A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. - Alexander V. Favorov; Mikhail S. Gelfand; Anna V. Gerasimova; Dmitry A. Ravcheev; Andrey A. Mironov; Vsevolod J. Makeev (Bioinform., 2005)

Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA. - Ludmila V. Danilova; Dmitri D. Pervouchine; Alexander V. Favorov; Andrey A. Mironov (J. Bioinform. Comput. Biol., 2006)

Motif discovery and motif finding from genome-mapped DNase footprint data. - Ivan V. Kulakovskiy; Alexander V. Favorov; Vsevolod J. Makeev (Bioinform., 2009)

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. - Elana J. Fertig; Jie Ding; Alexander V. Favorov; Giovanni Parmigiani; Michael F. Ochs (Bioinform., 2010)

Deep and wide digging for binding motifs in ChIP-Seq data. - Ivan V. Kulakovskiy; Valentina Boeva; Alexander V. Favorov; Vsevolod J. Makeev (Bioinform., 2010)

Identifying context-specific transcription factor targets from prior knowledge and gene expression data. - Elana J. Fertig; Alexander V. Favorov; Michael F. Ochs (BIBM, 2012)

A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure. - Anna A. Nilulova; Alexander V. Favorov; Vsevolod J. Makeev; Andrey A. Mironov (BIOINFORMATICS, 2012)

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package. - Alexander V. Favorov; Loris Mularoni; Leslie M. Cope; Yulia A. Medvedeva; Andrey A. Mironov; Vsevolod J. Makeev; Sarah J. Wheelan (PLoS Comput. Biol., 2012)

Fast assessment of the correlation between coverage-like genomic features and its statistical significance. - Elena D. Stavrovskaya; Andrey A. Mironov; Alexander V. Favorov (IWBBIO, 2013)

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. - Hilary S. Parker; Jeffrey T. Leek; Alexander V. Favorov; Michael Considine; Xiaoxin Xia; Sameer Chavan; Christine H. Chung; Elana J. Fertig (Bioinform., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data. - Elena D. Stavrovskaya; Tejasvi Niranjan; Elana J. Fertig; Sarah J. Wheelan; Alexander V. Favorov; Andrey A. Mironov (Bioinform., 2017)

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. - 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; et al. (Bioinform., 2017)

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. - 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; et al. (Bioinform., 2018)

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. - 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; et al. (Nucleic Acids Res., 2018)

VirGenA: a reference-based assembler for variable viral genomes. - Gennady G. Fedonin; Yury S. Fantin; Alexander V. Favorov; German A. Shipulin; Alexey D. Neverov (Briefings Bioinform., 2019)

Regression Expression Variation Analysis (REVA): a rank-based multi-dimensional measure of correlation. - Bahman Afsari; Alexander V. Favorov; Elana J. Fertig; Leslie Cope (ICMLA, 2022)