Author details

Full Name

David R Kelley

Affiliation

ORCID

Career Start Year

2008

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37531250	Individual cell types in C.Â elegans age differently and activate distinct cell-protective responses.		2023
38014075	An encyclopedia of enhancer-gene regulatory interactions in the human genome.	bioRxiv	2023
36564580	Author Correction: scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks.		2023
35119359	Novel insights from a multiomics dissection of the Hayflick limit.	Elife	2022
35941239	scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks.	Nature Methods	2022
36419176	The genetic and biochemical determinants of mRNA degradation rates in mammals.	Genome Biol	2022
34429411	The landscape of alternative polyadenylation in single cells of the developing mouse embryo.	Nat Commun	2021
33910007	Differentiation reveals latent features of aging and an energy barrier in murine myogenesis.	Cell Reports	2021
33627475	Semisupervised adversarial neural networks for single-cell classification.	Genome Research	2021
34608324	Effective gene expression prediction from sequence by integrating long-range interactions.	Nat Methods	2021
32943643	Evaluating the informativeness of deep learning annotations for human complex diseases.	Nat Commun	2020
33046897	Predicting 3D genome folding from DNA sequence with Akita.	Nat Methods	2020
32592658	Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning.		2020
32687525	Cross-species regulatory sequence activity prediction.	PLoS Computational Biology	2020
31754020	Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging.	Genome Research	2019
29358654	Genetic determinants and epigenetic effects of pioneer-factor occupancy.	Nat Genet	2018
30177862	Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk.	Nat Genet	2018
29588361	Sequential regulatory activity prediction across chromosomes with convolutional neural networks.	Genome Research	2018
28875933	lncRNA requirements for mouse acute myeloid leukemia and normal differentiation.	Elife	2017
28481342	Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.	Nat Genet	2017
26883116	Widespread RNA binding by chromatin-associated proteins.	Genome Biol	2016
27197224	Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks.	Genome Research	2016
24463464	Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.	Nat Struct Mol Biol	2014
25572935	Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.	Genome Biol	2014
23664763	Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.	Cell	2013
23401553	Long noncoding RNAs regulate adipogenesis.	Proc Natl Acad Sci U S A	2013
22102569	Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.	Nucleic Acids Res	2012
22383036	Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.	Nat Protoc	2012
22880081	Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.	PLoS One	2012
23181609	Transposable elements reveal a stem cell-specific class of long noncoding RNAs.		2012
21926179	Assemblathon 1: a competitive assessment of de novo short read assembly methods.	Genome Res	2011
21385041	Extracting between-pathway models from E-MAP interactions using expected graph compression.	J Comput Biol	2011
20219098	Detection and correction of false segmental duplications caused by genome mis-assembly.	Genome Biol	2010
21044341	Clustering metagenomic sequences with interpolated Markov models.	BMC Bioinformatics	2010
21114842	Quake: quality-aware detection and correction of sequencing errors.	Genome Biol	2010
19393038	A whole-genome assembly of the domestic cow, Bos taurus.	Genome Biol	2009
18452608	Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.	BMC Genomics	2008