Cole Trapnell

Also affiliated with Brotman Baty Institute, Allen Institute

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 1%percentile

25.9Author DataRank

Indexed papers

7in 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 7 indexed papers 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.

Comprehensive single-cell transcriptional profiling of a multicellular organism

Science(2017)10.1126/science.aam8940

Top 2%

8.4DataRank

Top 2%1581 citations

Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Xiaojie Qiu +9 more

Papers

Driven by 65 papers — median percentile 95. Top paper: “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions”.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Genome Biology(2013)10.1186/gb-2013-14-4-r36

N/A

22.2DataRank · unranked

13778 citations

Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg +1 more

Comprehensive single-cell transcriptional profiling of a multicellular organism

Science(2017)10.1126/science.aam8940

Top 2%

8.4DataRank

Top 2%1581 citations

Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Xiaojie Qiu +9 more

A human cell atlas of fetal gene expression

Science(2020)10.1126/science.aba7721

Top 3%

6.2DataRank

Top 3%842 citations

Diana R. O’Day, Hannah A. Pliner, Paul D. Kingsley, Mei Deng, Riza M. Daza +12 more

A human cell atlas of fetal chromatin accessibility

Science(2020)10.1126/science.aba7612

Top 3%

5.8DataRank

Top 3%466 citations

Andrew J. Hill, Riza M. Daza, Junyue Cao, Diana R. O’Day, Hannah A. Pliner +12 more

Systematic reconstruction of cellular trajectories across mouse embryogenesis

Nature Genetics(2022)10.1038/s41588-022-01018-x

Top 6%

3.8DataRank

Top 6%212 citations

Junyue Cao, Beth Martin, Tony Li, Ian Welsh, Sanjay Srivatsan +10 more

A single-cell time-lapse of mouse prenatal development from gastrula to birth

Nature(2024)10.1038/s41586-024-07069-w

N/A

3.2DataRank · unranked

181 citations

Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang +20 more

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Nature Protocols(2012)10.1038/nprot.2012.016

N/A

1.4DataRank · unranked

12835 citations

Adam Roberts, Reenal Pattni, Daehwan Kim, Cheryl A. Keller, Harold Pimentel +5 more

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Genes & Development(2011)10.1101/gad.17446611

N/A

1.2DataRank · unranked

3660 citations

Cole Trapnell, Barbara Tazon-Vega, Prisca Liberali, John L. Rinn, Loyal A. Goff +3 more

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Genome biology(2021)10.1186/s13059-021-02432-w

Top 22%

0.925DataRank

Top 22%27 citations

Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan +9 more

Predicting cellular responses to complex perturbations in high‐throughput screens

Molecular Systems Biology(2023)10.15252/msb.202211517

N/A

0.832DataRank · unranked

256 citations

Anna Klimovskaia Susmelj, Carlo De Donno, Leon Hetzel, Yuge Ji, Ignacio Ibarra Del Río +16 more

Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.04.502764

Top 27%

0.735DataRank

Top 27%22 citations

Sanjay Srivatsan, Madeleine Duran, Michael W. Dorrity, Brent Ewing, Tor Linbo +6 more

The regulatory potential of transposable elements in maize

Nature Plants(2025)10.1038/s41477-025-02002-z

N/A

0.525DataRank · unranked

17 citations

Morgan O. Hamm, Thomas W. Tullius, Joseph Min, Bryan Ramirez-Corona, Nicholas A. Mueth +9 more

The anatomy of successful computational biology software

Nature Biotechnology(2013)10.1038/nbt.2721

N/A

0.483DataRank · unranked

24 citations

Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski, Alexandra P. Lewis +6 more

Understanding genetic variants in context

eLife(2024)10.7554/elife.88231

N/A

0.403DataRank · unranked

10 citations

Stanley Fields, Frederick P. Roth, Lea M. Starita, Cole Trapnell, Judit Villén +3 more

A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

eLife(2023)10.7554/elife.92091

N/A

0.322DataRank · unranked

7 citations

Marcus Hooper, Levi Todd, Faith Kierney, Nicolai Blasdel, Cole Trapnell +2 more

Dystrophin deficiency impairs cell junction formation during embryonic myogenesis from pluripotent stem cells

iScience(2024)10.1016/j.isci.2024.110242

N/A

0.258DataRank · unranked

4 citations

Emmanuelle Massouridès, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L. Jackson +9 more

Dystrophin deficiency impairs cell junction formation during embryonic myogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.05.569919

N/A

0.208DataRank · unranked

2 citations

Emmanuelle Massouridès, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L. Jackson +9 more

Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.20.469409

N/A

0DataRank · unranked

5 citations

Kaitlyn A. Barrow, Lucille M. Rich, David F. Read, Cole Trapnell, Oghenemega Okoloko +5 more

Multipotent progenitors and hematopoietic stem cells arise independently during the endothelial to hematopoietic transition in the early mouse embryo

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.13.439736

N/A

0DataRank · unranked

1 citations

Barbara Varnum‐Finney, Sanjay Srivatsan, Stacey Dozono, Olivia G. Waltner, Adam Heck +7 more

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.12.443782

N/A

0DataRank · unranked

0 citations

Lauren M. Saunders, August A. Carr, Sanjay Srivatsan, Colten D. Eberhard, Blake Carrington +5 more

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.20.390765

N/A

0DataRank · unranked

4 citations

Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan +9 more

Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics

Nature Communications(2022)10.1038/s41467-022-28781-z

N/A

0DataRank · unranked

54 citations

Barbara Varnum‐Finney, Stacey Dozono, Tessa Dignum, Cynthia Nourigat-Mckay, Adam Heck +8 more

Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication

Scientific Reports(2022)10.1038/s41598-022-10763-2

N/A

0DataRank · unranked

30 citations

Kaitlyn A. Barrow, Lucille M. Rich, David F. Read, Cole Trapnell, Oghenemega Okoloko +5 more

Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

Nature Communications(2022)10.1038/s41467-022-30309-4

N/A

0DataRank · unranked

7 citations

Gregory T. Booth, Lauren M. Saunders, Sanjay Srivatsan, José L. McFaline‐Figueroa, Cole Trapnell +1 more

A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface

Journal of Biological Chemistry(2020)10.1074/jbc.ra120.013454

N/A

0DataRank · unranked

48 citations

Kerrie B. Collins, Stacey Aggarwal, Lauren M. Saunders, Ho-Tak Lau, Danny Suh +6 more

Proteostasis governs differential temperature sensitivity across embryonic cell types

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.04.502669

N/A

0DataRank · unranked

11 citations

Lauren M. Saunders, Madeleine Duran, Sanjay Srivatsan, Brent Ewing, Christine Queitsch +5 more

Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.12.496461

N/A

0DataRank · unranked

7 citations

Gregory T. Booth, Riza M. Daza, Dana L. Jackson, Rula Green Gladden, Sanjay Srivatsan +13 more

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.03.500325

N/A

0DataRank · unranked

5 citations

Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Rose Yinghan Behncke +28 more

Proteostasis governs differential temperature sensitivity across embryonic cell types

Cell(2023)10.1016/j.cell.2023.10.013

N/A

0DataRank · unranked

41 citations

Lauren M. Saunders, Madeleine Duran, Sanjay Srivatsan, Eliza Barkan, Dana L. Jackson +8 more

Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Nature(2023)10.1038/s41586-023-06548-w

N/A

0DataRank · unranked

36 citations

Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Oana V. Amarie +36 more

Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity

Cell Reports Methods(2023)10.1016/j.crmeth.2023.100548

N/A

0DataRank · unranked

33 citations

Akshayalakshmi Sridhar, Kiara C. Eldred, Sophia A. Cuschieri, Dawn Hoffer, Cole Trapnell +2 more

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

eLife(2023)10.7554/elife.86670

N/A

0DataRank · unranked

17 citations

Lauren M. Saunders, August A. Carr, Sanjay Srivatasan, Colten D. Eberhard, Blake Carrington +5 more

High-capacity sample multiplexing for single cell chromatin accessibility profiling

BMC Genomics(2023)10.1186/s12864-023-09832-1

N/A

0DataRank · unranked

3 citations

Riza M. Daza, Sanjay Srivatsan, José L. McFaline‐Figueroa, Rula Green Gladden, Andrew C. Mullen +4 more

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.05.535726

N/A

0DataRank · unranked

22 citations

Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang +20 more

Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.14.532666

N/A

0DataRank · unranked

10 citations

Rachel L. Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay Srivatsan, Ali Etemadi +27 more

Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.31.543087

N/A

0DataRank · unranked

9 citations

Akshayalakshmi Sridhar, Kiara C. Eldred, Sophia A. Cuschieri, Dawn Hoffer, Cole Trapnell +2 more

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.10.531983

N/A

0DataRank · unranked

6 citations

Sanjay Srivatsan, Andrew J. Hill, Molly Gasperini, Dana L. Jackson, Lauren M. Saunders +8 more

High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.05.531201

N/A

0DataRank · unranked

3 citations

Riza M. Daza, Sanjay Srivatsan, José L. McFaline‐Figueroa, Rula Green Gladden, Scott N. Furlan +3 more

Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.27.534417

N/A

0DataRank · unranked

2 citations

Sean Houghton, Ryan Schreiner, Lin Yang, Chaitanya R. Badwe, Véronique Voisin +20 more

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

(2023)10.7554/elife.86670.1

N/A

0DataRank · unranked

2 citations

Lauren M. Saunders, August A. Carr, Sanjay Srivatsan, Colten D. Eberhard, Blake Carrington +5 more

A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.26.559569

N/A

0DataRank · unranked

1 citations

Marcus Hooper, Levi Todd, Faith Kierney, Nicolai Blasdel, Cole Trapnell +2 more

Differentiation latency, cell division symmetry, and dormancy signatures define fetal liver HSCs at single cell resolution

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.01.543314

N/A

0DataRank · unranked

0 citations

Juliane I Mercoli, Adam Heck, Ian G. Phelps, Barbara Varnum‐Finney, Stacey Dozono +13 more

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

(2023)10.7554/elife.86670.3

N/A

0DataRank · unranked

0 citations

Lauren M. Saunders, August A. Carr, Sanjay Srivatsan, Colten D. Eberhard, Blake Carrington +5 more

Author Response: Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

(2023)10.7554/elife.86670.3.sa3

N/A

0DataRank · unranked

0 citations

Lauren M. Saunders, August A. Carr, Sanjay Srivatsan, Colten D. Eberhard, Blake Carrington +5 more

Reviewer #1 (Public Review): A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

(2023)10.7554/elife.92091.1.sa1

N/A

0DataRank · unranked

0 citations

Marcus Hooper, Levi Todd, Faith Kierney, Nicolai Blasdel, Cole Trapnell +2 more

A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

(2023)10.7554/elife.92091.1

N/A

0DataRank · unranked

0 citations

Marcus Hooper, Levi Todd, Faith Kierney, Nicolai Blasdel, Cole Trapnell +2 more

Dimensionality reduction by UMAP to visualize physical and genetic interactions

Nature Communications(2020)10.1038/s41467-020-15351-4

N/A

0DataRank · unranked

249 citations

Lauren M. Saunders, Christine Queitsch, Stanley Fields, Cole Trapnell, Michael W. Dorrity

Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies

Cell(2024)10.1016/j.cell.2024.05.025

N/A

0DataRank · unranked

56 citations

Ashish Phal, Rachel L. Redler, Thomas Schlichthaerle, Sanjay Srivatsan, Devon Duron Ehnes +35 more

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

Cell Genomics(2024)10.1016/j.xgen.2023.100487

N/A

0DataRank · unranked

17 citations

Sanjay Srivatsan, Andrew J. Hill, Molly Gasperini, Dana L. Jackson, Lauren M. Saunders +8 more

Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

Communications Biology(2024)10.1038/s42003-024-06582-y

N/A

0DataRank · unranked

14 citations

Gregory T. Booth, Riza M. Daza, Dana L. Jackson, Rula Green Gladden, Sanjay Srivatsan +15 more

Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.24.612755

N/A

0DataRank · unranked

1 citations

Xiaoyi Cheng, Clyde Campbell, Cole Trapnell, Raquel Espín-Palazón, Brandon Hadland +2 more

Reviewer #1 (Public Review): A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

(2024)10.7554/elife.92091.2.sa1

N/A

0DataRank · unranked

0 citations

Marcus Hooper, Levi Todd, Faith Kierney, Nicolai Blasdel, Cole Trapnell +2 more

An improved, high yield method for isolating nuclei from individual zebrafish embryos for single-nucleus RNA sequencing

arXiv (Cornell University)(2024)10.48550/arxiv.2411.15309

N/A

0DataRank · unranked

0 citations

Heidi Lee, Amy Tresenrider, Riza M. Daza, Andrew R. Mullen, Jay Shendure +3 more

Combinatorial mapping of E3 ubiquitin ligases to their target substrates

Molecular Cell(2025)10.1016/j.molcel.2025.01.016

N/A

0DataRank · unranked

20 citations

Diego Calderon, David Lee, Melodie Chiu, Shruti Jain, Florence M. Chardon +6 more

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Cell Systems(2020)10.1016/j.cels.2020.02.003

N/A

0DataRank · unranked

181 citations

Arman Rahimzamani, Li Wang, Bingcheng Ren, Qi Mao, Timothy Durham +5 more

Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells

Stem Cell Reports(2025)10.1016/j.stemcr.2025.102641

N/A

0DataRank · unranked

3 citations

Xiaoyi Cheng, Shuvra Dutta, Clyde Campbell, Cole Trapnell, Raquel Espín-Palazón +3 more

Differentiation latency and dormancy signatures define fetal liver hematopoietic stem cells at single-cell resolution

Cell Reports(2025)10.1016/j.celrep.2025.116289

N/A

0DataRank · unranked

1 citations

Juliane I Mercoli, Adam Heck, Ian G. Phelps, Barbara Varnum‐Finney, Stacey Dozono +13 more

A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.03.646654

N/A

0DataRank · unranked

6 citations

Eliza Barkan, Amy Tresenrider, Heidi Lee, Ryan Z. Friedman, Nicholas C Lammers +6 more

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.23.655669

N/A

0DataRank · unranked

4 citations

Chengxiang Qiu, Jean‐Benoît Lalanne, Beth Martin, Madeleine Duran, Cole Trapnell +4 more

An Improved, High-Yield Method for Isolating Nuclei from Individual Zebrafish Embryos for Single-Nucleus RNA Sequencing

Zebrafish(2025)10.1089/zeb.2024.0175

N/A

0DataRank · unranked

0 citations

Heidi Lee, Amy Tresenrider, Riza M. Daza, Andrew R. Mullen, Jay Shendure +3 more

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma

Molecular Systems Biology(2021)10.15252/msb.20209522

N/A

0DataRank · unranked

50 citations

Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin +12 more

Sci-fate characterizes the dynamics of gene expression in single cells

Nature Biotechnology(2020)10.1038/s41587-020-0480-9

N/A

0DataRank · unranked

183 citations

Wei Zhou, Frank J. Steemers, Cole Trapnell, Jay Shendure, Junyue Cao

Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo

Cell Reports(2021)10.1016/j.celrep.2021.109675

N/A

0DataRank · unranked

113 citations

Barbara Varnum‐Finney, Sanjay Srivatsan, Stacey Dozono, Olivia G. Waltner, Adam Heck +8 more

Engineering a niche supporting haematopoietic stem cell development using integrated single cell transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.25.427999

N/A

0DataRank · unranked

6 citations

Barbara Varnum‐Finney, Stacey Dozono, Tessa Dignum, Cynthia Nourigat-Mckay, Dana L. Jackson +6 more

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.08.447626

N/A

0DataRank · unranked

5 citations

Junyue Cao, Tony Li, Sanjay Srivatsan, Xingfan Huang, Diego Calderon +7 more

Cole Trapnell

Indexed papers

Top data-sharing exemplar

Papers