clusterMaker: a multi-algorithm clustering plugin for Cytoscape

by Morris, John H, Apeltsin, Leonard, Newman, Aaron M, Baumbach, Jan, Wittkop, Tobias, Su, Gang, Bader, Gary D, Ferrin, Thomas E
Published in BMC bioinformatics

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data

by Tran, Thinh N, Bader, Gary D
Published in PLoS computational biology

GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

by Warde-Farley, David, Donaldson, Sylva L, Comes, Ovi, Zuberi, Khalid, Badrawi, Rashad, Chao, Pauline, Franz, Max, Grouios, Chris, Kazi, Farzana, Lopes, Christian Tannus, Maitland, Anson, Mostafavi, Sara, Montojo, Jason, Shao, Quentin, Wright, George, Bader, Gary D, Morris, Quaid
Published in Nucleic acids research

Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion

by Lechman, Eric R., Gentner, Bernhard, van Galen, Peter, Giustacchini, Alice, Saini, Massimo, Boccalatte, Francesco E., Hiramatsu, Hidefumi, Restuccia, Umberto, Bachi, Angela, Voisin, Veronique, Bader, Gary D., Dick, John E., Naldini, Luigi
Published in Cell stem cell

Generation of Functional Liver Sinusoidal Endothelial Cells from Human Pluripotent Stem-Cell-Derived Venous Angioblasts

by Gage, Blair K., Liu, Jeff C., Innes, Brendan T., MacParland, Sonya A., McGilvray, Ian D., Bader, Gary D., Keller, Gordon M.
Published in Cell stem cell

Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia

by Cole, Alicia, Wang, Zezhou, Coyaud, Etienne, Voisin, Veronique, Gronda, Marcela, Jitkova, Yulia, Mattson, Rachel, Hurren, Rose, Babovic, Sonja, Maclean, Neil, Restall, Ian, Wang, Xiaoming, Jeyaraju, Danny V., Sukhai, Mahadeo A., Prabha, Swayam, Bashir, Shaheena, Ramakrishnan, Ashwin, Leung, Elisa, Qia, Yi Hua, Zhang, Nianxian, Combes, Kevin R., Ketela, Troy, Lin, Fengshu, Houry, Walid A., Aman, Ahmed, Al-awar, Rima, Zheng, Wei, Wienholds, Erno, Xu, Chang Jiang, Dick, John, Wang, Jean C.Y., Moffat, Jason, Minden, Mark D., Eaves, Connie J., Bader, Gary D., Hao, Zhenyue, Kornblau, Steven M., Raught, Brian, Schimmer, Aaron D.
Published in Cancer cell

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal

by Xie, Stephanie Z., Garcia-Prat, Laura, Voisin, Veronique, Ferrari, Robin, Gan, Olga I., Wagenblast, Elvin, Kaufmann, Kerstin B., Zeng, Andy G.X., Takayanagi, Shin-ichiro, Patel, Ishita, Lee, Esther K., Jargstorf, Joseph, Holmes, Gareth, Romm, Guy, Pan, Kristele, Shoong, Michelle, Vedi, Aditi, Luberto, Chiara, Minden, Mark D., Bader, Gary D., Laurenti, Elisa, Dick, John E.
Published in Cell stem cell

Cardioprotective Signature of Short-Term Caloric Restriction

by Noyan, Hossein, El-Mounayri, Omar, Isserlin, Ruth, Arab, Sara, Momen, Abdul, Cheng, Henry S, Wu, Jun, Afroze, Talat, Li, Ren-Ke, Fish, Jason E, Bader, Gary D, Husain, Mansoor
Published in PloS one

A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

by Labbé, Roselyne M., Irimia, Manuel, Currie, Ko W., Lin, Alexander, Zhu, Shu Jun, Brown, David D.R., Ross, Eric J., Voisin, Veronique, Bader, Gary D., Blencowe, Benjamin J., Pearson, Bret J.
Published in Stem cells (Dayton, Ohio)

Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer

by Jiang, Zhe, Ju, YoungJun, Ali, Amjad, Chung, Philip E D, Skowron, Patryk, Wang, Dong-Yu, Shrestha, Mariusz, Li, Huiqin, Liu, Jeff C, Vorobieva, Ioulia, Ghanbari-Azarnier, Ronak, Mwewa, Ethel, Koritzinsky, Marianne, Ben-David, Yaacov, Woodgett, James R, Perou, Charles M, Dupuy, Adam, Bader, Gary D, Egan, Sean E, Taylor, Michael D, Zacksenhaus, Eldad
Published in Nature communications

Proteome scanning to predict PDZ domain interactions using support vector machines

by Hui, Shirley, Bader, Gary D
Published in BMC bioinformatics

Combined deletion of Pten and p53 in mammary epithelium accelerates triple‐negative breast cancer with dependency on eEF2K

by Liu, Jeff C, Voisin, Veronique, Wang, Sharon, Wang, Dong‐Yu, Jones, Robert A, Datti, Alessandro, Uehling, David, Al‐awar, Rima, Egan, Sean E, Bader, Gary D, Tsao, Ming, Mak, Tak W, Zacksenhaus, Eldad
Published in EMBO molecular medicine

GeneMANIA prediction server 2013 update

by Zuberi, Khalid, Franz, Max, Rodriguez, Harold, Montojo, Jason, Lopes, Christian Tannus, Bader, Gary D, Morris, Quaid
Published in Nucleic acids research

Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2⁺:ERα⁻ breast cancer

by Liu, Jeff C., Voisin, Veronique, Bader, Gary D., Deng, Tao, Pusztai, Lajos, Symmans, William Fraser, Esteva, Francisco J., Egan, Sean E., Zacksenhaus, Eldad
Published in Proceedings of the National Academy of Sciences - PNAS

Single-cell transcriptomic profiling of the aging mouse brain

by Ximerakis, Methodios, Lipnick, Scott L, Innes, Brendan T, Simmons, Sean K, Adiconis, Xian, Dionne, Danielle, Mayweather, Brittany A, Nguyen, Lan, Niziolek, Zachary, Ozek, Ceren, Butty, Vincent L, Isserlin, Ruth, Buchanan, Sean M, Levine, Stuart S, Regev, Aviv, Bader, Gary D, Levin, Joshua Z, Rubin, Lee L
Published in Nature neuroscience

Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition

by Kool, Marcel, Jones, David T.W., Jäger, Natalie, Northcott, Paul A., Pugh, Trevor J., Hovestadt, Volker, Piro, Rosario M., Esparza, L. Adriana, Markant, Shirley L., Remke, Marc, Milde, Till, Bourdeaut, Franck, Ryzhova, Marina, Sturm, Dominik, Pfaff, Elke, Stark, Sebastian, Hutter, Sonja, Şeker-Cin, Huriye, Johann, Pascal, Bender, Sebastian, Schmidt, Christin, Rausch, Tobias, Shih, David, Reimand, Jüri, Sieber, Laura, Wittmann, Andrea, Linke, Linda, Witt, Hendrik, Weber, Ursula D., Zapatka, Marc, König, Rainer, Beroukhim, Rameen, Bergthold, Guillaume, van Sluis, Peter, Volckmann, Richard, Koster, Jan, Versteeg, Rogier, Schmidt, Sabine, Wolf, Stephan, Lawerenz, Chris, Bartholomae, Cynthia C., von Kalle, Christof, Unterberg, Andreas, Herold-Mende, Christel, Hofer, Silvia, Kulozik, Andreas E., von Deimling, Andreas, Scheurlen, Wolfram, Felsberg, Jörg, Reifenberger, Guido, Hasselblatt, Martin, Crawford, John R., Grant, Gerald A., Jabado, Nada, Perry, Arie, Cowdrey, Cynthia, Croul, Sydney, Zadeh, Gelareh, Korbel, Jan O., Doz, Francois, Delattre, Olivier, Bader, Gary D., McCabe, Martin G., Collins, V. Peter, Kieran, Mark W., Cho, Yoon-Jae, Pomeroy, Scott L., Witt, Olaf, Brors, Benedikt, Taylor, Michael D., Schüller, Ulrich, Korshunov, Andrey, Eils, Roland, Wechsler-Reya, Robert J., Lichter, Peter, Pfister, Stefan M.
Published in Cancer cell

Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells

by Rentas, Stefan, Holzapfel, Nicholas, Belew, Muluken S, Pratt, Gabriel, Voisin, Veronique, Wilhelm, Brian T, Bader, Gary D, Yeo, Gene W, Hope, Kristin J
Published in Nature (London)

The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety

by Shukla, Rammohan, Prevot, Thomas D., French, Leon, Isserlin, Ruth, Rocco, Brad R., Banasr, Mounira, Bader, Gary D., Sibille, Etienne
Published in Biological psychiatry (1969)

Hypophosphorylated pRb knock‐in mice exhibit hallmarks of aging and vitamin C‐preventable diabetes

by Jiang, Zhe, Li, Huiqin, Schroer, Stephanie A, Voisin, Veronique, Ju, YoungJun, Pacal, Marek, Erdmann, Natalie, Shi, Wei, Chung, Philip E D, Deng, Tao, Chen, Nien‐Jung, Ciavarra, Giovanni, Datti, Alessandro, Mak, Tak W, Harrington, Lea, Dick, Frederick A, Bader, Gary D, Bremner, Rod, Woo, Minna, Zacksenhaus, Eldad
Published in The EMBO journal

Mitochondrial carrier homolog 2 is necessary for AML survival

by Khan, Dilshad H., Mullokandov, Michael, Wu, Yan, Voisin, Veronique, Gronda, Marcela, Hurren, Rose, Wang, Xiaoming, MacLean, Neil, Jeyaraju, Danny V., Jitkova, Yulia, Xu, G. Wei, Laister, Rob, Seneviratne, Ayesh, Blatman, Zachary M., Ketela, Troy, Bader, Gary D., Marhon, Sajid A., De Carvalho, Daniel D., Minden, Mark D., Gross, Atan, Schimmer, Aaron D.
Published in Blood