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.

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Landscape of allele-specific transcription factor binding in the human genome von Abramov, Sergey, Boytsov, Alexandr, Bykova, Daria, Penzar, Dmitry D., Yevshin, Ivan, Kolmykov, Semyon K., Fridman, Marina V., Favorov, Alexander V., Vorontsov, Ilya E., Baulin, Eugene, Kolpakov, Fedor, Makeev, Vsevolod J., Kulakovskiy, Ivan V.

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HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers von Ren, Shuling, Gaykalova, Daria A., Guo, Theresa, Favorov, Alexander V., Fertig, Elana J., Tamayo, Pablo, Callejas-Valera, Juan Luis, Allevato, Mike, Gilardi, Mara, Santos, Jessica, Fukusumi, Takahito, Sakai, Akihiro, Ando, Mizuo, Sadat, Sayed, Liu, Chao, Xu, Guorong, Fisch, Kathleen M., Wang, Zhiyong, Molinolo, Alfredo A., Gutkind, J. Silvio, Ideker, Trey, Koch, Wayne M., Califano, Joseph A.

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Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers von Ando, Mizuo, Saito, Yuki, Xu, Guorong, Bui, Nam Q., Medetgul-Ernar, Kate, Pu, Minya, Fisch, Kathleen, Ren, Shuling, Sakai, Akihiro, Fukusumi, Takahito, Liu, Chao, Haft, Sunny, Pang, John, Mark, Adam, Gaykalova, Daria A., Guo, Theresa, Favorov, Alexander V., Yegnasubramanian, Srinivasan, Fertig, Elana J., Ha, Patrick, Tamayo, Pablo, Yamasoba, Tatsuya, Ideker, Trey, Messer, Karen, Califano, Joseph A.

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Assessing computational tools for the discovery of transcription factor binding sites von Eskin, Eleazar, Ye, Chun, Mironov, Andrei A, Fu, Yutao, Favorov, Alexander V, Pavesi, Giulio, Li, Nan, Pesole, Graziano, Vandenbogaert, Mathias, Noble, William Stafford, Weng, Zhiping, Régnier, Mireille, Sinha, Saurabh, Makeev, Vsevolod J, Kent, W James, De Moor, Bart, Simonis, Nicolas, Zhu, Zhou, Thijs, Gert, Bailey, Timothy L, Frith, Martin C, Workman, Christopher, Church, George M, Tompa, Martin, van Helden, Jacques

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A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers von Guo, Theresa, Sakai, Akihiro, Afsari, Bahman, Considine, Michael, Danilova, Ludmila, Favorov, Alexander V, Yegnasubramanian, Srinivasan, Kelley, Dylan Z, Flam, Emily, Ha, Patrick K, Khan, Zubair, Wheelan, Sarah J, Gutkind, J Silvio, Fertig, Elana J, Gaykalova, Daria A, Califano, Joseph

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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

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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.

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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.

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Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation von Lomakin, Yakov A., Zvyagin, Ivan V., Ovchinnikova, Leyla A., Kabilov, Marsel R., Staroverov, Dmitriy B., Mikelov, Artem, Tupikin, Alexey E., Zakharova, Maria Y., Bykova, Nadezda A., Mukhina, Vera S., Favorov, Alexander V., Ivanova, Maria, Simaniv, Taras, Rubtsov, Yury P., Chudakov, Dmitriy M., Zakharova, Maria N., Illarioshkin, Sergey N., Belogurov, Alexey A., Gabibov, Alexander G.

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Variants of the Coagulation and Inflammation Genes Are Replicably Associated with Myocardial Infarction and Epistatically Interact in Russians von Barsova, Rosa M, Lvovs, Dmitrijs, Titov, Boris V, Matveeva, Natalia A, Shakhnovich, Roman M, Sukhinina, Tatiana S, Kukava, Nino G, Ruda, Mikhail Ya, Karamova, Irina M, Nasibullin, Timur R, Mustafina, Olga E, Osmak, German J, Tsareva, Ekaterina Yu, Kulakova, Olga G, Favorov, Alexander V, Favorova, Olga O

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Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer von Afsari, Bahman, Guo, Theresa, Considine, Michael, Florea, Liliana, Kagohara, Luciane T, Stein-O'Brien, Genevieve L, Kelley, Dylan, Flam, Emily, Zambo, Kristina D, Ha, Patrick K, Geman, Donald, Ochs, Michael F, Califano, Joseph A, Gaykalova, Daria A, Favorov, Alexander V, Fertig, Elana J

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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.

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Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance von Stein-O'Brien, Genevieve, Kagohara, Luciane T, Li, Sijia, Thakar, Manjusha, Ranaweera, Ruchira, Ozawa, Hiroyuki, Cheng, Haixia, Considine, Michael, Schmitz, Sandra, Favorov, Alexander V, Danilova, Ludmila V, Califano, Joseph A, Izumchenko, Evgeny, Gaykalova, Daria A, Chung, Christine H, Fertig, Elana J

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Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers von Ando, Mizuo, Saito, Yuki, Xu, Guorong, Bui, Nam Q., Medetgul-Ernar, Kate, Pu, Minya, Fisch, Kathleen, Ren, Shuling, Sakai, Akihiro, Fukusumi, Takahito, Liu, Chao, Haft, Sunny, Pang, John, Mark, Adam, Gaykalova, Daria A., Guo, Theresa, Favorov, Alexander V., Yegnasubramanian, Srinivasan, Fertig, Elana J., Ha, Patrick, Tamayo, Pablo, Yamasoba, Tatsuya, Ideker, Trey, Messer, Karen, Califano, Joseph A.

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Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces von Deshpande, Atul, Loth, Melanie, Sidiropoulos, Dimitrios N, Zhang, Shuming, Yuan, Long, Bell, Alexander T F, Zhu, Qingfeng, Ho, Won Jin, Santa-Maria, Cesar, Gilkes, Daniele M, Williams, Stephen R, Uytingco, Cedric R, Chew, Jennifer, Hartnett, Andrej, Bent, Zachary W, Favorov, Alexander V, Popel, Aleksander S, Yarchoan, Mark, Kiemen, Ashley, Wu, Pei-Hsun, Fujikura, Kohei, Wirtz, Denis, Wood, Laura D, Zheng, Lei, Jaffee, Elizabeth M, Anders, Robert A, Danilova, Ludmila, Stein-O'Brien, Genevieve, Kagohara, Luciane T, Fertig, Elana J

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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

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Hidden Markov models for evolution and comparative genomics analysis von Bykova, Nadezda A, Favorov, Alexander V, Mironov, Andrey A

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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

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Inferring causal molecular networks: empirical assessment through a community-based effort von Hill, Steven M, Heiser, Laura M, Cokelaer, Thomas, Unger, Michael, Nesser, Nicole K, Carlin, Daniel E, Zhang, Yang, Sokolov, Artem, Paull, Evan O, Wong, Chris K, Graim, Kiley, Bivol, Adrian, Wang, Haizhou, Zhu, Fan, Afsari, Bahman, Danilova, Ludmila V, Favorov, Alexander V, Lee, Wai Shing, Taylor, Dane, Hu, Chenyue W, Long, Byron L, Noren, David P, Bisberg, Alexander J, Mills, Gordon B, Gray, Joe W, Kellen, Michael, Norman, Thea, Friend, Stephen, Qutub, Amina A, Fertig, Elana J, Guan, Yuanfang, Song, Mingzhou, Stuart, Joshua M, Spellman, Paul T, Koeppl, Heinz, Stolovitzky, Gustavo, Saez-Rodriguez, Julio, Mukherjee, Sach

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