Zobrazeno 1 - 10
of 16
pro vyhledávání: '"Surag Nair"'
Autor:
Rajiv Movva, Peyton Greenside, Georgi K Marinov, Surag Nair, Avanti Shrikumar, Anshul Kundaje
Publikováno v:
PLoS ONE, Vol 14, Iss 6, p e0218073 (2019)
The relationship between noncoding DNA sequence and gene expression is not well-understood. Massively parallel reporter assays (MPRAs), which quantify the regulatory activity of large libraries of DNA sequences in parallel, are a powerful approach to
Externí odkaz:
https://doaj.org/article/e40371fbb0544d5ea9bf64ac57fab03d
Publikováno v:
Bioinformatics
Motivation In silico saturation mutagenesis (ISM) is a popular approach in computational genomics for calculating feature attributions on biological sequences that proceeds by systematically perturbing each position in a sequence and recording the di
Autor:
Surag Nair, Arjun Barrett, Daofeng Li, Brian J. Raney, Brian T. Lee, Peter Kerpedjiev, Vivekanandan Ramalingam, Anusri Pampari, Fritz Lekschas, Ting Wang, Maximilian Haeussler, Anshul Kundaje
Publikováno v:
Nature genetics, vol 54, iss 11
Nat Genet
Nat Genet
High-throughput experimental platforms have revolutionized the ability to profile biochemical and functional properties of biological sequences such as DNA, RNA and proteins. By collating several data modalities with customizable tracks rendered usin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::87f6c0dd41a6d0a4f34f6c2f8dd5e2a6
https://escholarship.org/uc/item/8km025qx
https://escholarship.org/uc/item/8km025qx
Inbred mouse strains reveal the molecular basis of mammalian traits and diseases, particularly recessive ones. We utilized mouse community curated resources to set up an automated screen to discover novel testable gene function hypotheses. Using 11,8
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8e0418de01c92ab78541f6cf5eb061dc
https://doi.org/10.1101/2022.08.07.503105
https://doi.org/10.1101/2022.08.07.503105
Autor:
Surag Nair, Arjun Barrett, Daofeng Li, Brian J Raney, Brian T Lee, Peter Kerpedjiev, Vivekanandan Ramalingam, Anusri Pampari, Fritz Lekschas, Ting Wang, Maximilian Haeussler, Anshul Kundaje
We introduce the dynseq genome browser track, which displays DNA nucleotide characters scaled by user-specified, base-resolution scores provided in the BigWig file format. The dynseq track enables visualization of context-specific, informative genomi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d7b4c3a730ec84d04a16ee2f62c8f175
https://doi.org/10.1101/2022.05.26.493621
https://doi.org/10.1101/2022.05.26.493621
Autor:
Paul Cheng, Robert C. Wirka, Lee Shoa Clarke, Quanyi Zhao, Ramendra Kundu, Trieu Nguyen, Surag Nair, Disha Sharma, Hyun-jung Kim, Huitong Shi, Themistocles Assimes, Juyong Brian Kim, Anshul Kundaje, Thomas Quertermous
Publikováno v:
Circulation
Background: Smooth muscle cells (SMCs) transition into a number of different phenotypes during atherosclerosis, including those that resemble fibroblasts and chondrocytes, and make up the majority of cells in the atherosclerotic plaque. To better und
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1b422a68f2efe18e7ebd6b4bad68f53b
https://europepmc.org/articles/PMC8896308/
https://europepmc.org/articles/PMC8896308/
Autor:
Adam Frankish, Sílvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E Loveland, Jonathan M Mudge, Cristina Sisu, James C Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcıa Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M Schmitt, Jacob M Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S Choudhary, Mark Gerstein, Roderic Guigo, Tim J P Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L Tress, Paul Flicek
Publikováno v:
Frankish, Adam; Carbonell-Sala, Sílvia; Diekhans, Mark; Jungreis, Irwin; Loveland, Jane E; Mudge, Jonathan M; Sisu, Cristina; Wright, James C; Arnan, Carme; Barnes, If; Banerjee, Abhimanyu; Bennett, Ruth; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Calvet, Ferriol; Cerdán-Vélez, Daniel; Cunningham, Fiona; Davidson, Claire; Donaldson, Sarah; ... (2023). GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic acids research, 51(D1), D942-D949. Oxford University Press 10.1093/nar/gkac1071
Data availability: No new data were generated or analysed in support of this research. Copyright © The Author(s) 2022. GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::10247881d8c4fbceb604577e5be9e5ad
Autor:
Mohamed Ameen, Laksshman Sundaram, Abhimanyu Banerjee, Mengcheng Shen, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D. Wilson, Avyay Varadarajan, Nirmal Vadgama, Akshay Balsubramani, Joseph C. Wu, Jesse Engreitz, Kyle Farh, Ioannis Karakikes, Kevin C Wang, Thomas Quertermous, William Greenleaf, Anshul Kundaje
Publikováno v:
Cell. 185:4937-4953.e23
SummaryCongenital heart defects, the most common birth disorders, are the clinical manifestation of anomalies in fetal heart development - a complex process involving dynamic spatiotemporal coordination among various precursor cell lineages. This com
Autor:
Sean K. Wang, Surag Nair, Rui Li, Katerina Kraft, Anusri Pampari, Aman Patel, Joyce B. Kang, Christy Luong, Anshul Kundaje, Howard Y. Chang
Publikováno v:
Cell Genomics. 2:100164
Genome-wide association studies (GWAS) of eye disorders have identified hundreds of genetic variants associated with ocular disease. However, the vast majority of these variants are noncoding, making it challenging to interpret their function. Here,
Autor:
Surag Nair, Anna Shcherbina, Helen M. Blau, Thach Mai, David M Burns, Yu Xin Wang, Anshul Kundaje, Glenn J. Markov
Publikováno v:
Proc Natl Acad Sci U S A
Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming; yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epige
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::032aed4db589b2eaa8553beb1e3bb241
https://europepmc.org/articles/PMC8201948/
https://europepmc.org/articles/PMC8201948/