(orcid 0000-0002-9164-6231)
Gorin, Gennady; Carilli, Maria et al. (2022) Spectral neural approximations for models of transcriptional dynamics https://doi.org/10.1101/2022.06.16.496448
Gorin, Gennady; Pachter, Lior (2022) Monod: mechanistic analysis of single-cell RNA sequencing count data https://doi.org/10.1101/2022.06.11.495771
Booeshaghi, A. Sina; Pachter, Lior (2022) Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads https://doi.org/10.1101/2022.06.04.494845
Gálvez-Merchán, Ángel; Min, Kyung Hoi (Joseph) et al. (2022) Metadata retrieval from sequence databases with ffq https://doi.org/10.1101/2022.05.18.492548
Luebbert, Laura; Pachter, Lior (2022) Efficient querying of genomic reference databases with gget https://doi.org/10.1101/2022.05.17.492392
Booeshaghi, A. Sina; Hallgrímsdóttir, Ingileif B. et al. (2022) Depth normalization for single-cell genomics count data https://doi.org/10.1101/2022.05.06.490859
Gorin, Gennady; Fang, Meichen et al. (2022) RNA velocity unraveled https://doi.org/10.1101/2022.02.12.480214
Gao, Fan; Pachter, Lior (2021) Efficient pre-processing of Single-cell ATAC-seq data https://doi.org/10.1101/2021.12.08.471788
Gorin, Gennady; Vastola, John J. et al. (2021) Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments https://doi.org/10.1101/2021.09.06.459173
Chari, Tara; Banerjee, Joeyta et al. (2021) The Specious Art of Single-Cell Genomics https://doi.org/10.1101/2021.08.25.457696
Gorin, Gennady; Pachter, Lior (2021) Length Biases in Single-Cell RNA Sequencing of pre-mRNA https://doi.org/10.1101/2021.07.30.454514
Sierra, Noemie; Olsman, Noah et al. (2021) A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration https://doi.org/10.1101/2021.03.22.434850
Booeshaghi, A. Sina; Pachter, Lior (2021) Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing https://doi.org/10.1101/2021.01.25.428188
Gorin, Gennady; Pachter, Lior (2021) Direct simulation of a stochastically driven multi-step birth-death process https://doi.org/10.1101/2021.01.20.427480
Gorin, Gennady; Pachter, Lior (2020) Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production https://doi.org/10.1101/2020.09.25.312868
Booeshaghi, A. Sina; Tan, Fayth et al. (2020) Markedly heterogeneous COVID-19 testing plans among US colleges and universities https://doi.org/10.1101/2020.08.09.20171223
Booeshaghi, A. Sina; Pachter, Lior (2020) Decrease in ACE2 mRNA expression in aged mouse lung https://doi.org/10.1101/2020.04.02.021451
Svensson, Valentine; da Veiga Beltrame, Eduardo et al. (2019) Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq https://doi.org/10.1101/762773
Melsted, Páll; Booeshaghi, A. Sina et al. (2019) Modular and efficient pre-processing of single-cell RNA-seq https://doi.org/10.1101/673285
McGee, Warren A.; Pimentel, Harold et al. (2019) Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data https://doi.org/10.1101/564955
Yi, Lynn; Liu, Lauren et al. (2018) A direct comparison of genome alignment and transcriptome pseudoalignment https://doi.org/10.1101/444620
Ntranos, Vasilis; Yi, Lynn et al. (2018) Identification of transcriptional signatures for cell types from single-cell RNA-Seq https://doi.org/10.1101/258566
Melsted, Páll; Hateley, Shannon et al. (2017) Fusion detection and quantification by pseudoalignment https://doi.org/10.1101/166322
Pimentel, Harold; Conboy, John G. et al. (2016) Keep Me Around: Intron Retention Detection and Analysis https://resolver.caltech.edu/CaltechAUTHORS:20170306-132431515 (Submitted)
Bray, Nicolas L.; Pimentel, Harold et al. (2015) Near-optimal RNA-Seq quantification https://resolver.caltech.edu/CaltechAUTHORS:20170303-114628470
Tambe, Akshay; Doudna, Jennifer et al. (2014) Identifying RNA contacts from SHAPE-MaP by partial correlation analysis https://resolver.caltech.edu/CaltechAUTHORS:20170307-101642083 (Submitted)
Bray, Nicolas; Pachter, Lior (2012) Comment on "Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions" https://resolver.caltech.edu/CaltechAUTHORS:20170307-101423905 (Submitted)
Pachter, Lior (2011) Models for transcript quantification from RNA-Seq https://resolver.caltech.edu/CaltechAUTHORS:20170307-112830219 (Submitted)
Huggins, Peter; Pachter, Lior (2008) Selecting universities: personal preference and rankings https://resolver.caltech.edu/CaltechAUTHORS:20170306-145946949 (Submitted)
Schwartz, Ariel S.; Myers, Eugene W. et al. (2005) Alignment Metric Accuracy https://resolver.caltech.edu/CaltechAUTHORS:20170307-100435592 (Submitted)
Levy, Dan; Yoshida, Ruriko et al. (2005) Neighbor joining with phylogenetic diversity estimates https://resolver.caltech.edu/CaltechAUTHORS:20170307-090555699 (Submitted)
Guigó, Roderic; Birney, Ewan et al. (2004) Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models https://resolver.caltech.edu/CaltechAUTHORS:20170307-100841641 (Submitted)