<h1>Pachter, Lior</h1>
<h2>Monograph from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2>
<ul>
<li>Rich, Joseph M. and Moses, Lambda, el al. (2024) <a href="https://authors.library.caltech.edu/records/gzsw0-46t72">The impact of package selection and versioning on single-cell RNA-seq analysis</a>; PMCID PMC11014608; <a href="https://doi.org/10.1101/2024.04.04.588111">10.1101/2024.04.04.588111</a></li>
<li>Booeshaghi, A. Sina and Galvez-Merchán, Ángel, el al. (2024) <a href="https://authors.library.caltech.edu/records/e3z09-4wt43">Algorithms for a Commons Cell Atlas</a>; <a href="https://doi.org/10.1101/2024.03.23.586413">10.1101/2024.03.23.586413</a></li>
<li>Galvez-Merchán, Ángel and Booeshaghi, A. Sina, el al. (2024) <a href="https://authors.library.caltech.edu/records/74zne-hdv03">A human commons cell atlas reveals cell type specificity for OAS1 isoforms</a>; <a href="https://doi.org/10.1101/2024.03.23.586412">10.1101/2024.03.23.586412</a></li>
<li>Gorin, Gennady and Vastola, John J., el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257070000.17">Studying stochastic systems biology of the cell with single-cell genomics data</a>; PMCID PMC10245677; <a href="https://doi.org/10.1101/2023.05.17.541250">10.1101/2023.05.17.541250</a></li>
<li>Xiong, Lingyun and Liu, Jing, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257103000.21">Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney</a>; PMCID PMC10187285; <a href="https://doi.org/10.1101/2023.05.06.539585">10.1101/2023.05.06.539585</a></li>
<li>Sullivan, Delaney K. and Pachter, Lior (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230327-441955000.1">Flexible parsing and preprocessing of technical sequences with splitcode</a>; PMCID PMC10055216; <a href="https://doi.org/10.1101/2023.03.20.533521">10.1101/2023.03.20.533521</a></li>
<li>Booeshaghi, A. Sina and Chen, Xi, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230322-101294000.2">A machine-readable specification for genomics assays</a>; <a href="https://doi.org/10.1101/2023.03.17.533215">10.1101/2023.03.17.533215</a></li>
<li>Gorin, Gennady and Pachter, Lior (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182495000.36">The telegraph process is not a subordinator</a>; <a href="https://doi.org/10.1101/2023.01.17.524309">10.1101/2023.01.17.524309</a></li>
<li>Carilli, Maria and Gorin, Gennady, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182533000.39">Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data</a>; <a href="https://doi.org/10.1101/2023.01.13.523995">10.1101/2023.01.13.523995</a></li>
<li>Fenelon, Kelli D. and Gao, Fan, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182720000.54">Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos</a>; <a href="https://doi.org/10.1101/2022.12.15.519123">10.1101/2022.12.15.519123</a></li>
<li>Hjorleifsson, Kristján Eldjárn and Pachter, Lior, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182788000.61">Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes</a>; <a href="https://doi.org/10.1101/2022.12.02.518787">10.1101/2022.12.02.518787</a></li>
<li>Hjorleifsson, Kristján Eldjárn and Sullivan, Delaney K., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230316-182779000.60">Accurate quantification of single-nucleus and single-cell RNA-seq transcripts</a>; <a href="https://doi.org/10.1101/2022.12.02.518832">10.1101/2022.12.02.518832</a></li>
<li>Gorin, Gennady and Yoshida, Shawn, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230322-101567000.15">Transient and delay chemical master equations</a>; <a href="https://doi.org/10.1101/2022.10.17.512599">10.1101/2022.10.17.512599</a></li>
<li>Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph), el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230322-101653000.21">Quantifying orthogonal barcodes for sequence census assays</a>; <a href="https://doi.org/10.1101/2022.10.09.511501">10.1101/2022.10.09.511501</a></li>
<li>Gorin, Gennady and Carilli, Maria, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220706-964999000">Spectral neural approximations for models of transcriptional dynamics</a>; <a href="https://doi.org/10.1101/2022.06.16.496448">10.1101/2022.06.16.496448</a></li>
<li>Gorin, Gennady and Pachter, Lior (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220614-221628000">Monod: mechanistic analysis of single-cell RNA sequencing count data</a>; <a href="https://doi.org/10.1101/2022.06.11.495771">10.1101/2022.06.11.495771</a></li>
<li>Booeshaghi, A. Sina and Pachter, Lior (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220607-425123000">Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads</a>; <a href="https://doi.org/10.1101/2022.06.04.494845">10.1101/2022.06.04.494845</a></li>
<li>Gálvez-Merchán, Ángel and Min, Kyung Hoi (Joseph), el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220602-62681600">Metadata retrieval from sequence databases with ffq</a>; <a href="https://doi.org/10.1101/2022.05.18.492548">10.1101/2022.05.18.492548</a></li>
<li>Luebbert, Laura and Pachter, Lior (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220520-512432000">Efficient querying of genomic reference databases with gget</a>; <a href="https://doi.org/10.1101/2022.05.17.492392">10.1101/2022.05.17.492392</a></li>
<li>Booeshaghi, A. Sina and Hallgrímsdóttir, Ingileif B., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220509-762177400">Depth normalization for single-cell genomics count data</a>; <a href="https://doi.org/10.1101/2022.05.06.490859">10.1101/2022.05.06.490859</a></li>
<li>Gorin, Gennady and Fang, Meichen, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220214-147056100">RNA velocity unraveled</a>; <a href="https://doi.org/10.1101/2022.02.12.480214">10.1101/2022.02.12.480214</a></li>
<li>Gao, Fan and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20211210-240593000">Efficient pre-processing of Single-cell ATAC-seq data</a>; <a href="https://doi.org/10.1101/2021.12.08.471788">10.1101/2021.12.08.471788</a></li>
<li>Gorin, Gennady and Vastola, John J., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210907-221001270">Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments</a>; <a href="https://doi.org/10.1101/2021.09.06.459173">10.1101/2021.09.06.459173</a></li>
<li>Chari, Tara and Banerjee, Joeyta, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210831-175013923">The Specious Art of Single-Cell Genomics</a>; <a href="https://doi.org/10.1101/2021.08.25.457696">10.1101/2021.08.25.457696</a></li>
<li>Gorin, Gennady and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210802-221611892">Length Biases in Single-Cell RNA Sequencing of pre-mRNA</a>; <a href="https://doi.org/10.1101/2021.07.30.454514">10.1101/2021.07.30.454514</a></li>
<li>Sierra, Noemie and Olsman, Noah, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210324-071454082">A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration</a>; <a href="https://doi.org/10.1101/2021.03.22.434850">10.1101/2021.03.22.434850</a></li>
<li>Booeshaghi, A. Sina and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210126-131831766">Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing</a>; <a href="https://doi.org/10.1101/2021.01.25.428188">10.1101/2021.01.25.428188</a></li>
<li>Gorin, Gennady and Pachter, Lior (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210122-125501964">Direct simulation of a stochastically driven multi-step birth-death process</a>; <a href="https://doi.org/10.1101/2021.01.20.427480">10.1101/2021.01.20.427480</a></li>
<li>Gorin, Gennady and Pachter, Lior (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200928-131238226">Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production</a>; <a href="https://doi.org/10.1101/2020.09.25.312868">10.1101/2020.09.25.312868</a></li>
<li>Booeshaghi, A. Sina and Tan, Fayth, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200824-142429940">Markedly heterogeneous COVID-19 testing plans among US colleges and universities</a>; <a href="https://doi.org/10.1101/2020.08.09.20171223">10.1101/2020.08.09.20171223</a></li>
<li>Booeshaghi, A. Sina and Pachter, Lior (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200406-101324270">Decrease in ACE2 mRNA expression in aged mouse lung</a>; <a href="https://doi.org/10.1101/2020.04.02.021451">10.1101/2020.04.02.021451</a></li>
<li>Svensson, Valentine and da Veiga Beltrame, Eduardo, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190910-074005263">Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq</a>; <a href="https://doi.org/10.1101/762773">10.1101/762773</a></li>
<li>Melsted, Páll and Booeshaghi, A. Sina, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190617-153352518">Modular and efficient pre-processing of single-cell RNA-seq</a>; <a href="https://doi.org/10.1101/673285">10.1101/673285</a></li>
<li>McGee, Warren A. and Pimentel, Harold, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190304-085432513">Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data</a>; <a href="https://doi.org/10.1101/564955">10.1101/564955</a></li>
<li>Yi, Lynn and Liu, Lauren, el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181029-160959571">A direct comparison of genome alignment and transcriptome pseudoalignment</a>; <a href="https://doi.org/10.1101/444620">10.1101/444620</a></li>
<li>Ntranos, Vasilis and Yi, Lynn, el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181031-090523070">Identification of transcriptional signatures for cell types from single-cell RNA-Seq</a>; <a href="https://doi.org/10.1101/258566">10.1101/258566</a></li>
<li>Melsted, Páll and Hateley, Shannon, el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181029-134221299">Fusion detection and quantification by pseudoalignment</a>; <a href="https://doi.org/10.1101/166322">10.1101/166322</a></li>
<li>Pimentel, Harold and Conboy, John G., el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-132431515">Keep Me Around: Intron Retention Detection and Analysis</a>; <a href="https://doi.org/10.48550/arXiv.1510.00696">10.48550/arXiv.1510.00696</a></li>
<li>Bray, Nicolas L. and Pimentel, Harold, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170303-114628470">Near-optimal RNA-Seq quantification</a>; <a href="https://doi.org/10.48550/arXiv.1505.02710v2">10.48550/arXiv.1505.02710v2</a></li>
<li>Tambe, Akshay and Doudna, Jennifer, el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-101642083">Identifying RNA contacts from SHAPE-MaP by partial correlation analysis</a>; <a href="https://doi.org/10.48550/arXiv.1412.3800">10.48550/arXiv.1412.3800</a></li>
<li>Bray, Nicolas and Pachter, Lior (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-101423905">Comment on &quot;Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions&quot;</a>; <a href="https://doi.org/10.48550/arXiv.1212.3076">10.48550/arXiv.1212.3076</a></li>
<li>Pachter, Lior (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-112830219">Models for transcript quantification from RNA-Seq</a>; <a href="https://doi.org/10.48550/arXiv.1104.3889">10.48550/arXiv.1104.3889</a></li>
<li>Huggins, Peter and Pachter, Lior (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170306-145946949">Selecting universities: personal preference and rankings</a>; <a href="https://doi.org/10.48550/arXiv.0805.1026">10.48550/arXiv.0805.1026</a></li>
<li>Schwartz, Ariel S. and Myers, Eugene W., el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-100435592">Alignment Metric Accuracy</a>; <a href="https://doi.org/10.48550/arXiv.0510052">10.48550/arXiv.0510052</a></li>
<li>Levy, Dan and Yoshida, Ruriko, el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-090555699">Neighbor joining with phylogenetic diversity estimates</a>; <a href="https://doi.org/10.48550/arXiv.0508001">10.48550/arXiv.0508001</a></li>
<li>Guigó, Roderic and Birney, Ewan, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170307-100841641">Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models</a>; <a href="https://doi.org/10.48550/arXiv.0410008">10.48550/arXiv.0410008</a></li>
</ul>