Pachter, Lior

Monograph from CaltechAUTHORS

• Rebboah, Elisabeth and Weber, Ryan, el al. (2025) Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation; 10.1101/2025.04.21.649844
• Rich, Joseph M. and Moses, Lambda, el al. (2024) The impact of package selection and versioning on single-cell RNA-seq analysis; PMCID PMC11014608; 10.1101/2024.04.04.588111
• Booeshaghi, A. Sina and Galvez-Merchán, Ángel, el al. (2024) Algorithms for a Commons Cell Atlas; 10.1101/2024.03.23.586413
• Galvez-Merchán, Ángel and Booeshaghi, A. Sina, el al. (2024) A human commons cell atlas reveals cell type specificity for OAS1 isoforms; 10.1101/2024.03.23.586412
• Gorin, Gennady and Vastola, John J., el al. (2023) Studying stochastic systems biology of the cell with single-cell genomics data; PMCID PMC10245677; 10.1101/2023.05.17.541250
• Xiong, Lingyun and Liu, Jing, el al. (2023) Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney; PMCID PMC10187285; 10.1101/2023.05.06.539585
• Sullivan, Delaney K. and Pachter, Lior (2023) Flexible parsing and preprocessing of technical sequences with splitcode; PMCID PMC10055216; 10.1101/2023.03.20.533521
• Booeshaghi, A. Sina and Chen, Xi, el al. (2023) A machine-readable specification for genomics assays; 10.1101/2023.03.17.533215
• Gorin, Gennady and Pachter, Lior (2023) The telegraph process is not a subordinator; 10.1101/2023.01.17.524309
• Carilli, Maria and Gorin, Gennady, el al. (2023) Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data; 10.1101/2023.01.13.523995
• Fenelon, Kelli D. and Gao, Fan, el al. (2022) Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos; 10.1101/2022.12.15.519123
• Hjorleifsson, Kristján Eldjárn and Pachter, Lior, el al. (2022) Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes; 10.1101/2022.12.02.518787
• Hjorleifsson, Kristján Eldjárn and Sullivan, Delaney K., el al. (2022) Accurate quantification of single-nucleus and single-cell RNA-seq transcripts; 10.1101/2022.12.02.518832
• Gorin, Gennady and Yoshida, Shawn, el al. (2022) Transient and delay chemical master equations; 10.1101/2022.10.17.512599
• Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph), el al. (2022) Quantifying orthogonal barcodes for sequence census assays; 10.1101/2022.10.09.511501
• Gorin, Gennady and Carilli, Maria, el al. (2022) Spectral neural approximations for models of transcriptional dynamics; 10.1101/2022.06.16.496448
• Gorin, Gennady and Pachter, Lior (2022) Monod: mechanistic analysis of single-cell RNA sequencing count data; 10.1101/2022.06.11.495771
• Booeshaghi, A. Sina and Pachter, Lior (2022) Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads; 10.1101/2022.06.04.494845
• Gálvez-Merchán, Ángel and Min, Kyung Hoi (Joseph), el al. (2022) Metadata retrieval from sequence databases with ffq; 10.1101/2022.05.18.492548
• Luebbert, Laura and Pachter, Lior (2022) Efficient querying of genomic reference databases with gget; 10.1101/2022.05.17.492392
• Booeshaghi, A. Sina and Hallgrímsdóttir, Ingileif B., el al. (2022) Depth normalization for single-cell genomics count data; 10.1101/2022.05.06.490859
• Gorin, Gennady and Fang, Meichen, el al. (2022) RNA velocity unraveled; 10.1101/2022.02.12.480214
• Gao, Fan and Pachter, Lior (2021) Efficient pre-processing of Single-cell ATAC-seq data; 10.1101/2021.12.08.471788
• Gorin, Gennady and Vastola, John J., el al. (2021) Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments; 10.1101/2021.09.06.459173
• Chari, Tara and Banerjee, Joeyta, el al. (2021) The Specious Art of Single-Cell Genomics; 10.1101/2021.08.25.457696
• Gorin, Gennady and Pachter, Lior (2021) Length Biases in Single-Cell RNA Sequencing of pre-mRNA; 10.1101/2021.07.30.454514
• Sierra, Noemie and Olsman, Noah, el al. (2021) A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration; 10.1101/2021.03.22.434850
• Booeshaghi, A. Sina and Pachter, Lior (2021) Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing; 10.1101/2021.01.25.428188
• Gorin, Gennady and Pachter, Lior (2021) Direct simulation of a stochastically driven multi-step birth-death process; 10.1101/2021.01.20.427480
• Gorin, Gennady and Pachter, Lior (2020) Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production; 10.1101/2020.09.25.312868
• Booeshaghi, A. Sina and Tan, Fayth, el al. (2020) Markedly heterogeneous COVID-19 testing plans among US colleges and universities; 10.1101/2020.08.09.20171223
• Booeshaghi, A. Sina and Pachter, Lior (2020) Decrease in ACE2 mRNA expression in aged mouse lung; 10.1101/2020.04.02.021451
• Svensson, Valentine and da Veiga Beltrame, Eduardo, el al. (2019) Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq; 10.1101/762773
• Melsted, Páll and Booeshaghi, A. Sina, el al. (2019) Modular and efficient pre-processing of single-cell RNA-seq; 10.1101/673285
• McGee, Warren A. and Pimentel, Harold, el al. (2019) Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data; 10.1101/564955
• Yi, Lynn and Liu, Lauren, el al. (2018) A direct comparison of genome alignment and transcriptome pseudoalignment; 10.1101/444620
• Ntranos, Vasilis and Yi, Lynn, el al. (2018) Identification of transcriptional signatures for cell types from single-cell RNA-Seq; 10.1101/258566
• Melsted, Páll and Hateley, Shannon, el al. (2017) Fusion detection and quantification by pseudoalignment; 10.1101/166322
• Pimentel, Harold and Conboy, John G., el al. (2016) Keep Me Around: Intron Retention Detection and Analysis; 10.48550/arXiv.1510.00696
• Bray, Nicolas L. and Pimentel, Harold, el al. (2015) Near-optimal RNA-Seq quantification; 10.48550/arXiv.1505.02710v2
• Tambe, Akshay and Doudna, Jennifer, el al. (2014) Identifying RNA contacts from SHAPE-MaP by partial correlation analysis; 10.48550/arXiv.1412.3800
• Bray, Nicolas and Pachter, Lior (2012) Comment on "Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions"; 10.48550/arXiv.1212.3076
• Pachter, Lior (2011) Models for transcript quantification from RNA-Seq; 10.48550/arXiv.1104.3889
• Huggins, Peter and Pachter, Lior (2008) Selecting universities: personal preference and rankings; 10.48550/arXiv.0805.1026
• Schwartz, Ariel S. and Myers, Eugene W., el al. (2005) Alignment Metric Accuracy; 10.48550/arXiv.0510052
• Levy, Dan and Yoshida, Ruriko, el al. (2005) Neighbor joining with phylogenetic diversity estimates; 10.48550/arXiv.0508001
• Guigó, Roderic and Birney, Ewan, el al. (2004) Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models; 10.48550/arXiv.0410008