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A. Sivachenko · SciRah

Researcher profile · Semantic Scholar

A. Sivachenko

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A. Sivachenko — researcher profile on SciRah

h-index: 43
Works: 121
Citations: 102K

Most-cited papers

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
A. McKenna, Matthew G. Hanna, E. Banks, A. Sivachenko +7 more
2010Genome Research27K citations Open access
Semantic Scholar
A framework for variation discovery and genotyping using next-generation DNA sequencing data
M. DePristo, E. Banks, R. Poplin, K. Garimella +14 more
2011Nature Genetics11K citations Open access
Semantic Scholar
Comprehensive Molecular Characterization of Human Colon and Rectal Cancer
Donna M. Matthew N. Kyle Huyen H. Jennifer A. Gerald Chr Muzny Bainbridge Chang Dinh Drummond Fowler Kovar, Donna M. Matthew N. Kyle Huyen H. Jennifer A. Gerald Chr Muzny Bainbridge Chang Dinh Drummond Fowler Kovar, D. Muzny, M. Bainbridge +334 more
2012Nature7,917 citations Open access
Semantic Scholar
Comprehensive molecular portraits of human breast tumors
Daniel C. Robert S. Michael D. Heather Joelle Joshua F. L Koboldt Fulton McLellan Schmidt Kalicki-Veizer McM, Daniel C. Robert S. Michael D. Heather Joelle Joshua F. L Koboldt Fulton McLellan Schmidt Kalicki-Veizer McM, D. Koboldt, R. Fulton +377 more
2012Nature7,527 citations Open access
Semantic Scholar
Integrated Genomic Characterization of Endometrial Carcinoma
G. Getz, S. Gabriel, K. Cibulskis, E. Lander +268 more
2013Nature5,491 citations Open access
Semantic Scholar
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
K. Cibulskis, A. Sivachenko, D. Jaffe, C. Sougnez +6 more
2013Nature Biotechnology3,637 citations Open access
Semantic Scholar
Genome-scale DNA methylation maps of pluripotent and differentiated cells
A. Meissner, T. Mikkelsen, H. Gu, Marius Wernig +9 more
2008Nature2,613 citations Open access
Semantic Scholar
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
N. Stransky, A. Egloff, Aaron D. Tward, Aleksandar D. Kostic +35 more
2011Science2,556 citations Open access
Semantic Scholar
A Landscape of Driver Mutations in Melanoma
Eran Hodis, Ian R. Watson, G. Kryukov, S. Arold +36 more
2012Cell2,543 citations Open access
Semantic Scholar
Comprehensive Molecular Characterization of Urothelial Bladder Carcinoma
John N. Rehan Bradley M. Wenyi Roeland G. W. David Seth Weinstein Akbani Broom Wang Verhaak McConkey Lerne, John N. Rehan Bradley M. Wenyi Roeland G. W. David Weinstein Akbani Broom Wang Verhaak McConkey, J. Weinstein, R. Akbani +345 more
2014Nature2,115 citations Open access
Semantic Scholar
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing
M. Imieliński, A. Berger, P. Hammerman, Bryan Hernandez +41 more
2012Cell1,826 citations Open access
Semantic Scholar
Mutational heterogeneity in cancer and the search for new cancer genes
P. Stojanov, P. Polak, G. Kryukov, K. Cibulskis +2 more
20141,749 citations
Semantic Scholar
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
C. Barbieri, Sylvan C. Baca, Michael S. Lawrence, F. Demichelis +42 more
2012Nature Genetics1,538 citations Open access
Semantic Scholar
Initial genome sequencing and analysis of multiple myeloma
M. Chapman, Michael S. Lawrence, J. Keats, K. Cibulskis +46 more
2011Nature1,478 citations Open access
Semantic Scholar
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia
D. Landau, S. Carter, P. Stojanov, A. McKenna +22 more
2013Cell1,412 citations Open access
Semantic Scholar
Punctuated Evolution of Prostate Cancer Genomes
Sylvan C. Baca, D. Prandi, Michael S. Lawrence, J. Mosquera +39 more
2013Cell1,273 citations Open access
Semantic Scholar
SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia
Li-Li Wang, Michael S. Lawrence, Youzhong Wan, P. Stojanov +25 more
2011New England Journal of Medicine1,272 citations Open access
Semantic Scholar
The genomic complexity of primary human prostate cancer
M. Berger, Michael S. Lawrence, F. Demichelis, Y. Drier +37 more
2011Nature1,254 citations Open access
Semantic Scholar
Sequence analysis of mutations and translocations across breast cancer subtypes
S. Banerji, K. Cibulskis, C. Rangel-Escareño, Kristin K. Brown +43 more
2012Nature1,217 citations Open access
Semantic Scholar
Mutational heterogeneity in cancer and the search for new cancer genes
M. Lawrence, P. Stojanov, P. Polak, G. Kryukov +61 more
2013Nature1,179 citations Open access
Semantic Scholar
The genetic landscape of high-risk neuroblastoma
Trevor J Pugh, O. Morozova, E. Attiyeh, S. Asgharzadeh +56 more
2013Nature Genetics1,140 citations Open access
Semantic Scholar
Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
A. Dulak, P. Stojanov, Shouyong Peng, Michael S. Lawrence +35 more
2013Nature Genetics763 citations Open access
Semantic Scholar
MEDULLOBLASTOMA EXOME SEQUENCING UNCOVERS SUBTYPE-SPECIFIC SOMATIC MUTATIONS
Trevor J Pugh, S. D. Weeraratne, Tenley C. Archer, D. P. Pomeranz Krummel +39 more
2012Nature758 citations Open access
Semantic Scholar
Melanoma genome sequencing reveals frequent PREX2 mutations
M. Berger, Eran Hodis, T. Heffernan, Y. L. Deribe +44 more
2012Nature757 citations Open access
Semantic Scholar
Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine
E. V. Van Allen, N. Wagle, P. Stojanov, Danielle L. Perrin +32 more
2014Nature Medicine517 citations Open access
Semantic Scholar
The genomic landscape of pediatric Ewing sarcoma.
Brian D. Crompton, Chip Stewart, Amaro Taylor-Weiner, G. Alexe +30 more
2014Cancer Discovery492 citations Open access
Semantic Scholar
Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
X. Adiconis, Diego Borges-Rivera, R. Satija, D. DeLuca +10 more
2013Nature Methods488 citations Open access
Semantic Scholar
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
J. Perry, Adam Kiezun, Peter Tonzi, E. V. Van Allen +35 more
2014Proceedings of the National Academy of Sciences of the United States of America435 citations Open access
Semantic Scholar
Somatic mutation of CDKN1B in small intestine neuroendocrine tumors
J. Francis, Adam Kiezun, A. Ramos, S. Serra +43 more
2013Nature Genetics329 citations Open access
Semantic Scholar
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
A. Bass, Michael S. Lawrence, L. Brace, A. Ramos +36 more
2011Nature Genetics311 citations Open access
Semantic Scholar
Integrative analysis of the melanoma transcriptome.
M. Berger, J. Levin, K. Vijayendran, A. Sivachenko +22 more
2010Genome Research292 citations Open access
Semantic Scholar
Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients.
Youngwook Kim, P. Hammerman, Jaegil Kim, Ji-ae Yoon +30 more
2014Journal of Clinical Oncology195 citations Open access
Semantic Scholar
A Pan-Cancer Analysis of Transcriptome Changes Associated with Somatic Mutations in U2AF1 Reveals Commonly Altered Splicing Events
A. Brooks, P. Choi, L. de Waal, Tanaz Sharifnia +10 more
2014PLoS ONE175 citations Open access
Semantic Scholar
Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma
R. Liao, Joonil Jung, J. Tchaicha, M. Wilkerson +12 more
2013Cancer Research174 citations Open access
Semantic Scholar
Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data
J. Chen, Chang-Yu Shen, A. Sivachenko
2005Pacific Symposium on Biocomputing163 citations
Semantic Scholar
PRADA: pipeline for RNA sequencing data analysis
W. Torres-García, Si-Yuan Zheng, A. Sivachenko, R. Vegesna +6 more
2014Bioinform.157 citations Open access
Semantic Scholar
Isogenic cell models of cystic fibrosis-causing variants in natively expressing pulmonary epithelial cells.
H. Valley, K. Bukis, Alisa Bell, Yi Cheng +9 more
2019Journal of Cystic Fibrosis126 citations Open access
Semantic Scholar
Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA
K. Miranda, Daniel T. Bond, J. Levin, X. Adiconis +5 more
2014PLoS ONE110 citations Open access
Semantic Scholar
SF 3 B 1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia Citation
Lili Wang, Michael S. Lawrence, Youzhong Wan, P. Stojanov +25 more
201387 citations
Semantic Scholar
In vitro modulator responsiveness of 655 CFTR variants found in people with cystic fibrosis.
H. Bihler, A. Sivachenko, L. Millen, Priyanka Bhatt +15 more
2024Journal of Cystic Fibrosis78 citations Open access
Semantic Scholar
Molecular Networks in microarray Analysis
A. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo
2007J. Bioinform. Comput. Biol.73 citations
Semantic Scholar
RNA-Seq methods for imperfect samples: development, evaluation and applications
X. Adiconis, Lin Fan, D. DeLuca, A. Sivachenko +8 more
2011Genome Biology39 citations Open access
Semantic Scholar
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining
T. Huan, A. Sivachenko, Scott H. Harrison, J. Chen
2008BMC Bioinformatics39 citations Open access
Semantic Scholar
Exome sequencing identifies recurrent SPOP , FOXA 1 and MED 12 mutations in prostate cancer
Christopher E. Barbieri, S. Baca, Michael S. Lawrence, F. Demichelis +42 more
201333 citations
Semantic Scholar
LASERS, OPTICS, AND OPTOELECTRONICS 3467 Gain trimming of the resonant characteristics in vertically coupled InP microdisk switches
K. Djordjev, S. I. Choi, Sang-Jun Choi, P. Dapkus +32 more
200231 citations
Semantic Scholar
Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism
A. Sivachenko, A. Yuryev
2007Expert opinion on therapeutic targets29 citations
Semantic Scholar
Evidence for braggoriton excitations in opal photonic crystals infiltrated with highly polarizable dyes
N. Eradat, A. Sivachenko, M. Raikh, Z. Vardeny +2 more
200126 citations Open access
Semantic Scholar
Pathway analysis for design of promiscuous drugs and selective drug mixtures.
A. Sivachenko, Andrey A. Kalinin, A. Yuryev
2006Current Drug Discovery Technologies24 citations
Semantic Scholar
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
N. Stransky, A. Egloff, Aaron D. Tward, Aleksandar D. Kostic +40 more
201218 citations
Semantic Scholar
Identifying local gene expression patterns in biomolecular networks
A. Sivachenko, Y. Yuryev, N. Daraselia, I. Mazo
20052005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)12 citations
Semantic Scholar

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C. Sougnez — researcher profile on SciRah

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A. Ramos — researcher profile on SciRah