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1.

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior.

Kim, Dong-Wook; Yao, Zizhen; Graybuck, Lucas T; Kim, Tae Kyung; Nguyen, Thuc Nghi; Smith, Kimberly A; Fong, Olivia; Yi, Lynn; Koulena, Noushin; Pierson, Nico; Shah, Sheel; Lo, Liching; Pool, Allan-Hermann; Oka, Yuki; Pachter, Lior; Cai, Long; Tasic, Bosiljka; Zeng, Hongkui; Anderson, David J.

Cell ; 179(3): 713-728.e17, 2019 10 17.

Article in English | MEDLINE | ID: mdl-31626771

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7534821
https://dx.doi.org/10.1016/j.cell.2019.09.020

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2.

Isoform cell-type specificity in the mouse primary motor cortex.

Booeshaghi, A Sina; Yao, Zizhen; van Velthoven, Cindy; Smith, Kimberly; Tasic, Bosiljka; Zeng, Hongkui; Pachter, Lior.

Nature ; 598(7879): 195-199, 2021 10.

Article in English | MEDLINE | ID: mdl-34616073

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494650
https://dx.doi.org/10.1038/s41586-021-03969-3

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3.

RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq.

Svensson, Valentine; Pachter, Lior.

Mol Cell ; 72(1): 7-9, 2018 10 04.

Article in English | MEDLINE | ID: mdl-30290149

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4.

Museum of spatial transcriptomics.

Moses, Lambda; Pachter, Lior.

Nat Methods ; 19(5): 534-546, 2022 05.

Article in English | MEDLINE | ID: mdl-35273392

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5.

Flexible parsing, interpretation, and editing of technical sequences with splitcode.

Sullivan, Delaney K; Pachter, Lior.

Bioinformatics ; 2024 Jun 14.

Article in English | MEDLINE | ID: mdl-38876979

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6.

Fast and scalable querying of eukaryotic linear motifs with gget elm.

Luebbert, Laura; Hoang, Chi; Kumar, Manjeet; Pachter, Lior.

Bioinformatics ; 40(3)2024 Mar 04.

Article in English | MEDLINE | ID: mdl-38377393

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10927331
https://dx.doi.org/10.1093/bioinformatics/btae095

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7.

A machine-readable specification for genomics assays.

Booeshaghi, Ali Sina; Chen, Xi; Pachter, Lior.

Bioinformatics ; 40(4)2024 Mar 29.

Article in English | MEDLINE | ID: mdl-38579259

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11009023
https://dx.doi.org/10.1093/bioinformatics/btae168

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8.

Spectral neural approximations for models of transcriptional dynamics.

Gorin, Gennady; Carilli, Maria; Chari, Tara; Pachter, Lior.

Biophys J ; 2024 May 06.

Article in English | MEDLINE | ID: mdl-38715358

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9.

Efficient querying of genomic reference databases with gget.

Luebbert, Laura; Pachter, Lior.

Bioinformatics ; 39(1)2023 01 01.

Article in English | MEDLINE | ID: mdl-36610989

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835474
https://dx.doi.org/10.1093/bioinformatics/btac836

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10.

Metadata retrieval from sequence databases with ffq.

Gálvez-Merchán, Ángel; Min, Kyung Hoi Joseph; Pachter, Lior; Booeshaghi, A Sina.

Bioinformatics ; 39(1)2023 01 01.

Article in English | MEDLINE | ID: mdl-36610997

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9883619
https://dx.doi.org/10.1093/bioinformatics/btac667

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11.

The specious art of single-cell genomics.

Chari, Tara; Pachter, Lior.

PLoS Comput Biol ; 19(8): e1011288, 2023 08.

Article in English | MEDLINE | ID: mdl-37590228

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10434946
https://dx.doi.org/10.1371/journal.pcbi.1011288

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12.

RNA velocity unraveled.

Gorin, Gennady; Fang, Meichen; Chari, Tara; Pachter, Lior.

PLoS Comput Biol ; 18(9): e1010492, 2022 09.

Article in English | MEDLINE | ID: mdl-36094956

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9499228
https://dx.doi.org/10.1371/journal.pcbi.1010492

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13.

Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing.

Gorin, Gennady; Yoshida, Shawn; Pachter, Lior.

Bull Math Biol ; 85(11): 114, 2023 10 12.

Article in English | MEDLINE | ID: mdl-37828255

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14.

SWALO: scaffolding with assembly likelihood optimization.

Rahman, Atif; Pachter, Lior.

Nucleic Acids Res ; 49(20): e117, 2021 11 18.

Article in English | MEDLINE | ID: mdl-34417615

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8599790
https://dx.doi.org/10.1093/nar/gkab717

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15.

Modeling bursty transcription and splicing with the chemical master equation.

Gorin, Gennady; Pachter, Lior.

Biophys J ; 121(6): 1056-1069, 2022 03 15.

Article in English | MEDLINE | ID: mdl-35143775

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8943761
https://dx.doi.org/10.1016/j.bpj.2022.02.004

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16.

A discriminative learning approach to differential expression analysis for single-cell RNA-seq.

Ntranos, Vasilis; Yi, Lynn; Melsted, Páll; Pachter, Lior.

Nat Methods ; 16(2): 163-166, 2019 02.

Article in English | MEDLINE | ID: mdl-30664774

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17.

Interpretable factor models of single-cell RNA-seq via variational autoencoders.

Svensson, Valentine; Gayoso, Adam; Yosef, Nir; Pachter, Lior.

Bioinformatics ; 36(11): 3418-3421, 2020 06 01.

Article in English | MEDLINE | ID: mdl-32176273

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267837
https://dx.doi.org/10.1093/bioinformatics/btaa169

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18.

Expression reflects population structure.

Brown, Brielin C; Bray, Nicolas L; Pachter, Lior.

PLoS Genet ; 14(12): e1007841, 2018 12.

Article in English | MEDLINE | ID: mdl-30566439

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317812
https://dx.doi.org/10.1371/journal.pgen.1007841

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19.

Publisher Correction: Museum of spatial transcriptomics.

Moses, Lambda; Pachter, Lior.

Nat Methods ; 19(5): 628, 2022 May.

Article in English | MEDLINE | ID: mdl-35440782

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20.

Differential analysis of RNA-seq incorporating quantification uncertainty.

Pimentel, Harold; Bray, Nicolas L; Puente, Suzette; Melsted, Páll; Pachter, Lior.

Nat Methods ; 14(7): 687-690, 2017 Jul.

Article in English | MEDLINE | ID: mdl-28581496

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