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Wong, Valerie L. and Ellison, Christopher E., et el. (2014) Structural Variation among Wild and Industrial Strains of Penicillium chrysogenum ; PLoS ONE; Vol. 9; No. 5; Art. No. e96784; PMCID PMC4019546; 10.1371/journal.pone.0096784
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Pimentel, Harold and Parra, Marilynn, et el. (2014) A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis ; Nucleic Acids Research; Vol. 42; No. 6; 4031-4042; PMCID PMC3973340; 10.1093/nar/gkt1388
Roberts, Adam and Feng, Harvey, et el. (2013) Fragment assignment in the cloud with eXpress-D ; BMC Bioinformatics; Vol. 14; Art. No. 358; PMCID PMC3881492; 10.1186/1471-2105-14-358
Roberts, Adam and Schaeffer, Lorian, et el. (2013) Updating RNA-Seq analyses after re-annotation ; Bioinformatics; Vol. 29; No. 13; 1631-1637; PMCID PMC3694665; 10.1093/bioinformatics/btt197
Kleinman, Aaron and Harel, Matan, et el. (2013) Affine and Projective Tree Metric Theorems ; Annals of Combinatorics; Vol. 17; No. 1; 205-228; 10.1007/s00026-012-0173-2
Rahman, Atif and Pachter, Lior (2013) CGAL: computing genome assembly likelihoods ; Genome Biology; Vol. 14; No. 1; Art. No. R8; PMCID PMC3663106; 10.1186/gb-2013-14-1-r8
Roberts, Adam and Pachter, Lior (2013) Streaming fragment assignment for real-time analysis of sequencing experiments ; Nature Methods; Vol. 10; No. 1; 71-73; PMCID PMC3880119; 10.1038/nmeth.2251
Trapnell, Cole and Hendrickson, David G., et el. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq ; Nature Biotechnology; Vol. 31; No. 1; 46-53; PMCID PMC3869392; 10.1038/nbt.2450
Mortimer, Stefanie A. and Trapnell, Cole, et el. (2012) SHAPE-Seq: High-Throughput RNA Structure Analysis ; ISBN 9780470559277; Current Protocols in Chemical Biology; 275-297; 10.1002/9780470559277.ch120019
Hower, Valerie and Starfield, Richard, et el. (2012) Quantifying uniformity of mapped reads ; Bioinformatics; Vol. 28; No. 20; 2680-2682; PMCID PMC3467739; 10.1093/bioinformatics/bts451
Pachter, Lior (2012) A closer look at RNA editing ; Nature Biotechnology; Vol. 30; No. 3; 246-247; 10.1038/nbt.2156
Trapnell, Cole and Roberts, Adam, et el. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks ; Nature Protocols; Vol. 7; No. 3; 562-578; PMCID PMC3334321; 10.1038/nprot.2012.016
Martin, David I. K. and Singer, Meromit, et el. (2011) Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states ; Genome Research; Vol. 21; No. 12; 2049-2057; PMCID PMC3227095; 10.1101/gr.122721.111
Roberts, Adam and Pachter, Lior (2011) RNA-Seq and find: entering the RNA deep field ; Genome Medicine; Vol. 3; No. 11; Art. No. 74; PMCID PMC3308029; 10.1186/gm290
Meacham, Frazer and Boffelli, Dario, et el. (2011) Identification and correction of systematic error in high-throughput sequence data ; BMC Bioinformatics; Vol. 12; Art. No. 451; PMCID PMC3295828; 10.1186/1471-2105-12-451
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Aviran, Sharon and Lucks, Julius B., et el. (2011) RNA structure characterization from chemical mapping experiments ; ISBN 978-1-4577-1817-5; 49th Annual Allerton Conference on Communication, Control, and Computing; 1743-1750; 10.1109/Allerton.2011.6120379
Snir, Sagi and Pachter, Lior (2011) Tracing the Most Parsimonious Indel History ; Journal of Computational Biology; Vol. 18; No. 8; 967-986; 10.1089/cmb.2010.0325
Levy, Dan and Pachter, Lior (2011) The neighbor-net algorithm ; Advances in Applied Mathematics; Vol. 47; No. 2; 240-258; 10.1016/j.aam.2010.09.002
Lucks, Julius B. and Mortimer, Stefanie A., et el. (2011) Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 27; 11063-11068; PMCID PMC3131332; 10.1073/pnas.1106501108
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Roberts, Adam and Trapnell, Cole, et el. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias ; Genome Biology; Vol. 12; No. 3; Art. No. R22; PMCID PMC3129672; 10.1186/gb-2011-12-3-r22
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Willerth, Stephanie M. and Pedro, Hélder A. M., et el. (2010) Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology ; PLOS ONE; Vol. 5; No. 10; Art. No. e13564; PMCID PMC2962647; 10.1371/journal.pone.0013564
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Singer, Meromit and Boffelli, Dario, et el. (2010) MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations ; PLOS Computational Biology; Vol. 6; No. 8; Art. No. e1000888; PMCID PMC2924245; 10.1371/journal.pcbi.1000888
Levin, Tera C. and Glazer, Andrew M., et el. (2010) Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study ; PLOS ONE; Vol. 5; No. 7; Art. No. e11645; PMCID PMC2912228; 10.1371/journal.pone.0011645
Lapuk, Anna and Marr, Henry, et el. (2010) Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer ; Molecular Cancer Research; Vol. 8; No. 7; 961-974; PMCID PMC2911965; 10.1158/1541-7786.MCR-09-0528
Trapnell, Cole and Williams, Brian A., et el. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation ; Nature Biotechnology; Vol. 28; No. 5; 511-515; PMCID PMC3146043; 10.1038/nbt.1621
Bradley, Robert K. and Li, Xiao-Yong, et el. (2010) Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species ; PLoS Biology; Vol. 8; No. 3; Art. No. e1000343; PMCID PMC2843597; 10.1371/journal.pbio.1000343
Hilty, Markus and Burke, Conor, et el. (2010) Disordered Microbial Communities in Asthmatic Airways ; PLOS ONE; Vol. 5; No. 1; Art. No. e8578; PMCID PMC2798952; 10.1371/journal.pone.0008578
Morton, Jason and Pachter, Lior, et el. (2009) Convex Rank Tests and Semigraphoids ; SIAM Journal on Discrete Mathematics; Vol. 23; No. 3; 1117-1134; 10.1137/080715822
Trapnell, Cole and Pachter, Lior, et el. (2009) TopHat: discovering splice junctions with RNA-Seq ; Bioinformatics; Vol. 25; No. 9; 1105-1111; PMCID PMC2672628; 10.1093/bioinformatics/btp120
Bradley, Robert K. and Roberts, Adam, et el. (2009) Fast Statistical Alignment ; PLOS Computational Biology; Vol. 5; No. 5; Art. No. e1000392; PMCID PMC2684580; 10.1371/journal.pcbi.1000392
Mihaescu, Radu and Levy, Dan, et el. (2009) Why neighbor-joining works ; Algorithmica; Vol. 54; No. 1; 1-24; 10.1007/s00453-007-9116-4
Bradley, Robert K. and Pachter, Lior, et el. (2008) Specific alignment of structured RNA: stochastic grammars and sequence annealing ; Bioinformatics; Vol. 24; No. 23; 2677-2683; PMCID PMC2732270; 10.1093/bioinformatics/btn495
Mihaescu, Radu and Pachter, Lior (2008) Combinatorics of least squares trees ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 36; 13206-13211; PMCID PMC2533170; 10.1073/pnas.0802089105
Dequéant, Mary-Lee and Ahnert, Sebastian, et el. (2008) Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock ; PLOS ONE; Vol. 3; No. 8; Art. No. e2856; PMCID PMC2481401; 10.1371/journal.pone.0002856
Satija, Rahul and Pachter, Lior, et el. (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements ; Bioinformatics; Vol. 24; No. 10; 1236-1242; 10.1093/bioinformatics/btn104
Tesler, Glenn and Eriksson, Nicholas, et el. (2008) Viral Population Estimation Using Pyrosequencing ; PLoS Computational Biology; Vol. 4; No. 5; Art. No. e1000074; PMCID PMC2323617; 10.1371/journal.pcbi.1000074
Eickmeyer, Kord and Huggins, Peter, et el. (2008) On the optimality of the neighbor-joining algorithm ; Algorithms for Molecular Biology; Vol. 3; Art. No. 5; PMCID PMC2430562; 10.1186/1748-7188-3-5
Stark, Alexander and Pachter, Lior (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures ; Nature; Vol. 450; No. 7167; 219-232; PMCID PMC2474711; 10.1038/nature06340
Clark, Andrew G. and Pachter, Lior, et el. (2007) Evolution of genes and genomes on the Drosophila phylogeny ; Nature; Vol. 450; No. 7167; 203-218; 10.1038/nature06341
Huggins, Peter and Pachter, Lior, et el. (2007) Towards the Human Genotope ; Bulletin of Mathematical Biology; Vol. 69; No. 8; 2723-2735; 10.1007/s11538-007-9244-7
Begun, David J. and Holloway, Alisha K., et el. (2007) Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans ; PLoS Biology; Vol. 5; No. 11; Art. No. e310; PMCID PMC2062478; 10.1371/journal.pbio.0050310
Beerenwinkel, Niko and Pachter, Lior, et el. (2007) Epistasis and Shapes of Fitness Landscapes ; Statistica Sinica; Vol. 17; No. 4; 1317-1342; 10.48550/arXiv.0603034
Morton, Jason and Pachter, Lior, et el. (2007) The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies ; Statistical Applications in Genetics and Molecular Biology; Vol. 6; Art. No. 21; 10.2202/1544-6115.1286
Chatterji, Sourav and Pachter, Lior (2007) Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor ; Genomics; Vol. 90; No. 1; 44-48; PMCID PMC2034525; 10.1016/j.ygeno.2007.03.008
Birney, Ewan and Pachter, Lior, et el. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project ; Nature; Vol. 447; No. 7146; 799-816; PMCID PMC2212820; 10.1038/nature05874
Margulies, Elliott H. and Pachter, Lior, et el. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome ; Genome Research; Vol. 17; No. 6; 760-774; PMCID PMC1891336; 10.1101/gr.6034307
Pachter, Lior (2007) Interpreting the unculturable majority ; Nature Methods; Vol. 4; No. 6; 479-480; 10.1038/nmeth0607-479
Beerenwinkel, Niko and Pachter, Lior, et el. (2007) Analysis of epistatic interactions and fitness landscapes using a new geometric approach ; BMC Evolutionary Biology; Vol. 7; Art. No. 60; PMCID PMC1865543; 10.1186/1471-2148-7-60
Pachter, Lior and Sturmfels, Bernd (2007) The Mathematics of Phylogenomics ; SIAM Review; Vol. 49; No. 1; 3-31; 10.1137/050632634
Schwartz, Ariel S. and Pachter, Lior (2007) Multiple alignment by sequence annealing ; Bioinformatics; Vol. 23; No. 2; e24-e29; 10.1093/bioinformatics/btl311
Pachter, Lior (2007) An introduction to reconstructing ancestral genomes ; ISBN 978-0-8218-3964-5; Modeling and Simulation of Biological Networks; 10-29; 10.48550/arXiv.0612046
Morton, Jason and Pachter, Lior, et el. (2006) Geometry of rank tests ; ISBN 9788086742144; Proceedings of the 3rd European Workshop on Probabilistic Graphical Models; Art. No.7; 10.48550/arXiv.0605173
Dewey, Colin N. and Huggins, Peter M., et el. (2006) Parametric Alignment of Drosophila Genomes ; PLoS Computational Biology; Vol. 2; No. 6; Art. No. e73; PMCID PMC1480539; 10.1371/journal.pcbi.0020073
Dewey, Colin N. and Pachter, Lior (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment ; Human Molecular Genetics; Vol. 15; No. Suppl. 1; R51-R56; 10.1093/hmg/ddl056
Chatterji, Sourav and Pachter, Lior (2006) Reference based annotation with GeneMapper ; Genome Biology; Vol. 7; No. 4; Art. No. R29; PMCID PMC1557983; 10.1186/gb-2006-7-4-r29
Snir, Sagi and Pachter, Lior (2006) Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes ; ISBN 978-3-540-33295-4; Research in Computational Molecular Biology; 265-280; 10.1007/11732990_23
Lall, Sabbi and Grün, Dominic, et el. (2006) A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans ; Current Biology; Vol. 16; No. 5; 460-471; 10.1016/j.cub.2006.01.050
Levy, Dan and Yoshida, Ruriko, et el. (2006) Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates ; Molecular Biology and Evolution; Vol. 23; No. 3; 491-498; 10.1093/molbev/msj059
Caspi, Anat and Pachter, Lior (2006) Identification of transposable elements using multiple alignments of related genomes ; Genome Research; Vol. 16; No. 2; 260-270; PMCID PMC1361722; 10.1101/gr.4361206
Chen, Kevin and Pachter, Lior (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities ; PLoS Computational Biology; Vol. 1; No. 2; Art. No. e24; PMCID PMC1185649; 10.1371/journal.pcbi.0010024
Chatterji, Sourav and Pachter, Lior (2005) Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling ; Journal of Computational Biology; Vol. 12; No. 6; 599-608; 10.1089/cmb.2005.12.599
McAuliffe, Jon D. and Jordan, Michael I., et el. (2005) Subtree power analysis and species selection for comparative genomics ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 102; No. 22; 7900-7905; PMCID PMC1142384; 10.1073/pnas.0502790102
Alexandersson, Marina and Bray, Nicolas, et el. (2005) Pair hidden Markov models ; ISBN 9780470011539; Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics; Art. No. 4:4.2:17; 10.1002/047001153X.g402215
Hillier, LaDeana W. and Pachter, Lior, et el. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution ; Nature; Vol. 432; No. 7018; 695-716; 10.1038/nature03154
Boffelli, Dario and Weer, Claire V., et el. (2004) Intraspecies sequence comparisons for annotating genomes ; Genome Research; Vol. 14; No. 12; 2406-2411; PMCID PMC534664; 10.1101/gr.3199704
Pachter, Lior and Sturmfels, Bernd (2004) Parametric Inference for Biological Sequence Analysis ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 46; 16138-16143; PMCID PMC528961; 10.1073/pnas.0406011101
Pachter, Lior and Sturmfels, Bernd (2004) Tropical Geometry of Statistical Models ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 46; 16132-16137; PMCID PMC528960; 10.1073/pnas.0406010101
Feingold, E. A. and Pachter, L., et el. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project ; Science; Vol. 306; No. 5696; 636-640; 10.1126/science.1105136
McAuliffe, Jon D. and Pachter, Lior, et el. (2004) Multiple-sequence functional annotation and the generalized hidden Markov phylogeny ; Bioinformatics; Vol. 20; No. 12; 1850-1860; 10.1093/bioinformatics/bth153
Frazer, Kelly A. and Pachter, Lior, et el. (2004) VISTA: computational tools for comparative genomics ; Nucleic Acids Research; Vol. 32; No. Suppl. 2; W273-W279; PMCID PMC441596; 10.1093/nar/gkh458
Pachter, L. and Speyer, D. (2004) Reconstructing Trees from Subtree Weights ; Applied Mathematics Letters; Vol. 17; No. 6; 615-621; 10.1016/S0893-9659(04)90095-X
Gibbs, Richard A. and Pachter, Lior, et el. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution ; Nature; Vol. 428; No. 6982; 493-521; 10.1038/nature02426
Chakrabarti, Kushal and Pachter, Lior (2004) Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER ; Genome Research; Vol. 14; No. 4; 716-720; PMCID PMC383318; 10.1101/gr.1957004
Yap, Von Bing and Pachter, Lior (2004) Identification of Evolutionary Hotspots in the Rodent Genomes ; Genome Research; Vol. 14; No. 4; 574-579; PMCID PMC383301; 10.1101/gr.1967904
Dewey, Colin and Wu, Jia Qian, et el. (2004) Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat ; Genome Research; Vol. 14; No. 4; 661-664; PMCID PMC383310; 10.1101/gr.1939804
Bray, Nicolas and Pachter, Lior (2004) MAVID: Constrained ancestral alignment of multiple sequences ; Genome Research; Vol. 14; No. 4; 693-699; PMCID PMC383315; 10.1101/gr.1960404
Chatterji, Sourav and Pachter, Lior (2004) Multiple organism gene finding by collapsed Gibbs sampling ; ISBN 1-58113-755-9; Proceedings of the eighth annual international conference on Computational molecular biology (RECOMB '04); 187-193; 10.1145/974614.974639
Cawley, Simon L. and Pachter, Lior (2003) HMM sampling and applications to gene finding and alternative splicing ; Bioinformatics; Vol. 19; No. Suppl 2; ii36-ii41; 10.1093/bioinformatics/btg1057
Lam, Fumei and Pachter, Lior (2003) Forcing numbers of stop signs ; Theoretical Computer Science; Vol. 303; No. 2-3; 409-416; 10.1016/S0304-3975(02)00499-1
Cawley, Simon and Pachter, Lior, et el. (2003) SLAM web server for comparative gene finding and alignment ; Nucleic Acids Research; Vol. 31; No. 13; 3507-3509; PMCID PMC168989; 10.1093/nar/gkg583
Bray, Nicolas and Pachter, Lior (2003) MAVID multiple alignment server ; Nucleic Acids Research; Vol. 31; No. 13; 3525-3526; PMCID PMC169029; 10.1093/nar/gkg623
Lam, Fumei and Alexandersson, Marina, et el. (2003) Picking Alignments from (Steiner) Trees ; Journal of Computational Biology; Vol. 10; No. 3-4; 509-520; 10.1089/10665270360688156
Alexandersson, Marina and Cawley, Simon, et el. (2003) SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model ; Genome Research; Vol. 13; No. 3; 496-502; PMCID PMC430255; 10.1101/gr.424203
Boffelli, Dario and McAuliffe, Jon, et el. (2003) Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome ; Science; Vol. 299; No. 5611; 1391-1394; 10.1126/science.1081331
Bray, Nick and Dubchak, Inna, et el. (2003) AVID: A Global Alignment Program ; Genome Research; Vol. 13; No. 1; 97-102; PMCID PMC430967; 10.1101/gr.789803
Couronne, Olivier and Poliakov, Alexander, et el. (2003) Strategies and Tools for Whole-Genome Alignments ; Genome Research; Vol. 13; No. 1; 73-80; PMCID PMC430965; 10.1101/gr.762503
Waterston, Robert H. and Pachter, Lior, et el. (2002) Initial sequencing and comparative analysis of the mouse genome ; Nature; Vol. 420; No. 6915; 520-562; 10.1038/nature01262
Pachter, Lior and Alexandersson, Marina, et el. (2002) Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems ; Journal of Computational Biology; Vol. 9; No. 2; 389-399; 10.1089/10665270252935520
Benos, Panayiotis and Pachter, Lior (2002) From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies ; Genome Research; Vol. 11; No. 5; 710-730; PMCID PMC311117; 10.1101/gr.173801
Loots, Gabriela G. and Ovcharenko, Ivan, et el. (2002) rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites ; Genome Research; Vol. 12; No. 5; 832-839; PMCID PMC186580; 10.1101/gr.225502
Pachter, Lior and Lam, Fumei, et el. (2002) Picking alignments from (Steiner) trees ; ISBN 1-58113-498-3; Proceedings of the sixth annual international conference on Computational biology (RECOMB '02); 246-253; 10.1145/565196.565228
Dubchak, Inna and Pachter, Lior (2002) The computational challenges of applying comparative-based computational methods to whole genomes ; Briefings in Bioinformatics; Vol. 3; No. 1; 18-22; 10.1093/bib/3.1.18
Peter, Annette and Pachter, Lior (2002) Mapping and identification of essential gene functions on the X chromosome of Drosophila ; EMBO Reports; Vol. 3; No. 1; 34-38; PMCID PMC1083931; 10.1093/embo-reports/kvf012
Pachter, L. S. and Pachter, M. (2001) Optimal paths for avoiding a radiating source ; ISBN 9780780370616; Proceedings of the 40th IEEE Conference on Decision and Control : December 4-7, 2001 : Hyatt Regency Grand Cypress, Orlando, Florida, USA; 3581-3586; 10.1109/CDC.2001.980415
Pachter, Lior and Alexandersson, Marina, et el. (2001) Applications of generalized pair hidden Markov models to alignment and gene finding problems ; ISBN 1-58113-353-7; Proceedings of the fifth annual international conference on Computational biology (RECOMB '01); 241-248; 10.1145/369133.369227
Mayor, Chris and Brudno, Michael, et el. (2000) VISTA : visualizing global DNA sequence alignments of arbitrary length ; Bioinformatics; Vol. 16; No. 11; 1046-1047; 10.1093/bioinformatics/16.11.1046
Dubchak, Inna and Brudno, Michael, et el. (2000) Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons ; Genome Research; Vol. 10; No. 9; 1304-1306; PMCID PMC310906; 10.1101/gr.142200
Batzoglou, Serafim and Pachter, Lior, et el. (2000) Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction ; Genome Research; Vol. 10; No. 7; 950-958; PMCID PMC310911; 10.1101/gr.10.7.950
Batzoglou, Serafim and Pachter, Lior, et el. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction ; ISBN 1-58113-186-0; Proceedings of the fourth annual international conference on Computational molecular biology (RECOMB '00); 46-53; 10.1145/332306.332326
Pachter, Lior and Batzoglou, Serafim, et el. (1999) A Dictionary-Based Approach for Gene Annotation ; Journal of Computational Biology; Vol. 6; No. 3-4; 419-430; 10.1089/106652799318364
Pachter, Lior and Batzoglou, Serafim, et el. (1999) A dictionary based approach for gene annotation ; ISBN 1-58113-069-4; Proceedings of the third annual international conference on Computational molecular biology (RECOMB '99); 285-294; 10.1145/299432.299504
Pachter, Lior and Kim, Peter (1998) Forcing matchings on square grids ; Discrete Mathematics; Vol. 190; No. 1-3; 287-294; 10.1016/S0012-365X(97)00266-5
Kleitman, D. and Pachter, L. (1998) Finding Convex Sets Among Points in the Plane ; Discrete and Computational Geometry; Vol. 19; No. 3; 405-410; 10.1007/PL00009358
Batzoglou, Serafim and Berger, Bonnie, et el. (1998) Recent Developments in Computational Gene Recognition ; Documenta Mathematica; Vol. ICM I; 649-658
Pachter, Lior (1997) Constructing status injective graphs ; Discrete Applied Mathematics; Vol. 80; No. 1; 107-113; 10.1016/S0166-218X(97)00073-5
Pachter, Lior (1997) Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes ; Electronic Journal of Combinatorics; Vol. 4; No. 1; Art. No. R29
Pachter, Lior and Snevily, Hunter S., et el. (1995) On pebbling graphs
