The case for cloud computing in genome informatics von Stein, Lincoln D

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The International Cancer Genome Consortium Data Portal von Zhang, Junjun, Bajari, Rosita, Andric, Dusan, Gerthoffert, Francois, Lepsa, Alexandru, Nahal-Bose, Hardeep, Stein, Lincoln D., Ferretti, Vincent

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A human functional protein interaction network and its application to cancer data analysis von Wu, Guanming, Feng, Xin, Stein, Lincoln

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Impact of outdated gene annotations on pathway enrichment analysis von Wadi, Lina, Meyer, Mona, Weiser, Joel, Stein, Lincoln D, Reimand, Jüri

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Redefining genomic privacy: trust and empowerment von Erlich, Yaniv, Williams, James B, Glazer, David, Yocum, Kenneth, Farahany, Nita, Olson, Maynard, Narayanan, Arvind, Stein, Lincoln D, Witkowski, Jan A, Kain, Robert C

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Distinct routes of lineage development reshape the human blood hierarchy across ontogeny von Notta, Faiyaz, Zandi, Sasan, Takayama, Naoya, Dobson, Stephanie, Gan, Olga I., Wilson, Gavin, Kaufmann, Kerstin B., McLeod, Jessica, Laurenti, Elisa, Dunant, Cyrille F., McPherson, John D., Stein, Lincoln D., Dror, Yigal, Dick, John E.

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Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution von Chan-Seng-Yue, Michelle, Kim, Jaeseung C., Wilson, Gavin W., Ng, Karen, Figueroa, Eugenia Flores, O’Kane, Grainne M., Connor, Ashton A., Denroche, Robert E., Grant, Robert C., McLeod, Jessica, Wilson, Julie M., Jang, Gun Ho, Zhang, Amy, Dodd, Anna, Liang, Sheng-Ben, Borgida, Ayelet, Chadwick, Dianne, Kalimuthu, Sangeetha, Lungu, Ilinca, Bartlett, John M. S., Krzyzanowski, Paul M., Sandhu, Vandana, Tiriac, Hervé, Froeling, Fieke E. M., Karasinska, Joanna M., Topham, James T., Renouf, Daniel J., Schaeffer, David F., Jones, Steven J. M., Marra, Marco A., Laskin, Janessa, Chetty, Runjan, Stein, Lincoln D., Zogopoulos, George, Haibe-Kains, Benjamin, Campbell, Peter J., Tuveson, David A., Knox, Jennifer J., Fischer, Sandra E., Gallinger, Steven, Notta, Faiyaz

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The U1 spliceosomal RNA is recurrently mutated in multiple cancers von Shuai, Shimin, Suzuki, Hiromichi, Diaz-Navarro, Ander, Nadeu, Ferran, Kumar, Sachin A., Gutierrez-Fernandez, Ana, Delgado, Julio, Pinyol, Magda, López-Otín, Carlos, Puente, Xose S., Taylor, Michael D., Campo, Elías, Stein, Lincoln D.

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Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges von Stein, Lincoln D

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The reactome pathway knowledgebase von Jassal, Bijay, Matthews, Lisa, Viteri, Guilherme, Gong, Chuqiao, Lorente, Pascual, Fabregat, Antonio, Sidiropoulos, Konstantinos, Cook, Justin, Gillespie, Marc, Haw, Robin, Loney, Fred, May, Bruce, Milacic, Marija, Rothfels, Karen, Sevilla, Cristoffer, Shamovsky, Veronica, Shorser, Solomon, Varusai, Thawfeek, Weiser, Joel, Wu, Guanming, Stein, Lincoln, Hermjakob, Henning, D’Eustachio, Peter

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JBrowse 2: a modular genome browser with views of synteny and structural variation von Diesh, Colin, Stevens, Garrett J, Xie, Peter, De Jesus Martinez, Teresa, Hershberg, Elliot A, Leung, Angel, Guo, Emma, Dider, Shihab, Zhang, Junjun, Bridge, Caroline, Hogue, Gregory, Duncan, Andrew, Morgan, Matthew, Flores, Tia, Bimber, Benjamin N, Haw, Robin, Cain, Scott, Buels, Robert M, Stein, Lincoln D, Holmes, Ian H

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Reactome pathway analysis: a high-performance in-memory approach von Fabregat, Antonio, Sidiropoulos, Konstantinos, Viteri, Guilherme, Forner, Oscar, Marin-Garcia, Pablo, Arnau, Vicente, D'Eustachio, Peter, Stein, Lincoln, Hermjakob, Henning

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The reactome pathway knowledgebase 2022 von Gillespie, Marc, Jassal, Bijay, Stephan, Ralf, Milacic, Marija, Rothfels, Karen, Senff-Ribeiro, Andrea, Griss, Johannes, Sevilla, Cristoffer, Matthews, Lisa, Gong, Chuqiao, Deng, Chuan, Varusai, Thawfeek, Ragueneau, Eliot, Haider, Yusra, May, Bruce, Shamovsky, Veronica, Weiser, Joel, Brunson, Timothy, Sanati, Nasim, Beckman, Liam, Shao, Xiang, Fabregat, Antonio, Sidiropoulos, Konstantinos, Murillo, Julieth, Viteri, Guilherme, Cook, Justin, Shorser, Solomon, Bader, Gary, Demir, Emek, Sander, Chris, Haw, Robin, Wu, Guanming, Stein, Lincoln, Hermjakob, Henning, D’Eustachio, Peter

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Create a cloud commons von Stein, Lincoln D

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A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns von Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W., Connor, Ashton A., Denroche, Robert E., Liang, Sheng-Ben, Brown, Andrew M. K., Kim, Jaeseung C., Wang, Tao, Simpson, Jared T., Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E., Heisler, Lawrence, Hollingsworth, Michael A., Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars G. T., Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M., Shlush, Liran I., Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M., Yung, Christina K., Zogopoulos, George, Bartlett, John M. S., Alexandrov, Ludmil B., Real, Francisco X., Cleary, Sean P., Roehrl, Michael H., McPherson, John D., Stein, Lincoln D., Hudson, Thomas J., Campbell, Peter J., Gallinger, Steven

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Inferring clonal evolution of tumors from single nucleotide somatic mutations von Jiao, Wei, Vembu, Shankar, Deshwar, Amit G, Stein, Lincoln, Morris, Quaid

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Reactome diagram viewer: data structures and strategies to boost performance von Fabregat, Antonio, Sidiropoulos, Konstantinos, Viteri, Guilherme, Marin-Garcia, Pablo, Ping, Peipei, Stein, Lincoln, D'Eustachio, Peter, Hermjakob, Henning

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JBrowse: a next-generation genome browser von Skinner, Mitchell E, Uzilov, Andrew V, Stein, Lincoln D, Mungall, Christopher J, Holmes, Ian H

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Spatial genomic heterogeneity within localized, multifocal prostate cancer von Boutros, Paul C, Fraser, Michael, Harding, Nicholas J, de Borja, Richard, Trudel, Dominique, Lalonde, Emilie, Meng, Alice, Hennings-Yeomans, Pablo H, McPherson, Andrew, Sabelnykova, Veronica Y, Zia, Amin, Fox, Natalie S, Livingstone, Julie, Shiah, Yu-Jia, Wang, Jianxin, Beck, Timothy A, Have, Cherry L, Chong, Taryne, Sam, Michelle, Johns, Jeremy, Timms, Lee, Buchner, Nicholas, Wong, Ada, Watson, John D, Simmons, Trent T, P'ng, Christine, Zafarana, Gaetano, Nguyen, Francis, Luo, Xuemei, Chu, Kenneth C, Prokopec, Stephenie D, Sykes, Jenna, Dal Pra, Alan, Berlin, Alejandro, Brown, Andrew, Chan-Seng-Yue, Michelle A, Yousif, Fouad, Denroche, Robert E, Chong, Lauren C, Chen, Gregory M, Jung, Esther, Fung, Clement, Starmans, Maud H W, Chen, Hanbo, Govind, Shaylan K, Hawley, James, D'Costa, Alister, Pintilie, Melania, Waggott, Daryl, Hach, Faraz, Lambin, Philippe, Muthuswamy, Lakshmi B, Cooper, Colin, Eeles, Rosalind, Neal, David, Tetu, Bernard, Sahinalp, Cenk, Stein, Lincoln D, Fleshner, Neil, Shah, Sohrab P, Collins, Colin C, Hudson, Thomas J, McPherson, John D, van der Kwast, Theodorus, Bristow, Robert G

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Reactome graph database: Efficient access to complex pathway data von Fabregat, Antonio, Korninger, Florian, Viteri, Guilherme, Sidiropoulos, Konstantinos, Marin-Garcia, Pablo, Ping, Peipei, Wu, Guanming, Stein, Lincoln, D'Eustachio, Peter, Hermjakob, Henning

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