Amit Deshwar
Amit Deshwar
Deep Genomics
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Pan-cancer analysis of whole genomes
Nature 578 (7793), 82-93, 2020
The evolutionary history of 2,658 cancers
M Gerstung, C Jolly, I Leshchiner, SC Dentro, S Gonzalez, D Rosebrock, ...
Nature 578 (7793), 122-128, 2020
PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
AG Deshwar, S Vembu, CK Yung, GH Jang, L Stein, Q Morris
Genome biology 16, 1-20, 2015
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
SC Dentro, I Leshchiner, K Haase, M Tarabichi, J Wintersinger, ...
Cell 184 (8), 2239-2254. e39, 2021
Inferring clonal evolution of tumors from single nucleotide somatic mutations
W Jiao, S Vembu, AG Deshwar, L Stein, Q Morris
BMC bioinformatics 15, 1-16, 2014
A practical guide to cancer subclonal reconstruction from DNA sequencing
M Tarabichi, A Salcedo, AG Deshwar, M Ni Leathlobhair, J Wintersinger, ...
Nature methods 18 (2), 144-155, 2021
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction
G Quon, S Haider, AG Deshwar, A Cui, PC Boutros, Q Morris
Genome medicine 5, 1-20, 2013
Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism
DU Kemaladewi, E Maino, E Hyatt, H Hou, M Ding, KM Place, X Zhu, ...
Nature medicine 23 (8), 984-989, 2017
A community effort to create standards for evaluating tumor subclonal reconstruction
A Salcedo, M Tarabichi, SMG Espiritu, AG Deshwar, M David, NM Wilson, ...
Nature biotechnology 38 (1), 97-107, 2020
COSSMO: predicting competitive alternative splice site selection using deep learning
H Bretschneider, S Gandhi, AG Deshwar, K Zuberi, BJ Frey
Bioinformatics 34 (13), i429-i437, 2018
Transcriptome-wide off-target effects of steric-blocking oligonucleotides
EM Holgersen, S Gandhi, Y Zhou, J Kim, B Vaz, J Bogojeski, M Bugno, ...
nucleic acid therapeutics 31 (6), 392-403, 2021
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Y Rubanova, R Shi, CF Harrigan, R Li, J Wintersinger, N Sahin, ...
Nature communications 11 (1), 731, 2020
Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types
SC Dentro, I Leshchiner, K Haase, M Tarabichi, J Wintersinger, ...
BioRxiv, 312041, 2018
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
CV Anghel, G Quon, S Haider, F Nguyen, AG Deshwar, QD Morris, ...
BMC bioinformatics 16, 1-11, 2015
PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
SC Dentro, I Leshchiner, K Haase, M Tarabichi, J Wintersinger, ...
Cell 184 (8), 2239-54, 2021
PLIDA: cross-platform gene expression normalization using perturbed topic models
AG Deshwar, Q Morris
Bioinformatics 30 (7), 956-961, 2014
Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression
AM Mezlini, B Wang, A Deshwar, Q Morris, A Goldenberg
PloS one 8 (10), e73168, 2013
An RNA foundation model enables discovery of disease mechanisms and candidate therapeutics
A Celaj, AJ Gao, TTY Lau, EM Holgersen, A Lo, V Lodaya, CB Cole, ...
bioRxiv, 2023.09. 20.558508, 2023
ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping
D Merico, C Spickett, M O’Hara, B Kakaradov, AG Deshwar, P Fradkin, ...
NPJ genomic medicine 5 (1), 16, 2020
Relapsing-remitting multiple sclerosis classification using elastic net logistic regression on gene expression data
C Zhao, AG Deshwar, Q Morris
Systems Biomedicine 1 (4), 247-253, 2013
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