Lior Pachter

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 7%percentile

0.165Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation

Cell Genomics(2025)10.1016/j.xgen.2025.101108

Top 70%

0.165DataRank

Top 70%2 citations

Ryan Weber, Elnaz Abdollahzadeh, Nikhila Swarna, Delaney K. Sullivan, Diane Trout +21 more

Papers

Driven by 59 papers — median percentile 30. Top paper: “A Python library for probabilistic analysis of single-cell omics data”.

A Python library for probabilistic analysis of single-cell omics data

Nature Biotechnology(2022)10.1038/s41587-021-01206-w

N/A

9.4DataRank · unranked

825 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong +24 more

PSCA-CAR T cell therapy in metastatic castration-resistant prostate cancer: a phase 1 trial

Nature Medicine(2024)10.1038/s41591-024-02979-8

N/A

1.8DataRank · unranked

124 citations

M. Suzette Blanchard, Lauren Adkins, Laura Luebbert, Neena A. Leggett, Stephanie N. Shishido +23 more

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

eLife(2020)10.7554/elife.59610

N/A

1.3DataRank · unranked

54 citations

Fan Gao, Yasuno Iwasaki, Peng He, Lior Pachter, J. Peter Gergen +2 more

Deciphering the impact of genomic variation on function

Nature(2024)10.1038/s41586-024-07510-0

N/A

1.1DataRank · unranked

89 citations

Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon +95 more

Isoform cell-type specificity in the mouse primary motor cortex

Nature(2021)10.1038/s41586-021-03969-3

N/A

0.685DataRank · unranked

95 citations

Zizhen Yao, Cindy T. J. van Velthoven, Kimberly A. Smith, Bosiljka Tasic, Hongkui Zeng +2 more

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples

Nature Biomedical Engineering(2021)10.1038/s41551-021-00754-5

N/A

0.655DataRank · unranked

78 citations

Laila Sathe, Chetan Munugala, Eric M. Jones, Molly Gasperini, Nathan B. Lubock +36 more

Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney

Developmental Cell(2023)10.1016/j.devcel.2023.08.010

N/A

0.596DataRank · unranked

52 citations

Jing Liu, Seung Yub Han, Kari Koppitch, Jinjin Guo, Megan K. Rommelfanger +8 more

Metadata retrieval from sequence databases with ffq

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.18.492548

N/A

0.385DataRank · unranked

12 citations

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

A machine-readable specification for genomics assays

Bioinformatics(2024)10.1093/bioinformatics/btae168

N/A

0.385DataRank · unranked

12 citations

Xi Chen, Lior Pachter, A. Sina Booeshaghi

Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.06.539585

N/A

0.208DataRank · unranked

3 citations

Jianjun Liu, Seung Yub Han, Kari Koppitch, Jinjin Guo, Megan K. Rommelfanger +7 more

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation

Cell Genomics(2025)10.1016/j.xgen.2025.101108

Top 70%

0.165DataRank

Top 70%2 citations

Ryan Weber, Elnaz Abdollahzadeh, Nikhila Swarna, Delaney K. Sullivan, Diane Trout +21 more

Determining gene specificity from multivariate single-cell RNA sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.21.689845

N/A

0.104DataRank · unranked

1 citations

A. Sina Booeshaghi, Elisabeth Rebboah, M. Grace Gordon, Pooja Kathail, Taibo Li +6 more

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

UNC Libraries(2021)10.17615/1d8m-k379

N/A

0DataRank · unranked

1 citations

Charles H. Langley, Alisha K. Holloway, Phillip M Nista, LaDeana W. Hillier, Corbin D. Jones +8 more

Length Biases in Single-Cell RNA Sequencing of pre-mRNA

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.30.454514

N/A

0DataRank · unranked

11 citations

Lior Pachter, Gennady Gorin

Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.22.427844

N/A

0DataRank · unranked

9 citations

Brandon Weissbourd, Jase Gehring, Anna Ferraioli, Lucas Leclère, Makenna Herl +7 more

Assessing the multimodal tradeoff

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.08.471788

N/A

0DataRank · unranked

8 citations

Fan Gao, Lior Pachter, A. Sina Booeshaghi

Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.25.428188

N/A

0DataRank · unranked

4 citations

Lior Pachter, A. Sina Booeshaghi

Direct simulation of a stochastically driven multi-step birth-death process

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.20.427480

N/A

0DataRank · unranked

2 citations

Lior Pachter, Gennady Gorin

RNA velocity unraveled

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010492

N/A

0DataRank · unranked

189 citations

Meichen Fang, Tara Chari, Lior Pachter, Gennady Gorin

Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments

Nature Communications(2022)10.1038/s41467-022-34857-7

N/A

0DataRank · unranked

55 citations

John J. Vastola, Meichen Fang, Lior Pachter, Gennady Gorin

Modeling bursty transcription and splicing with the chemical master equation

Biophysical Journal(2022)10.1016/j.bpj.2022.02.004

N/A

0DataRank · unranked

48 citations

Lior Pachter, Gennady Gorin

Metadata retrieval from sequence databases with ffq

Bioinformatics(2022)10.1093/bioinformatics/btac667

N/A

0DataRank · unranked

33 citations

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

Monod : model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.11.495771

N/A

0DataRank · unranked

18 citations

Tara Chari, Maria Carilli, John J. Vastola, Lior Pachter, Gennady Gorin

Transient and delay chemical master equations

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.17.512599

N/A

0DataRank · unranked

7 citations

Shawn Yoshida, Lior Pachter, Gennady Gorin

Efficient querying of genomic reference databases with gget

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.17.492392

N/A

0DataRank · unranked

6 citations

Lior Pachter, Laura Luebbert

The specious art of single-cell genomics

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011288

N/A

0DataRank · unranked

322 citations

Lior Pachter, Tara Chari

Efficient querying of genomic reference databases with gget

Bioinformatics(2023)10.1093/bioinformatics/btac836

N/A

0DataRank · unranked

41 citations

Lior Pachter, Laura Luebbert

Studying stochastic systems biology of the cell with single-cell genomics data

Cell Systems(2023)10.1016/j.cels.2023.08.004

N/A

0DataRank · unranked

41 citations

John J. Vastola, Lior Pachter, Gennady Gorin

Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing

Bulletin of Mathematical Biology(2023)10.1007/s11538-023-01213-9

N/A

0DataRank · unranked

12 citations

Shawn Yoshida, Lior Pachter, Gennady Gorin

Voyager: exploratory single-cell genomics data analysis with geospatial statistics

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.20.549945

N/A

0DataRank · unranked

57 citations

Pétur Helgi Einarsson, Kayla Jackson, Laura Luebbert, A. Sina Booeshaghi, Sindri Emmanúel Antonsson +4 more

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.21.568164

N/A

0DataRank · unranked

30 citations

Kyung Hoi Min, Kristján Eldjárn Hjörleifsson, Laura Luebbert, Guillaume Holley, Lambda Moses +7 more

A machine-readable specification for genomics assays

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.17.533215

N/A

0DataRank · unranked

9 citations

Xi Chen, Lior Pachter, A. Sina Booeshaghi

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.11.571168

N/A

0DataRank · unranked

7 citations

Delaney K. Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari +2 more

Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.17.558131

N/A

0DataRank · unranked

6 citations

Gennady Gorin, Lior Pachter, Tara Chari

Studying stochastic systems biology of the cell with single-cell genomics data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.17.541250

N/A

0DataRank · unranked

4 citations

John J. Vastola, Lior Pachter, Gennady Gorin

Universal preprocessing of single-cell genomics data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.14.543267

N/A

0DataRank · unranked

4 citations

Delaney K. Sullivan, Lior Pachter, A. Sina Booeshaghi

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.20.533521

N/A

0DataRank · unranked

3 citations

Lior Pachter, Delaney K. Sullivan

The telegraph process is not a subordinator

太陽/風力エネルギー講演論文集 = Proceedings of JSES/JWEA Joint Conference(2023)10.1101/2023.01.17.524309

N/A

0DataRank · unranked

0 citations

Lior Pachter, Gennady Gorin

Spectral neural approximations for models of transcriptional dynamics

Biophysical Journal(2024)10.1016/j.bpj.2024.04.034

N/A

0DataRank · unranked

15 citations

Maria Carilli, Tara Chari, Lior Pachter, Gennady Gorin

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

Bioinformatics(2024)10.1093/bioinformatics/btae331

N/A

0DataRank · unranked

11 citations

Lior Pachter, Delaney K. Sullivan

The impact of package selection and versioning on single-cell RNA-seq analysis

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.04.588111

N/A

0DataRank · unranked

35 citations

Lambda Moses, Pétur Helgi Einarsson, Kayla Jackson, Laura Luebbert, A. Sina Booeshaghi +6 more

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

Bioinformatics(2020)10.1093/bioinformatics/btaa169

N/A

0DataRank · unranked

221 citations

Adam Gayoso, Nir Yosef, Lior Pachter, Valentine Svensson

Estimating cis and trans contributions to differences in gene regulation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.13.603403

N/A

0DataRank · unranked

4 citations

Maria Carilli, Lior Pachter, Ingileif B. Hallgrímsdóttir

Stochastic Modeling of Biophysical Responses to Perturbation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.04.602131

N/A

0DataRank · unranked

0 citations

Gennady Gorin, Lior Pachter, Tara Chari

Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes

Nature Biotechnology(2025)10.1038/s41587-025-02614-y

N/A

0DataRank · unranked

11 citations

Delaney K. Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari +2 more

Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data

Nature Methods(2025)10.1038/s41592-025-02832-x

N/A

0DataRank · unranked

6 citations

Tara Chari, Maria Carilli, John J. Vastola, Lior Pachter, Gennady Gorin

Pseudoassembly of k-mers

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.11.653354

N/A

0DataRank · unranked

2 citations

Mayuko Boffelli, Lior Pachter, Delaney K. Sullivan

Long-read sequencing transcriptome quantification with lr-kallisto

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.19.604364

N/A

0DataRank · unranked

14 citations

Delaney K. Sullivan, A. Sina Booeshaghi, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr +12 more

Protein velocity and acceleration from single-cell multiomics experiments

Genome biology(2020)10.1186/s13059-020-1945-3

N/A

0DataRank · unranked

98 citations

Valentine Svensson, Lior Pachter, Gennady Gorin

RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

PLoS ONE(2020)10.1371/journal.pone.0232946

N/A

0DataRank · unranked

21 citations

Lior Pachter, David Tse, Sreeram Kannan, Shunfu Mao

Special function methods for bursty models of transcription

Physical review. E(2020)10.1103/physreve.102.022409

N/A

0DataRank · unranked

26 citations

Lior Pachter, Gennady Gorin

A faster implementation of association mapping from k-mers

BIO-PROTOCOL(2020)10.21769/bioprotoc.3815

N/A

0DataRank · unranked

3 citations

Jaiaid Mobin, Ibrahim Asadullah Tahmid, Lior Pachter, Atif Rahman, Zakaria Mehrab

Intrinsic and extrinsic noise are distinguishable in a synthesis – export – degradation model of mRNA production

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.25.312868

N/A

0DataRank · unranked

15 citations

Lior Pachter, Gennady Gorin

Isoform cell type specificity in the mouse primary motor cortex

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.05.977991

N/A

0DataRank · unranked

6 citations

Zizhen Yao, Cindy T. J. van Velthoven, Kimberly A. Smith, Bosiljka Tasic, Hongkui Zeng +2 more

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.06.188003

N/A

0DataRank · unranked

2 citations

Jonathan L. Robinson, Jens Nielsen, Lior Pachter, Johan Gustafsson

Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types

Science Advances(2021)10.1126/sciadv.abh1683

N/A

0DataRank · unranked

127 citations

Brandon Weissbourd, Jase Gehring, Anna Ferraioli, Lucas Leclère, Makenna Herl +7 more

Normalization of single-cell RNA-seq counts by log( x + 1) or log(1 + x )

Bioinformatics(2021)10.1093/bioinformatics/btab085

N/A

0DataRank · unranked

82 citations

Lior Pachter, A. Sina Booeshaghi

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Genome biology(2021)10.1186/s13059-021-02386-z

N/A

0DataRank · unranked

9 citations

Jonathan L. Robinson, Jens Nielsen, Lior Pachter, Johan Gustafsson

SWALO: scaffolding with assembly likelihood optimization

Nucleic Acids Research(2021)10.1093/nar/gkab717

N/A

0DataRank · unranked

4 citations

Lior Pachter, Atif Rahman

Lior Pachter

Indexed papers

Top data-sharing exemplar

Papers