Alexander V. Favorov

16 papers C 1Journal 12Unranked 3
YearRankTypeTitle / Venue / Authors
2022 C conf
Regression Expression Variation Analysis (REVA): a rank-based multi-dimensional measure of correlation.
ICMLA
Bahman Afsari, Alexander V. Favorov, Elana J. Fertig, Leslie Cope
2019 J jnl
VirGenA: a reference-based assembler for variable viral genomes.
Briefings Bioinform.
Gennady G. Fedonin, Yury S. Fantin, Alexander V. Favorov, German A. Shipulin, Alexey D. Neverov
2018 J jnl
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.
Nucleic Acids Res.
Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander V. Favorov, Ryan M. Layer, Andrey A. Mironov, Aaron R. Quinlan, Nathan C. Sheffield, Gosia Trynka, Geir Kjetil Sandve
2018 J jnl
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Bioinform.
Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane T. Kagohara, Genevieve L. Stein-O'Brien, Dylan Kelley, Emily Flam, Kristina D. Zambo, Patrick K. Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana J. Fertig
2017 J jnl
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Bioinform.
Genevieve L. Stein-O'Brien, Jacob L. Carey, Waishing Lee, Michael Considine, Alexander V. Favorov, Emily Flam, Theresa Guo, Sijia Li, Luigi Marchionni, Thomas Sherman, Shawn Sivy, Daria A. Gaykalova, Ronald McKay, Michael F. Ochs, Carlo Colantuoni, Elana J. Fertig
2017 J jnl
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.
Bioinform.
Elena D. Stavrovskaya, Tejasvi Niranjan, Elana J. Fertig, Sarah J. Wheelan, Alexander V. Favorov, Andrey A. Mironov
2014 J jnl
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.
Bioinform.
Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, Elana J. Fertig
2013 — conf
Fast assessment of the correlation between coverage-like genomic features and its statistical significance.
IWBBIO
Elena D. Stavrovskaya, Andrey A. Mironov, Alexander V. Favorov
2012 — conf
A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure.
BIOINFORMATICS
Anna A. Nilulova, Alexander V. Favorov, Vsevolod J. Makeev, Andrey A. Mironov
2012 J jnl
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package.
PLoS Comput. Biol.
Alexander V. Favorov, Loris Mularoni, Leslie M. Cope, Yulia A. Medvedeva, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan
2012 — conf
Identifying context-specific transcription factor targets from prior knowledge and gene expression data.
BIBM
Elana J. Fertig, Alexander V. Favorov, Michael F. Ochs
2010 J jnl
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
Bioinform.
Elana J. Fertig, Jie Ding, Alexander V. Favorov, Giovanni Parmigiani, Michael F. Ochs
2010 J jnl
Deep and wide digging for binding motifs in ChIP-Seq data.
Bioinform.
Ivan V. Kulakovskiy, Valentina Boeva, Alexander V. Favorov, Vsevolod J. Makeev
2009 J jnl
Motif discovery and motif finding from genome-mapped DNase footprint data.
Bioinform.
Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev
2006 J jnl
Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA.
J. Bioinform. Comput. Biol.
Ludmila V. Danilova, Dmitri D. Pervouchine, Alexander V. Favorov, Andrey A. Mironov
2005 J jnl
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Bioinform.
Alexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod J. Makeev