Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs by Körner, Heinz, Sofia, Heidi J, Zumft, Walter G

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iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching by Kuo, Tsung-Ting, Jiang, Xiaoqian, Tang, Haixu, Wang, XiaoFeng, Bath, Tyler, Bu, Diyue, Wang, Lei, Harmanci, Arif, Zhang, Shaojie, Zhi, Degui, Sofia, Heidi J, Ohno-Machado, Lucila

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The Human Pangenome Project: a global resource to map genomic diversity by Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A., Lucas, Julian K., Phillippy, Adam M., Popejoy, Alice B., Asri, Mobin, Carson, Caryn, Chaisson, Mark J. P., Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L., Fulton, Robert S., Garrison, Erik P., Garrison, Nanibaa’ A., Graves-Lindsay, Tina A., Ji, Hanlee, Kenny, Eimear E., Koenig, Barbara A., Li, Daofeng, Marschall, Tobias, McMichael, Joshua F., Novak, Adam M., Purushotham, Deepak, Schneider, Valerie A., Schultz, Baergen I., Smith, Michael W., Sofia, Heidi J., Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H., Paten, Benedict, Jarvis, Erich D., Hall, Ira M., Eichler, Evan E., Haussler, David

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third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family by Staroń, Anna, Sofia, Heidi J, Dietrich, Sascha, Ulrich, Luke E, Liesegang, Heiko, Mascher, Thorsten

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FAVOR: functional annotation of variants online resource and annotator for variation across the human genome by Zhou, Hufeng, Arapoglou, Theodore, Li, Xihao, Li, Zilin, Zheng, Xiuwen, Moore, Jill, Asok, Abhijith, Kumar, Sushant, Blue, Elizabeth E, Buyske, Steven, Cox, Nancy, Felsenfeld, Adam, Gerstein, Mark, Kenny, Eimear, Li, Bingshan, Matise, Tara, Philippakis, Anthony, Rehm, Heidi L, Sofia, Heidi J, Snyder, Grace, Weng, Zhiping, Neale, Benjamin, Sunyaev, Shamil R, Lin, Xihong

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Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and info... by Sofia, H J, Chen, G, Hetzler, B G, Reyes-Spindola, J F, Miller, N E

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The Data Use Ontology to streamline responsible access to human biomedical datasets by Lawson, Jonathan, Cabili, Moran N., Kerry, Giselle, Boughtwood, Tiffany, Thorogood, Adrian, Alper, Pinar, Bowers, Sarion R., Boyles, Rebecca R., Brookes, Anthony J., Brush, Matthew, Burdett, Tony, Clissold, Hayley, Donnelly, Stacey, Dyke, Stephanie O.M., Freeberg, Mallory A., Haendel, Melissa A., Hata, Chihiro, Holub, Petr, Jeanson, Francis, Jene, Aina, Kawashima, Minae, Kawashima, Shuichi, Konopko, Melissa, Kyomugisha, Irene, Li, Haoyuan, Linden, Mikael, Rodriguez, Laura Lyman, Morita, Mizuki, Mulder, Nicola, Muller, Jean, Nagaie, Satoshi, Nasir, Jamal, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura D., Pandya, Ravi N., Parkinson, Helen, Philippakis, Anthony A., Prasser, Fabian, Rambla, Jordi, Reinold, Kathy, Rushton, Gregory A., Saltzman, Andrea, Saunders, Gary, Sofia, Heidi J., Spalding, John D., Swertz, Morris A., Tulchinsky, Ilia, van Enckevort, Esther J., Varma, Susheel, Voisin, Craig, Yamamoto, Natsuko, Yamasaki, Chisato, Zass, Lyndon, Guidry Auvil, Jaime M., Nyrönen, Tommi H., Courtot, Mélanie

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BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment by Chin, Jr, George, Chavarria, Daniel G, Nakamura, Grant C, Sofia, Heidi J

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A Conserved Structural Module Regulates Transcriptional Responses to Diverse Stress Signals in Bacteria by Campbell, Elizabeth A., Greenwell, Roger, Anthony, Jennifer R., Wang, Sheng, Lim, Lionel, Das, Kalyan, Sofia, Heidi J., Donohue, Timothy J., Darst, Seth A.

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Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer by Kim, Jaegil, Bellmunt, Joaquim, Cherniack, Andrew D., Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Shukla, Sachet A., Sanchez-Vega, Francisco, Reuter, Victor E., Sadeghi, Sara, Pedamallu, Chandra Sekhar, Lu, Yiling, Klimczak, Leszek J., Zhang, Jiexin, Choo, Caleb, Leraas, Kristen M., Lichtenberg, Tara M., Schultz, Nicholaus, Getz, Gad, Mills, Gordon B., Al-Ahmadie, Hikmat, Alexopoulou, Iakovina, Ally, Adrian, Beaver, Allison, Bellmunt, Joaquim, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Brooks, Denise, Broom, Bradley M., Bshara, Wiam, Bullman, Susan, Burks, Eric, Carvalho, Benilton S., Carvalho, Andre L., Castro, Mauro A.A., Chagas, Vinicius S., Cherniack, Andrew D., Cortessis, Victoria K., Czerniak, Bogdan A., Daneshmand, Siamak, Dhalla, Noreen, Egea, Sophie C., Engel, Jay, Felau, Ina, Gastier-Foster, Julie M., Getz, Gad, Gordenin, Dmitry A., Hansel, Donna E., Harr, Jodi, Hartmann, Arndt, Hinoue, Toshinori, Jones, Steven J.M., Kahnoski, Richard J., Kasaian, Katayoon, Lai, Phillip H., Lane, Brian R., Liu, Jia, Lolla, Laxmi, Lotan, Yair, Lu, Yiling, Lucchesi, Fabiano R., Mallery, David, Marra, Marco A., Mills, Gordon B., Mungall, Karen L., Ojesina, Akinyemi I., Parekh, Dipen J., Sekhar Pedamallu, Chandra, Pihl, Todd, Rathmell, W. Kimryn, Robertson, A. Gordon, Sadeghi, Sara, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Scapulatempo-Neto, Cristovam, Schuckman, Anne K., Shukla, Sachet A., Simko, Jeff, Sipahimalani, Payal, Sorcini, Andrea, Stoehr, Robert, Su, Xiaoping, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh, Tse, Kane, Wach, Sven, Wang, Zhining, Weinstein, John N., Wise, Lisa, Wong, Tina, Wu, Ye, Zach, Leigh Anne, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Jiexin, Zwarthoff, Ellen C., Weinstein, John N.

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Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma by Carlsen, Rebecca, Chuah, Eric, Clarke, Amanda, Holt, Robert A., Mayo, Michael, Schein, Jacqueline E., Thiessen, Nina, Cheung, Dorothy, Bowlby, Reanne, Shinbrot, Eve, Donehower, Lawrence A., Bowen, Jay, Helsel, Carmen, Leraas, Kristen M., Wise, Lisa, Shih, Juliann, Cherniack, Andrew D., Saksena, Gordon, Pedamallu, Chandra Sekhar, Chin, Lynda, Cho, Juok, Defreitas, Timothy, Meier, Sam, Lawrence, Michael, Hu, Jianhong, Wang, Min, Morton, Donna, Korchina, Viktoriya, Lewis, Lora, Bellair, Michelle, Lee, Sandra, Shmulevich, Ilya, Zhang, Wei, Liu, Yuexin, Iype, Lisa, Makhlouf, Hala, Kakar, Sanjay, Yeh, Matthew M., Kleiner, David E., El-Serag, Hashem B., Mishra, Lopa, Ling, Shiyun, Su, Xiaoping, Chen, Jian, Tong, Pan, Aburatani, Hiroyuki, Tatsuno, Kenji, Seiser, Eric, Gao, Jianjiong, Ochoa, Angelica, Shen, Ronglai, Arora, Arshi, Radenbaugh, Amie, Moore, David D., Totoki, Yasushi, Shibata, Tatsuhiro, Yau, Christina, Slagle, Betty L., Ojesina, Akinyemi I., Koire, Amanda, Hsu, Teng-Kuei, Felau, Ina, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Hutter, Carolyn M., Sofia, Heidi J., Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Wu, Ye, Pihl, Todd, Huang, Mei, Junior, Carlos Gilberto Carlotti, Silva, Orlando de Castro, Ahn, Keun Soo, Moser, Catherine D., Giordano, Thomas J., Crain, Daniel, Curley, Erin, Morris, Scott, Paulauskis, Joseph, Shelton, Candace, Shelton, Troy, Roberts, Lewis R., Hagedorn, Curt H., O'Brien, Daniel R., Perou, Charles M., Skelly, Tara, Veluvolu, Umadevi, Balu, Saianand, Hoyle, Alan P., Jefferys, Stuart R., Meng, Shaowu, Mose, Lisle E., Simons, Janae V., Hoadley, Katherine A., Shen, Hui, Berrios, Mario, Laird, Peter W.

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A draft human pangenome reference by Liao, Wen-Wei, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cook, Daniel E., Cook-Deegan, Robert M., Diekhans, Mark, Ebert, Peter, Fedrigo, Olivier, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Koenig, Barbara A., Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M. D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J. P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict

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Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer by Ciriello, Giovanni, Gatza, Michael L., Wilkerson, Matthew D., Rhie, Suhn K., Pastore, Alessandro, McLellan, Michael, Bowlby, Reanne, Lester, Susan C., Tse, Gary M.K., Chen, Yunn-Yi, Jensen, Kristin, Johnson, Nicole B., Mills, Gordon B., Robertson, Gordon, Benz, Christopher, Sander, Chris, Hoadley, Katherine A., King, Tari A., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Barr, Thomas, Beck, Andrew, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Cherniack, Andrew D., Chin, Lynda, Davidsen, Tanja, Demchok, John A., Dennison, Jennifer B., Ding, Li, Ferguson, Martin L., Gabriel, Stacey B., Gao, JianJiong, Gastier-Foster, Julie M., Gatza, Michael L., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gibson, William J., Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holbrook, Andrea, Hoyle, Alan P., Hu, Hai, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Ju, Zhenlin, Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lin, Pei, Liu, Jia, Liu, Wenbin, Maglinte, Dennis T., Mardis, Elaine, Marra, Marco A., McAllister, Cynthia, McLellan, Michael, Meng, Shaowu, Mills, Gordon B., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Noble, Michael S., Olopade, Olufunmilayo, Perou, Charles M., Saksena, Gordon, Schumacher, Steven E., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Sander, Chris, Sheth, Margi, Shi, Yan, Shih, Juliann, Shelley, Carl Simon, Simons, Janae V., Sofia, Heidi J., Sougnez, Carrie, Sun, Charlie, Van Den Berg, David J., Wan, Yunhu, Wang, Zhining, Wise, Lisa, Wiznerowicz, Maciej, Wu, Junyuan, Yang, Liming, Yau, Christina, Zack, Travis I., Zhang, Hailei, Zhang, Jiashan, Perou, Charles M.

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Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma by Robertson, A. Gordon, Lichtenberg, Tara M., Else, Tobias, Ling, Shiyun, Jefferys, Stuart R., Wenz, Brandon, Korpershoek, Esther, Amelio, Antonio L., Makowski, Liza, Gimenez-Roqueplo, Anne-Paule, Amar, Laurence, Arachchi, Harindra, Asa, Sylvia L., Balasundaram, Miruna, Balu, Saianand, Benz, Christopher, Bodenheimer, Tom, Boice, Lori, Bowen, Jay, Brooks, Denise, Cherniack, Andrew D., Cho, Juok, Cope, Leslie, Danilova, Ludmila, Deutschbein, Timo, Dhalla, Noreen, Eng, Charis, Eschbacher, Jennifer, Fassnacht, Martin, Ferguson, Martin L., Fiddes, Ian, Fishbein, Lauren, Frazer, Scott, Gastier-Foster, Julie M., Getz, Gad, Ghayee, Hans K., Haussler, David, Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holt, Robert A., Huang, Mei, Johnson, Amy R., Jones, Steven J.M., Kebebew, Electron, Korpershoek, Esther, Lee, Darlene, Lerario, Antonio, Leshchiner, Ignaty, Lin, Pei, Liu, Jia, Lolla, Laxmi, Lotan, Yair, Lu, Yiling, Makowski, Liza, Mallery, David, Marra, Marco A., Merino, Maria J., Mete, Ozgur, Meyerson, Matthew, Morris, Scott, Mose, Lisle E., Naresh, Rashi, Newton, Yulia, Ng, Sam, Ni, Ying, Pacak, Karel, Paul, Evan, Penny, Robert, Pihl, Todd, Rao, Arjun, Roach, Jeffrey, Salama, Sofie, Saller, Charles, Sandusky, George, Sbiera, Silviu, Schein, Jacqueline E., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Sokolov, Artem, Soloway, Matthew G., Thorne, Leigh B., Timmers, Henri J., Tse, Kane, van Berkel, Anouk, Veluvolu, Umadevi, Voet, Doug, Wan, Yunhu, Wang, Tracy S., Weinstein, John N., Wenz, Brandon, Wilkerson, Matthew D., Wise, Lisa, Wong, Christopher, Zhang, Jiashan (Julia), Zhu, Jingchun, Zmuda, Erik, Pacak, Karel, Wilkerson, Matthew D.

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Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer by Wang, Yumeng, Xu, Xiaoyan, Maglic, Dejan, Dill, Michael T, Mojumdar, Kamalika, Ng, Patrick Kwok-Shing, Jeong, Kang Jin, Tsang, Yiu Huen, Moreno, Daniela, Bhavana, Venkata Hemanjani, Peng, Xinxin, Ge, Zhongqi, Chen, Hu, Li, Jun, Chen, Zhongyuan, Zhang, Huiwen, Han, Leng, Du, Di, Creighton, Chad J, Mills, Gordon B, Camargo, Fernando, Liang, Han

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Pangenome graph construction from genome alignments with Minigraph-Cactus by Hickey, Glenn, Monlong, Jean, Ebler, Jana, Novak, Adam M., Eizenga, Jordan M., Gao, Yan, Marschall, Tobias, Li, Heng, Paten, Benedict

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Integrated Molecular Characterization of Uterine Carcinosarcoma by Cherniack, Andrew D., Murray, Bradley A., Hu, Xin, Ling, Shiyun, Soslow, Robert A., Zuna, Rosemary E., Laird, Peter W., Kucherlapati, Raju, Mills, Gordon B., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Bodenheimer, Tom, Bogomolniy, Faina, Brooks, Denise, Carlsen, Rebecca, Cherniack, Andrew D., Cho, Juok, Chuah, Eric, Chudamani, Sudha, David, Mutch, Ferguson, Martin L., Frick, Jessica, Gabriel, Stacey, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gupta, Manaswi, Heiman, David I., Hess, Julian, Hoffmann, Robert, Holt, Robert A., Hu, Xin, Hutter, Carolyn M., Jefferys, Stuart R., Kanchi, Rupa S., Kandoth, Cyriac, Kerr, Sarah, Kim, Jaegil, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Leshchiner, Ignaty, Levine, Douglas A., Lichtenberg, Tara M., Ling, Shiyun, Liu, Jia, Liu, Wenbin, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Moore, Richard A., Mose, Lisle E., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Parker, Joel S., Perou, Charles M., Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Salvesen, Helga B., Sheth, Margi, Shi, Yan, Shih, Juliann, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Sun, Charlie, Tan, Donghui, Tarnuzzer, Roy, Thorne, Leigh B., Tseng, Jill, Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Wan, Yunhu, Wang, Chen, Weisenberger, Daniel J., Wilkerson, Matthew D., Winterhoff, Boris, Wong, Tina, Yang, Liming, Zhang, Hailei, Zhu, Jing-chun, Zuna, Rosemary E., Weinstein, John N.

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Recombination between heterologous human acrocentric chromosomes by Guarracino, Andrea, Buonaiuto, Silvia, de Lima, Leonardo Gomes, Potapova, Tamara, Rhie, Arang, Koren, Sergey, Rubinstein, Boris, Fischer, Christian, Gerton, Jennifer L., Phillippy, Adam M., Colonna, Vincenza, Garrison, Erik

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Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family by Buchko, Garry W, Sofia, Heidi J

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Increased mutation and gene conversion within human segmental duplications by Vollger, Mitchell R., Dishuck, Philip C., Harvey, William T., DeWitt, William S., Guitart, Xavi, Goldberg, Michael E., Rozanski, Allison N., Lucas, Julian, Asri, Mobin, Munson, Katherine M., Lewis, Alexandra P., Hoekzema, Kendra, Logsdon, Glennis A., Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, Eichler, Evan E.

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