David R Kelley

ORCID

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 18

Top Venues

bioRxiv : the preprint server for biology

Nature methods

Genome research

Nature communications

Calico LLC

University of Maryland at College Park (PHD)

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

Affiliation History

Calico LLC

United States

Harvard University

United States

Postdoctoral fellow :: Stem Cell and Regenerative Biology

Education History

University of Maryland at College Park

United States

PHD :: Computer Science

Syracuse University

United States

BSC :: Computer Science

Publications

Andreas R Gschwind, Kristy S Mualim, Alireza Karbalayghareh, Maya U Sheth, Kushal K Dey, Evelyn Jagoda, Ramil N Nurtdinov, Wang Xi, Anthony S Tan, Hank Jones, X Rosa Ma, David Yao, Joseph Nasser, Žiga Avsec, Benjamin T James, Muhammad Saad Shamim, Neva C Durand, Suhas S P Rao, Ragini Mahajan, Benjamin R Doughty, Kalina Andreeva, Jacob C Ulirsch, Kaili Fan, Elizabeth M Perez, Tri C Nguyen, David R Kelley, Hilary K Finucane, Jill E Moore, Nishigandha Phalke, Manolis Kellis, Michael C Bassik, Alkes L Price, Michael A Beer, Roderic Guigo, John A Stamatoyannopoulos, Erez Lieberman Aiden, William J Greenleaf, Christina S Leslie, Lars M Steinmetz, Anshul Kundaje, Jesse M Engreitz
An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv : the preprint server for biology (2023)
Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz
Rewriting regulatory DNA to dissect and reprogram gene expression. bioRxiv : the preprint server for biology (2023)
Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz
Rewriting regulatory DNA to dissect and reprogram gene expression. bioRxiv : the preprint server for biology (2023)
Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz
Rewriting regulatory DNA to dissect and reprogram gene expression. bioRxiv : the preprint server for biology (2023)
Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz
Rewriting regulatory DNA to dissect and reprogram gene expression. bioRxiv : the preprint server for biology (2023)
Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz
Rewriting regulatory DNA to dissect and reprogram gene expression. bioRxiv : the preprint server for biology (2023)
Han Yuan, David R Kelley
scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks. Nature methods 19 (9) (2022)
Han Yuan, David R Kelley
Author Correction: scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks. Nature methods (2022)
Jacob C Kimmel, David R Kelley
Semisupervised adversarial neural networks for single-cell classification. Genome research 31 (10) (2021)
Žiga Avsec, Vikram Agarwal, Daniel Visentin, Joseph R Ledsam, Agnieszka Grabska-Barwinska, Kyle R Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, David R Kelley
Effective gene expression prediction from sequence by integrating long-range interactions. Nature methods 18 (10) (2021)
Vikram Agarwal, Sereno Lopez-Darwin, David R Kelley, Jay Shendure
The landscape of alternative polyadenylation in single cells of the developing mouse embryo. Nature communications 12 (1) (2021)
Qingbo S Wang, David R Kelley, Jacob C Ulirsch, Masahiro Kanai, Shuvom Sadhuka, Ran Cui, Carlos Albors, Nathan Cheng, Yukinori Okada, null null, François Aguet, Kristin G Ardlie, Daniel G MacArthur, Hilary K Finucane
Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs. Nature communications 12 (1) (2021)
Geoffrey Fudenberg, David R Kelley, Katherine S Pollard
Predicting 3D genome folding from DNA sequence with Akita. Nature methods 17 (11) (2020)
David R Kelley
Cross-species regulatory sequence activity prediction. PLoS computational biology 16 (7) (2020)
Kushal K Dey, Bryce van de Geijn, Samuel Sungil Kim, Farhad Hormozdiari, David R Kelley, Alkes L Price
Evaluating the informativeness of deep learning annotations for human complex diseases. Nature communications 11 (1) (2020)
Jacob C Kimmel, Lolita Penland, Nimrod D Rubinstein, David G Hendrickson, David R Kelley, Adam Z Rosenthal
Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging. Genome research 29 (12) (2019)
David R Kelley, Yakir A Reshef, Maxwell Bileschi, David Belanger, Cory Y McLean, Jasper Snoek
Sequential regulatory activity prediction across chromosomes with convolutional neural networks. Genome research 28 (5) (2018)
Julie Donaghey, Sudhir Thakurela, Jocelyn Charlton, Jennifer S Chen, Zachary D Smith, Hongcang Gu, Ramona Pop, Kendell Clement, Elena K Stamenova, Rahul Karnik, David R Kelley, Casey A Gifford, Davide Cacchiarelli, John L Rinn, Andreas Gnirke, Michael J Ziller, Alexander Meissner
Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nature genetics 50 (2) (2018)

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Publication Activity (10 Years)

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David R Kelley