Zobrazeno 1 - 10
of 58
pro vyhledávání: '"Abhinav Nellore"'
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-22 (2022)
Abstract Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is comp
Externí odkaz:
https://doaj.org/article/ea62db3678a941dabe74f0c088a5f2e6
Autor:
Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen, Ben Langmead
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-40 (2021)
Abstract We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recoun
Externí odkaz:
https://doaj.org/article/8ffd406a24644e9286dbf6b7448b3e96
Publikováno v:
Genome Medicine, Vol 12, Iss 1, Pp 1-16 (2020)
Abstract Background Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as a result. However, T
Externí odkaz:
https://doaj.org/article/020f9dccb61e4868af0dd53ce442a9c8
Autor:
Jonathan P. Ling, Christopher Wilks, Rone Charles, Patrick J. Leavey, Devlina Ghosh, Lizhi Jiang, Clayton P. Santiago, Bo Pang, Anand Venkataraman, Brian S. Clark, Abhinav Nellore, Ben Langmead, Seth Blackshaw
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)
The increasing amount of raw RNA-seq data calls for new computational methods to mine information. Here, the authors present ASCOT, a computational resource to identify splice variants in RNA-seq data, and apply it to splicing patterns in neurons and
Externí odkaz:
https://doaj.org/article/7ea8584150d14155b401fb552d0229f2
Autor:
Mary A. Wood, Mayur Paralkar, Mihir P. Paralkar, Austin Nguyen, Adam J. Struck, Kyle Ellrott, Adam Margolin, Abhinav Nellore, Reid F. Thompson
Publikováno v:
BMC Cancer, Vol 18, Iss 1, Pp 1-15 (2018)
Abstract Background Tumor neoantigens are drivers of cancer immunotherapy response; however, current prediction tools produce many candidates requiring further prioritization. Additional filtration criteria and population-level understanding may assi
Externí odkaz:
https://doaj.org/article/f1cc876bd8654bfd9c5b53d659bf98bc
Publikováno v:
F1000Research, Vol 6 (2017)
The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be accessed via the recount2 website and the recount Bioconductor package. This workflow explains
Externí odkaz:
https://doaj.org/article/5cafe792c1e54b3393e984f3e3ad1c66
Publikováno v:
HLA. 99:607-613
HLA is a critical component of the viral antigen presentation pathway. We investigated the relationship between severity of SARS-CoV-2 disease and HLA type in 3,235 individuals with confirmed SARS-CoV-2 infection. We found only the DPB1 locus to be a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2c890992335cc1466ffbc1da7fdf2d46
https://doi.org/10.1111/tan.14574
https://doi.org/10.1111/tan.14574
Publikováno v:
Bioinformatics Advances. 3
SummaryThousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but they remain underutilized for experiment planning, replication and cross-study and cross-platform analyses. To
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::3bb85247d184a4b9d974d7c228698e7c
https://doi.org/10.1093/bioadv/vbad020
https://doi.org/10.1093/bioadv/vbad020
A large number of machine learning-based Major Histocompatibility Complex (MHC) binding affinity (BA) prediction tools have been developed and are widely used for both investigational and therapeutic applications, so it is important to explore differ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2bc14b192455f3cf12d1c2c65cb6cd2b
https://doi.org/10.1101/2022.12.04.518984
https://doi.org/10.1101/2022.12.04.518984
Autor:
Sean K. Maden, Brian Walsh, Kyle Ellrott, Kasper D. Hansen, Reid F. Thompson, Abhinav Nellore
Thousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but they remain underutilized for experiment planning, replication, and cross-study and cross-platform analyses. To facili
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6c62601118a05388b63e74f2d5d68dc8
https://doi.org/10.1101/2022.05.19.492680
https://doi.org/10.1101/2022.05.19.492680