Lior Pachter

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 76

Top Topics

Gene Expression

Top Venues

bioRxiv : the preprint server for biology

Bioinformatics (Oxford, England)

Genome biology and evolution

This page only lists publications with an associated author ORCID identifier.

Publications

Tara Chari, Gennady Gorin, Lior Pachter
Stochastic Modeling of Biophysical Responses to Perturbation. bioRxiv : the preprint server for biology (2024)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods (2024)
Delaney K Sullivan, Lior Pachter
Flexible parsing, interpretation, and editing of technical sequences with splitcode. Bioinformatics (Oxford, England) 40 (6) (2024)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2024)
Rebekah Loving, Delaney K Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Yahan Liang, Ghassan Filimban, Shimako Kawauchi, Conrad G Oakes, Diane Trout, Brian A Williams, Grant R MacGregor, Barbara J Wold, Ali Mortazavi, Lior Pachter
Long-read sequencing transcriptome quantification with lr-kallisto. bioRxiv : the preprint server for biology (2024)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2024)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2024)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2024)
Joseph Matthew Rich, Lambda Moses, Pétur Helgi Einarsson, Kayla C Jackson, Laura Luebbert, Ali Sina Booeshaghi, Sindri Antonsson, Delaney K Sullivan, Nicolas L Bray, Páll Melsted, Lior Pachter
The impact of package selection and versioning on single-cell RNA-seq analysis. bioRxiv : the preprint server for biology (2024)
Noémie C Sierra, Noah Olsman, Lynn Yi, Lior Pachter, Lea Goentoro, David A Gold
A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration. Genome biology and evolution 16 (6) (2024)
Kayla C Jackson, Ali Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Lior Pachter
Identification of spatial homogeneous regions in tissues with concordex. bioRxiv : the preprint server for biology (2024)
Delaney K Sullivan, Lior Pachter
Flexible parsing, interpretation, and editing of technical sequences with splitcode. Bioinformatics (Oxford, England) 40 (6) (2024)
Ali Sina Booeshaghi, Xi Chen, Lior Pachter
A machine-readable specification for genomics assays. Bioinformatics (Oxford, England) 40 (4) (2024)
Kayla C Jackson, Ali Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Lior Pachter
Identification of spatial homogeneous regions in tissues with concordex. bioRxiv : the preprint server for biology (2024)
Kayla C Jackson, Ali Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Lior Pachter
Identification of spatial homogeneous regions in tissues with concordex. bioRxiv : the preprint server for biology (2024)
Tara Chari, Gennady Gorin, Lior Pachter
Stochastic Modeling of Biophysical Responses to Perturbation. bioRxiv : the preprint server for biology (2024)
Joseph Matthew Rich, Lambda Moses, Pétur Helgi Einarsson, Kayla C Jackson, Laura Luebbert, Ali Sina Booeshaghi, Sindri Antonsson, Delaney K Sullivan, Nicolas L Bray, Páll Melsted, Lior Pachter
The impact of package selection and versioning on single-cell RNA-seq analysis. bioRxiv : the preprint server for biology (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods 21 (8) (2024)
Ali Sina Booeshaghi, Xi Chen, Lior Pachter
A machine-readable specification for genomics assays. Bioinformatics (Oxford, England) 40 (4) (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods 21 (8) (2024)
Rebekah Loving, Delaney K Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Yahan Liang, Ghassan Filimban, Shimako Kawauchi, Conrad G Oakes, Diane Trout, Brian A Williams, Grant R MacGregor, Barbara J Wold, Ali Mortazavi, Lior Pachter
Long-read sequencing transcriptome quantification with lr-kallisto. bioRxiv : the preprint server for biology (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods (2024)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nature methods (2024)
Noemie Sierra, Noah Olsman, Lynn Yi, Lior Pachter, Lea Goentoro, David A Gold
A novel approach to comparative RNA-Seq does not support a conserved set of orthologs underlying animal regeneration. Genome biology and evolution (2024)
Ali Sina Booeshaghi, Xi Chen, Lior Pachter
A machine-readable specification for genomics assays. Bioinformatics (Oxford, England) 40 (4) (2024)
Noémie C Sierra, Noah Olsman, Lynn Yi, Lior Pachter, Lea Goentoro, David A Gold
A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration. Genome biology and evolution 16 (6) (2024)
Noémie C Sierra, Noah Olsman, Lynn Yi, Lior Pachter, Lea Goentoro, David A Gold
A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration. Genome biology and evolution 16 (6) (2024)
Rebekah Loving, Delaney K Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Yahan Liang, Ghassan Filimban, Shimako Kawauchi, Conrad G Oakes, Diane Trout, Brian A Williams, Grant R MacGregor, Barbara J Wold, Ali Mortazavi, Lior Pachter
Long-read sequencing transcriptome quantification with lr-kallisto. bioRxiv : the preprint server for biology (2024)
Laura Luebbert, Chi Hoang, Manjeet Kumar, Lior Pachter
Fast and scalable querying of eukaryotic linear motifs with gget elm. Bioinformatics (Oxford, England) 40 (3) (2024)
Delaney K Sullivan, Lior Pachter
Flexible parsing, interpretation, and editing of technical sequences with splitcode. Bioinformatics (Oxford, England) 40 (6) (2024)
Noémie C Sierra, Noah Olsman, Lynn Yi, Lior Pachter, Lea Goentoro, David A Gold
A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration. Genome biology and evolution 16 (6) (2024)
Delaney K Sullivan, Lior Pachter
Flexible parsing, interpretation, and editing of technical sequences with splitcode. Bioinformatics (Oxford, England) 40 (6) (2024)
Tara Chari, Gennady Gorin, Lior Pachter
Stochastic Modeling of Biophysical Responses to Perturbation. bioRxiv : the preprint server for biology (2024)
Joseph Matthew Rich, Lambda Moses, Pétur Helgi Einarsson, Kayla C Jackson, Laura Luebbert, Ali Sina Booeshaghi, Sindri Antonsson, Delaney K Sullivan, Nicolas L Bray, Páll Melsted, Lior Pachter
The impact of package selection and versioning on single-cell RNA-seq analysis. bioRxiv : the preprint server for biology (2024)
Gennady Gorin, John J Vastola, Lior Pachter
Studying stochastic systems biology of the cell with single-cell genomics data. bioRxiv : the preprint server for biology (2023)
Gennady Gorin, Lior Pachter
The telegraph process is not a subordinator. bioRxiv : the preprint server for biology (2023)
Lambda Moses, Pétur Helgi Einarsson, Kayla C Jackson, Laura Luebbert, Ali Sina Booeshaghi, Sindri Antonsson, Nicolas L Bray, Páll Melsted, Lior Pachter
Voyager: exploratory single-cell genomics data analysis with geospatial statistics. bioRxiv : the preprint server for biology (2023)
Ali Sina Booeshaghi, Kyung Hoi Joseph Min, Jase Gehring, Lior Pachter
Quantifying orthogonal barcodes for sequence census assays. Bioinformatics advances 4 (1) (2023)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data. bioRxiv : the preprint server for biology (2023)
Delaney K Sullivan, Lior Pachter
Flexible parsing and preprocessing of technical sequences with splitcode. bioRxiv : the preprint server for biology (2023)
Zsofia Torok, Laura Luebbert, Jordan Feldman, Alison Duffy, Alexander A Nevue, Shelyn Wongso, Claudio V Mello, Adrienne Fairhall, Lior Pachter, Walter G Gonzalez, Carlos Lois
Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons. bioRxiv : the preprint server for biology (2023)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2023)
Lingyun Ivy Xiong, Jing Liu, Seung Yub Han, Kari Koppitch, Jin-Jin Guo, Megan Rommelfanger, Fan Gao, Ingileif B Hallgrimsdottir, Lior Pachter, Junhyong Kim, Adam L MacLean, Andrew P McMahon
Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. bioRxiv : the preprint server for biology (2023)
Tara Chari, Lior Pachter
The specious art of single-cell genomics. PLoS computational biology 19 (8) (2023)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data. bioRxiv : the preprint server for biology (2023)
Gennady Gorin, Lior Pachter
The telegraph process is not a subordinator. bioRxiv : the preprint server for biology (2023)
Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior Pachter
Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data. bioRxiv : the preprint server for biology (2023)
Delaney K Sullivan, Lior Pachter
Flexible parsing and preprocessing of technical sequences with splitcode. bioRxiv : the preprint server for biology (2023)
Delaney K Sullivan, Lior Pachter
Flexible parsing and preprocessing of technical sequences with splitcode. bioRxiv : the preprint server for biology (2023)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2023)
Tara Chari, Gennady Gorin, Lior Pachter
Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data. bioRxiv : the preprint server for biology (2023)
Lingyun Ivy Xiong, Jing Liu, Seung Yub Han, Kari Koppitch, Jin-Jin Guo, Megan Rommelfanger, Fan Gao, Ingileif B Hallgrimsdottir, Lior Pachter, Junhyong Kim, Adam L MacLean, Andrew P McMahon
Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. bioRxiv : the preprint server for biology (2023)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2023)
Lingyun Ivy Xiong, Jing Liu, Seung Yub Han, Kari Koppitch, Jin-Jin Guo, Megan Rommelfanger, Fan Gao, Ingileif B Hallgrimsdottir, Lior Pachter, Junhyong Kim, Adam L MacLean, Andrew P McMahon
Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. bioRxiv : the preprint server for biology (2023)
Ali Sina Booeshaghi, Xi Chen, Lior Pachter
A machine-readable specification for genomics assays. bioRxiv : the preprint server for biology (2023)
Delaney K Sullivan, Kyung Hoi Joseph Min, Kristján Eldjárn Hjörleifsson, Laura Luebbert, Guillaume Holley, Lambda Moses, Johan Gustafsson, Nicolas L Bray, Harold Pimentel, Ali Sina Booeshaghi, Páll Melsted, Lior Pachter
kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq. bioRxiv : the preprint server for biology (2023)
Ali Sina Booeshaghi, Kyung Hoi Joseph Min, Jase Gehring, Lior Pachter
Quantifying orthogonal barcodes for sequence census assays. Bioinformatics advances 4 (1) (2023)
Fairlie Reese, Brian A Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang, Beatrice Borsari, Samuel J Morabito, Heidi Yahan Liang, Cassandra J McGill, Sorena Rahmanian, Jasmine Sakr, Shan Jiang, Weihua Zeng, Klebea Carvalho, Annika K Weimer, Louise A Dionne, Ariel McShane, Karan Bedi, Shaimae I Elhajjajy, Sean Upchurch, Jennifer Jou, Ingrid Youngworth, Aditi K Narayanan, Paul Sud, Otto Jolanki, Benjamin C Hitz, Meenakshi S Kagda, Michael Paul Snyder, Benjamin C Hitz, Jill E Moore, Nishigandha Phalke, David A Bennett, Laura G Reinholdt, Mats Ljungman, Michael A Beer, Mark B Gerstein, Lior Pachter, Roderic Guigo, Barbara J Wold, Ali Mortazavi
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv : the preprint server for biology (2023)
Laura Luebbert, Delaney K Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter
Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. bioRxiv : the preprint server for biology (2023)
Ali Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter
Author Correction: Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Scientific reports 13 (1) (2023)
Ali Sina Booeshaghi, Delaney K Sullivan, Lior Pachter
Universal preprocessing of single-cell genomics data. bioRxiv : the preprint server for biology (2023)
Gennady Gorin, John J Vastola, Meichen Fang, Lior Pachter
Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nature communications 13 (1) (2022)
Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling A Xu, Tal Ashuach, Mariano Gabitto, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-López, Lior Pachter, Fabian Joachim Theis, Aaron Streets, Michael I Jordan, Jeffrey Regier, Nir Yosef
A Python library for probabilistic analysis of single-cell omics data. Nature biotechnology 40 (2) (2022)
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
RNA velocity unraveled. PLoS computational biology 18 (9) (2022)
Gennady Gorin, John J Vastola, Meichen Fang, Lior Pachter
Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nature communications 13 (1) (2022)
Gennady Gorin, John J Vastola, Meichen Fang, Lior Pachter
Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nature communications 13 (1) (2022)
Gennady Gorin, John J Vastola, Meichen Fang, Lior Pachter
Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nature communications 13 (1) (2022)
Lambda Moses, Lior Pachter
Museum of spatial transcriptomics. Nature methods 19 (5) (2022)
Johan Gustafsson, Jonathan Robinson, Jens Nielsen, Lior Pachter
BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq. Genome biology 22 (1) (2021)
Tara Chari, Brandon Weissbourd, Jase Gehring, Anna Ferraioli, Marion Lechable, Makenna Herl, Fan Gao, Sandra Chevalier, Richard R Copley, Evelyn Houliston, David J Anderson, Lior Pachter
Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types. Science advances 7 (48) (2021)
Páll Melsted, A Sina Booeshaghi, Lauren Liu, Fan Gao, Lambda Lu, Kyung Hoi Joseph Min, Eduardo da Veiga Beltrame, Kristján Eldjárn Hjörleifsson, Jase Gehring, Lior Pachter
Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nature biotechnology 39 (7) (2021)
Gennady Gorin, Valentine Svensson, Lior Pachter
Protein velocity and acceleration from single-cell multiomics experiments. Genome biology 21 (1) (2020)
Ali Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter
Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Scientific reports 9 (1) (2019)
Jase Gehring, Jong Hwee Park, Sisi Chen, Matthew Thomson, Lior Pachter
Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins. Nature biotechnology 38 (1) (2019)
Vasilis Ntranos, Lynn Yi, Páll Melsted, Lior Pachter
A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nature methods 16 (2) (2019)