Sasha Favorov

Research output

Research output per year 1999 2009 2010 2011 2012 2014 2015 2017 2018 2019 2020 2022 2023

• 108 Article
• 9 Review article
• 4 Comment/debate
• 3 Conference contribution

Research output per year

Research output per year

Search results

• 2023

  Erratum: Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces (Cell Systems (2023) 14(4) (285–301.e4), (S2405471223000807), (10.1016/j.cels.2023.03.004))

  Deshpande, A., Loth, M., Sidiropoulos, D. N., Zhang, S., Yuan, L., Bell, A. T. F., Zhu, Q., Ho, W. J., Santa-Maria, C., Gilkes, D. M., Williams, S. R., Uytingco, C. R., Chew, J., Hartnett, A., Bent, Z. W., Favorov, S., Popel, A. S., Yarchoan, M., Kiemen, A., Wu, P. H., & 10 othersFujikura, K., Wirtz, D., Wood, L. D., Zheng, L., Jaffee, E. M., Anders, R. A., Danilova, L., Stein-O'Brien, G., Kagohara, L. T. & Fertig, E. J., Aug 16 2023, In: Cell Systems. 14, 8, p. 722 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Confusion 100%
  • Tumor Microenvironment 94%
  • Emotions 71%

• Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

  Deshpande, A., Loth, M., Sidiropoulos, D. N., Zhang, S., Yuan, L., Bell, A. T. F., Zhu, Q., Ho, W. J., Santa-Maria, C., Gilkes, D. M., Williams, S. R., Uytingco, C. R., Chew, J., Hartnett, A., Bent, Z. W., Favorov, S., Popel, A. S., Yarchoan, M., Kiemen, A., Wu, P. H., & 10 othersFujikura, K., Wirtz, D., Wood, L. D., Zheng, L., Jaffee, E. M., Anders, R. A., Danilova, L., Stein-O'Brien, G., Kagohara, L. T. & Fertig, E. J., Apr 19 2023, In: Cell Systems. 14, 4, p. 285-301.e4

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Tumor Microenvironment 100%
  • Cell Communication 60%
  • Small Cytoplasmic RNA 57%
  • Technology 41%
  • Spatial Analysis 41%
• 2022

  Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)

  FANTOM consortium, Dec 1 2022, In: Nature communications. 13, 1, 1200.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • document markup languages 100%
  • microsatellites 87%
  • communication networks 71%
  • Microsatellite Repeats 58%
  • Communication 50%

• Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation

  Lomakin, Y. A., Zvyagin, I. V., Ovchinnikova, L. A., Kabilov, M. R., Staroverov, D. B., Mikelov, A., Tupikin, A. E., Zakharova, M. Y., Bykova, N. A., Mukhina, V. S., Favorov, A. V., Ivanova, M., Simaniv, T., Rubtsov, Y. P., Chudakov, D. M., Zakharova, M. N., Illarioshkin, S. N., Belogurov, A. A. & Gabibov, A. G., Aug 16 2022, In: Frontiers in immunology. 13, 803229.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Multiple Sclerosis 100%
  • Regulatory B-Lymphocytes 97%
  • B-Lymphocytes 87%
  • B-Lymphoid Precursor Cells 38%
  • Tissue Donors 38%

• Hobotnica: Exploring molecular signature quality

  Stupnikov, A., Medvedeva, Y., Sizykh, A., Budkina, A., Favorov, A., Afsari, B., Wheelan, S. & Marchionni, L., 2022, In: F1000Research. 10, 1260.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pipeline 100%
  • Phenotype 52%
  • Computational Biology 27%

• Investigation of the Role of PUFA Metabolism in Breast Cancer Using a Rank-Based Random Forest Algorithm

  Guryleva, M. V., Penzar, D. D., Chistyakov, D. V., Mironov, A. A., Favorov, A. V. & Sergeeva, M. G., Oct 2022, In: Cancers. 14, 19, 4663.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Unsaturated Fatty Acids 100%
  • Breast Neoplasms 59%
  • Genes 37%
  • Oxylipins 16%
  • Area Under Curve 15%

• Multiple Sclerosis Is Associated with Immunoglobulin Germline Gene Variation of Transitional B Cells

  Lomakin, Y. A., Ovchinnikova, L. A., Zakharova, M. N., Ivanova, M. V., Simaniv, T. O., Kabilov, M. R., Bykova, N. A., Mukhina, V. S., Kaminskaya, A. N., Tupikin, A. E., Zakharova, M. Y., Favorov, A. V., Illarioshkin, S. N., Belogurov, A. A. & Gabibov, A. G., 2022, In: Acta Naturae. 14, 4-55, p. 84-93 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Immunoglobulin Genes 100%
  • B-Lymphoid Precursor Cells 94%
  • Antiinflammatory 75%
  • Multiple Sclerosis 69%
  • Regulatory B-Lymphocytes 59%

• Regression Expression Variation Analysis (REVA): A rank-based multi-dimensional measure of correlation

  Afsari, B., Favorov, A. V., Fertig, E. J. & Cope, L., 2022, Proceedings - 21st IEEE International Conference on Machine Learning and Applications, ICMLA 2022. Wani, M. A., Kantardzic, M., Palade, V., Neagu, D., Yang, L. & Chan, K-Y. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1063-1070 8 p. (Proceedings - 21st IEEE International Conference on Machine Learning and Applications, ICMLA 2022).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Statistics 100%
  • Gene expression 48%
  • Cells 43%
  • Labels 37%
  • Learning algorithms 36%
• 2021

  Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

  FANTOM consortium, Dec 1 2021, In: Nature communications. 12, 1, 3297.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • microsatellites 100%
  • Microsatellite Repeats 67%
  • caps 48%
  • gene expression 37%
  • Tandem Repeat Sequences 20%

• Landscape of allele-specific transcription factor binding in the human genome

  Abramov, S., Boytsov, A., Bykova, D., Penzar, D. D., Yevshin, I., Kolmykov, S. K., Fridman, M. V., Favorov, A. V., Vorontsov, I. E., Baulin, E., Kolpakov, F., Makeev, V. J. & Kulakovskiy, I. V., May 12 2021, In: Nature communications. 12, 1, 2751.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • genome 100%
  • Enhancer 91%
  • Human Genome 80%
  • Transcription Factors 57%
  • Alleles 56%

• Newly identified members of FGFR1 splice variants engage in cross-talk with AXL/AKT axis in salivary adenoid cystic carcinoma

  Humtsoe, J. O., Kim, H. S., Leonard, B., Ling, S., Keam, B., Marchionni, L., Afsari, B., Considine, M., Favorov, A. V., Fertig, E. J., Kang, H. & Ha, P. K., Feb 15 2021, In: Cancer Research. 81, 4, p. 1001-1013 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Adenoid Cystic Carcinoma 100%
  • Alternative Splicing 13%
  • Salivary Glands 12%
  • RNA Sequence Analysis 6%
  • Neoplasms 5%

• Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding

  Busa, V. F., Favorov, A. V., Fertig, E. J. & Leung, A. K. L., Oct 25 2021, In: Cell Reports Methods. 1, 6, 100088.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Structure 100%
  • RNA 89%
  • RNA-Binding Proteins 85%
  • Protein Binding 73%
  • Transcriptome 68%

• Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer

  Afsari, B., Kuo, A., Zhang, Y., Li, L., Lahouel, K., Danilova, L., Favorov, A., Rosenquist, T., Grollman, A. P., Kinzler, K. W., Cope, L., Vogelstein, B. & Tomasetti, C., Jan 2021, In: eLife. 10, p. 1-71 71 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Mutation 100%
  • Obesity 82%
  • Neoplasms 38%
  • Environmental Exposure 25%
  • Reaction Yield 23%
• 2020

  Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma

  Guo, T., Zambo, K. D. A., Zamuner, F. T., Ou, T., Hopkins, C., Kelley, D. Z., Wulf, H. A., Winkler, E., Erbe, R., Danilova, L., Considine, M., Sidransky, D., Favorov, S., Florea, L., Fertig, E. J. & Gaykalova, D., Sep 1 2020, In: Epigenetics. 15, 9, p. 959-971 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Alternative Splicing 100%
  • Chromatin 81%
  • Squamous Cell Carcinoma 76%
  • Neoplasms 29%
  • Cell Line 16%
  4 Scopus citations

• Erratum: Functional annotation of human long noncoding RNAs via molecular phenotyping (Genome Research (2020) 30 (1060-1072) DOI: 10.1101/gr.254219.119)

  Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J. C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Li, J., Ooi, C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonetti, A., & 97 othersBono, H., Borsari, B., Brombacher, F., Cameron, C. J. F., Cannistraci, C. V., Cardenas, R., Cardon, M., Chang, H., Dostie, J., Ducoli, L., Favorov, A., Fort, A., Garrido, D., Gil, N., Gimenez, J., Guler, R., Handoko, L., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, K., Hayatsu, N., Heutink, P., Hirose, T., Imada, E. L., Itoh, M., Kaczkowski, B., Kanhere, A., Kawabata, E., Kawaji, H., Kawashima, T., Thomas Kelly, S., Kojima, M., Kondo, N., Koseki, H., Kouno, T., Kratz, A., Kurowska-Stolarska, M., Kwon, A. T. J., Leek, J., Lennartsson, A., Lizio, M., López-Redondo, F., Luginbühl, J., Maeda, S., Makeev, V. J., Marchionni, L., Medvedeva, Y. A., Minoda, A., Müller, F., Muñoz-Aguirre, M., Murata, M., Nishiyori, H., Nitta, K. R., Noguchi, S., Noro, Y., Nurtdinov, R., Okazaki, Y., Orlando, V., Paquette, D., Parr, C. J. C., Rackham, O. J. L., Rizzu, P., Martinez, D. F. S., Sandelin, A., Sanjana, P., Semple, C. A. M., Shibayama, Y., Sivaraman, D. M., Suzuki, T., Szumowski, S. C., Tagami, M., Taylor, M. S., Terao, C., Thodberg, M., Thongjuea, S., Tripathi, V., Ulitsky, I., Verardo, R., Vorontsov, I. E., Yamamoto, C., Young, R. S., Kenneth Baillie, J., Forrest, A. R. R., Guigó, R., Hoffman, M. M., Hon, C. C., Kasukawa, T., Kauppinen, S., Kere, J., Lenhard, B., Schneider, C., Suzuki, H., Yagi, K., de Hoon, M. J. L., Shin, J. W. & Carninci, P., Oct 2020, In: Genome research. 30, 9, p. 1377 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Long Noncoding RNA 100%
  • Biochemistry 82%
  • Biophysics 63%
  • Genome 62%
  • Names 43%

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

  Lopatina, T., Favaro, E., Danilova, L., Fertig, E. J., Favorov, A. V., Kagohara, L. T., Martone, T., Bussolati, B., Romagnoli, R., Albera, R., Pecorari, G., Brizzi, M. F., Camussi, G. & Gaykalova, D. A., Sep 9 2020, In: Frontiers in Cell and Developmental Biology. 8, 698.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Extracellular Vesicles 100%
  • Immunosuppressive Agents 70%
  • Endothelial Cells 62%
  • Neoplasms 27%
  • Mesenchymal Stem Cells 27%
  3 Scopus citations

• Functional annotation of human long noncoding RNAs via molecular phenotyping

  Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J. C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonetti, A., Bono, H., & 96 othersBorsari, B., Brombacher, F., Cameron, C. J. F., Cannistraci, C. V., Cardenas, R., Cardon, M., Chang, H., Dostie, J., Ducoli, L., Favorov, A., Fort, A., Garrido, D., Gil, N., Gimenez, J., Guler, R., Handoko, L., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, K., Hayatsu, N., Heutink, P., Hirose, T., Imada, E. L., Itoh, M., Kaczkowski, B., Kanhere, A., Kawabata, E., Kawaji, H., Kawashima, T., Kelly, S. T., Kojima, M., Kondo, N., Koseki, H., Kouno, T., Kratz, A., Kurowska-Stolarska, M., Kwon, A. T. J., Leek, J., Lennartsson, A., Lizio, M., López-Redondo, F., Luginbühl, J., Maeda, S., Makeev, V. J., Marchionni, L., Medvedeva, Y. A., Minoda, A., Müller, F., Muñoz-Aguirre, M., Murata, M., Nishiyori, H., Nitta, K. R., Noguchi, S., Noro, Y., Nurtdinov, R., Okazaki, Y., Orlando, V., Paquette, D., Parr, C. J. C., Rackham, O. J. L., Rizzu, P., Martinez, D. F. S., Sandelin, A., Sanjana, P., Semple, C. A. M., Shibayama, Y., Sivaraman, D. M., Suzuki, T., Szumowski, S. C., Tagami, M., Taylor, M. S., Terao, C., Thodberg, M., Thongjuea, S., Tripathi, V., Ulitsky, I., Verardo, R., Vorontsov, I. E., Yamamoto, C., Young, R. S., Baillie, J. K., Forrest, A. R. R., Guigó, R., Hoffman, M. M., Hon, C. C., Kasukawa, T., Kauppinen, S., Kere, J., Lenhard, B., Schneider, C., Suzuki, H., Yagi, K., De Hoon, M. J. L., Shin, J. W. & Carninci, P., Jul 2020, In: Genome research. 30, 7, p. 1060-1072 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Long Noncoding RNA 100%
  • Gene Expression 41%
  • Phenotype 27%
  • Antisense Oligonucleotides 26%
  • High-Throughput Nucleotide Sequencing 22%
  19 Scopus citations

• HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers

  Ren, S., Gaykalova, D. A., Guo, T., Favorov, A. V., Fertig, E. J., Tamayo, P., Callejas-Valera, J. L., Allevato, M., Gilardi, M., Santos, J., Fukusumi, T., Sakai, A., Ando, M., Sadat, S., Liu, C., Xu, G., Fisch, K. M., Wang, Z., Molinolo, A. A., Gutkind, J. S., & 3 othersIdeker, T., Koch, W. M. & Califano, J. A., Oct 1 2020, In: Oncogene. 39, 40, p. 6327-6339 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pharyngeal Neoplasms 100%
  • Fibroblast Growth Factor Receptors 87%
  • Carcinogenesis 51%
  • Genome 45%
  • Uterine Cervical Neoplasms 31%
  5 Scopus citations

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

  Erbe, R., Kessler, M. D., Favorov, A. V., Easwaran, H., Gaykalova, D. A. & Fertig, E. J., Jul 9 2020, In: Nucleic acids research. 48, 12, p. E68-E68

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Chromatin Immunoprecipitation Sequencing 100%
  • Machine Learning 87%
  • Datasets 61%
  • Small Cytoplasmic RNA 34%
  • Cluster Analysis 17%
  3 Scopus citations

• Protective Allele for Multiple Sclerosis HLA-DRB1*01:01 Provides Kinetic Discrimination of Myelin and Exogenous Antigenic Peptides

  Mamedov, A., Vorobyeva, N., Filimonova, I., Zakharova, M., Kiselev, I., Bashinskaya, V., Baulina, N., Boyko, A., Favorov, A., Kulakova, O., Ziganshin, R., Smirnov, I., Poroshina, A., Shilovskiy, I., Khaitov, M., Sykulev, Y., Favorova, O., Vlassov, V., Gabibov, A. & Belogurov, A., Jan 17 2020, In: Frontiers in immunology. 10, 3088.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Myelin Sheath 100%
  • HLA Antigens 99%
  • Multiple Sclerosis 85%
  • Alleles 70%
  • Kinetics 70%
  3 Scopus citations

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

  Saito, Y., Favorov, A. V., Forman, M., Ren, S., Sakai, A., Fukusumi, T., Liu, C., Sadat, S., Ando, M., Xu, G., Khan, Z., Pang, J., Valsamakis, A., Fisch, K. M. & Califano, J. A., Apr 1 2020, In: Head and Neck. 42, 4, p. 688-697 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Human papillomavirus 16 100%
  • Squamous Cell Carcinoma of Head and Neck 94%
  • DNA 47%
  • Polymerase Chain Reaction 37%
  • Body Fluids 23%
  1 Scopus citations

• Recounting the FANTOM CAGE-Associated Transcriptome

  Imada, E. L., Sanchez, D. F., Collado-Torres, L., Wilks, C., Matam, T., Dinalankara, W., Stupnikov, A., Lobo-Pereira, F., Yip, C. W., Yasuzawa, K., Kondo, N., Itoh, M., Suzuki, H., Kasukawa, T., Hon, C. C., De Hoon, M. J. L., Shin, J. W., Carninci, P., Jaffe, A. E., Leek, J. T., & 4 othersFavorov, A., Franco, G. R., Langmead, B. & Marchionni, L., Jul 2020, In: Genome research. 30, 7, p. 1073-1081 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Long Noncoding RNA 100%
  • Transcriptome 85%
  • Atlases 79%
  • Genes 29%
  • Molecular Sequence Annotation 24%
  2 Scopus citations

• Senescence and entrenchment in evolution of amino acid sites

  Stolyarova, A. V., Nabieva, E., Ptushenko, V. V., Favorov, A. V., Popova, A. V., Neverov, A. D. & Bazykin, G. A., Dec 1 2020, In: Nature communications. 11, 1, 4603.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • genome 100%
  • amino acids 88%
  • Amino Acids 53%
  • Insect Genome 48%
  • Alleles 37%
  1 Scopus citations
• 2019

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

  Popova, A. V., Safina, K. R., Ptushenko, V. V., Stolyarova, A. V., Favorov, A. V., Neverov, A. D. & Bazykin, G. A., Oct 15 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 42, p. 21104-21112 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Influenza A virus 100%
  • Membrane Proteins 75%
  • Herd Immunity 67%
  • Alleles 66%
  • Amino Acids 63%
  2 Scopus citations

• Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

  Ando, M., Saito, Y., Xu, G., Bui, N. Q., Medetgul-Ernar, K., Pu, M., Fisch, K., Ren, S., Sakai, A., Fukusumi, T., Liu, C., Haft, S., Pang, J., Mark, A., Gaykalova, D. A., Guo, T., Favorov, A. V., Yegnasubramanian, S., Fertig, E. J., Ha, P., & 5 othersTamayo, P., Yamasoba, T., Ideker, T., Messer, K. & Califano, J. A., Dec 1 2019, In: Nature communications. 10, 1, 2188.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • methylation 100%
  • chromatin 81%
  • Transcription Initiation Site 73%
  • DNA Methylation 62%
  • cancer 59%
  21 Scopus citations

• Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

  Flam, E. L., Danilova, L., Kelley, D. Z., Stavrovskaya, E., Guo, T., Considine, M., Qian, J., Califano, J. A., Favorov, A., Fertig, E. J. & Gaykalova, D. A., Dec 1 2019, In: Scientific reports. 9, 1, 15034.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Gene Expression 100%
  • Chromatin 55%
  • Neoplasms 53%
  • Genetic Enhancer Elements 53%
  • Genes 41%
  1 Scopus citations

• Differential variation analysis enables detection of tumor heterogeneity using single-cell RNA-sequencing data

  Davis-Marcisak, E. F., Sherman, T. D., Orugunta, P., Stein-O'Brien, G. L., Puram, S. V., Roussos Torres, E. T., Hopkins, A. C., Jaffee, E. M., Favorov, A. V., Afsari, B., Goff, L. A. & Fertig, E. J., Oct 1 2019, In: Cancer Research. 79, 19, p. 5102-5112 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Sequence Analysis 100%
  • Neoplasms 28%
  • Squamous Cell Carcinoma of Head and Neck 19%
  • Neoplasm Metastasis 11%
  • Public Sector 10%
  5 Scopus citations

• Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers (Nature Communications, (2019), 10, 1, (2188), 10.1038/s41467-019-09937-w)

  Ando, M., Saito, Y., Xu, G., Bui, N. Q., Medetgul-Ernar, K., Pu, M., Fisch, K., Ren, S., Sakai, A., Fukusumi, T., Liu, C., Haft, S., Pang, J., Mark, A., Gaykalova, D. A., Guo, T., Favorov, A. V., Yegnasubramanian, S., Fertig, E. J., Ha, P., & 5 othersTamayo, P., Yamasoba, T., Ideker, T., Messer, K. & Califano, J. A., Dec 1 2019, In: Nature communications. 10, 1, 2415.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • methylation 100%
  • chromatin 81%
  • Transcription Initiation Site 73%
  • medicine 67%
  • DNA Methylation 62%
  1 Scopus citations

• VirGenA: A reference-based assembler for variable viral genomes

  Fedonin, G. G., Fantin, Y. S., Favorov, A. V., Shipulin, G. A. & Neverov, A. D., Jan 18 2019, In: Briefings in bioinformatics. 20, 1, p. 15-25 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Viral Genome 100%
  • Genomics 91%
  • Contamination 84%
  • Genotype 62%
  • Pathogens 39%
  6 Scopus citations

• What do neighbors tell about you: The local context of cis-regulatory modules complicates prediction of regulatory variants

  Penzar, D. D., Zinkevich, A. O., Vorontsov, I. E., Sitnik, V. V., Favorov, A. V., Makeev, V. J. & Kulakovskiy, I. V., 2019, In: Frontiers in Genetics. 10, OCT, 1078.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Machine Learning 100%
  • Information Storage and Retrieval 80%
  • Nucleic Acid Regulatory Sequences 50%
  • Genomics 44%
  • Mutagenesis 43%
  1 Scopus citations
• 2018

  Coloc-stats: A unified web interface to perform colocalization analysis of genomic features

  Simovski, B., Kanduri, C., Gundersen, S., Titov, D., Domanska, D., Bock, C., Bossini-Castillo, L., Chikina, M., Favorov, A., Layer, R. M., Mironov, A. A., Quinlan, A. R., Sheffield, N. C., Trynka, G. & Sandve, G. K., Jul 2 2018, In: Nucleic acids research. 46, W1, p. W186-W193

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genomics 100%
  • Research Personnel 69%
  8 Scopus citations

• Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma

  Ren, S., Gaykalova, D., Wang, J., Guo, T., Danilova, L., Favorov, A., Fertig, E., Bishop, J., Khan, Z., Flam, E., Wysocki, P. T., DeJong, P., Ando, M., Liu, C., Sakai, A., Fukusumi, T., Haft, S., Sadat, S. & Califano, J. A., Nov 15 2018, In: International Journal of Cancer. 143, 10, p. 2425-2436 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Squamous Cell Carcinoma 100%
  • Methylation 67%
  • DNA Methylation 44%
  • Genome 30%
  • Methyl CpG Binding Domain 25%
  12 Scopus citations

• Enter the Matrix: Factorization Uncovers Knowledge from Omics

  Stein-O'Brien, G. L., Arora, R., Culhane, A. C., Favorov, S., Garmire, L. X., Greene, C. S., Goff, L. A., Li, Y., Ngom, A., Ochs, M. F., Xu, Y. & Fertig, E. J., Oct 2018, In: Trends in Genetics. 34, 10, p. 790-805 16 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Kinetics 100%
  46 Scopus citations

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

  Kagohara, L. T., Stein-O'Brien, G. L., Kelley, D., Flam, E., Wick, H. C., Danilova, L. V., Easwaran, H., Favorov, A. V., Qian, J., Gaykalova, D. A. & Fertig, E. J., Jan 1 2018, In: Briefings in Functional Genomics. 17, 1, p. 49-63 15 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Gene Expression Regulation 100%
  • Epigenomics 81%
  • Histone 33%
  • DNA Sequence 32%
  • Acetylation 31%
  49 Scopus citations

• Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

  Kelley, D. Z., Flam, E. L., Guo, T., Danilova, L. V., Zamuner, F. T., Bohrson, C., Considine, M., Windsor, E. J., Bishop, J. A., Zhang, C., Koch, W. M., Sidransky, D., Westra, W. H., Chung, C. H., Califano, J. A., Wheelan, S., Favorov, S., Florea, L., Fertig, E. J. & Gaykalova, D., Dec 2018, In: Translational Research. 202, p. 109-119 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Squamous Cell Carcinoma of Head and Neck 100%
  • Alternative Splicing 97%
  • Biological Marker 80%
  • event 43%
  • Protein 37%
  5 Scopus citations

• Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance

  Stein-O'Brien, G., Kagohara, L. T., Li, S., Thakar, M., Ranaweera, R., Ozawa, H., Cheng, H., Considine, M., Schmitz, S., Favorov, A. V., Danilova, L. V., Califano, J. A., Izumchenko, E., Gaykalova, D. A., Chung, C. H. & Fertig, E. J., May 23 2018, In: Genome Medicine. 10, 1, 37.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Epigenomics 100%
  • Molecular Dynamics Simulation 84%
  • DNA Methylation 75%
  • Phenotype 45%
  • RNA Sequence Analysis 42%
  8 Scopus citations

• Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer

  Afsari, B., Guo, T., Considine, M., Florea, L., Kagohara, L. T., Stein-O'Brien, G. L., Kelley, D., Flam, E., Zambo, K. D., Ha, P. K., Geman, D., Ochs, M. F., Califano, J. A., Gaykalova, D. A., Favorov, A. V. & Fertig, E. J., Jun 1 2018, In: Bioinformatics. 34, 11, p. 1859-1867 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Tumor 100%
  • Cancer 96%
  • Tumors 96%
  • Gene 92%
  • Genes 89%
  4 Scopus citations
• 2017

  A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers

  Guo, T., Sakai, A., Afsari, B., Considine, M., Danilova, L., Favorov, A. V., Yegnasubramanian, S., Kelley, D. Z., Flam, E., Ha, P. K., Khan, Z., Wheelan, S. J., Gutkind, J. S., Fertig, E. J., Gaykalova, D. A. & Califano, J., Oct 1 2017, In: Cancer Research. 77, 19, p. 5248-5258 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Oropharyngeal Neoplasms 100%
  • Alternative Splicing 81%
  • Methylation 68%
  • Squamous Cell Carcinoma 47%
  • RNA Sequence Analysis 42%
  22 Scopus citations

• Association of combinations of polymorphisms in fibroblast growth factor receptor 2 gene with breast cancer among various ethnic groups

  Aitkhozhina, N. A., Khanseitova, A. K., Nigmatova, V. G., Neupokoeva, A. S., Sharafutdinova, D. A., Ashirbekov, E. E., Favorov, A. V. & Balmukhanov, T. S., Sep 1 2017, In: Russian Journal of Genetics. 53, 9, p. 1042-1047 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Receptor, Fibroblast Growth Factor, Type 2 100%
  • Alleles 48%
  • Breast Neoplasms 42%
  • Kazakhstan 33%
  • Genes 26%

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

  Finegersh, A., Kulich, S., Guo, T., Favorov, A. V., Fertig, E. J., Danilova, L. V., Gaykalova, D. A., Califano, J. A. & Duvvuri, U., Dec 1 2017, In: Scientific reports. 7, 1, 15173.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • CpG Islands 100%
  • Squamous Cell Carcinoma of Head and Neck 92%
  • DNA Methylation 81%
  • Keratinocytes 40%
  • Methylation 37%
  10 Scopus citations

• Genetic risk factors for myocardial infarction more clearly manifest for early age of first onset

  Titov, B. V., Osmak, G. J., Matveeva, N. A., Kukava, N. G., Shakhnovich, R. M., Favorov, A. V., Ruda, M. Y. & Favorova, O. O., Aug 1 2017, In: Molecular Biology Reports. 44, 4, p. 315-321 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Age of Onset 100%
  • Myocardial Infarction 77%
  • Single Nucleotide Polymorphism 17%
  • Genetic Testing 10%
  • Interleukin-4 9%
  5 Scopus citations

• 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

  Kelley, D. Z., Flam, E. L., Izumchenko, E., Danilova, L. V., Wulf, H. A., Guo, T., Singman, D. A., Afsari, B., Skaist, A. M., Considine, M., Welch, J. A., Stavrovskaya, E., Bishop, J. A., Westra, W. H., Khan, Z., Koch, W. M., Sidransky, D., Wheelan, S. J., Califano, J. A., Favorov, A. V., & 2 othersFertig, E. J. & Gaykalova, D. A., Dec 1 2017, In: Cancer Research. 77, 23, p. 6538-6550 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Chromatin Immunoprecipitation Sequencing 100%
  • RNA-Seq 90%
  • Chromatin 68%
  • Neck 58%
  • Head 56%
  15 Scopus citations

• Multilocus analysis of genetic susceptibility to myocardial infarction in Russians: Replication study

  Kukava, N. G., Titov, B. V., Osmak, G. J., Matveeva, N. A., Kulakova, O. G., Favorov, A. V., Shakhnovich, R. M., Ruda, M. Y. & Favorova, O. O., 2017, In: Acta Naturae. 9, 4, p. 74-83 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genetic Predisposition to Disease 100%
  • Marker 85%
  • Myocardial Infarction 71%
  • Composite Material 32%
  • Genetic Markers 29%
  3 Scopus citations

• PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

  Stein-O'Brien, G. L., Carey, J. L., Lee, W. S., Considine, M., Favorov, A. V., Flam, E., Guo, T., Li, S., Marchionni, L., Sherman, T., Sivy, S., Gaykalova, D. A., McKay, R. D., Ochs, M. F., Colantuoni, C. & Fertig, E. J., Jun 15 2017, In: Bioinformatics. 33, 12, p. 1892-1894 3 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Biomarkers 100%
  • Matrix Factorization 97%
  • Data-driven 88%
  • Genome 85%
  • Genomics 81%
  12 Scopus citations

• Pharmacogenetics of glatiramer acetate therapy for multiple sclerosis: The impact of genome-wide association studies identified disease risk loci

  Kulakova, O., Bashinskaya, V., Kiselev, I., Baulina, N., Tsareva, E., Nikolaev, R., Kozin, M., Shchur, S., Favorov, A., Boyko, A. & Favorova, O., Nov 2017, In: Pharmacogenomics. 18, 17, p. 1563-1574 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Pharmacogenetics 78%
  • Genome-Wide Association Study 71%
  • Multiple Sclerosis 60%
  • HLA-DRB1 Chains 15%
  • Therapeutics 11%
  6 Scopus citations

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

  Stavrovskaya, E. D., Niranjan, T., Fertig, E. J., Wheelan, S. J., Favorov, A. V. & Mironov, A. A., Oct 15 2017, In: Bioinformatics. 33, 20, p. 3158-3165 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genome 100%
  • Genomics 94%
  • Interval 52%
  • Galaxies 25%
  • Poly A 20%
  10 Scopus citations

• The combined effects of myocardial infarction risk factors: Simulation of the combined effects of gene variants, age, and smoking and an analysis of their interaction

  Osmak, G. J., Lvovs, D., Titov, B. V., Matveeva, N. A., Favorova, O. O. & Favorov, S., Jan 1 2017, In: Biophysics (Russian Federation). 62, 1, p. 123-128 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Myocardial Infarction 100%
  • Smoking 99%
  • Genes 55%
  • Alleles 50%
  • Non-Smokers 34%

• Transcriptional mechanisms of resistance to anti-PD-1 therapy

  Ascierto, M. L., Makohon-Moore, A., Lipson, E. J., Taube, J. M., McMiller, T. L., Berger, A. E., Fan, J., Kaunitz, G. J., Cottrell, T. R., Kohutek, Z. A., Favorov, A., Makarov, V., Riaz, N., Chan, T. A., Cope, L., Hruban, R. H., Pardoll, D. M., Taylor, B. S., Solit, D. B., Iacobuzio-Donahue, C. A., & 1 othersTopalian, S. L., Jun 15 2017, In: Clinical Cancer Research. 23, 12, p. 3168-3180 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Melanoma 100%
  • Clonal Evolution 55%
  • Biomarkers 52%
  • Neoplasm Metastasis 49%
  • Whole Exome Sequencing 47%
  38 Scopus citations
• 2016

  CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network

  Fertig, E. J., Ozawa, H., Thakar, M., Howard, J. D., Kagohara, L. T., Krigsfeld, G., Ranaweera, R. S., Hughes, R. M., Perez, J., Jones, S., Favorov, A. V., Carey, J., Stein-O'Brien, G., Gaykalova, D. A., Ochs, M. F. & Chung, C. H., 2016, In: Oncotarget. 7, 45, p. 73845-73864 20 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Psychological Inhibition 100%
  • Transcription Factor AP-2 66%
  • Phosphatidylinositol 3-Kinases 60%
  • Transcriptome 56%
  • Genes 49%
  6 Scopus citations

• Inferring causal molecular networks: Empirical assessment through a community-based effort

  Hill, S. M., Heiser, L. M., Cokelaer, T., Linger, M., Nesser, N. K., Carlin, D. E., Zhang, Y., Sokolov, A., Paull, E. O., Wong, C. K., Graim, K., Bivol, A., Wang, H., Zhu, F., Afsari, B., Danilova, L. V., Favorov, A. V., Lee, W. S., Taylor, D., Hu, C. W., & 115 othersLong, B. L., Noren, D. P., Bisberg, A. J., Mills, G. B., Gray, J. W., Kellen, M., Norman, T., Friend, S., Qutub, A. A., Fertig, E. J., Guan, Y., Song, M., Stuart, J. M., Spellman, P. T., Koeppl, H., Stolovitzky, G., Saez-Rodriguez, J., Mukherjee, S., Al-Ouran, R., Anton, B., Arodz, T., Sichani, O. A., Bagheri, N., Berlow, N., Bohler, A., Bonet, J., Bonneau, R., Budak, G., Bunescu, R., Caglar, M., Cai, B., Cai, C., Carlon, A., Chen, L., Ciaccio, M. F., Cooper, G., Coort, S., Creighton, C. J., Daneshmand, S. M. H., De La Fuente, A., Di Camillo, B., Dutta-Moscato, J., Emmett, K., Evelo, C., Fassia, M. K. H., Finotello, F., Finkle, J. D., Gao, X., Garcia-Garcia, J., Ghosh, S., Giaretta, A., Großeholz, R., Guinney, J., Hafemeister, C., Hahn, O., Haider, S., Hase, T., Hodgson, J., Hoff, B., Hsu, C. H., Hu, Y., Huang, X., Jalili, M., Jiang, X., Kacprowski, T., Kaderali, L., Kang, M., Kannan, V., Kikuchi, K., Kim, D. C., Kitano, H., Knapp, B., Komatsoulis, G., Krämer, A., Kursa, M. B., Kutmon, M., Li, Y., Liang, X., Liu, Z., Liu, Y., Lu, S., Lu, X., Manfrini, M., Matos, M. R. A., Meerzaman, D., Min, W., Müller, C. L., Neapolitan, R. E., Oliva, B., Opiyo, S. O., Pal, R., Palinkas, A., Planas-Iglesias, J., Poglayen, D., Sambo, F., Sanavia, T., Sharifi-Zarchi, A., Slawek, J., Streck, A., Strunz, S., Tegnér, J., Thobe, K., Toffolo, G. M., Trifoglio, E., Unger, M., Wan, Q., Welch, L., Wu, J. J., Xue, A. Y., Yamanaka, R., Yan, C., Zairis, S., Zengerling, M., Zenil, H. & Zi, Z., Mar 30 2016, In: Nature Methods. 13, 4, p. 310-322 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Phosphoproteins 100%
  • Learning 62%
  • Nonlinear Dynamics 55%
  • Computer Simulation 40%
  • Cell Line 25%
  124 Scopus citations