SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency

por Yi, Ming, Stephens, Robert M.
Publicado 2008

AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations

por Vuong, Hue, Stephens, Robert M, Volfovsky, Natalia
Publicado 2012

GradientScanSurv—An exhaustive association test method for gene expression data with censored survival outcome

por Yi, Ming, Zhu, Ruoqing, Stephens, Robert M.
Publicado 2018

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis

por Yi, Ming, Mudunuri, Uma, Che, Anney, Stephens, Robert M
Publicado 2009

SRAdb: query and use public next-generation sequencing data from within R

por Zhu, Yuelin, Stephens, Robert M, Meltzer, Paul S, Davis, Sean R
Publicado 2013

ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications

por Yi, Ming, Nissley, Dwight V., McCormick, Frank, Stephens, Robert M.
Publicado 2020

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data

por Yi, Ming, Zhao, Yongmei, Jia, Li, He, Mei, Kebebew, Electron, Stephens, Robert M.
Publicado 2014

Tumor RAS Gene Expression Levels Are Influenced by the Mutational Status of RAS Genes and Both Upstream and Downstream RAS Pathway Genes

por Stephens, Robert M, Yi, Ming, Kessing, Bailey, Nissley, Dwight V, McCormick, Frank
Publicado 2017

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

por Yi, Ming, Horton, Jay D, Cohen, Jonathan C, Hobbs, Helen H, Stephens, Robert M
Publicado 2006

Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22

por Volfovsky, Natalia, Oleksyk, Taras K, Cruz, Kristine C, Truelove, Ann L, Stephens, Robert M, Smith, Michael W
Publicado 2009

MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains

por Akagi, Keiko, Stephens, Robert M., Li, Jingfeng, Evdokimov, Evgenji, Kuehn, Michael R., Volfovsky, Natalia, Symer, David E.
Publicado 2010

Knowledge and Theme Discovery across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data

por Mudunuri, Uma S., Khouja, Mohamad, Repetski, Stephen, Venkataraman, Girish, Che, Anney, Luke, Brian T., Girard, F. Pascal, Stephens, Robert M.
Publicado 2013

Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage

por Zhu, Min, Yi, Ming, Kim, Chang Hee, Deng, Chuxia, Li, Yi, Medina, Daniel, Stephens, Robert M, Green, Jeffrey E
Publicado 2011

Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

por Jiang, Hongying, Yi, Ming, Mu, Jianbing, Zhang, Louie, Ivens, Al, Klimczak, Leszek J, Huyen, Yentram, Stephens, Robert M, Su, Xin-zhuan
Publicado 2008

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes

por Cer, Regina Z., Bruce, Kevin H., Mudunuri, Uma S., Yi, Ming, Volfovsky, Natalia, Luke, Brian T., Bacolla, Albino, Collins, Jack R., Stephens, Robert M.
Publicado 2011

Reconciling Apparent Conflicts between Mitochondrial and Nuclear Phylogenies in African Elephants

por Ishida, Yasuko, Oleksyk, Taras K., Georgiadis, Nicholas J., David, Victor A., Zhao, Kai, Stephens, Robert M., Kolokotronis, Sergios-Orestis, Roca, Alfred L.
Publicado 2011

RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy

por Shao, Wei, Kearney, Mary, Maldarelli, Frank, Mellors, John W, Stephens, Robert M, Lifson, Jeffrey D, KewalRamani, Vineet N, Ambrose, Zandrea, Coffin, John M, Palmer, Sarah E
Publicado 2009

Introducing the non-B DNA Motif Search Tool (nBMST)

por Cer, Regina Z, Bruce, Kevin H, Donohue, Duncan E, Temiz, Alpay N, Bacolla, Albino, Mudunuri, Uma S, Yi, Ming, Volfovsky, Natalia, Luke, Brian T, Collins, Jack R, Stephens, Robert M
Publicado 2011

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

por Shao, Wei, Boltz, Valerie F, Spindler, Jonathan E, Kearney, Mary F, Maldarelli, Frank, Mellors, John W, Stewart, Claudia, Volfovsky, Natalia, Levitsky, Alexander, Stephens, Robert M, Coffin, John M
Publicado 2013

The somatic autosomal mutation matrix in cancer genomes

por Temiz, Nuri A., Donohue, Duncan E., Bacolla, Albino, Vasquez, Karen M., Cooper, David N., Mudunuri, Uma, Ivanic, Joseph, Cer, Regina Z., Yi, Ming, Stephens, Robert M., Collins, Jack R., Luke, Brian T.
Publicado 2015