David R. Kelley - Publications, H-index & Citations

David R. Kelley

calico life sciences llc

47H指数

112论文数

2.8W被引数

收录论文 36

发表时间

An encyclopedia of human enhancer–gene regulatory interactions 人类增强子-基因调控互作百科全书

Nature

IF48.5

2026-07-15

OAAI

Andreas R. Gschwind; Kristy S. Mualim; Alireza Karbalayghareh; Maya U. Sheth; Kushal K. Dey; Evelyn Jagoda; Ramil N. Nurtdinov; Wang Xi; Anthony S. Tan; James Galante; Hank Jones; X. Rosa Ma; David Yao; Dulguun Amgalan; Judhajeet Ray; Chad J. Munger; Joseph Nasser; Žiga Avsec; Benjamin T. James; Muhammad S. 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; Zhiping Weng; Manolis Kellis; Michael C. Bassik; Berk Ustun; Alkes L. Price; Michael A. Beer; Roderic Guigó; John A. Stamatoyannopoulos; Erez Lieberman Aiden; William J. Greenleaf; Christina S. Leslie; Lars M. Steinmetz; Anshul Kundaje; Jesse M. Engreitz

Teaching an old dog new cells 教老狗新细胞

Nature Methods

IF32.1

2026-05-25

PREAI

Johannes Linder; David R. Kelley

Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts 参数高效的微调可以将调控序列模型可扩展地转移到新的环境中

Genome Biology

IF9.4

2026-01-30

OAAI

Han Yuan; Johannes Linder; David R. Kelley

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2 解读CTCF介导的基因组折叠序列语法与AkitaV2

plos biology

IF3.6

2025-02-04

OAAI

Smaruj, Paulina N.; Kamulegeya, Fahad; Kelley, David R.

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

CELL REPORTS

IF6.9

2023-08-01

OAAI

Roux, Antoine Emile; Yuan, Han; Podshivalova, Katie; Hendrickson, David; Kerr, Rex; Kenyon, Cynthia; Kelley, David

scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks (vol 19, pg 1088, 2022)

NATURE METHODS

IF32.1

2022-12-23

OAAI

Yuan, Han; Kelley, David R. R.

The genetic and biochemical determinants of mRNA degradation rates in mammals 哺乳动物mRNA降解速率的遗传和生化决定因素

GENOME BIOLOGY

IF9.4

2022-11-23

OAAI

Agarwal, Vikram; Kelley, David R.

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

NATURE METHODS

IF32.1

2022-08-08

OAAI

Yuan, Han; Kelley, David R.

Effective gene expression prediction from sequence by integrating long-range interactions 通过整合长程相互作用从序列中有效预测基因表达

NATURE METHODS

IF32.1

2021-10-04

411

OAAI

Avsec, Ziga; Agarwal, Vikram; Visentin, Daniel; Ledsam, Joseph R.; Grabska-Barwinska, Agnieszka; Taylor, Kyle R.; Assael, Yannis; Jumper, John; Kohli, Pushmeet; Kelley, David R.

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

NATURE COMMUNICATIONS

IF15.7

2021-08-24

OAAI

Agarwal, Vikram; Lopez-Darwin, Sereno; Kelley, David R.; Shendure, Jay

Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs 利用监督学习进行cis-eqtl的功能信息精细映射，可以识别额外的20,913个假定的因果eqtl

NATURE COMMUNICATIONS

IF15.7

2021-06-07

OAAI

Wang, Qingbo S.; Kelley, David R.; Ulirsch, Jacob; Kanai, Masahiro; Sadhuka, Shuvom; Cui, Ran; Albors, Carlos; Cheng, Nathan; Okada, Yukinori; Aguet, Francois; Ardlie, Kristin G.; MacArthur, Daniel G.; Finucane, Hilary K.

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

CELL REPORTS

IF6.9

2021-04-01

OAAI

Kimmel, Jacob C.; Yi, Nelda; Roy, Margaret; Hendrickson, David G.; Kelley, David R.

Semisupervised adversarial neural networks for single-cell classification 用于单细胞分类的半监督对抗神经网络

GENOME RESEARCH

IF5.5

2021-02-24

OAAI

Kimmel, Jacob C.; Kelley, David R.

Predicting 3D genome folding from DNA sequence with Akita

NATURE METHODS

IF32.1

2020-10-12

148

OAAI

Fudenberg, Geoff; Kelley, David R.; Pollard, Katherine S.

Evaluating the informativeness of deep learning annotations for human complex diseases

NATURE COMMUNICATIONS

IF15.7

2020-09-17

OAAI

Dey, Kushal K.; van de Geijn, Bryce; Kim, Samuel Sungil; Hormozdiari, Farhad; Kelley, David R.; Price, Alkes L.

Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning Solo: 通过半监督深度学习在单细胞rna-seq中识别双峰

CELL SYSTEMS

IF7.7

2020-07-01

104

OAAI

Bernstein, Nicholas J.; Fong, Nicole L.; Lam, Irene; Roy, Margaret A.; Hendrickson, David G.; Kelley, David R.

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging (vol 29, pg 2088, 2019)

GENOME RESEARCH

IF5.5

2020-01-09

OAAI

Kimmel, Jacob C.; Penland, Lolita; Rubinstein, Nimrod D.; Hendrickson, David G.; Kelley, David R.; Rosenthal, Adam Z.

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging 鼠单细胞rna-seq揭示了衰老的细胞身份和组织特异性轨迹

GENOME RESEARCH

IF5.5

2019-11-21

105

OAAI

Kimmel, Jacob C.; Penland, Lolita; Rubinstein, Nimrod D.; Hendrickson, David G.; Kelley, David R.; Rosenthal, Adam Z.

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk 检测转录因子结合对多基因疾病风险的全基因组定向效应

NATURE GENETICS

IF31.8

2018-09-03

OAAI

Reshef, Yakir A.; Finucane, Hilary K.; Kelley, David R.; Gusev, Alexander; Kotliar, Dylan; Ulirsch, Jacob C.; Hormozdiari, Farhad; Nasser, Joseph; O'Connor, Luke; van de Geijn, Bryce; Loh, Po-Ru; Grossman, Sharon R.; Bhatia, Gaurav; Gazel, Steven; Palamara, Pier Francesco; Pinello, Luca; Patterson, Nick; Adams, Ryan P.; Price, Alkes L.

Sequential regulatory activity prediction across chromosomes with convolutional neural networks 基于卷积神经网络的跨染色体序列调控活动预测

GENOME RESEARCH

IF5.5

2018-03-27

281

OAAI

Kelley, David R.; Reshef, Yakir A.; Bileschi, Maxwell; Belanger, David; McLean, Cory Y.; Snoek, Jasper

研究方向