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Alexander V. Favorov · SciRah

Researcher profile · Semantic Scholar

Alexander V. Favorov

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Alexander V. Favorov — researcher profile on SciRah

h-index: 25
Works: 107
Citations: 2,612

Most-cited papers

Enter the Matrix: Factorization Uncovers Knowledge from Omics
G. Stein-O'Brien, R. Arora, A. Culhane, Alexander V. Favorov +8 more
2018Trends in Genetics231 citations Open access
Semantic Scholar
Inferring causal molecular networks: empirical assessment through a community-based effort
S. Hill, L. Heiser, T. Cokelaer, Michael Unger +34 more
2016Nature Methods229 citations Open access
Semantic Scholar
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
Alexander V. Favorov, L. Mularoni, L. Cope, Y. Medvedeva +3 more
2012PLoS Comput. Biol.178 citations Open access
Semantic Scholar
Deep and wide digging for binding motifs in ChIP-Seq data
I. Kulakovskiy, V. Boeva, Alexander V. Favorov, V. Makeev
2010Bioinform.165 citations Open access
Semantic Scholar
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
Alexander V. Favorov, M. Gelfand, A. Gerasimova, D. Ravcheev +2 more
2005Bioinform.126 citations Open access
Semantic Scholar
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction
H. Parker, J. Leek, Alexander V. Favorov, M. Considine +4 more
2014Bioinform.123 citations Open access
Semantic Scholar
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
L. Kagohara, G. Stein-O'Brien, Dylan Kelley, Emily Flam +7 more
2017bioRxiv112 citations Open access
Semantic Scholar
A Markov Chain Monte Carlo Technique for Identification of Combinations of Allelic Variants Underlying Complex Diseases in Humans
Alexander V. Favorov, Timophey V. Andreewski, M. Sudomoina, O. Favorova +2 more
2005Genetics103 citations Open access
Semantic Scholar
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data
E. Fertig, Jie Ding, Alexander V. Favorov, G. Parmigiani +1 more
2010Bioinform.96 citations Open access
Semantic Scholar
HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers
Shu-Ling Ren, Daria A. Gaykalova, Theresa Guo, Alexander V. Favorov +19 more
2020Oncogene93 citations Open access
Semantic Scholar
Transcriptional mechanisms of resistance to anti-PD-1 therapy
M. Ascierto, Alvin P. Makohon-Moore, E. Lipson, J. Taube +17 more
2017Clinical Cancer Research78 citations Open access
Semantic Scholar
A review of genome-wide association studies for multiple sclerosis: classical and hypothesis-driven approaches
V. Bashinskaya, O. Kulakova, A. Boyko, Alexander V. Favorov +1 more
2015Human Genetics76 citations
Semantic Scholar
Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA
L. V. Danilova, D. Pervouchine, Alexander V. Favorov, A. Mironov
2006J. Bioinform. Comput. Biol.65 citations
Semantic Scholar
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
G. Stein-O'Brien, J. Carey, Wai-Shing Lee, M. Considine +12 more
2016bioRxiv53 citations Open access
Semantic Scholar
Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks
Dylan Kelley, Emily Flam, E. Izumchenko, L. Danilova +18 more
2017Cancer Research51 citations Open access
Semantic Scholar
A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers
Theresa Guo, Akihiro Sakai, Bahman Afsari, M. Considine +12 more
2017Cancer Research43 citations Open access
Semantic Scholar
Discovery and development of differentially methylated regions in human papillomavirus‐related oropharyngeal squamous cell carcinoma
Shu-Ling Ren, Daria A. Gaykalova, J. Wang, Theresa Guo +15 more
2018International Journal of Cancer42 citations Open access
Semantic Scholar
Genetic polymorphisms, their allele combinations and IFN-β treatment response in Irish multiple sclerosis patients
C. O'Doherty, Alexander V. Favorov, S. Heggarty, C. Graham +6 more
2009Pharmacogenomics (London)39 citations Open access
Semantic Scholar
Motif discovery and motif finding from genome-mapped DNase footprint data
I. Kulakovskiy, Alexander V. Favorov, V. Makeev
2009Bioinform.37 citations Open access
Semantic Scholar
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance
G. Stein-O'Brien, L. Kagohara, Si-Jia Li, Manjusha Thakar +12 more
2018Genome Medicine31 citations Open access
Semantic Scholar
Conserved and species-specific alternative splicing in mammalian genomes
R. Nurtdinov, A. Neverov, Alexander V. Favorov, A. Mironov +1 more
2007BMC Evolutionary Biology31 citations Open access
Semantic Scholar
Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma
Theresa Guo, Kristina D. Zambo, Fernando T. Zamuner, Tingting Ou +12 more
2020Epigenetics29 citations Open access
Semantic Scholar
Protective Allele for Multiple Sclerosis HLA-DRB1*01:01 Provides Kinetic Discrimination of Myelin and Exogenous Antigenic Peptides
A. Mamedov, Nadezhda L. Vorobyeva, I. Filimonova, M. Zakharova +16 more
2020Frontiers in Immunology27 citations Open access
Semantic Scholar
Heavy-light chain interrelations of MS-associated immunoglobulins probed by deep sequencing and rational variation.
Y. Lomakin, M. Zakharova, A. Stepanov, M. Dronina +20 more
2014Molecular Immunology26 citations Open access
Semantic Scholar
Three allele combinations associated with Multiple Sclerosis
O. Favorova, Alexander V. Favorov, A. Boiko, T. V. Andreewski +6 more
2006BMC Medical Genetics26 citations Open access
Semantic Scholar
Allelic combinations of immune-response genes associated with glatiramer acetate treatment response in Russian multiple sclerosis patients.
E. Tsareva, O. Kulakova, A. Boyko, S. Shchur +5 more
2012Pharmacogenomics (London)25 citations
Semantic Scholar
DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma
A. Finegersh, S. Kulich, Theresa Guo, Alexander V. Favorov +5 more
2017Scientific Reports23 citations Open access
Semantic Scholar
StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
E. Stavrovskaya, T. Niranjan, E. Fertig, S. Wheelan +2 more
2017bioRxiv23 citations Open access
Semantic Scholar
Variants of the Coagulation and Inflammation Genes Are Replicably Associated with Myocardial Infarction and Epistatically Interact in Russians
R. M. Barsova, D. Lvovs, B. Titov, N. Matveeva +12 more
2015PLoS ONE22 citations Open access
Semantic Scholar
Comparative pharmacogenetics of multiple sclerosis: IFN-β versus glatiramer acetate.
O. Kulakova, E. Tsareva, D. Lvovs, Alexander V. Favorov +2 more
2014Pharmacogenomics (London)20 citations
Semantic Scholar
Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer
Bahman Afsari, Albert Kuo, Yifan Zhang, Lu Li +9 more
2021eLife17 citations Open access
Semantic Scholar
VirGenA: a reference‐based assembler for variable viral genomes
Gennady G. Fedonin, Yu S Fantin, Alexander V. Favorov, G. Shipulin +1 more
2017Briefings Bioinform.16 citations Open access
Semantic Scholar
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
E. Fertig, Hiroyuki Ozawa, Manjusha Thakar, J. Howard +12 more
2016OncoTarget15 citations Open access
Semantic Scholar
Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms
Yuri S. Fantin, A. Neverov, Alexander V. Favorov, Maria V. Alvarez-Figueroa +10 more
2013PLoS ONE15 citations Open access
Semantic Scholar
Allelic combinations of immune-response genes as possible composite markers of IFN-β efficacy in multiple sclerosis patients.
O. Kulakova, E. Tsareva, A. Boyko, S. Shchur +5 more
2012Pharmacogenomics (London)15 citations
Semantic Scholar
Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation
Y. Lomakin, I. Zvyagin, L. A. Ovchinnikova, Marsel R Kabilov +15 more
2022Frontiers in Immunology14 citations Open access
Semantic Scholar
Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer
Emily Flam, L. Danilova, Dylan Kelley, E. Stavrovskaya +7 more
2019Scientific Reports14 citations Open access
Semantic Scholar
Weak Negative and Positive Selection and the Drift Load at Splice Sites
S. Denisov, G. Bazykin, R. Sutormin, Alexander V. Favorov +3 more
2014Genome Biology and Evolution14 citations Open access
Semantic Scholar
Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma.
Dylan Kelley, Emily Flam, Theresa Guo, L. Danilova +16 more
2018Translational Research: The Journal of Laboratory and Clinical Medicine13 citations Open access
Semantic Scholar
Pharmacogenetics of glatiramer acetate therapy for multiple sclerosis: the impact of genome-wide association studies identified disease risk loci.
O. Kulakova, V. Bashinskaya, I. Kiselev, N. Baulina +7 more
2017Pharmacogenomics (London)13 citations
Semantic Scholar
Genetic risk factors for myocardial infarction more clearly manifest for early age of first onset
B. Titov, G. Osmak, N. Matveeva, N. Kukava +4 more
2017Molecular Biology Reports13 citations
Semantic Scholar
Hidden Markov Models for Evolution and Comparative Genomics Analysis
N. Bykova, Alexander V. Favorov, A. Mironov
2013PLoS ONE13 citations Open access
Semantic Scholar
Multilocus Analysis of Genetic Susceptibility to Myocardial Infarction in Russians: Replication Study
N. Kukava, B. Titov, G. Osmak, N. Matveeva +5 more
2017Acta Naturae12 citations Open access
Semantic Scholar
CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation
A. A. Nikulova, Alexander V. Favorov, R. Sutormin, V. Makeev +1 more
2012Nucleic Acids Research11 citations Open access
Semantic Scholar
Pharmacogenomics of multiple sclerosis: Association of immune response gene polymorphisms with copaxone treatment efficacy
E. Tsareva, O. Kulakova, O. Makarycheva, A. N. Boyko +9 more
2011Molecular Biology11 citations
Semantic Scholar
Investigation of the Role of PUFA Metabolism in Breast Cancer Using a Rank-Based Random Forest Algorithm
Mariia V. Guryleva, Dmitry D. Penzar, D. Chistyakov, A. Mironov +2 more
2022Cancers10 citations Open access
Semantic Scholar
Allele-specific nonstationarity in evolution of influenza A virus surface proteins
A. Popova, Ksenia R. Safina, V. Ptushenko, A. Stolyarova +3 more
2019Proceedings of the National Academy of Sciences of the United States of America10 citations Open access
Semantic Scholar
Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer
Bahman Afsari, Theresa Guo, M. Considine, Liliana D. Florea +12 more
2016bioRxiv10 citations Open access
Semantic Scholar
Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development
E. Fertig, L. Danilova, Alexander V. Favorov, M. Ochs
2011Front. Gene.10 citations Open access
Semantic Scholar
Complex analysis of association of inflammation gene polymorphisms with myocardial infarction
M. Sudomoina, T. Sukhinina, R. M. Barsova, Alexander V. Favorov +8 more
2010Molecular Biology10 citations
Semantic Scholar

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