Hidden Markov Models for Evolution and Comparative Genomics Analysis

von Bykova, Nadezda A., Favorov, Alexander V., Mironov, Andrey A.
Veröffentlicht 2013

Identifying Context-Specific Transcription Factor Targets from Prior Knowledge and Gene Expression Data

von Fertig, Elana J, Favorov, Alexander V, Ochs, Michael F
Veröffentlicht 2013

Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development

von Fertig, Elana J., Danilova, Ludmila V., Favorov, Alexander V., Ochs, Michael F.
Veröffentlicht 2011

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

von Fertig, Elana J., Ding, Jie, Favorov, Alexander V., Parmigiani, Giovanni, Ochs, Michael F.
Veröffentlicht 2010

Conserved and species-specific alternative splicing in mammalian genomes

von Nurtdinov, Ramil N, Neverov, Alexey D, Favorov, Alexander V, Mironov, Andrey A, Gelfand, Mikhail S
Veröffentlicht 2007

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation

von Nikulova, Anna A., Favorov, Alexander V., Sutormin, Roman A., Makeev, Vsevolod J., Mironov, Andrey A.
Veröffentlicht 2012

Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets

von Erbe, Rossin, Kessler, Michael D, Favorov, Alexander V, Easwaran, Hariharan, Gaykalova, Daria A, Fertig, Elana J
Veröffentlicht in Nucleic Acids Res (2020)

A Markov Chain Monte Carlo Technique for Identification of Combinations of Allelic Variants Underlying Complex Diseases in Humans

von Favorov, Alexander V., Andreewski, Timophey V., Sudomoina, Marina A., Favorova, Olga O., Parmigiani, Giovanni, Ochs, Michael F.
Veröffentlicht 2005

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data

von Stavrovskaya, Elena D, Niranjan, Tejasvi, Fertig, Elana J, Wheelan, Sarah J, Favorov, Alexander V, Mironov, Andrey A
Veröffentlicht in Bioinformatics (2017)

Weak Negative and Positive Selection and the Drift Load at Splice Sites

von Denisov, Stepan V., Bazykin, Georgii A., Sutormin, Roman, Favorov, Alexander V., Mironov, Andrey A., Gelfand, Mikhail S., Kondrashov, Alexey S.
Veröffentlicht 2014

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

von Parker, Hilary S., Leek, Jeffrey T., Favorov, Alexander V., Considine, Michael, Xia, Xiaoxin, Chavan, Sameer, Chung, Christine H., Fertig, Elana J.
Veröffentlicht 2014

Allele-specific nonstationarity in evolution of influenza A virus surface proteins

von Popova, Anfisa V., Safina, Ksenia R., Ptushenko, Vasily V., Stolyarova, Anastasia V., Favorov, Alexander V., Neverov, Alexey D., Bazykin, Georgii A.
Veröffentlicht in Proc Natl Acad Sci U S A (2019)

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

von Penzar, Dmitry D., Zinkevich, Arsenii O., Vorontsov, Ilya E., Sitnik, Vasily V., Favorov, Alexander V., Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Veröffentlicht in Front Genet (2019)

DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma

von Finegersh, Andrey, Kulich, Scott, Guo, Theresa, Favorov, Alexander V., Fertig, Elana J., Danilova, Ludmila V., Gaykalova, Daria A., Califano, Joseph A., Duvvuri, Umamaheswar
Veröffentlicht in Sci Rep (2017)

Natural variation of gene models in Drosophila melanogaster

von Kurmangaliyev, Yerbol Z, Favorov, Alexander V, Osman, Noha M, Lehmann, Kjong-Van, Campo, Daniel, Salomon, Matthew P, Tower, John, Gelfand, Mikhail S, Nuzhdin, Sergey V
Veröffentlicht in BMC Genomics (2015)

Three allele combinations associated with Multiple Sclerosis

von Favorova, Olga O, Favorov, Alexander V, Boiko, Alexey N, Andreewski, Timofey V, Sudomoina, Marina A, Alekseenkov, Alexey D, Kulakova, Olga G, Gusev, Eugenyi I, Parmigiani, Giovanni, Ochs, Michael F
Veröffentlicht 2006

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis

von Kagohara, Luciane T, Stein-O’Brien, Genevieve L, Kelley, Dylan, Flam, Emily, Wick, Heather C, Danilova, Ludmila V, Easwaran, Hariharan, Favorov, Alexander V, Qian, Jiang, Gaykalova, Daria A, Fertig, Elana J
Veröffentlicht in Brief Funct Genomics (2017)

Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells

von Lopatina, Tatiana, Favaro, Enrica, Danilova, Ludmila, Fertig, Elana J., Favorov, Alexander V., Kagohara, Luciane T., Martone, Tiziana, Bussolati, Benedetta, Romagnoli, Renato, Albera, Roberto, Pecorari, Giancarlo, Brizzi, Maria Felice, Camussi, Giovanni, Gaykalova, Daria A.
Veröffentlicht in Front Cell Dev Biol (2020)

Enter the Matrix: Factorization Uncovers Knowledge from Omics

von Stein-O’Brien, Genevieve L., Arora, Raman, Culhane, Aedin C., Favorov, Alexander V., Garmire, Lana X., Greene, Casey S., Goff, Loyal A., Li, Yifeng, Ngom, Aloune, Ochs, Michael F., Xu, Yanxun, Fertig, Elana J.
Veröffentlicht in Trends Genet (2018)

Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

von Saito, Yuki, Favorov, Alexander V., Forman, Michael, Ren, Shuling, Sakai, Akihiro, Fukusumi, Takahito, Liu, Chao, Sadat, Sayed, Ando, Mizuo, Xu, Guorong, Khan, Zubair, Pang, John, Valsamakis, Alex, Fisch, Kathleen M., Califano, Joseph A.
Veröffentlicht in Head Neck (2019)