Kancherla, Jayaram and Kroll, Matthew and Lathia, Kanan and Li, Yang Eric and Lucero, Jacinta D. and Luo, Chongyuan and Mahurkar, Anup and McMillen, Delissa and Nadaf, Naeem M. and Nery, Joseph R. and Nguyen, Thuc Nghi and Niu, Sheng-Yong and Ntranos, Vasilis and Orvis, Joshua and Osteen, Julia K. and Pham, Thanh and Pinto-Duarte, Antonio and Poirion, Olivier and Preissl, Sebastian and Purdom, Elizabeth and Rimorin, Christine and Risso, Davide and Rivkin, Angeline C. and Smith, Kimberly and Street, Kelly and Sulc, Josef and Svensson, Valentine and Tieu, Michael and Torkelson, Amy and Tung, Herman and Vaishnav, Eeshit Dhaval and Vanderburg, Charles R. and van Velthoven, Cindy and Wang, Xinxin and White, Owen R. and Huang, Z. Josh and Kharchenko, Peter V. and Pachter, Lior and Ngai, John and Regev, Aviv and Tasic, Bosiljka and Welch, Joshua D. and Gillis, Jesse and Macosko, Evan Z. and Ren, Bing and Ecker, Joseph R. and Zeng, Hongkui and Mukamel, Eran A.",
    title = "A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200303-153620082",
    id = "https://authors.library.caltech.edu/records/13dbk-bh430",
    issn = "0028-0836",
    doi = "10.1038/s41586-021-03500-8",
    volume = "598",
    number = "7879",
    pmcid = "PMC8494649",
    pages = "103-110"
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@article{https://authors.library.caltech.edu/records/mb2qc-b8r09,
    authors = "Booeshaghi, A. Sina and Yao, Zizhen and van Velthoven, Cindy and Smith, Kimberly and Tasic, Bosiljka and Zeng, Hongkui and Pachter, Lior",
    title = "Isoform cell-type specificity in the mouse primary motor cortex",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200306-130944112",
    id = "https://authors.library.caltech.edu/records/mb2qc-b8r09",
    issn = "0028-0836",
    doi = "10.1038/s41586-021-03969-3",
    volume = "598",
    number = "7879",
    pmcid = "PMC8494650",
    pages = "195-199"
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@article{https://authors.library.caltech.edu/records/06pjn-hnt60,
    authors = "Booeshaghi, A. Sina and Kil, Yeokyoung and Min, Kyung Hoi and Gehring, Jase and Pachter, Lior",
    title = "Low-cost, scalable, and automated fluid sampling for fluidics applications",
    journal = "HardwareX",
    publisher = "Elsevier",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210129-070700034",
    id = "https://authors.library.caltech.edu/records/06pjn-hnt60",
    issn = "2468-0672",
    doi = "10.1016/j.ohx.2021.e00201",
    volume = "10",
    pages = "Art. No. e00201"
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@article{https://authors.library.caltech.edu/records/jp119-47j39,
    authors = "Booeshaghi, A. Sina and Pachter, Lior",
    title = "Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200520-084505912",
    id = "https://authors.library.caltech.edu/records/jp119-47j39",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btab085",
    volume = "37",
    number = "15",
    pmcid = "PMC7989636",
    pages = "2223-2224"
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@article{https://authors.library.caltech.edu/records/05kjw-6t056,
    authors = "Bloom, Joshua S. and Sathe, Laila and Munugala, Chetan and Jones, Eric M. and Gasperini, Molly and Lubock, Nathan B. and Yarza, Fauna and Thompson, Erin M. and Kovary, Kyle M. and Park, Jimin and Marquette, Dawn and Kay, Stephania and Lucas, Mark and Love, TreQuan and Booeshaghi, A. Sina and Brandenberg, Oliver F. and Guo, Longhua and Boocock, James and Hochman, Myles and Simpkins, Scott W. and Lin, Isabella and LaPierre, Nathan and Hong, Duke and Zhang, Yi and Oland, Gabriel and Choe, Bianca Judy and Chandrasekaran, Sukantha and Hilt, Evann E. and Butte, Manish J. and Damoiseaux, Robert and Kravit, Clifford and Cooper, Aaron R. and Yin, Yi and Pachter, Lior and Garner, Omai B. and Flint, Jonathan and Eskin, Eleazar and Luo, Chongyuan and Kosuri, Sriram and Kruglyak, Leonid and Arboleda, Valerie A.",
    title = "Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples",
    journal = "Nature Biomedical Engineering",
    publisher = "Nature Publishing Group",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20201119-132151980",
    id = "https://authors.library.caltech.edu/records/05kjw-6t056",
    issn = "2157-846X",
    doi = "10.1038/s41551-021-00754-5",
    volume = "5",
    number = "7",
    pmcid = "PMC7480060",
    pages = "657-665"
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@article{https://authors.library.caltech.edu/records/ykq5c-d8h82,
    authors = "Bloom, Joshua S. and Sathe, Laila and Munugala, Chetan and Jones, Eric M. and Gasperini, Molly and Lubock, Nathan B. and Yarza, Fauna and Thompson, Erin M. and Kovary, Kyle M. and Park, Jimin and Marquette, Dawn and Kay, Stephania and Lucas, Mark and Love, TreQuan and Booeshaghi, A. Sina and Brandenberg, Oliver F. and Guo, Longhua and Boocock, James and Hochman, Myles and Simpkins, Scott W. and Lin, Isabella and LaPierre, Nathan and Hong, Duke and Zhang, Yi and Oland, Gabriel and Choe, Bianca Judy and Chandrasekaran, Sukantha and Hilt, Evann E. and Butte, Manish J. and Damoiseaux, Robert and Kravit, Clifford and Cooper, Aaron R. and Yin, Yi and Pachter, Lior and Garner, Omai B. and Flint, Jonathan and Eskin, Eleazar and Luo, Chongyuan and Kosuri, Sriram and Kruglyak, Leonid and Arboleda, Valerie A.",
    title = "Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples",
    journal = "Nature Biomedical Engineering",
    publisher = "Nature Publishing Group",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20201119-132151980",
    id = "https://authors.library.caltech.edu/records/ykq5c-d8h82",
    issn = "2157-846X",
    doi = "10.1038/s41551-021-00754-5",
    volume = "5",
    number = "7",
    pmcid = "PMC7480060",
    pages = "657-665"
}


@article{https://authors.library.caltech.edu/records/363j8-nw138,
    authors = "Melsted, Páll and Booeshaghi, A. Sina and Liu, Lauren and Gao, Fan and Lu, Lambda and Min, Kyung Hoi and da Veiga Beltrame, Eduardo and Hjorleifsson, Kristján Eldjárn and Gehring, Jase and Pachter, Lior",
    title = "Modular, efficient and constant-memory single-cell RNA-seq preprocessing",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210405-142728694",
    id = "https://authors.library.caltech.edu/records/363j8-nw138",
    issn = "1087-0156",
    doi = "10.1038/s41587-021-00870-2",
    volume = "39",
    number = "7",
    pages = "813-818"
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@article{https://authors.library.caltech.edu/records/anq5b-hzp82,
    authors = "Gustafsson, Johan and Robinson, Jonathan and Nielsen, Jens and Pachter, Lior",
    title = "BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200707-114817234",
    id = "https://authors.library.caltech.edu/records/anq5b-hzp82",
    issn = "1474-760X",
    doi = "10.1186/s13059-021-02386-z",
    volume = "22",
    pmcid = "PMC8188791",
    pages = "Art. No. 174"
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@article{https://authors.library.caltech.edu/records/t6026-vtf40,
    authors = "Gorin, Gennady and Pachter, Lior",
    title = "Analysis of Length Biases in Single-Cell RNA Sequencing of Unspliced mRNA by Markov Modeling",
    journal = "Biophysical Journal",
    publisher = "Biophysical Society",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210503-100056268",
    id = "https://authors.library.caltech.edu/records/t6026-vtf40",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2020.11.706",
    volume = "120",
    number = "3",
    pages = "81A"
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@article{https://authors.library.caltech.edu/records/8h643-s8r26,
    authors = "Vastola, John J. and Gorin, Gennady and Pachter, Lior and Holmes, William R.",
    title = "Learning the Dynamics of Bursty Transcription and Splicing using Ultra-Fast Parameter Inference and New Analytical Solutions of the Chemical Master Equation",
    journal = "Biophysical Journal",
    publisher = "Biophysical Society",
    year = "2021",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210503-102227319",
    id = "https://authors.library.caltech.edu/records/8h643-s8r26",
    issn = "0006-3495",
    doi = "10.1016/j.bpj.2020.11.1018",
    volume = "120",
    number = "3",
    pages = "135A"
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@article{https://authors.library.caltech.edu/records/r5anw-4eh31,
    authors = "Booeshaghi, A. Sina and Lubock, Nathan B. and Cooper, Aaron R. and Simpkins, Scott W. and Bloom, Joshua S. and Gehring, Jase and Luebbert, Laura and Kosuri, Sriram and Pachter, Lior",
    title = "Reliable and accurate diagnostics from highly multiplexed sequencing assays",
    journal = "Scientific Reports",
    publisher = "Nature Publishing Group",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200601-101849395",
    id = "https://authors.library.caltech.edu/records/r5anw-4eh31",
    issn = "2045-2322",
    doi = "10.1038/s41598-020-78942-7",
    volume = "10",
    pmcid = "PMC7730459",
    pages = "Art. No. 21759"
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@article{https://authors.library.caltech.edu/records/fvv0w-xy358,
    authors = "Svensson, Valentine and da Veiga Beltrame, Eduardo and Pachter, Lior",
    title = "A curated database reveals trends in single cell transcriptomics",
    journal = "Database: The Journal of Biological Databases and Curation",
    publisher = "Oxford University Press",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190821-092511308",
    id = "https://authors.library.caltech.edu/records/fvv0w-xy358",
    issn = "1758-0463",
    doi = "10.1093/database/baaa073",
    volume = "2020",
    pmcid = "PMC7698659",
    pages = "Art. No. baaa073"
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@article{https://authors.library.caltech.edu/records/bkjds-vsh60,
    authors = "Mehrab, Zakaria and Mobin, Jaiaid and Tahmid, Ibrahim Asadullah and Pachter, Lior and Rahman, Atif",
    title = "A faster implementation of association mapping from k-mers",
    journal = "Bio-protocol",
    publisher = "Bio-Protocol",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20210309-074448590",
    id = "https://authors.library.caltech.edu/records/bkjds-vsh60",
    issn = "2331-8325",
    doi = "10.21769/bioprotoc.3815",
    volume = "10",
    number = "21",
    pages = "Art. No. e3815"
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@article{https://authors.library.caltech.edu/records/ampr3-ja254,
    authors = "Gorin, Gennady and Pachter, Lior",
    title = "Special function methods for bursty models of transcription",
    journal = "Physical Review E",
    publisher = "American Physical Society",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200909-153753998",
    id = "https://authors.library.caltech.edu/records/ampr3-ja254",
    issn = "2470-0045",
    doi = "10.1103/physreve.102.022409",
    volume = "102",
    number = "2",
    pages = "Art. No. 022409"
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@article{https://authors.library.caltech.edu/records/nn6dw-xb480,
    authors = "Koromila, Theodora and Gao, Fan and Iwasaki, Yasuno and He, Peng and Pachter, Lior and Gergen, J. Peter and Stathopoulos, Angelike",
    title = "Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos",
    journal = "eLife",
    publisher = "eLife Sciences Publications",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20191125-141648000",
    id = "https://authors.library.caltech.edu/records/nn6dw-xb480",
    issn = "2050-084X",
    doi = "10.7554/eLife.59610",
    volume = "9",
    pmcid = "PMC7417190",
    pages = "Art. No. e59610"
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@article{https://authors.library.caltech.edu/records/zc0e4-j1959,
    authors = "Mao, Shunfu and Pachter, Lior and Tse, David and Kannan, Sreeram",
    title = "RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition",
    journal = "PLoS ONE",
    publisher = "Public Library of Science",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200602-124021279",
    id = "https://authors.library.caltech.edu/records/zc0e4-j1959",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0232946",
    volume = "15",
    number = "6",
    pmcid = "PMC7266320",
    pages = "Art. No. e0232946"
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@article{https://authors.library.caltech.edu/records/2pyfk-v8764,
    authors = "Svensson, Valentine and Gayoso, Adam and Yosef, Nir and Pachter, Lior",
    title = "Interpretable factor models of single-cell RNA-seq via variational autoencoders",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190816-135915873",
    id = "https://authors.library.caltech.edu/records/2pyfk-v8764",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btaa169",
    volume = "36",
    number = "11",
    pmcid = "PMC7267837",
    pages = "3418-3421"
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@article{https://authors.library.caltech.edu/records/akk2e-ngb36,
    authors = "Gorin, Gennady and Svensson, Valentine and Pachter, Lior",
    title = "RNA velocity and protein acceleration from single-cell multiomics experiments",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190607-122759859",
    id = "https://authors.library.caltech.edu/records/akk2e-ngb36",
    issn = "1465-6906",
    doi = "10.1186/s13059-020-1945-3",
    volume = "21",
    pmcid = "PMC7029606",
    pages = "Art. No. 39"
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@article{https://authors.library.caltech.edu/records/m07dw-3jq86,
    authors = "Gehring, Jase and Park, Jong Hwee and Chen, Sisi and Thomson, Matthew and Pachter, Lior",
    title = "Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2020",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181030-145533155",
    id = "https://authors.library.caltech.edu/records/m07dw-3jq86",
    issn = "1087-0156",
    doi = "10.1038/s41587-019-0372-z",
    volume = "38",
    number = "1",
    pages = "35-38"
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@article{https://authors.library.caltech.edu/records/x39ya-h3a68,
    authors = "Gao, Fan and da Veiga Beltrame, Eduardo and Gehring, Jase A. and Hjoerleifsson, Kristin E. Edljarn and Lu, Lambda and Melsted, Paull and Ntranos, Vasilis and Pachter, Lior and Svensson, Valentine",
    title = "The BUS Format for Single-Cell RNA-Seq Processing and Analysis",
    journal = "Journal of Biomolecular Techniques",
    publisher = "Association of Biomolecular Resource Facilities",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200106-081503232",
    id = "https://authors.library.caltech.edu/records/x39ya-h3a68",
    issn = "1524-0215",
    volume = "30",
    number = "S1",
    pmcid = "PMC6938108",
    pages = "S62"
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@article{https://authors.library.caltech.edu/records/jk166-h3s87,
    authors = "Melsted, Páll and Ntranos, Vasilis and Pachter, Lior",
    title = "Barcode, UMI, Set format and BUStools",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526289",
    id = "https://authors.library.caltech.edu/records/jk166-h3s87",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btz279",
    volume = "35",
    number = "21",
    pages = "4472-4473"
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@article{https://authors.library.caltech.edu/records/e3g77-5qr43,
    authors = "Kim, Dong-Wook and Yao, Zizhen and Graybuck, Lucas T. and Kim, Tae Kyung and Nguyen, Thuc Nghi and Smith, Kimberly A. and Fong, Olivia and Yi, Lynn and Koulena, Noushin and Pierson, Nico and Shah, Sheel and Lo, Liching and Pool, Allan-Hermann and Oka, Yuki and Pachter, Lior and Cai, Long and Tasic, Bosiljka and Zeng, Hongkui and Anderson, David J.",
    title = "Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior",
    journal = "Cell",
    publisher = "Cell Press",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20191017-094121433",
    id = "https://authors.library.caltech.edu/records/e3g77-5qr43",
    issn = "0092-8674",
    doi = "10.1016/j.cell.2019.09.020",
    volume = "179",
    number = "3",
    pmcid = "PMC7534821",
    pages = "713-728"
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@article{https://authors.library.caltech.edu/records/gyqah-rvc67,
    authors = "Wright, Matthew and Goin, Dana and Smed, Mette and Pachter, Lior and Nelson, J. Lee and Jewell, Nicholas and Olsen, Jørn and Hetland, Merete Lund and Zoffmann, Vibeke and Jawaheer, Damini",
    title = "Investigating the Post-Partum Flare in Rheumatoid Arthritis Using Transcriptome Analysis",
    journal = "Arthritis and Rheumatology",
    publisher = "Wiley",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200206-130336877",
    id = "https://authors.library.caltech.edu/records/gyqah-rvc67",
    issn = "2326-5191",
    doi = "10.1002/art.41108",
    volume = "71",
    number = "S10",
    pages = "Art. No. 1940"
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@article{https://authors.library.caltech.edu/records/rcg7y-rez41,
    authors = "Pathi, Amogh and Smed, Mette and Pachter, Lior and Purdom, Elizabeth and Wright, Matthew and Jewell, Nicholas and Nelson, J. Lee and Olsen, Jørn and Hetland, Merete Lund and Zoffmann, Vibeke and Jawaheer, Damini",
    title = "The Pre-pregnancy Rheumatoid Arthritis Gene Expression Signature Correlates with Improvement or Worsening of Disease Activity During Pregnancy: A Pilot Study",
    journal = "Arthritis and Rheumatology",
    publisher = "Wiley",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200206-125453251",
    id = "https://authors.library.caltech.edu/records/rcg7y-rez41",
    issn = "2326-5191",
    doi = "10.1002/art.41108",
    volume = "71",
    number = "S10",
    pages = "Art. No. 1938"
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@article{https://authors.library.caltech.edu/records/b2hv9-6t971,
    authors = "McCurdy, Shannon and Molinaro, Annette and Pachter, Lior",
    title = "Factor analysis for survival time prediction with informative censoring and diverse covariates",
    journal = "Statistics in Medicine",
    publisher = "Wiley",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190610-075805993",
    id = "https://authors.library.caltech.edu/records/b2hv9-6t971",
    issn = "0277-6715",
    doi = "10.1002/sim.8151",
    volume = "38",
    number = "20",
    pages = "3719-3732"
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@article{https://authors.library.caltech.edu/records/f2956-nyy34,
    authors = "Booeshaghi, A. Sina and da Veiga Beltrame, Eduardo and Bannon, Dylan and Gehring, Jase and Pachter, Lior",
    title = "Principles of open source bioinstrumentation applied to the poseidon syringe pump system",
    journal = "Scientific Reports",
    publisher = "Nature Publishing Group",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190827-103540654",
    id = "https://authors.library.caltech.edu/records/f2956-nyy34",
    issn = "2045-2322",
    doi = "10.1038/s41598-019-48815-9",
    volume = "9",
    pmcid = "PMC6711986",
    pages = "12385"
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@article{https://authors.library.caltech.edu/records/cpbyk-8yg76,
    authors = "Ntranos, Vasilis and Yi, Lynn and Melsted, Páll and Pachter, Lior",
    title = "A discriminative learning approach to differential expression analysis for single-cell RNA-seq",
    journal = "Nature Methods",
    publisher = "Nature Publishing Group",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190123-095919155",
    id = "https://authors.library.caltech.edu/records/cpbyk-8yg76",
    issn = "1548-7091",
    doi = "10.1038/s41592-018-0303-9",
    volume = "16",
    number = "2",
    pages = "163-166"
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@article{https://authors.library.caltech.edu/records/26j43-gs111,
    authors = "McCurdy, Shannon R. and Ntranos, Vasilis and Pachter, Lior",
    title = "Deterministic column subset selection for single-cell RNA-Seq",
    journal = "PLoS ONE",
    publisher = "Public Library of Science",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181029-133340286",
    id = "https://authors.library.caltech.edu/records/26j43-gs111",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0210571",
    volume = "14",
    number = "1",
    pmcid = "PMC6347249",
    pages = "Art. No. e0210571"
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@article{https://authors.library.caltech.edu/records/a5jaw-w3h87,
    authors = "Tambe, Akshay and Pachter, Lior",
    title = "Barcode identification for single cell genomics",
    journal = "BMC Bioinformatics",
    publisher = "BioMed Central",
    year = "2019",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181029-144423877",
    id = "https://authors.library.caltech.edu/records/a5jaw-w3h87",
    issn = "1471-2105",
    doi = "10.1186/s12859-019-2612-0",
    volume = "20",
    pmcid = "PMC6337828",
    pages = "Art. No. 32"
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@article{https://authors.library.caltech.edu/records/wt9yb-wny62,
    authors = "Brown, Brielin C. and Bray, Nicolas L. and Pachter, Lior",
    title = "Expression reflects population structure",
    journal = "PLoS Genetics",
    publisher = "Public Library of Science",
    year = "2018",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181008-162020262",
    id = "https://authors.library.caltech.edu/records/wt9yb-wny62",
    issn = "1553-7390",
    doi = "10.1371/journal.pgen.1007841",
    volume = "14",
    number = "12",
    pmcid = "PMC6317812",
    pages = "Art. No. e1007841"
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@article{https://authors.library.caltech.edu/records/qhp6e-5ta13,
    authors = "Svensson, Valentine and Pachter, Lior",
    title = "RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq",
    journal = "Molecular Cell",
    publisher = "Elsevier",
    year = "2018",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181004-091624887",
    id = "https://authors.library.caltech.edu/records/qhp6e-5ta13",
    issn = "1097-2765",
    doi = "10.1016/j.molcel.2018.09.026",
    volume = "72",
    number = "1",
    pages = "7-9"
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@article{https://authors.library.caltech.edu/records/qbnnk-nye38,
    authors = "Tunney, Robert and McGlincy, Nicholas J. and Graham, Monica E. and Naddaf, Nicki and Pachter, Lior and Lareau, Liana F.",
    title = "Accurate design of translational output by a neural network model of ribosome distribution",
    journal = "Nature Structural \& Molecular Biology",
    publisher = "Nature Publishing Group",
    year = "2018",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180423-152534642",
    id = "https://authors.library.caltech.edu/records/qbnnk-nye38",
    issn = "1545-9985",
    doi = "10.1038/s41594-018-0080-2",
    volume = "25",
    number = "7",
    pmcid = "PMC6457438",
    pages = "577-582"
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@article{https://authors.library.caltech.edu/records/q0xz8-h1p26,
    authors = "Rahman, Atif and Hallgrímsdóttir, Ingileif and Eisen, Michael and Pachter, Lior",
    title = "Association mapping from sequencing reads using k-mers",
    journal = "eLife",
    publisher = "eLife Sciences Publications",
    year = "2018",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190503-134759852",
    id = "https://authors.library.caltech.edu/records/q0xz8-h1p26",
    issn = "2050-084X",
    doi = "10.7554/elife.32920",
    volume = "7",
    pmcid = "PMC6044908",
    pages = "Art. No. e32920"
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@article{https://authors.library.caltech.edu/records/st76a-kg126,
    authors = "Yi, Lynn and Pimentel, Harold and Bray, Nicolas L. and Pachter, Lior",
    title = "Gene-level differential analysis at transcript-level resolution",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2018",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180416-090553011",
    id = "https://authors.library.caltech.edu/records/st76a-kg126",
    issn = "1474-760X",
    doi = "10.1186/s13059-018-1419-z",
    volume = "19",
    pmcid = "PMC5896116",
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@article{https://authors.library.caltech.edu/records/nf54s-9xm95,
    authors = "Goin, Dana E. and Smed, Mette and Jewell, Nicholas and Pachter, Lior and Nelson, J. Lee and Kjaergaard, Hanne and Olsen, Jørn and Hetland, Merete Lund and Ottesen, Bent and Zoffmann, Vibeke and Jawaheer, Damini",
    title = "Longitudinal Changes in Gene Expression Associated with Disease Activity during Pregnancy and Post-Partum Among Women with Rheumatoid Arthritis",
    journal = "Arthritis and Rheumatology",
    publisher = "Wiley",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20171113-143256428",
    id = "https://authors.library.caltech.edu/records/nf54s-9xm95",
    issn = "2326-5191",
    doi = "10.1002/art.40321",
    volume = "69",
    number = "S10",
    pages = "Art. No. 2432"
}


@article{https://authors.library.caltech.edu/records/3hhxt-h4x56,
    authors = "Goin, Dana E. and Smed, Mette and Pachter, Lior and Purdom, Elizabeth and Nelson, J. Lee and Kjaergaard, Hanne and Olsen, Jørn and Hetland, Merete Lund and Ottesen, Bent and Zoffmann, Vibeke and Jawaheer, Damini",
    title = "Transcriptome Analysis in Women with Rheumatoid Arthritis Who Improve or Worsen during Pregnancy",
    journal = "Arthritis and Rheumatology",
    publisher = "Wiley",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20171113-145148333",
    id = "https://authors.library.caltech.edu/records/3hhxt-h4x56",
    issn = "2326-5191",
    doi = "10.1002/art.40321",
    volume = "69",
    number = "S10",
    pages = "Art. No. 2433"
}


@article{https://authors.library.caltech.edu/records/15tce-gp284,
    authors = "Schaeffer, L. and Pimentel, H. and Bray, N. and Melsted, P. and Pachter, L.",
    title = "Pseudoalignment for metagenomic read assignment",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-131027010",
    id = "https://authors.library.caltech.edu/records/15tce-gp284",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btx106",
    volume = "33",
    number = "14",
    pmcid = "PMC5870846",
    pages = "2082-2088"
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@article{https://authors.library.caltech.edu/records/kmsft-gtd43,
    authors = "Pimentel, Harold and Bray, Nicolas L. and Puente, Suzette and Melsted, Páll and Pachter, Lior",
    title = "Differential analysis of RNA-seq incorporating quantification uncertainty",
    journal = "Nature Methods",
    publisher = "Nature Publishing Group",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170612-084553487",
    id = "https://authors.library.caltech.edu/records/kmsft-gtd43",
    issn = "1548-7091",
    doi = "10.1038/nmeth.4324",
    volume = "14",
    number = "7",
    pages = "687-690"
}


@article{https://authors.library.caltech.edu/records/jbjbb-4as73,
    authors = "Goin, Dana E. and Smed, Mette Kiel and Pachter, Lior and Purdom, Elizabeth and Nelson, J. Lee and Kjærgaard, Hanne and Olsen, Jørn and Hetland, Merete Lund and Zoffmann, Vibeke and Ottesen, Bent and Jawaheer, Damini",
    title = "Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study",
    journal = "Arthritis Research and Therapy",
    publisher = "BioMed Central",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170531-131446160",
    id = "https://authors.library.caltech.edu/records/jbjbb-4as73",
    issn = "1478-6362",
    doi = "10.1186/s13075-017-1312-2",
    volume = "19",
    number = "1",
    pmcid = "PMC5445464",
    pages = "Art. No. 104"
}


@article{https://authors.library.caltech.edu/records/7czc6-vfq51,
    authors = "Li, Bo and Tambe, Akshay and Aviran, Sharon and Pachter, Lior",
    title = "PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays",
    journal = "Cell Systems",
    publisher = "Cell Press",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170510-142406445",
    id = "https://authors.library.caltech.edu/records/7czc6-vfq51",
    issn = "2405-4712",
    doi = "10.1016/j.cels.2017.04.007",
    volume = "4",
    number = "5",
    pmcid = "PMC5758053",
    pages = "568-574"
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@article{https://authors.library.caltech.edu/records/tfn4w-6em19,
    authors = "Yi, Lynn and Pimentel, Harold and Pachter, Lior",
    title = "Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways",
    journal = "PLoS ONE",
    publisher = "Public Library of Science",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170505-103858288",
    id = "https://authors.library.caltech.edu/records/tfn4w-6em19",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0175744",
    volume = "12",
    number = "4",
    pmcid = "PMC5407828",
    pages = "Art. No. e0175744"
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@article{https://authors.library.caltech.edu/records/nbtgs-bmj74,
    authors = "McAuliffe, Jon D. and Jordan, Michael I. and Pachter, Lior",
    title = "Subtree power analysis finds optimal species for comparative genomics",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2017",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-090057219",
    id = "https://authors.library.caltech.edu/records/nbtgs-bmj74",
    issn = "0027-8424",
    doi = "10.1073/pnas.0502790102",
    volume = "102",
    number = "22",
    pmcid = "PMC1142384",
    pages = "7900-7905"
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@article{https://authors.library.caltech.edu/records/fw493-kaf67,
    authors = "Pimentel, Harold and Sturmfels, Pascal and Bray, Nicolas and Melsted, Páll and Pachter, Lior",
    title = "The Lair: a resource for exploratory analysis of published RNA-Seq data",
    journal = "BMC Bioinformatics",
    publisher = "BioMed Central",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190506-141348569",
    id = "https://authors.library.caltech.edu/records/fw493-kaf67",
    issn = "1471-2105",
    doi = "10.1186/s12859-016-1357-2",
    volume = "17",
    number = "1",
    pmcid = "PMC5131447",
    pages = "Art. No. 490"
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@article{https://authors.library.caltech.edu/records/cz0cp-gge47,
    authors = "Fu, Audrey Qiuyan and Pachter, Lior",
    title = "Estimating intrinsic and extrinsic noise from single-cell gene expression measurements",
    journal = "Statistical Applications in Genetics and Molecular Biology",
    publisher = "De Gruyter",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-150123048",
    id = "https://authors.library.caltech.edu/records/cz0cp-gge47",
    issn = "2194-6302",
    doi = "10.1515/sagmb-2016-0002",
    volume = "15",
    number = "6",
    pmcid = "PMC5518956",
    pages = "447-471"
}


@article{https://authors.library.caltech.edu/records/pv1dd-91s03,
    authors = "Chen, Xi and Love, J. Christopher and Navin, Nicholas E. and Pachter, Lior and Stubbington, Michael J. T. and Svensson, Valentine and Sweedler, Jonathan V. and Teichmann, Sarah A.",
    title = "Single-cell analysis at the threshold",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190503-153138885",
    id = "https://authors.library.caltech.edu/records/pv1dd-91s03",
    issn = "1087-0156",
    doi = "10.1038/nbt.3721",
    volume = "34",
    number = "11",
    pages = "1111-1118"
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@article{https://authors.library.caltech.edu/records/jj12q-40t75,
    authors = "Hateley, Shannon and Hosamani, Ravikumar and Bhardwaj, Shilpa R. and Pachter, Lior and Bhattacharya, Sharmila",
    title = "Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity",
    journal = "Genomics",
    publisher = "Elsevier",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-154829565",
    id = "https://authors.library.caltech.edu/records/jj12q-40t75",
    issn = "0888-7543",
    doi = "10.1016/j.ygeno.2016.09.002",
    volume = "108",
    number = "3-4",
    pages = "158-167"
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@article{https://authors.library.caltech.edu/records/3dew4-m0c86,
    authors = "Ntranos, Vasilis and Kamath, Govinda M. and Zhang, Jesse M. and Pachter, Lior and Tse, David N.",
    title = "Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190503-155957743",
    id = "https://authors.library.caltech.edu/records/3dew4-m0c86",
    issn = "1474-760X",
    doi = "10.1186/s13059-016-0970-8",
    volume = "17",
    number = "1",
    pmcid = "PMC4881296",
    pages = "Art. No. 112"
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@article{https://authors.library.caltech.edu/records/9cqwz-arv02,
    authors = "Bray, Nicolas L. and Pimentel, Harold and Melsted, Páll and Pachter, Lior",
    title = "Near-optimal probabilistic RNA-seq quantification",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190506-110012992",
    id = "https://authors.library.caltech.edu/records/9cqwz-arv02",
    issn = "1087-0156",
    doi = "10.1038/nbt.3519",
    volume = "34",
    number = "5",
    pages = "525-527"
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@article{https://authors.library.caltech.edu/records/6h7fw-ebc29,
    authors = "Pimentel, Harold and Parra, Marilyn and Gee, Sherry L. and Mohandas, Narla and Pachter, Lior and Conboy, John G.",
    title = "A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2016",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-131213123",
    id = "https://authors.library.caltech.edu/records/6h7fw-ebc29",
    issn = "0305-1048",
    doi = "10.1093/nar/gkv1168",
    volume = "44",
    number = "2",
    pmcid = "PMC4737145",
    pages = "838-851"
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@article{https://authors.library.caltech.edu/records/2n03m-r5660,
    authors = "Mittal, Anuradha and Pachter, Lior and Nelson, J. Lee and Kjærgaard, Hanne and Smed, Mette Kiel and Gildengorin, Virginia L. and Zoffmann, Vibeke and Hetland, Merete Lund and Jewell, Nicholas P. and Olsen, Jørn and Jawaheer, Damini",
    title = "Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis",
    journal = "PLOS ONE",
    publisher = "Public Library of Science",
    year = "2015",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-124807271",
    id = "https://authors.library.caltech.edu/records/2n03m-r5660",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0145204",
    volume = "10",
    number = "12",
    pmcid = "PMC4684291",
    pages = "Art. No. e0145204"
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@article{https://authors.library.caltech.edu/records/nrkwk-ccq57,
    authors = "Hanchate, Naresh K. and Kondoh, Kunio and Lu, Zhonglua and Kuang, Donghui and Ye, Xiaolan and Qiu, Xiaojie and Pachter, Lior and Trapnell, Cole and Buck, Linda B.",
    title = "Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis",
    journal = "Science",
    publisher = "American Association for the Advancement of Science",
    year = "2015",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-130217211",
    id = "https://authors.library.caltech.edu/records/nrkwk-ccq57",
    issn = "0036-8075",
    doi = "10.1126/science.aad2456",
    volume = "350",
    number = "6265",
    pmcid = "PMC5642900",
    pages = "1251-1255"
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@article{https://authors.library.caltech.edu/records/bj6ys-b0g23,
    authors = "Paten, Benedict and Diekhans, Mark and Druker, Brian J. and Friend, Stephen and Guinney, Justin and Gassner, Nadine and Guttman, Mitchell and Kent, W. James and Mantey, Patrick and Margolin, Adam A. and Massie, Matt and Novak, Adam M. and Nothaft, Frank and Pachter, Lior and Patterson, David and Smuga-Otto, Maciej and Stuart, Joshua M. and Van't Veer, Laura and Wold, Barbara and Haussler, David",
    title = "The NIH BD2K center for big data in translational genomics",
    journal = "Journal of the American Medical Informatics Association",
    publisher = "American Medical Informatics Association",
    year = "2015",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20150721-085701041",
    id = "https://authors.library.caltech.edu/records/bj6ys-b0g23",
    issn = "1067-5027",
    doi = "10.1093/jamia/ocv047",
    volume = "22",
    number = "6",
    pmcid = "PMC5009913",
    pages = "1143-1147"
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@article{https://authors.library.caltech.edu/records/vg27x-zhk63,
    authors = "Brat, Daniel J. and Pachter, Lior",
    title = "Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas",
    journal = "New England Journal of Medicine",
    publisher = "Massachusetts Medical Society",
    year = "2015",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-132106100",
    id = "https://authors.library.caltech.edu/records/vg27x-zhk63",
    issn = "0028-4793",
    doi = "10.1056/NEJMoa1402121",
    volume = "372",
    number = "26",
    pmcid = "PMC4530011",
    pages = "2481-2498"
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@article{https://authors.library.caltech.edu/records/3y9vj-fab67,
    authors = "Singer, Meromit and Pachter, Lior",
    title = "Controlling for conservation in genome-wide DNA methylation studies",
    journal = "BMC Genomics",
    publisher = "BioMed Central",
    year = "2015",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-133219740",
    id = "https://authors.library.caltech.edu/records/3y9vj-fab67",
    issn = "1471-2164",
    doi = "10.1186/s12864-015-1604-3",
    volume = "16",
    pmcid = "PMC4448855",
    pages = "Art. No. 420"
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@article{https://authors.library.caltech.edu/records/qbbbd-k1850,
    authors = "Singer, Meromit and Kosti, Idit and Pachter, Lior and Mandel-Gutfreund, Yael",
    title = "A diverse epigenetic landscape at human exons with implication for expression",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2015",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-133948010",
    id = "https://authors.library.caltech.edu/records/qbbbd-k1850",
    issn = "0305-1048",
    doi = "10.1093/nar/gkv153",
    volume = "43",
    number = "7",
    pmcid = "PMC4402514",
    pages = "3498-3508"
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@article{https://authors.library.caltech.edu/records/acq1h-k9e77,
    authors = "Aviran, Sharon and Pachter, Lior",
    title = "Rational experiment design for sequencing-based RNA structure mapping",
    journal = "RNA",
    publisher = "RNA Society",
    year = "2014",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-134607827",
    id = "https://authors.library.caltech.edu/records/acq1h-k9e77",
    issn = "1355-8382",
    doi = "10.1261/rna.043844.113",
    volume = "20",
    number = "12",
    pmcid = "PMC4238353",
    pages = "1864-1877"
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@article{https://authors.library.caltech.edu/records/57pcw-w6930,
    authors = "Forster, Ryan and Chiba, Kunitoshi and Schaeffer, Lorian and Regalado, Samuel G. and Lai, Christine S. and Gao, Qing and Kiani, Samira and Farin, Henner F. and Clevers, Hans and Cost, Gregory J. and Chan, Andy and Rebar, Edward J. and Urnov, Fyodor D. and Gregory, Philip D. and Pachter, Lior and Jaenisch, Rudolf and Hockemeyer, Dirk",
    title = "Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells",
    journal = "Stem Cell Reports",
    publisher = "Elsevier",
    year = "2014",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-141031221",
    id = "https://authors.library.caltech.edu/records/57pcw-w6930",
    issn = "2213-6711",
    doi = "10.1016/j.stemcr.2014.05.001",
    volume = "2",
    number = "6",
    pmcid = "PMC4050346",
    pages = "838-852"
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@article{https://authors.library.caltech.edu/records/ffw23-m8n84,
    authors = "Wong, Valerie L. and Ellison, Christopher E. and Eisen, Michael B. and Pachter, Lior and Brem, Rachel B.",
    title = "Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum",
    journal = "PLoS ONE",
    publisher = "Public Library of Science",
    year = "2014",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190507-112223935",
    id = "https://authors.library.caltech.edu/records/ffw23-m8n84",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0096784",
    volume = "9",
    number = "5",
    pmcid = "PMC4019546",
    pages = "Art. No. e96784"
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@article{https://authors.library.caltech.edu/records/xw760-6ct89,
    authors = "Takayama, Sachiko and Dhahbi, Joseph and Roberts, Adam and Mao, Guanxiong and Heo, Seok-Jin and Pachter, Lior and Martin, David I. K. and Boffelli, Dario",
    title = "Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2014",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-142644662",
    id = "https://authors.library.caltech.edu/records/xw760-6ct89",
    issn = "1088-9051",
    doi = "10.1101/gr.162412.113",
    volume = "24",
    number = "5",
    pmcid = "PMC4009611",
    pages = "821-830"
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@article{https://authors.library.caltech.edu/records/jjxxg-g1y43,
    authors = "Pimentel, Harold and Parra, Marilynn and Gee, Sherry and Ghanem, Dana and An, Xiuli and Li, Jie and Mohandas, Narla and Pachter, Lior and Conboy, John G.",
    title = "A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2014",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-143819723",
    id = "https://authors.library.caltech.edu/records/jjxxg-g1y43",
    issn = "0305-1048",
    doi = "10.1093/nar/gkt1388",
    volume = "42",
    number = "6",
    pmcid = "PMC3973340",
    pages = "4031-4042"
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@article{https://authors.library.caltech.edu/records/v52pv-abs78,
    authors = "Roberts, Adam and Feng, Harvey and Pachter, Lior",
    title = "Fragment assignment in the cloud with eXpress-D",
    journal = "BMC Bioinformatics",
    publisher = "BioMed Central",
    year = "2013",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-144424899",
    id = "https://authors.library.caltech.edu/records/v52pv-abs78",
    issn = "1471-2105",
    doi = "10.1186/1471-2105-14-358",
    volume = "14",
    pmcid = "PMC3881492",
    pages = "Art. No. 358"
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@article{https://authors.library.caltech.edu/records/55r0e-gyg95,
    authors = "Roberts, Adam and Schaeffer, Lorian and Pachter, Lior",
    title = "Updating RNA-Seq analyses after re-annotation",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2013",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-154642805",
    id = "https://authors.library.caltech.edu/records/55r0e-gyg95",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btt197",
    volume = "29",
    number = "13",
    pmcid = "PMC3694665",
    pages = "1631-1637"
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@article{https://authors.library.caltech.edu/records/h7bt6-gaq50,
    authors = "Kleinman, Aaron and Harel, Matan and Pachter, Lior",
    title = "Affine and Projective Tree Metric Theorems",
    journal = "Annals of Combinatorics",
    publisher = "Springer",
    year = "2013",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-162557287",
    id = "https://authors.library.caltech.edu/records/h7bt6-gaq50",
    issn = "0218-0006",
    doi = "10.1007/s00026-012-0173-2",
    volume = "17",
    number = "1",
    pages = "205-228"
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@article{https://authors.library.caltech.edu/records/x5dqz-e3w34,
    authors = "Rahman, Atif and Pachter, Lior",
    title = "CGAL: computing genome assembly likelihoods",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2013",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-155431520",
    id = "https://authors.library.caltech.edu/records/x5dqz-e3w34",
    issn = "1465-6906",
    doi = "10.1186/gb-2013-14-1-r8",
    volume = "14",
    number = "1",
    pmcid = "PMC3663106",
    pages = "Art. No. R8"
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@article{https://authors.library.caltech.edu/records/3jby4-nxg71,
    authors = "Trapnell, Cole and Hendrickson, David G. and Sauvageau, Martin and Goff, Loyal and Rinn, John L. and Pachter, Lior",
    title = "Differential analysis of gene regulation at transcript resolution with RNA-seq",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2013",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-161532491",
    id = "https://authors.library.caltech.edu/records/3jby4-nxg71",
    issn = "1087-0156",
    doi = "10.1038/nbt.2450",
    volume = "31",
    number = "1",
    pmcid = "PMC3869392",
    pages = "46-53"
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@article{https://authors.library.caltech.edu/records/fa8tb-0xm37,
    authors = "Roberts, Adam and Pachter, Lior",
    title = "Streaming fragment assignment for real-time analysis of sequencing experiments",
    journal = "Nature Methods",
    publisher = "Nature Publishing Group",
    year = "2013",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-163300268",
    id = "https://authors.library.caltech.edu/records/fa8tb-0xm37",
    issn = "1548-7091",
    doi = "10.1038/nmeth.2251",
    volume = "10",
    number = "1",
    pmcid = "PMC3880119",
    pages = "71-73"
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@article{https://authors.library.caltech.edu/records/eas5h-yyq14,
    authors = "Hower, Valerie and Starfield, Richard and Roberts, Adam and Pachter, Lior",
    title = "Quantifying uniformity of mapped reads",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2012",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-164056261",
    id = "https://authors.library.caltech.edu/records/eas5h-yyq14",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/bts451",
    volume = "28",
    number = "20",
    pmcid = "PMC3467739",
    pages = "2680-2682"
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@article{https://authors.library.caltech.edu/records/dnfee-gqw75,
    authors = "Pachter, Lior",
    title = "A closer look at RNA editing",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2012",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-164721967",
    id = "https://authors.library.caltech.edu/records/dnfee-gqw75",
    issn = "1087-0156",
    doi = "10.1038/nbt.2156",
    volume = "30",
    number = "3",
    pages = "246-247"
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@article{https://authors.library.caltech.edu/records/x492k-9n169,
    authors = "Trapnell, Cole and Roberts, Adam and Goff, Loyal and Pertea, Geo and Kim, Daehwan and Kelley, David R. and Pimentel, Harold and Salzberg, Steven L. and Rinn, John L. and Pachter, Lior",
    title = "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks",
    journal = "Nature Protocols",
    publisher = "Nature Publishing Group",
    year = "2012",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170303-165006599",
    id = "https://authors.library.caltech.edu/records/x492k-9n169",
    issn = "1754-2189",
    doi = "10.1038/nprot.2012.016",
    volume = "7",
    number = "3",
    pmcid = "PMC3334321",
    pages = "562-578"
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@article{https://authors.library.caltech.edu/records/1bb4r-e4p39,
    authors = "Martin, David I. K. and Singer, Meromit and Dhahbi, Joseph and Mao, Guanxiong and Zhang, Lu and Schroth, Gary P. and Pachter, Lior and Boffelli, Dario",
    title = "Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-101015596",
    id = "https://authors.library.caltech.edu/records/1bb4r-e4p39",
    issn = "1088-9051",
    doi = "10.1101/gr.122721.111",
    volume = "21",
    number = "12",
    pmcid = "PMC3227095",
    pages = "2049-2057"
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@article{https://authors.library.caltech.edu/records/fbtq8-9m762,
    authors = "Roberts, Adam and Pachter, Lior",
    title = "RNA-Seq and find: entering the RNA deep field",
    journal = "Genome Medicine",
    publisher = "BioMed Central",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-093511106",
    id = "https://authors.library.caltech.edu/records/fbtq8-9m762",
    issn = "1756-994X",
    doi = "10.1186/gm290",
    volume = "3",
    number = "11",
    pmcid = "PMC3308029",
    pages = "Art. No. 74"
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@article{https://authors.library.caltech.edu/records/khkgx-4cj35,
    authors = "Meacham, Frazer and Boffelli, Dario and Dhahbi, Joseph and Martin, David I. K. and Singer, Meromit and Pachter, Lior",
    title = "Identification and correction of systematic error in high-throughput sequence data",
    journal = "BMC Bioinformatics",
    publisher = "BioMed Central",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-095020310",
    id = "https://authors.library.caltech.edu/records/khkgx-4cj35",
    issn = "1471-2105",
    doi = "10.1186/1471-2105-12-451",
    volume = "12",
    pmcid = "PMC3295828",
    pages = "Art. No. 451"
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@article{https://authors.library.caltech.edu/records/4dgap-m4a79,
    authors = "Singer, Meromit and Engström, Alexander and Schönhuth, Alexander and Pachter, Lior",
    title = "Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains",
    journal = "Statistical Applications in Genetics and Molecular Biology",
    publisher = "De Gruyter",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-100428893",
    id = "https://authors.library.caltech.edu/records/4dgap-m4a79",
    issn = "2194-6302",
    doi = "10.2202/1544-6115.1677",
    volume = "10",
    number = "1",
    pages = "Art. No. 43"
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@article{https://authors.library.caltech.edu/records/381cc-ttw35,
    authors = "Roberts, Adam and Pimentel, Harold and Trapnell, Cole and Pachter, Lior",
    title = "Identification of novel transcripts in annotated genomes using RNA-Seq",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-101954304",
    id = "https://authors.library.caltech.edu/records/381cc-ttw35",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btr355",
    volume = "27",
    number = "17",
    pages = "2325-2329"
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@article{https://authors.library.caltech.edu/records/t7zmb-bhs07,
    authors = "Levy, Dan and Pachter, Lior",
    title = "The neighbor-net algorithm",
    journal = "Advances in Applied Mathematics",
    publisher = "Elsevier",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-113043756",
    id = "https://authors.library.caltech.edu/records/t7zmb-bhs07",
    issn = "0196-8858",
    doi = "10.1016/j.aam.2010.09.002",
    volume = "47",
    number = "2",
    pages = "240-258"
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@article{https://authors.library.caltech.edu/records/kg7s1-59c84,
    authors = "Snir, Sagi and Pachter, Lior",
    title = "Tracing the Most Parsimonious Indel History",
    journal = "Journal of Computational Biology",
    publisher = "Mary Ann Liebert, Inc.",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-102549258",
    id = "https://authors.library.caltech.edu/records/kg7s1-59c84",
    issn = "1066-5277",
    doi = "10.1089/cmb.2010.0325",
    volume = "18",
    number = "8",
    pages = "967-986"
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@article{https://authors.library.caltech.edu/records/c0y2x-zwa90,
    authors = "Aviran, Sharon and Trapnell, Cole and Lucks, Julius B. and Mortimer, Stefanie A. and Luo, Shujun and Schroth, Gary P. and Doudna, Jennifer A. and Arkin, Adam P. and Pachter, Lior",
    title = "Modeling and automation of sequencing-based characterization of RNA structure",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-103050792",
    id = "https://authors.library.caltech.edu/records/c0y2x-zwa90",
    issn = "0027-8424",
    doi = "10.1073/pnas.1106541108",
    volume = "108",
    number = "27",
    pmcid = "PMC3131376",
    pages = "11069-11074"
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@article{https://authors.library.caltech.edu/records/8ca3h-68a74,
    authors = "Lucks, Julius B. and Mortimer, Stefanie A. and Trapnell, Cole and Luo, Shujun and Aviran, Sharon and Schroth, Gary P. and Pachter, Lior and Doudna, Jennifer A. and Arkin, Adam P.",
    title = "Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-104204159",
    id = "https://authors.library.caltech.edu/records/8ca3h-68a74",
    issn = "0027-8424",
    doi = "10.1073/pnas.1106501108",
    volume = "108",
    number = "27",
    pmcid = "PMC3131332",
    pages = "11063-11068"
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@article{https://authors.library.caltech.edu/records/tkpa3-pje63,
    authors = "Roberts, Adam and Trapnell, Cole and Donaghey, Julie and Rinn, John L. and Pachter, Lior",
    title = "Improving RNA-Seq expression estimates by correcting for fragment bias",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-105110860",
    id = "https://authors.library.caltech.edu/records/tkpa3-pje63",
    issn = "1465-6906",
    doi = "10.1186/gb-2011-12-3-r22",
    volume = "12",
    number = "3",
    pmcid = "PMC3129672",
    pages = "Art. No. R22"
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@article{https://authors.library.caltech.edu/records/3k62z-3jg56,
    authors = "Hower, Valerie and Evans, Steven N. and Pachter, Lior",
    title = "Shape-based peak identification for ChIP-Seq",
    journal = "BMC Bioinformatics",
    publisher = "BioMed Central",
    year = "2011",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-111327579",
    id = "https://authors.library.caltech.edu/records/3k62z-3jg56",
    issn = "1471-2105",
    doi = "10.1186/1471-2105-12-15",
    volume = "12",
    pmcid = "PMC3032669",
    pages = "Art. No. 15"
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@article{https://authors.library.caltech.edu/records/445ny-3rj08,
    authors = "Willerth, Stephanie M. and Pedro, Hélder A. M. and Pachter, Lior and Humeau, Laurent M. and Arkin, Adam P. and Schaffer, David V.",
    title = "Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology",
    journal = "PLOS ONE",
    publisher = "Public Library of Science",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-114844988",
    id = "https://authors.library.caltech.edu/records/445ny-3rj08",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0013564",
    volume = "5",
    number = "10",
    pmcid = "PMC2962647",
    pages = "Art. No. e13564"
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@article{https://authors.library.caltech.edu/records/egmr2-mf591,
    authors = "Evans, Steven N. and Hower, Valerie and Pachter, Lior",
    title = "Coverage statistics for sequence census methods",
    journal = "BMC Bioinformatics",
    publisher = "BioMed Central",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-122114222",
    id = "https://authors.library.caltech.edu/records/egmr2-mf591",
    issn = "1471-2105",
    doi = "10.1186/1471-2105-11-430",
    volume = "11",
    pmcid = "PMC2940910",
    pages = "Art. No. 430"
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@article{https://authors.library.caltech.edu/records/vzhec-44b69,
    authors = "Singer, Meromit and Boffelli, Dario and Dhahbi, Joseph and Schönhuth, Alexander and Schroth, Gary P. and Martin, David I. K. and Pachter, Lior",
    title = "MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations",
    journal = "PLOS Computational Biology",
    publisher = "Public Library of Science",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-121310345",
    id = "https://authors.library.caltech.edu/records/vzhec-44b69",
    issn = "1553-7358",
    doi = "10.1371/journal.pcbi.1000888",
    volume = "6",
    number = "8",
    pmcid = "PMC2924245",
    pages = "Art. No. e1000888"
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@article{https://authors.library.caltech.edu/records/1sq2y-r7n90,
    authors = "Levin, Tera C. and Glazer, Andrew M. and Pachter, Lior and Brem, Rachel B. and Eisen, Michael B.",
    title = "Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study",
    journal = "PLOS ONE",
    publisher = "Public Library of Science",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-123004736",
    id = "https://authors.library.caltech.edu/records/1sq2y-r7n90",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0011645",
    volume = "5",
    number = "7",
    pmcid = "PMC2912228",
    pages = "Art. No. e11645"
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@article{https://authors.library.caltech.edu/records/q1bwm-dea54,
    authors = "Lapuk, Anna and Marr, Henry and Jakkula, Lakshmi and Pedro, Helder and Bhattacharya, Sanchita and Purdom, Elizabeth and Hu, Zhi and Simpson, Ken and Pachter, Lior and Durinck, Steffen and Wang, Nicholas and Parvin, Bahram and Fontenay, Gerald and Speed, Terence and Garbe, James and Stampfer, Martha and Bayandorian, Hovig and Dorton, Shannon and Clark, Tyson A. and Schweitzer, Anthony and Wyrobek, Andrew and Feiler, Heidi and Spellman, Paul and Conboy, John and Gray, Joe W.",
    title = "Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer",
    journal = "Molecular Cancer Research",
    publisher = "American Association for Cancer Research",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-123614363",
    id = "https://authors.library.caltech.edu/records/q1bwm-dea54",
    issn = "1541-7786",
    doi = "10.1158/1541-7786.MCR-09-0528",
    volume = "8",
    number = "7",
    pmcid = "PMC2911965",
    pages = "961-974"
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@article{https://authors.library.caltech.edu/records/wvkv3-hv456,
    authors = "Trapnell, Cole and Williams, Brian A. and Pertea, Geo and Mortazavi, Ali and Kwan, Gordon and van Baren, Marijke J. and Salzberg, Steven L. and Wold, Barbara J. and Pachter, Lior",
    title = "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation",
    journal = "Nature Biotechnology",
    publisher = "Nature Publishing Group",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20100601-111602154",
    id = "https://authors.library.caltech.edu/records/wvkv3-hv456",
    issn = "1087-0156",
    doi = "10.1038/nbt.1621",
    volume = "28",
    number = "5",
    pmcid = "PMC3146043",
    pages = "511-515"
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@article{https://authors.library.caltech.edu/records/y0yeq-t0p17,
    authors = "Bradley, Robert K. and Li, Xiao-Yong and Trapnell, Cole and Davidson, Stuart and Pachter, Lior and Chu, Hou Cheng and Tonkin, Leath A. and Biggin, Mark D. and Eisen, Michael B.",
    title = "Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species",
    journal = "PLoS Biology",
    publisher = "Public Library of Science",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-125457377",
    id = "https://authors.library.caltech.edu/records/y0yeq-t0p17",
    issn = "1545-7885",
    doi = "10.1371/journal.pbio.1000343",
    volume = "8",
    number = "3",
    pmcid = "PMC2843597",
    pages = "Art. No. e1000343"
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@article{https://authors.library.caltech.edu/records/2jf89-zme75,
    authors = "Hilty, Markus and Burke, Conor and Pedro, Helder and Cardenas, Paul and Bush, Andy and Bossley, Cara and Davies, Jane and Ervine, Aaron and Poulter, Len and Pachter, Lior and Moffatt, Miriam F. and Cookson, William O. C.",
    title = "Disordered Microbial Communities in Asthmatic Airways",
    journal = "PLOS ONE",
    publisher = "Public Library of Science",
    year = "2010",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-131319458",
    id = "https://authors.library.caltech.edu/records/2jf89-zme75",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0008578",
    volume = "5",
    number = "1",
    pmcid = "PMC2798952",
    pages = "Art. No. e8578"
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@article{https://authors.library.caltech.edu/records/fbdkt-n0b22,
    authors = "Morton, Jason and Pachter, Lior and Shiu, Anne and Sturmfels, Bernd and Wienand, Oliver",
    title = "Convex Rank Tests and Semigraphoids",
    journal = "SIAM Journal on Discrete Mathematics",
    publisher = "Society for Industrial and Applied Mathematics",
    year = "2009",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-133921221",
    id = "https://authors.library.caltech.edu/records/fbdkt-n0b22",
    issn = "0895-4801",
    doi = "10.1137/080715822",
    volume = "23",
    number = "3",
    pages = "1117-1134"
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@article{https://authors.library.caltech.edu/records/6d8hx-6w537,
    authors = "Trapnell, Cole and Pachter, Lior and Salzberg, Steven L.",
    title = "TopHat: discovering splice junctions with RNA-Seq",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2009",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-141357019",
    id = "https://authors.library.caltech.edu/records/6d8hx-6w537",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btp120",
    volume = "25",
    number = "9",
    pmcid = "PMC2672628",
    pages = "1105-1111"
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@article{https://authors.library.caltech.edu/records/rbmj2-r9288,
    authors = "Bradley, Robert K. and Roberts, Adam and Smoot, Michael and Juvekar, Sudeep and Do, Jaeyoung and Dewey, Colin and Holmes, Ian and Pachter, Lior",
    title = "Fast Statistical Alignment",
    journal = "PLOS Computational Biology",
    publisher = "Public Library of Science",
    year = "2009",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-135830452",
    id = "https://authors.library.caltech.edu/records/rbmj2-r9288",
    issn = "1553-7358",
    doi = "10.1371/journal.pcbi.1000392",
    volume = "5",
    number = "5",
    pmcid = "PMC2684580",
    pages = "Art. No. e1000392"
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@article{https://authors.library.caltech.edu/records/8c606-67x34,
    authors = "Mihaescu, Radu and Levy, Dan and Pachter, Lior",
    title = "Why neighbor-joining works",
    journal = "Algorithmica",
    publisher = "Springer",
    year = "2009",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-094400293",
    id = "https://authors.library.caltech.edu/records/8c606-67x34",
    issn = "0178-4617",
    doi = "10.1007/s00453-007-9116-4",
    volume = "54",
    number = "1",
    pages = "1-24"
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@article{https://authors.library.caltech.edu/records/64b05-1m385,
    authors = "Bradley, Robert K. and Pachter, Lior and Holmes, Ian",
    title = "Specific alignment of structured RNA: stochastic grammars and sequence annealing",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2008",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-103825678",
    id = "https://authors.library.caltech.edu/records/64b05-1m385",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btn495",
    volume = "24",
    number = "23",
    pmcid = "PMC2732270",
    pages = "2677-2683"
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@article{https://authors.library.caltech.edu/records/newbg-mqk69,
    authors = "Mihaescu, Radu and Pachter, Lior",
    title = "Combinatorics of least squares trees",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2008",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-144249240",
    id = "https://authors.library.caltech.edu/records/newbg-mqk69",
    issn = "0027-8424",
    doi = "10.1073/pnas.0802089105",
    volume = "105",
    number = "36",
    pmcid = "PMC2533170",
    pages = "13206-13211"
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@article{https://authors.library.caltech.edu/records/xmecw-c0d24,
    authors = "Dequéant, Mary-Lee and Ahnert, Sebastian and Edelsbrunner, Herbert and Fink, Thomas M. A. and Glynn, Earl F. and Hattem, Gaye and Kudlicki, Andrzej and Mileyko, Yuriy and Morton, Jason and Mushegian, Arcady R. and Pachter, Lior and Rowicka, Maga and Shiu, Anne and Sturmfels, Bernd and Pourquié, Olivier",
    title = "Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock",
    journal = "PLOS ONE",
    publisher = "Public Library of Science",
    year = "2008",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-104539290",
    id = "https://authors.library.caltech.edu/records/xmecw-c0d24",
    issn = "1932-6203",
    doi = "10.1371/journal.pone.0002856",
    volume = "3",
    number = "8",
    pmcid = "PMC2481401",
    pages = "Art. No. e2856"
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@article{https://authors.library.caltech.edu/records/pc0jh-45q03,
    authors = "Satija, Rahul and Pachter, Lior and Hein, Jotun",
    title = "Combining statistical alignment and phylogenetic footprinting to detect regulatory elements",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2008",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-111036850",
    id = "https://authors.library.caltech.edu/records/pc0jh-45q03",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btn104",
    volume = "24",
    number = "10",
    pages = "1236-1242"
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@article{https://authors.library.caltech.edu/records/096a7-06d87,
    authors = "Tesler, Glenn and Eriksson, Nicholas and Pachter, Lior and Mitsuya, Yumi and Rhee, Soo-Yon and Wang, Chunlin and Gharizadeh, Baback and Ronaghi, Mostafa and Shafer, Robert W. and Beerenwinkel, Niko",
    title = "Viral Population Estimation Using Pyrosequencing",
    journal = "PLoS Computational Biology",
    publisher = "Public Library of Science",
    year = "2008",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-133352205",
    id = "https://authors.library.caltech.edu/records/096a7-06d87",
    issn = "1553-7358",
    doi = "10.1371/journal.pcbi.1000074",
    volume = "4",
    number = "5",
    pmcid = "PMC2323617",
    pages = "Art. No. e1000074"
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@article{https://authors.library.caltech.edu/records/mdrpa-46960,
    authors = "Eickmeyer, Kord and Huggins, Peter and Pachter, Lior and Yoshida, Ruriko",
    title = "On the optimality of the neighbor-joining algorithm",
    journal = "Algorithms for Molecular Biology",
    publisher = "BioMed Central",
    year = "2008",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-143033087",
    id = "https://authors.library.caltech.edu/records/mdrpa-46960",
    issn = "1748-7188",
    doi = "10.1186/1748-7188-3-5",
    volume = "3",
    pmcid = "PMC2430562",
    pages = "Art. No. 5"
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@article{https://authors.library.caltech.edu/records/crp2q-p2j11,
    authors = "Stark, Alexander and Pachter, Lior",
    title = "Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-112926954",
    id = "https://authors.library.caltech.edu/records/crp2q-p2j11",
    issn = "0028-0836",
    doi = "10.1038/nature06340",
    volume = "450",
    number = "7167",
    pmcid = "PMC2474711",
    pages = "219-232"
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@article{https://authors.library.caltech.edu/records/04wc6-q2j80,
    authors = "Clark, Andrew G. and Pachter, Lior",
    title = "Evolution of genes and genomes on the Drosophila phylogeny",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-113900780",
    id = "https://authors.library.caltech.edu/records/04wc6-q2j80",
    issn = "0028-0836",
    doi = "10.1038/nature06341",
    volume = "450",
    number = "7167",
    pages = "203-218"
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@article{https://authors.library.caltech.edu/records/qj3nn-jb436,
    authors = "Begun, David J. and Holloway, Alisha K. and Stevens, Kristian and Hillier, LaDeana W. and Poh, Yu-Ping and Hahn, Matthew W. and Nista, Phillip M. and Jones, Corbin D. and Kern, Andrew D. and Dewey, Colin N. and Pachter, Lior and Myers, Eugene and Langley, Charles H.",
    title = "Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans",
    journal = "PLoS Biology",
    publisher = "Public Library of Science",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-114846354",
    id = "https://authors.library.caltech.edu/records/qj3nn-jb436",
    issn = "1545-7885",
    doi = "10.1371/journal.pbio.0050310",
    volume = "5",
    number = "11",
    pmcid = "PMC2062478",
    pages = "Art. No. e310"
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@article{https://authors.library.caltech.edu/records/yenc3-ndk14,
    authors = "Huggins, Peter and Pachter, Lior and Sturmfels, Bernd",
    title = "Towards the Human Genotope",
    journal = "Bulletin of Mathematical Biology",
    publisher = "Springer",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-095818473",
    id = "https://authors.library.caltech.edu/records/yenc3-ndk14",
    issn = "0092-8240",
    doi = "10.1007/s11538-007-9244-7",
    volume = "69",
    number = "8",
    pages = "2723-2735"
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@article{https://authors.library.caltech.edu/records/znssb-fyb07,
    authors = "Beerenwinkel, Niko and Pachter, Lior and Sturmfels, Bernd",
    title = "Epistasis and Shapes of Fitness Landscapes",
    journal = "Statistica Sinica",
    publisher = "Institute of Statistical Science, Academia Sinica",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-094958898",
    id = "https://authors.library.caltech.edu/records/znssb-fyb07",
    issn = "1017-0405",
    doi = "10.48550/arXiv.0603034",
    volume = "17",
    number = "4",
    pages = "1317-1342"
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@article{https://authors.library.caltech.edu/records/47a83-v6n34,
    authors = "Morton, Jason and Pachter, Lior and Shiu, Anne and Sturmfels, Bernd",
    title = "The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies",
    journal = "Statistical Applications in Genetics and Molecular Biology",
    publisher = "De Gruyter",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170306-154012533",
    id = "https://authors.library.caltech.edu/records/47a83-v6n34",
    issn = "2194-6302",
    doi = "10.2202/1544-6115.1286",
    volume = "6",
    pages = "Art. No. 21"
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@article{https://authors.library.caltech.edu/records/q89db-2cr95,
    authors = "Chatterji, Sourav and Pachter, Lior",
    title = "Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor",
    journal = "Genomics",
    publisher = "Elsevier",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-130932831",
    id = "https://authors.library.caltech.edu/records/q89db-2cr95",
    issn = "0888-7543",
    doi = "10.1016/j.ygeno.2007.03.008",
    volume = "90",
    number = "1",
    pmcid = "PMC2034525",
    pages = "44-48"
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@article{https://authors.library.caltech.edu/records/0dpmy-1bc16,
    authors = "Birney, Ewan and Pachter, Lior",
    title = "Identification and analysis of functional elements in 1\% of the human genome by the ENCODE pilot project",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-121815071",
    id = "https://authors.library.caltech.edu/records/0dpmy-1bc16",
    issn = "0028-0836",
    doi = "10.1038/nature05874",
    volume = "447",
    number = "7146",
    pmcid = "PMC2212820",
    pages = "799-816"
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@article{https://authors.library.caltech.edu/records/jz1bx-4kd75,
    authors = "Margulies, Elliott H. and Pachter, Lior",
    title = "Analyses of deep mammalian sequence alignments and constraint predictions for 1\% of the human genome",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-125526948",
    id = "https://authors.library.caltech.edu/records/jz1bx-4kd75",
    issn = "1088-9051",
    doi = "10.1101/gr.6034307",
    volume = "17",
    number = "6",
    pmcid = "PMC1891336",
    pages = "760-774"
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@article{https://authors.library.caltech.edu/records/tmz64-b0883,
    authors = "Pachter, Lior",
    title = "Interpreting the unculturable majority",
    journal = "Nature Methods",
    publisher = "Nature Publishing Group",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-131612759",
    id = "https://authors.library.caltech.edu/records/tmz64-b0883",
    issn = "1548-7091",
    doi = "10.1038/nmeth0607-479",
    volume = "4",
    number = "6",
    pages = "479-480"
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@article{https://authors.library.caltech.edu/records/1wmws-xht65,
    authors = "Beerenwinkel, Niko and Pachter, Lior and Sturmfels, Bernd and Elena, Santiago F. and Lenski, Richard E.",
    title = "Analysis of epistatic interactions and fitness landscapes using a new geometric approach",
    journal = "BMC Evolutionary Biology",
    publisher = "BioMed Central",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-131928305",
    id = "https://authors.library.caltech.edu/records/1wmws-xht65",
    issn = "1471-2148",
    doi = "10.1186/1471-2148-7-60",
    volume = "7",
    pmcid = "PMC1865543",
    pages = "Art. No. 60"
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@article{https://authors.library.caltech.edu/records/737t0-a8613,
    authors = "Pachter, Lior and Sturmfels, Bernd",
    title = "The Mathematics of Phylogenomics",
    journal = "SIAM Review",
    publisher = "Society for Industrial and Applied Mathematics",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-085456375",
    id = "https://authors.library.caltech.edu/records/737t0-a8613",
    issn = "0036-1445",
    doi = "10.1137/050632634",
    volume = "49",
    number = "1",
    pages = "3-31"
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@article{https://authors.library.caltech.edu/records/pmyqk-7z667,
    authors = "Schwartz, Ariel S. and Pachter, Lior",
    title = "Multiple alignment by sequence annealing",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2007",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-134453947",
    id = "https://authors.library.caltech.edu/records/pmyqk-7z667",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btl311",
    volume = "23",
    number = "2",
    pages = "e24-e29"
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@article{https://authors.library.caltech.edu/records/kk2y6-qk074,
    authors = "Dewey, Colin N. and Huggins, Peter M. and Woods, Kevin and Sturmfels, Bernd and Pachter, Lior",
    title = "Parametric Alignment of Drosophila Genomes",
    journal = "PLoS Computational Biology",
    publisher = "Public Library of Science",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-090954418",
    id = "https://authors.library.caltech.edu/records/kk2y6-qk074",
    issn = "1553-734X",
    doi = "10.1371/journal.pcbi.0020073",
    volume = "2",
    number = "6",
    pmcid = "PMC1480539",
    pages = "Art. No. e73"
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@article{https://authors.library.caltech.edu/records/9rzxt-bad89,
    authors = "Dewey, Colin N. and Pachter, Lior",
    title = "Evolution at the nucleotide level: the problem of multiple whole-genome alignment",
    journal = "Human Molecular Genetics",
    publisher = "Oxford University Press",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-162320251",
    id = "https://authors.library.caltech.edu/records/9rzxt-bad89",
    issn = "0964-6906",
    doi = "10.1093/hmg/ddl056",
    volume = "15",
    number = "Suppl. 1",
    pages = "R51-R56"
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@article{https://authors.library.caltech.edu/records/4g2cj-jb389,
    authors = "Chatterji, Sourav and Pachter, Lior",
    title = "Reference based annotation with GeneMapper",
    journal = "Genome Biology",
    publisher = "BioMed Central",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-162728814",
    id = "https://authors.library.caltech.edu/records/4g2cj-jb389",
    issn = "1465-6906",
    doi = "10.1186/gb-2006-7-4-r29",
    volume = "7",
    number = "4",
    pmcid = "PMC1557983",
    pages = "Art. No. R29"
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@article{https://authors.library.caltech.edu/records/rfdxr-1as30,
    authors = "Lall, Sabbi and Grün, Dominic and Krek, Azra and Chen, Kevin and Wang, Yi-Lu and Dewey, Colin N. and Sood, Pranidhi and Colombo, Teresa and Bray, Nicolas and MacMenamin, Philip and Kao, Huey-Ling and Gunsalus, Kristin C. and Pachter, Lior and Piano, Fabio and Rajewsky, Nikolaus",
    title = "A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans",
    journal = "Current Biology",
    publisher = "Cell Press",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-164849681",
    id = "https://authors.library.caltech.edu/records/rfdxr-1as30",
    issn = "0960-9822",
    doi = "10.1016/j.cub.2006.01.050",
    volume = "16",
    number = "5",
    pages = "460-471"
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@article{https://authors.library.caltech.edu/records/1hgt0-34a86,
    authors = "Levy, Dan and Yoshida, Ruriko and Pachter, Lior",
    title = "Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates",
    journal = "Molecular Biology and Evolution",
    publisher = "Oxford University Press",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-164418033",
    id = "https://authors.library.caltech.edu/records/1hgt0-34a86",
    issn = "0737-4038",
    doi = "10.1093/molbev/msj059",
    volume = "23",
    number = "3",
    pages = "491-498"
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    authors = "Caspi, Anat and Pachter, Lior",
    title = "Identification of transposable elements using multiple alignments of related genomes",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2006",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-111109017",
    id = "https://authors.library.caltech.edu/records/y9ss2-0wq61",
    issn = "1088-9051",
    doi = "10.1101/gr.4361206",
    volume = "16",
    number = "2",
    pmcid = "PMC1361722",
    pages = "260-270"
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@article{https://authors.library.caltech.edu/records/czhmv-7p908,
    authors = "Chen, Kevin and Pachter, Lior",
    title = "Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities",
    journal = "PLoS Computational Biology",
    publisher = "Public Library of Science",
    year = "2005",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-124940796",
    id = "https://authors.library.caltech.edu/records/czhmv-7p908",
    issn = "1553-734X",
    doi = "10.1371/journal.pcbi.0010024",
    volume = "1",
    number = "2",
    pmcid = "PMC1185649",
    pages = "Art. No. e24"
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@article{https://authors.library.caltech.edu/records/yf5ce-tav61,
    authors = "Chatterji, Sourav and Pachter, Lior",
    title = "Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling",
    journal = "Journal of Computational Biology",
    publisher = "Mary Ann Liebert, Inc.",
    year = "2005",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-125857130",
    id = "https://authors.library.caltech.edu/records/yf5ce-tav61",
    issn = "1066-5277",
    doi = "10.1089/cmb.2005.12.599",
    volume = "12",
    number = "6",
    pages = "599-608"
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@article{https://authors.library.caltech.edu/records/dejyt-dqe25,
    authors = "McAuliffe, Jon D. and Jordan, Michael I. and Pachter, Lior",
    title = "Subtree power analysis and species selection for comparative genomics",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2005",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20190503-150942109",
    id = "https://authors.library.caltech.edu/records/dejyt-dqe25",
    issn = "0027-8424",
    doi = "10.1073/pnas.0502790102",
    volume = "102",
    number = "22",
    pmcid = "PMC1142384",
    pages = "7900-7905"
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@article{https://authors.library.caltech.edu/records/tr080-6rv26,
    authors = "Hillier, LaDeana W. and Pachter, Lior",
    title = "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-130340353",
    id = "https://authors.library.caltech.edu/records/tr080-6rv26",
    issn = "0028-0836",
    doi = "10.1038/nature03154",
    volume = "432",
    number = "7018",
    pages = "695-716"
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@article{https://authors.library.caltech.edu/records/q9x6k-rkc63,
    authors = "Boffelli, Dario and Weer, Claire V. and Weng, Li and Lewis, Keith D. and Shoukry, Malak I. and Pachter, Lior and Keys, David N. and Rubin, Edward M.",
    title = "Intraspecies sequence comparisons for annotating genomes",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-131651119",
    id = "https://authors.library.caltech.edu/records/q9x6k-rkc63",
    issn = "1088-9051",
    doi = "10.1101/gr.3199704",
    volume = "14",
    number = "12",
    pmcid = "PMC534664",
    pages = "2406-2411"
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@article{https://authors.library.caltech.edu/records/hn6be-bya11,
    authors = "Pachter, Lior and Sturmfels, Bernd",
    title = "Parametric Inference for Biological Sequence Analysis",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-081738298",
    id = "https://authors.library.caltech.edu/records/hn6be-bya11",
    issn = "0027-8424",
    doi = "10.1073/pnas.0406011101",
    volume = "101",
    number = "46",
    pmcid = "PMC528961",
    pages = "16138-16143"
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@article{https://authors.library.caltech.edu/records/9npck-fag88,
    authors = "Pachter, Lior and Sturmfels, Bernd",
    title = "Tropical Geometry of Statistical Models",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    publisher = "National Academy of Sciences",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-073504137",
    id = "https://authors.library.caltech.edu/records/9npck-fag88",
    issn = "0027-8424",
    doi = "10.1073/pnas.0406010101",
    volume = "101",
    number = "46",
    pmcid = "PMC528960",
    pages = "16132-16137"
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@article{https://authors.library.caltech.edu/records/h1p73-wax92,
    authors = "Feingold, E. A. and Pachter, L.",
    title = "The ENCODE (ENCyclopedia Of DNA Elements) Project",
    journal = "Science",
    publisher = "American Association for the Advancement of Science",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-133717579",
    id = "https://authors.library.caltech.edu/records/h1p73-wax92",
    issn = "0036-8075",
    doi = "10.1126/science.1105136",
    volume = "306",
    number = "5696",
    pages = "636-640"
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@article{https://authors.library.caltech.edu/records/h1v4b-fzh55,
    authors = "McAuliffe, Jon D. and Pachter, Lior and Jordan, Michael I.",
    title = "Multiple-sequence functional annotation and the generalized hidden Markov phylogeny",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-135943475",
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    issn = "1367-4803",
    doi = "10.1093/bioinformatics/bth153",
    volume = "20",
    number = "12",
    pages = "1850-1860"
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@article{https://authors.library.caltech.edu/records/w4ajn-sw675,
    authors = "Frazer, Kelly A. and Pachter, Lior and Poliakov, Alexander and Rubin, Edward M. and Dubchak, Inna",
    title = "VISTA: computational tools for comparative genomics",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-140652072",
    id = "https://authors.library.caltech.edu/records/w4ajn-sw675",
    issn = "0305-1048",
    doi = "10.1093/nar/gkh458",
    volume = "32",
    number = "Suppl. 2",
    pmcid = "PMC441596",
    pages = "W273-W279"
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@article{https://authors.library.caltech.edu/records/2v174-rtt49,
    authors = "Pachter, L. and Speyer, D.",
    title = "Reconstructing Trees from Subtree Weights",
    journal = "Applied Mathematics Letters",
    publisher = "Elsevier",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-080948323",
    id = "https://authors.library.caltech.edu/records/2v174-rtt49",
    issn = "0893-9659",
    doi = "10.1016/S0893-9659(04)90095-X",
    volume = "17",
    number = "6",
    pages = "615-621"
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@article{https://authors.library.caltech.edu/records/t95d7-66x59,
    authors = "Gibbs, Richard A. and Pachter, Lior",
    title = "Genome sequence of the Brown Norway rat yields insights into mammalian evolution",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-145138306",
    id = "https://authors.library.caltech.edu/records/t95d7-66x59",
    issn = "0028-0836",
    doi = "10.1038/nature02426",
    volume = "428",
    number = "6982",
    pages = "493-521"
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@article{https://authors.library.caltech.edu/records/9kwva-gf330,
    authors = "Dewey, Colin and Wu, Jia Qian and Cawley, Simon and Alexandersson, Marina and Gibbs, Richard and Pachter, Lior",
    title = "Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-144150791",
    id = "https://authors.library.caltech.edu/records/9kwva-gf330",
    issn = "1088-9051",
    doi = "10.1101/gr.1939804",
    volume = "14",
    number = "4",
    pmcid = "PMC383310",
    pages = "661-664"
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@article{https://authors.library.caltech.edu/records/vf6w0-hrb56,
    authors = "Yap, Von Bing and Pachter, Lior",
    title = "Identification of Evolutionary Hotspots in the Rodent Genomes",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-144803591",
    id = "https://authors.library.caltech.edu/records/vf6w0-hrb56",
    issn = "1088-9051",
    doi = "10.1101/gr.1967904",
    volume = "14",
    number = "4",
    pmcid = "PMC383301",
    pages = "574-579"
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@article{https://authors.library.caltech.edu/records/nb32q-zt780,
    authors = "Bray, Nicolas and Pachter, Lior",
    title = "MAVID: Constrained ancestral alignment of multiple sequences",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170307-074220313",
    id = "https://authors.library.caltech.edu/records/nb32q-zt780",
    issn = "1088-9051",
    doi = "10.1101/gr.1960404",
    volume = "14",
    number = "4",
    pmcid = "PMC383315",
    pages = "693-699"
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@article{https://authors.library.caltech.edu/records/bzm2q-a6208,
    authors = "Chakrabarti, Kushal and Pachter, Lior",
    title = "Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2004",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-142044905",
    id = "https://authors.library.caltech.edu/records/bzm2q-a6208",
    issn = "1088-9051",
    doi = "10.1101/gr.1957004",
    volume = "14",
    number = "4",
    pmcid = "PMC383318",
    pages = "716-720"
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@article{https://authors.library.caltech.edu/records/dkg16-32f71,
    authors = "Cawley, Simon L. and Pachter, Lior",
    title = "HMM sampling and applications to gene finding and alternative splicing",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-151105303",
    id = "https://authors.library.caltech.edu/records/dkg16-32f71",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btg1057",
    volume = "19",
    number = "Suppl 2",
    pages = "ii36-ii41"
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@article{https://authors.library.caltech.edu/records/n5qhb-91b08,
    authors = "Lam, Fumei and Pachter, Lior",
    title = "Forcing numbers of stop signs",
    journal = "Theoretical Computer Science",
    publisher = "Elsevier",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-151538288",
    id = "https://authors.library.caltech.edu/records/n5qhb-91b08",
    issn = "0304-3975",
    doi = "10.1016/S0304-3975(02)00499-1",
    volume = "303",
    number = "2-3",
    pages = "409-416"
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@article{https://authors.library.caltech.edu/records/07qjz-fdj71,
    authors = "Bray, Nicolas and Pachter, Lior",
    title = "MAVID multiple alignment server",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-152103068",
    id = "https://authors.library.caltech.edu/records/07qjz-fdj71",
    issn = "1362-4962",
    doi = "10.1093/nar/gkg623",
    volume = "31",
    number = "13",
    pmcid = "PMC169029",
    pages = "3525-3526"
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@article{https://authors.library.caltech.edu/records/s4hgs-n2n71,
    authors = "Cawley, Simon and Pachter, Lior and Alexandersson, Marina",
    title = "SLAM web server for comparative gene finding and alignment",
    journal = "Nucleic Acids Research",
    publisher = "Oxford University Press",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-152527629",
    id = "https://authors.library.caltech.edu/records/s4hgs-n2n71",
    issn = "1362-4962",
    doi = "10.1093/nar/gkg583",
    volume = "31",
    number = "13",
    pmcid = "PMC168989",
    pages = "3507-3509"
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@article{https://authors.library.caltech.edu/records/azh9j-rwv53,
    authors = "Lam, Fumei and Alexandersson, Marina and Pachter, Lior",
    title = "Picking Alignments from (Steiner) Trees",
    journal = "Journal of Computational Biology",
    publisher = "Mary Ann Liebert, Inc.",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-153301235",
    id = "https://authors.library.caltech.edu/records/azh9j-rwv53",
    issn = "1066-5277",
    doi = "10.1089/10665270360688156",
    volume = "10",
    number = "3-4",
    pages = "509-520"
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@article{https://authors.library.caltech.edu/records/ahkxa-cwz69,
    authors = "Alexandersson, Marina and Cawley, Simon and Pachter, Lior",
    title = "SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-154151410",
    id = "https://authors.library.caltech.edu/records/ahkxa-cwz69",
    issn = "1088-9051",
    doi = "10.1101/gr.424203",
    volume = "13",
    number = "3",
    pmcid = "PMC430255",
    pages = "496-502"
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@article{https://authors.library.caltech.edu/records/hty8p-scq52,
    authors = "Boffelli, Dario and McAuliffe, Jon and Ovcharenko, Dmitriy and Lewis, Keith D. and Ovcharenko, Ivan and Pachter, Lior and Rubin, Edward M.",
    title = "Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome",
    journal = "Science",
    publisher = "American Association for the Advancement of Science",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-154624549",
    id = "https://authors.library.caltech.edu/records/hty8p-scq52",
    issn = "0036-8075",
    doi = "10.1126/science.1081331",
    volume = "299",
    number = "5611",
    pages = "1391-1394"
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@article{https://authors.library.caltech.edu/records/ps1wq-rss05,
    authors = "Bray, Nick and Dubchak, Inna and Pachter, Lior",
    title = "AVID: A Global Alignment Program",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-155631683",
    id = "https://authors.library.caltech.edu/records/ps1wq-rss05",
    issn = "1088-9051",
    doi = "10.1101/gr.789803",
    volume = "13",
    number = "1",
    pmcid = "PMC430967",
    pages = "97-102"
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@article{https://authors.library.caltech.edu/records/2yrxj-wqw78,
    authors = "Couronne, Olivier and Poliakov, Alexander and Bray, Nicolas and Ishkhanov, Tigran and Ryaboy, Dmitriy and Rubin, Edward and Pachter, Lior and Dubchak, Inna",
    title = "Strategies and Tools for Whole-Genome Alignments",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2003",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170308-160145750",
    id = "https://authors.library.caltech.edu/records/2yrxj-wqw78",
    issn = "1088-9051",
    doi = "10.1101/gr.762503",
    volume = "13",
    number = "1",
    pmcid = "PMC430965",
    pages = "73-80"
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@article{https://authors.library.caltech.edu/records/0x565-8ph71,
    authors = "Waterston, Robert H. and Pachter, Lior",
    title = "Initial sequencing and comparative analysis of the mouse genome",
    journal = "Nature",
    publisher = "Nature Publishing Group",
    year = "2002",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-090859678",
    id = "https://authors.library.caltech.edu/records/0x565-8ph71",
    issn = "0028-0836",
    doi = "10.1038/nature01262",
    volume = "420",
    number = "6915",
    pages = "520-562"
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@article{https://authors.library.caltech.edu/records/nvtfr-fpx06,
    authors = "Pachter, Lior and Alexandersson, Marina and Cawley, Simon",
    title = "Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems",
    journal = "Journal of Computational Biology",
    publisher = "Mary Ann Liebert, Inc.",
    year = "2002",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-092737635",
    id = "https://authors.library.caltech.edu/records/nvtfr-fpx06",
    issn = "1066-5277",
    doi = "10.1089/10665270252935520",
    volume = "9",
    number = "2",
    pages = "389-399"
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@article{https://authors.library.caltech.edu/records/mg9tz-23986,
    authors = "Benos, Panayiotis and Pachter, Lior",
    title = "From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2002",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-100309238",
    id = "https://authors.library.caltech.edu/records/mg9tz-23986",
    issn = "1088-9051",
    doi = "10.1101/gr.173801",
    volume = "11",
    number = "5",
    pmcid = "PMC311117",
    pages = "710-730"
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@article{https://authors.library.caltech.edu/records/0947j-v2n07,
    authors = "Loots, Gabriela G. and Ovcharenko, Ivan and Pachter, Lior and Dubchak, Inna and Rubin, Edward M.",
    title = "rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2002",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-093325277",
    id = "https://authors.library.caltech.edu/records/0947j-v2n07",
    issn = "1088-9051",
    doi = "10.1101/gr.225502",
    volume = "12",
    number = "5",
    pmcid = "PMC186580",
    pages = "832-839"
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@article{https://authors.library.caltech.edu/records/3f346-d0z81,
    authors = "Dubchak, Inna and Pachter, Lior",
    title = "The computational challenges of applying comparative-based computational methods to whole genomes",
    journal = "Briefings in Bioinformatics",
    publisher = "Oxford University Press",
    year = "2002",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-093904962",
    id = "https://authors.library.caltech.edu/records/3f346-d0z81",
    issn = "1467-5463",
    doi = "10.1093/bib/3.1.18",
    volume = "3",
    number = "1",
    pages = "18-22"
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@article{https://authors.library.caltech.edu/records/hnyxk-9bm85,
    authors = "Peter, Annette and Pachter, Lior",
    title = "Mapping and identification of essential gene functions on the X chromosome of Drosophila",
    journal = "EMBO Reports",
    publisher = "European Molecular Biology Organization",
    year = "2002",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-095230836",
    id = "https://authors.library.caltech.edu/records/hnyxk-9bm85",
    issn = "1469-221X",
    doi = "10.1093/embo-reports/kvf012",
    volume = "3",
    number = "1",
    pmcid = "PMC1083931",
    pages = "34-38"
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@article{https://authors.library.caltech.edu/records/tjked-pcn03,
    authors = "Mayor, Chris and Brudno, Michael and Schwartz, Jody R. and Poliakov, Alexander and Rubin, Edward M. and Frazer, Kelly A. and Pachter, Lior S. and Dubchak, Inna",
    title = "VISTA : visualizing global DNA sequence alignments of arbitrary length",
    journal = "Bioinformatics",
    publisher = "Oxford University Press",
    year = "2000",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-104254761",
    id = "https://authors.library.caltech.edu/records/tjked-pcn03",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/16.11.1046",
    volume = "16",
    number = "11",
    pages = "1046-1047"
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@article{https://authors.library.caltech.edu/records/yas84-r6j70,
    authors = "Dubchak, Inna and Brudno, Michael and Loots, Gabriela G. and Pachter, Lior and Mayor, Chris and Rubin, Edward M. and Frazer, Kelly A.",
    title = "Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2000",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-111029375",
    id = "https://authors.library.caltech.edu/records/yas84-r6j70",
    issn = "1088-9051",
    doi = "10.1101/gr.142200",
    volume = "10",
    number = "9",
    pmcid = "PMC310906",
    pages = "1304-1306"
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@article{https://authors.library.caltech.edu/records/9zeww-dy998,
    authors = "Batzoglou, Serafim and Pachter, Lior and Mesirov, Jill P. and Berger, Bonnie and Lander, Eric S.",
    title = "Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction",
    journal = "Genome Research",
    publisher = "Cold Spring Harbor Laboratory Press",
    year = "2000",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-110441139",
    id = "https://authors.library.caltech.edu/records/9zeww-dy998",
    issn = "1088-9051",
    doi = "10.1101/gr.10.7.950",
    volume = "10",
    number = "7",
    pmcid = "PMC310911",
    pages = "950-958"
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@article{https://authors.library.caltech.edu/records/vh6dd-k6133,
    authors = "Pachter, Lior and Batzoglou, Serafim and Spitkovsky, Valentin I. and Banks, Eric and Lander, Eric S. and Kleitman, Daniel J. and Berger, Bonnie",
    title = "A Dictionary-Based Approach for Gene Annotation",
    journal = "Journal of Computational Biology",
    publisher = "Mary Ann Liebert, Inc.",
    year = "1999",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-113000311",
    id = "https://authors.library.caltech.edu/records/vh6dd-k6133",
    issn = "1066-5277",
    doi = "10.1089/106652799318364",
    volume = "6",
    number = "3-4",
    pages = "419-430"
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@article{https://authors.library.caltech.edu/records/8cx0q-kp250,
    authors = "Pachter, Lior and Kim, Peter",
    title = "Forcing matchings on square grids",
    journal = "Discrete Mathematics",
    publisher = "Elsevier",
    year = "1998",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-141622723",
    id = "https://authors.library.caltech.edu/records/8cx0q-kp250",
    issn = "0012-365X",
    doi = "10.1016/S0012-365X(97)00266-5",
    volume = "190",
    number = "1-3",
    pages = "287-294"
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@article{https://authors.library.caltech.edu/records/xbfv1-a5n80,
    authors = "Kleitman, D. and Pachter, L.",
    title = "Finding Convex Sets Among Points in the Plane",
    journal = "Discrete and Computational Geometry",
    publisher = "Springer",
    year = "1998",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-114305555",
    id = "https://authors.library.caltech.edu/records/xbfv1-a5n80",
    issn = "0179-5376",
    doi = "10.1007/PL00009358",
    volume = "19",
    number = "3",
    pages = "405-410"
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@article{https://authors.library.caltech.edu/records/jxxfj-d1y91,
    authors = "Batzoglou, Serafim and Berger, Bonnie and Kleitman, Daniel J. and Lander, Eric S. and Pachter, Lior",
    title = "Recent Developments in Computational Gene Recognition",
    journal = "Documenta Mathematica",
    publisher = "Deutsche Mathematiker-Vereinigung (DMV)",
    year = "1998",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-142440565",
    id = "https://authors.library.caltech.edu/records/jxxfj-d1y91",
    issn = "1431-0635",
    volume = "ICM I",
    pages = "649-658"
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@article{https://authors.library.caltech.edu/records/ccpk8-h2947,
    authors = "Pachter, Lior",
    title = "Constructing status injective graphs",
    journal = "Discrete Applied Mathematics",
    publisher = "Elsevier",
    year = "1997",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-143338663",
    id = "https://authors.library.caltech.edu/records/ccpk8-h2947",
    issn = "0166-218X",
    doi = "10.1016/S0166-218X(97)00073-5",
    volume = "80",
    number = "1",
    pages = "107-113"
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@article{https://authors.library.caltech.edu/records/mxdck-d5b36,
    authors = "Pachter, Lior",
    title = "Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes",
    journal = "Electronic Journal of Combinatorics",
    publisher = "Electronic Journal of Combinatorics",
    year = "1997",
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20170309-144854496",
    id = "https://authors.library.caltech.edu/records/mxdck-d5b36",
    issn = "1077-8926",
    volume = "4",
    number = "1",
    pages = "Art. No. R29"
}