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Anshul Kundaje
Researcher at Stanford University
Publications - 252
Citations - 43164
Anshul Kundaje is an academic researcher from Stanford University. The author has contributed to research in topics: Chromatin & Gene. The author has an hindex of 60, co-authored 203 publications receiving 32299 citations. Previous affiliations of Anshul Kundaje include Microsoft & Columbia University.
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Learning Important Features Through Propagating Activation Differences
TL;DR: DeepLIFT as mentioned in this paper decomposes the output prediction of a neural network on a specific input by backpropagating the contributions of all neurons in the network to every feature of the input.
Journal ArticleDOI
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Jill Moore,Michael J. Purcaro,Henry Pratt,Charles B. Epstein,Noam Shoresh,Jessika Adrian,Trupti Kawli,Carrie A. Davis,Alexander Dobin,Rajinder Kaul,Jessica Halow,Eric L. Van Nostrand,Peter Freese,David U. Gorkin,David U. Gorkin,Yin Shen,Yin Shen,Yupeng He,Mark Mackiewicz,Florencia Pauli-Behn,Brian A. Williams,Ali Mortazavi,Cheryl A. Keller,Xiao-Ou Zhang,Shaimae I. Elhajjajy,Jack Huey,Diane E. Dickel,Valentina Snetkova,Xintao Wei,Xiaofeng Wang,Xiaofeng Wang,Juan Carlos Rivera-Mulia,Juan Carlos Rivera-Mulia,Joel Rozowsky,Jing Zhang,Surya B. Chhetri,Jialing Zhang,Alec Victorsen,Kevin P. White,Axel Visel,Axel Visel,Gene W. Yeo,Christopher B. Burge,Eric Lécuyer,Eric Lécuyer,David M. Gilbert,Job Dekker,John L. Rinn,Eric M. Mendenhall,Joseph R. Ecker,Manolis Kellis,Manolis Kellis,Robert J. Klein,William Stafford Noble,Anshul Kundaje,Roderic Guigó,Peggy J. Farnham,J. Michael Cherry,Richard M. Myers,Bing Ren,Bing Ren,Brenton R. Graveley,Mark Gerstein,Len A. Pennacchio,Len A. Pennacchio,Michael Snyder,Bradley E. Bernstein,Barbara J. Wold,Ross C. Hardison,Thomas R. Gingeras,John A. Stamatoyannopoulos,Zhiping Weng,Zhiping Weng,Zhiping Weng +73 more
TL;DR: The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development.
Journal ArticleDOI
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
M. Ryan Corces,Jason D. Buenrostro,Jason D. Buenrostro,Beijing Wu,Peyton Greenside,Steven M. Chan,Julie L. Koenig,Michael Snyder,Jonathan K. Pritchard,Jonathan K. Pritchard,Anshul Kundaje,William J. Greenleaf,Ravindra Majeti,Howard Y. Chang +13 more
TL;DR: The chromatin accessibility and transcriptional landscapes in 13 human primary blood cell types that span the hematopoietic hierarchy are defined and 'enhancer cytometry' is enabled for enumeration of pure cell types from complex populations.
Journal ArticleDOI
The ENCODE Blacklist: Identification of Problematic Regions of the Genome.
TL;DR: The ENCODE blacklist is defined- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment.
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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Jie Wang,Jiali Zhuang,Sowmya Iyer,Sowmya Iyer,Xinying Lin,Troy W. Whitfield,Melissa C. Greven,Brian G. Pierce,Xianjun Dong,Anshul Kundaje,Yong Cheng,Oliver J. Rando,Ewan Birney,Richard M. Myers,William Stafford Noble,Michael Snyder,Zhiping Weng +16 more
TL;DR: An integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones.