Personal information

Activities

Employment (2)

Calico LLC: South San Francisco, CA, US

2016 to present | PI
Employment
Source: Self-asserted source
David Kelley

Harvard University: Cambridge, MA, US

2011 to 2016 | Postdoctoral fellow (Stem Cell and Regenerative Biology)
Employment
Source: Self-asserted source
David Kelley

Education and qualifications (2)

University of Maryland at College Park: College Park, MD, US

2007 to 2011 | PhD (Computer Science)
Education
Source: Self-asserted source
David Kelley

Syracuse University: Syracuse, NY, US

2003 to 2007 | BS (Computer Science)
Education
Source: Self-asserted source
David Kelley

Works (31)

Selective State Space Models Outperform Transformers at Predicting RNA-Seq Read Coverage

2025-02-17 | Preprint
Contributors: Ian H Holmes; Johannes Linder; David R Kelley
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Crossref

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2

PLOS Computational Biology
2025-02-04 | Journal article
Contributors: Paulina N. Smaruj; Maxwell Wing Libbrecht; Fahad Kamulegeya; David R. Kelley; Geoffrey Fudenberg
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Crossref

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

Nature Genetics
2025-01-08 | Journal article
Contributors: Johannes Linder; Divyanshi Srivastava; Han Yuan; Vikram Agarwal; David R. Kelley
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Crossref

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2

2024-08-04 | Preprint
Contributors: Paulina N. Smaruj; Fahad Kamulegeya; David R. Kelley; Geoffrey Fudenberg
Source: check_circle
Crossref

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

2023-09-01 | Preprint
Contributors: Johannes Linder; Divyanshi Srivastava; Han Yuan; Vikram Agarwal; David R. Kelley
Source: check_circle
Crossref

Individual cell types in C. elegans age differently and activate distinct cell-protective responses

Cell Reports
2023-08 | Journal article
Contributors: Antoine Emile Roux; Han Yuan; Katie Podshivalova; David Hendrickson; Rex Kerr; Cynthia Kenyon; David Kelley
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Crossref

Author Correction: scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks

Nature Methods
2023-01 | Journal article
Contributors: Han Yuan; David R. Kelley
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Crossref

scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks

Nature Methods
2022-09 | Journal article
Contributors: Han Yuan; David R. Kelley
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Crossref

The complete cell atlas of an aging multicellular organism

2022-06-16 | Preprint
Contributors: Antoine E. Roux; Han Yuan; Katie Podshivalova; David Hendrickson; Rex Kerr; Cynthia Kenyon; David R. Kelley
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Crossref

The genetic and biochemical determinants of mRNA degradation rates in mammals

2022-03-19 | Preprint
Contributors: Vikram Agarwal; David Kelley
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Crossref

Effective gene expression prediction from sequence by integrating long-range interactions

Nature Methods
2021-10 | Journal article
Contributors: Žiga Avsec; Vikram Agarwal; Daniel Visentin; Joseph R. Ledsam; Agnieszka Grabska-Barwinska; Kyle R. Taylor; Yannis Assael; John Jumper; Pushmeet Kohli; David R. Kelley
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Crossref

Semisupervised adversarial neural networks for single-cell classification

Genome Research
2021-10-24 | Journal article
Contributors: Jacob C. Kimmel; David R. Kelley
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Crossref

scBasset: Sequence-based modeling of single cell ATAC-seq using convolutional neural networks

2021-09-10 | Other
Contributors: Han Yuan; David R Kelley
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Crossref

The landscape of alternative polyadenylation in single cells of the developing mouse embryo

Nature Communications
2021-08-24 | Journal article
Contributors: Vikram Agarwal; Sereno Lopez-Darwin; David R. Kelley; Jay Shendure
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Crossref

Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs

Nature Communications
2021-06-07 | Journal article
Contributors: Qingbo S. Wang; David R. Kelley; Jacob Ulirsch; Masahiro Kanai; Shuvom Sadhuka; Ran Cui; Carlos Albors; Nathan Cheng; Yukinori Okada; Koichi Matsuda et al.
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Crossref

Differentiation reveals latent features of aging and an energy barrier in murine myogenesis

Cell Reports
2021-04 | Journal article
Contributors: Jacob C. Kimmel; Nelda Yi; Margaret Roy; David G. Hendrickson; David R. Kelley
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Crossref

Effective gene expression prediction from sequence by integrating long-range interactions

2021-04-08 | Other
Contributors: Žiga Avsec; Vikram Agarwal; Daniel Visentin; Joseph R. Ledsam; Agnieszka Grabska-Barwinska; Kyle R. Taylor; Yannis Assael; John Jumper; Pushmeet Kohli; David R. Kelley
Source: check_circle
Crossref

The landscape of alternative polyadenylation in single cells of the developing mouse embryo

2021-01-22 | Preprint
Contributors: Vikram Agarwal; Sereno Lopez-Darwin; David R. Kelley; Jay Shendure
Source: check_circle
Crossref

Predicting 3D genome folding from DNA sequence with Akita

Nature Methods
2020-11-12 | Journal article
Contributors: Geoff Fudenberg; David R. Kelley; Katherine S. Pollard
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Evaluating the informativeness of deep learning annotations for human complex diseases

Nature Communications
2020-09-17 | Journal article
Contributors: Kushal K. Dey; Bryce van de Geijn; Samuel Sungil Kim; Farhad Hormozdiari; David R. Kelley; Alkes L. Price
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Crossref

Cross-species regulatory sequence activity prediction

PLOS Computational Biology
2020-07-20 | Journal article
Contributors: David R. Kelley; Jian Ma
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Crossref

scNym: Semi-supervised adversarial neural networks for single cell classification

2020-06-05 | Preprint
Contributors: Jacob C. Kimmel; David R. Kelley
Source: check_circle
Crossref

Differentiation reveals the plasticity of age-related change in murine muscle progenitors

2020-03-06 | Preprint
Contributors: Jacob C. Kimmel; David G. Hendrickson; David R. Kelley
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Crossref

Corrigendum: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

Genome Research
2020-01 | Journal article
Contributors: Jacob C. Kimmel; Lolita Penland; Nimrod D. Rubinstein; David G. Hendrickson; David R. Kelley; Adam Z. Rosenthal
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Crossref

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

Genome Research
2019-12-21 | Journal article
Contributors: Jacob C. Kimmel; Lolita Penland; Nimrod D. Rubinstein; David G. Hendrickson; David R. Kelley; Adam Z. Rosenthal
Source: check_circle
Crossref

Solo: doublet identification via semi-supervised deep learning

2019-11-14 | Other
Contributors: Nicholas Bernstein; Nicole Fong; Irene Lam; Margaret Roy; David G. Hendrickson; David R. Kelley
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Crossref

Predicting 3D genome folding from DNA sequence

2019-10-10 | Other
Contributors: Geoff Fudenberg; David R. Kelley; Katherine S. Pollard
Source: check_circle
Crossref

A murine aging cell atlas reveals cell identity and tissue-specific trajectories of aging

2019-06-06 | Other
Contributors: Jacob C. Kimmel; Lolita Penland; Nimrod D. Rubinstein; David G. Hendrickson; David R. Kelley; Adam Z. Rosenthal
Source: check_circle
Crossref

Cross-species regulatory sequence activity prediction

2019-06-05 | Other
Contributors: David R. Kelley
Source: check_circle
Crossref

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

Genome Research
2018-05-27 | Journal article
Contributors: David R. Kelley; Yakir A. Reshef; Maxwell Bileschi; David Belanger; Cory Y. McLean; Jasper Snoek
Source: check_circle
Crossref

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

2017-07-10 | Preprint
Contributors: David R. Kelley; Yakir A. Reshef; Maxwell Bileschi; David Belanger; Cory Y. McLean; Jasper Snoek
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Peer review (13 reviews for 8 publications/grants)

Review activity for F1000Research. (1)
Review activity for Genome biology. (1)
Review activity for Nature (1)
Review activity for Nature biotechnology. (1)
Review activity for Nature communications (2)
Review activity for Nature genetics. (2)
Review activity for Nature methods. (3)
Review activity for PLoS computational biology. (2)