Zobrazeno 1 - 10
of 61
pro vyhledávání: '"Kushal K, Dey"'
Autor:
Samuel Joseph Kaplan, Wilfred Wong, Jielin Yan, Julian Pulecio, Hyein S. Cho, Qianzi Li, Jiahui Zhao, Jayanti Leslie-Iyer, Jonathan Kazakov, Dylan Murphy, Renhe Luo, Kushal K. Dey, Effie Apostolou, Christina S. Leslie, Danwei Huangfu
Publikováno v:
Cell Reports, Vol 43, Iss 8, Pp 114640- (2024)
Summary: Functional enhancer annotation is critical for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants. However, unbiased enhancer discovery in disease-relevant contexts remains challe
Externí odkaz:
https://doaj.org/article/18884ea54402465ca393dbb1bcd2118f
Autor:
Samuel S. Kim, Buu Truong, Karthik Jagadeesh, Kushal K. Dey, Amber Z. Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L. Price
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-11 (2024)
Abstract Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized ce
Externí odkaz:
https://doaj.org/article/85297281a64c4afc81f239e94e41ce07
Autor:
Samuel S. Kim, Kushal K. Dey, Omer Weissbrod, Carla Márquez-Luna, Steven Gazal, Alkes L. Price
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-15 (2020)
Pathogenicity scores are instrumental in prioritizing variants for Mendelian disease, yet their application to common disease is largely unexplored. Here, the authors assess the utility of pathogenicity scores for 41 complex traits and develop a fram
Externí odkaz:
https://doaj.org/article/a9c384dedfce4fe695bcccca771f0514
Autor:
Kushal K. Dey, Bryce van de Geijn, Samuel Sungil Kim, Farhad Hormozdiari, David R. Kelley, Alkes L. Price
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
Deep learning models have shown great promise in predicting regulatory effects from DNA sequence. Here the authors evaluate sequence-based epigenomic deep learning models and conclude that these models are not yet ready to inform our knowledge of hum
Externí odkaz:
https://doaj.org/article/e966c41c45b24c86a35cad7f34f42b80
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-8 (2019)
Multiple drivers maintain unique species assemblages at multiple biogeographic scales. Here, the authors show that the freezing line is a key barrier generating evolutionary differences in temperate and tropical bird communities across a steep elevat
Externí odkaz:
https://doaj.org/article/4a7e12d8fd0b449989ef41eef463ddc8
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)
Abstract Background Sequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesti
Externí odkaz:
https://doaj.org/article/8c4f4c382f5043249985545c3cc23fe5
Autor:
Daniel J. Weiner, Ajay Nadig, Karthik A. Jagadeesh, Kushal K. Dey, Benjamin M. Neale, Elise B. Robinson, Konrad J. Karczewski, Luke J. O’Connor
Publikováno v:
Nature. 614:492-499
Autor:
Karthik A. Jagadeesh, Kushal K. Dey, Daniel T. Montoro, Rahul Mohan, Steven Gazal, Jesse M. Engreitz, Ramnik J. Xavier, Alkes L. Price, Aviv Regev
Publikováno v:
Nature Genetics. 54:1479-1492
Autor:
Steven Gazal, Omer Weissbrod, Farhad Hormozdiari, Kushal K. Dey, Joseph Nasser, Karthik A. Jagadeesh, Daniel J. Weiner, Huwenbo Shi, Charles P. Fulco, Luke J. O’Connor, Bogdan Pasaniuc, Jesse M. Engreitz, Alkes L. Price
Publikováno v:
Nature genetics, vol 54, iss 6
Nat Genet
Nat Genet
Disease-associated single-nucleotide polymorphisms (SNPs) generally do not implicate target genes, as most disease SNPs are regulatory. Many SNP-to-gene (S2G) linking strategies have been developed to link regulatory SNPs to the genes that they regul
Autor:
Kathryn Geiger-Schuller, Basak Eraslan, Olena Kuksenko, Kushal K. Dey, Karthik A. Jagadeesh, Pratiksha I. Thakore, Ozge Karayel, Andrea R. Yung, Anugraha Rajagopalan, Ana M Meireles, Karren Dai Yang, Liat Amir-Zilberstein, Toni Delorey, Devan Phillips, Raktima Raychowdhury, Christine Moussion, Alkes L. Price, Nir Hacohen, John G. Doench, Caroline Uhler, Orit Rozenblatt-Rosen, Aviv Regev
Publikováno v:
bioRxiv
E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3d8f305a048b8acb0f805d0af1ceb7e
https://europepmc.org/articles/PMC9900845/
https://europepmc.org/articles/PMC9900845/