Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

by Merid, Simon Kebede, Goranskaya, Daria, Alexeyenko, Andrey
Published 2014

Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD

by Heijtz, Rochellys Diaz, Alexeyenko, Andrey, Castellanos, F Xavier
Published 2007

Comparative interactomics with Funcoup 2.0

by Alexeyenko, Andrey, Schmitt, Thomas, Tjärnberg, Andreas, Guala, Dmitri, Frings, Oliver, Sonnhammer, Erik L. L.
Published 2012

Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression

by Frings, Oliver, Mank, Judith E., Alexeyenko, Andrey, Sonnhammer, Erik L. L.
Published 2012

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

by McCormack, Theodore, Frings, Oliver, Alexeyenko, Andrey, Sonnhammer, Erik L. L.
Published 2013

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

by Alexeyenko, Andrey, Lee, Woojoo, Pernemalm, Maria, Guegan, Justin, Dessen, Philippe, Lazar, Vladimir, Lehtiö, Janne, Pawitan, Yudi
Published 2012

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population

by Lee, Woojoo, Alexeyenko, Andrey, Pernemalm, Maria, Guegan, Justine, Dessen, Philippe, Lazar, Vladimir, Lehtiö, Janne, Pawitan, Yudi
Published 2015

Novel Genes and Pathways Modulated by Syndecan-1: Implications for the Proliferation and Cell-Cycle Regulation of Malignant Mesothelioma Cells

by Szatmári, Tünde, Mundt, Filip, Heidari-Hamedani, Ghazal, Zong, Fang, Ferolla, Elena, Alexeyenko, Andrey, Hjerpe, Anders, Dobra, Katalin
Published 2012

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines

by Akan, Pelin, Alexeyenko, Andrey, Costea, Paul Igor, Hedberg, Lilia, Solnestam, Beata Werne, Lundin, Sverker, Hällman, Jimmie, Lundberg, Emma, Uhlén, Mathias, Lundeberg, Joakim
Published 2012

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools

by Alexeyenko, Andrey, Nystedt, Björn, Vezzi, Francesco, Sherwood, Ellen, Ye, Rosa, Knudsen, Bjarne, Simonsen, Martin, Turner, Benjamin, de Jong, Pieter, Wu, Cheng-Cang, Lundeberg, Joakim
Published 2014

Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis

by Bersani, Cinzia, Huss, Mikael, Giacomello, Stefania, Xu, Li-Di, Bianchi, Julie, Eriksson, Sofi, Jerhammar, Fredrik, Alexeyenko, Andrey, Vilborg, Anna, Lundeberg, Joakim, Lui, Weng-Onn, Wiman, Klas G.
Published 2015

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth

by Alexeyenko, Andrey, Alkasalias, Twana, Pavlova, Tatiana, Szekely, Laszlo, Kashuba, Vladimir, Rundqvist, Helene, Wiklund, Peter, Egevad, Lars, Csermely, Peter, Korcsmaros, Tamas, Guven, Hayrettin, Klein, George
Published 2015

High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans

by Hunt-Newbury, Rebecca, Viveiros, Ryan, Johnsen, Robert, Mah, Allan, Anastas, Dina, Fang, Lily, Halfnight, Erin, Lee, David, Lin, John, Lorch, Adam, McKay, Sheldon, Okada, H. Mark, Pan, Jie, Schulz, Ana K, Tu, Domena, Wong, Kim, Zhao, Z, Alexeyenko, Andrey, Burglin, Thomas, Sonnhammer, Eric, Schnabel, Ralf, Jones, Steven J, Marra, Marco A, Baillie, David L, Moerman, Donald G
Published 2007

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis

by Dmitriev, Alexey A., Rosenberg, Eugenia E., Krasnov, George S., Gerashchenko, Ganna V., Gordiyuk, Vasily V., Pavlova, Tatiana V., Kudryavtseva, Anna V., Beniaminov, Artemy D., Belova, Anastasia A., Bondarenko, Yuriy N., Danilets, Rostislav O., Glukhov, Alexander I., Kondratov, Aleksandr G., Alexeyenko, Andrey, Alekseev, Boris Y., Klein, George, Senchenko, Vera N., Kashuba, Vladimir I.
Published 2015

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

by Brownstein, Catherine A, Beggs, Alan H, Homer, Nils, Merriman, Barry, Yu, Timothy W, Flannery, Katherine C, DeChene, Elizabeth T, Towne, Meghan C, Savage, Sarah K, Price, Emily N, Holm, Ingrid A, Luquette, Lovelace J, Lyon, Elaine, Majzoub, Joseph, Neupert, Peter, McCallie Jr, David, Szolovits, Peter, Willard, Huntington F, Mendelsohn, Nancy J, Temme, Renee, Finkel, Richard S, Yum, Sabrina W, Medne, Livija, Sunyaev, Shamil R, Adzhubey, Ivan, Cassa, Christopher A, de Bakker, Paul IW, Duzkale, Hatice, Dworzyński, Piotr, Fairbrother, William, Francioli, Laurent, Funke, Birgit H, Giovanni, Monica A, Handsaker, Robert E, Lage, Kasper, Lebo, Matthew S, Lek, Monkol, Leshchiner, Ignaty, MacArthur, Daniel G, McLaughlin, Heather M, Murray, Michael F, Pers, Tune H, Polak, Paz P, Raychaudhuri, Soumya, Rehm, Heidi L, Soemedi, Rachel, Stitziel, Nathan O, Vestecka, Sara, Supper, Jochen, Gugenmus, Claudia, Klocke, Bernward, Hahn, Alexander, Schubach, Max, Menzel, Mortiz, Biskup, Saskia, Freisinger, Peter, Deng, Mario, Braun, Martin, Perner, Sven, Smith, Richard JH, Andorf, Janeen L, Huang, Jian, Ryckman, Kelli, Sheffield, Val C, Stone, Edwin M, Bair, Thomas, Black-Ziegelbein, E Ann, Braun, Terry A, Darbro, Benjamin, DeLuca, Adam P, Kolbe, Diana L, Scheetz, Todd E, Shearer, Aiden E, Sompallae, Rama, Wang, Kai, Bassuk, Alexander G, Edens, Erik, Mathews, Katherine, Moore, Steven A, Shchelochkov, Oleg A, Trapane, Pamela, Bossler, Aaron, Campbell, Colleen A, Heusel, Jonathan W, Kwitek, Anne, Maga, Tara, Panzer, Karin, Wassink, Thomas, Van Daele, Douglas, Azaiez, Hela, Booth, Kevin, Meyer, Nic, Segal, Michael M, Williams, Marc S, Tromp, Gerard, White, Peter, Corsmeier, Donald, Fitzgerald-Butt, Sara, Herman, Gail, Lamb-Thrush, Devon, McBride, Kim L, Newsom, David, Pierson, Christopher R, Rakowsky, Alexander T, Maver, Aleš, Lovrečić, Luca, Palandačić, Anja, Peterlin, Borut, Torkamani, Ali, Wedell, Anna, Huss, Mikael, Alexeyenko, Andrey, Lindvall, Jessica M, Magnusson, Måns, Nilsson, Daniel, Stranneheim, Henrik, Taylan, Fulya, Gilissen, Christian, Hoischen, Alexander, van Bon, Bregje, Yntema, Helger, Nelen, Marcel, Zhang, Weidong, Sager, Jason, Zhang, Lu, Blair, Kathryn, Kural, Deniz, Cariaso, Michael, Lennon, Greg G, Javed, Asif, Agrawal, Saloni, Ng, Pauline C, Sandhu, Komal S, Krishna, Shuba, Veeramachaneni, Vamsi, Isakov, Ofer, Halperin, Eran, Friedman, Eitan, Shomron, Noam, Glusman, Gustavo, Roach, Jared C, Caballero, Juan, Cox, Hannah C, Mauldin, Denise, Ament, Seth A, Rowen, Lee, Richards, Daniel R, Lucas, F Anthony San, Gonzalez-Garay, Manuel L, Caskey, C Thomas, Bai, Yu, Huang, Ying, Fang, Fang, Zhang, Yan, Wang, Zhengyuan, Barrera, Jorge, Garcia-Lobo, Juan M, González-Lamuño, Domingo, Llorca, Javier, Rodriguez, Maria C, Varela, Ignacio, Reese, Martin G, De La Vega, Francisco M, Kiruluta, Edward, Cargill, Michele, Hart, Reece K, Sorenson, Jon M, Lyon, Gholson J, Stevenson, David A, Bray, Bruce E, Moore, Barry M, Eilbeck, Karen, Yandell, Mark, Zhao, Hongyu, Hou, Lin, Chen, Xiaowei, Yan, Xiting, Chen, Mengjie, Li, Cong, Yang, Can, Gunel, Murat, Li, Peining, Kong, Yong, Alexander, Austin C, Albertyn, Zayed I, Boycott, Kym M, Bulman, Dennis E, Gordon, Paul MK, Innes, A Micheil, Knoppers, Bartha M, Majewski, Jacek, Marshall, Christian R, Parboosingh, Jillian S, Sawyer, Sarah L, Samuels, Mark E, Schwartzentruber, Jeremy, Kohane, Isaac S, Margulies, David M
Published 2014