Anshul Kundaje
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Explore the profile of Anshul Kundaje including associated specialties, affiliations and a list of published articles.
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179
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19672
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Recent Articles
11.
Sheth M, Qiu W, Ma X, Gschwind A, Jagoda E, Tan A, et al.
bioRxiv
. 2024 Nov;
PMID: 39605382
Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interactions from single-cell datasets has...
12.
Marinov G, Doughty B, Kundaje A, Greenleaf W
Genome Res
. 2024 Nov;
35(1):109-123.
PMID: 39572228
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a...
13.
Mudge J, Carbonell-Sala S, Diekhans M, Martinez J, Hunt T, Jungreis I, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D966-D975.
PMID: 39565199
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome...
14.
Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Madry T, et al.
bioRxiv
. 2024 Nov;
PMID: 39554180
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse...
15.
Esplin E, Hanson C, Wu S, Horning A, Barapour N, Nevins S, et al.
Nat Cancer
. 2024 Oct;
5(11):1737-1753.
PMID: 39478120
Familial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected persons and is an ideal model to study transitions of early precancer states to colorectal...
16.
Zhu Y, Lee H, White S, Weimer A, Monte E, Horning A, et al.
Nat Cancer
. 2024 Oct;
5(11):1697-1712.
PMID: 39478119
Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution...
17.
Levin-Konigsberg R, Mitra K, Spees K, Nigam A, Liu K, Januel C, et al.
Dev Cell
. 2024 Oct;
60(2):220-235.e7.
PMID: 39476838
Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity cause ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH)....
18.
Valbuena R, Nigam A, Tycko J, Suzuki P, Spees K, Aradhana , et al.
bioRxiv
. 2024 Oct;
PMID: 39386603
Regulatory proteins have evolved diverse repressor domains (RDs) to enable precise context-specific repression of transcription. However, our understanding of how sequence variation impacts the functional activity of RDs is limited....
19.
Zhou B, Arthur J, Guo H, Kim T, Huang Y, Pattni R, et al.
Cell
. 2024 Oct;
187(23):6687-6706.e25.
PMID: 39353437
Complex structural variations (cxSVs) are often overlooked in genome analyses due to detection challenges. We developed ARC-SV, a probabilistic and machine-learning-based method that enables accurate detection and reconstruction of cxSVs...
20.
Jha A, Hristov B, Wang X, Wang S, Greenleaf W, Kundaje A, et al.
bioRxiv
. 2024 Sep;
PMID: 39345598
Three-dimensional nuclear DNA architecture comprises well-studied intra-chromosomal () folding and less characterized inter-chromosomal () interfaces. Current predictive models of 3D genome folding can effectively infer pairwise -chromatin interactions from the...