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Impact of outdated gene annotations on pathway enrichment analysis von Wadi, Lina, Meyer, Mona, Weiser, Joel, Stein, Lincoln D, Reimand, Jüri

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

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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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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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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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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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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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scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy von Ocasio, Jennifer Karin, Babcock, Benjamin, Malawsky, Daniel, Weir, Seth J., Loo, Lipin, Simon, Jeremy M., Zylka, Mark J., Hwang, Duhyeong, Dismuke, Taylor, Sokolsky, Marina, Rosen, Elias P., Vibhakar, Rajeev, Zhang, Jiao, Saulnier, Olivier, Vladoiu, Maria, El-Hamamy, Ibrahim, Stein, Lincoln D., Taylor, Michael D., Smith, Kyle S., Northcott, Paul A., Colaneri, Alejandro, Wilhelmsen, Kirk, Gershon, Timothy R.

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Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks von Zhu, Helen, Uusküla-Reimand, Liis, Isaev, Keren, Wadi, Lina, Alizada, Azad, Shuai, Shimin, Huang, Vincent, Aduluso-Nwaobasi, Dike, Paczkowska, Marta, Abd-Rabbo, Diala, Ocsenas, Oliver, Liang, Minggao, Thompson, J. Drew, Li, Yao, Ruan, Luyao, Krassowski, Michal, Dzneladze, Irakli, Simpson, Jared T., Lupien, Mathieu, Stein, Lincoln D., Boutros, Paul C., Wilson, Michael D., Reimand, Jüri

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Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy von Atienza, Joshua, Benedict, Anjalee, Stein, Lincoln D, Pirzada, Kashif, White, Cheryl, Pai, Shraddha

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Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis von Thomas, Cristel G, Wang, Wei, Jovelin, Richard, Ghosh, Rajarshi, Lomasko, Tatiana, Trinh, Quang, Kruglyak, Leonid, Stein, Lincoln D, Cutter, Asher D

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Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer von Gendoo, Deena M A, Denroche, Robert E, Zhang, Amy, Radulovich, Nikolina, Jang, Gun Ho, Lemire, Mathieu, Fischer, Sandra, Chadwick, Dianne, Lungu, Ilinca M, Ibrahimov, Emin, Cao, Ping-Jiang, Stein, Lincoln D, Wilson, Julie M, Bartlett, John M S, Tsao, Ming-Sound, Dhani, Neesha, Hedley, David, Gallinger, Steven, Haibe-Kains, Benjamin

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Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma von Feigin, Michael E, Garvin, Tyler, Bailey, Peter, Waddell, Nicola, Chang, David K, Kelley, David R, Shuai, Shimin, Gallinger, Steven, McPherson, John D, Grimmond, Sean M, Khurana, Ekta, Stein, Lincoln D, Biankin, Andrew V, Schatz, Michael C, Tuveson, David A

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A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours von Hamed, Akram A., Kunz, Daniel J., El-Hamamy, Ibrahim, Trinh, Quang M., Subedar, Omar D., Richards, Laura M., Foltz, Warren, Bullivant, Garrett, Ware, Matthaeus, Vladoiu, Maria C., Zhang, Jiao, Raj, Antony M., Pugh, Trevor J., Taylor, Michael D., Teichmann, Sarah A., Stein, Lincoln D., Simons, Benjamin D., Dirks, Peter B.

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Plasma circulating tumor DNA as a potential tool for disease monitoring in head and neck cancer von Egyud, Matthew, Sridhar, Praveen, Devaiah, Anand, Yamada, Emiko, Saunders, Stefanie, Ståhlberg, Anders, Filges, Stefan, Krzyzanowski, Paul M., Kalatskaya, Irina, Jiao, Wei, Stein, Lincoln D., Jalisi, Scharukh, Godfrey, Tony E.

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