Genomic profiling of mycosis fungoides identifies patients at high risk of disease progression

Authors: Fléchon, Léa, Arib, Inès, Dutta, Ankit K., Hasan Bou Issa, Lama, Sklavenitis-Pistofidis, Romanos, Tilmont, Rémi, Stewart, Chip, Dubois, Romain, Poulain, Stéphanie, Copin, Marie-Christine, Javed, Sahir, Nudel, Morgane, Cavalieri, Doriane, Escure, Guillaume, Gower, Nicolas, Chauvet, Paul, Gazeau, Nicolas, Saade, Cynthia, Thiam, Marietou Binta, Ouelkite-Oumouchal, Aïcha, Gaggero, Silvia, Cailliau, Émeline, Faiz, Sarah, Carpentier, Olivier, Duployez, Nicolas, Idziorek, Thierry, Mortier, Laurent, Figeac, Martin, Preudhomme, Claude, Quesnel, Bruno, Mitra, Suman, Morschhauser, Franck, Getz, Gad, Ghobrial, Irene M., Manier, Salomon

Source: In Blood Advances 25 June 2024 8(12):3109-3119

DLBclass: a probabilistic molecular classifier to guide clinical investigation and practice in diffuse large B-cell lymphoma

Authors: Chapuy, Björn ^{1, 2, 3, 7, ∗}, Wood, Timothy ⁴, Stewart, Chip ⁴, Dunford, Andrew ⁴, Wienand, Kirsty ^{1, 4}, Khan, Sumbul Jawed ¹, Serin, Nazli ³, Wang, Meng ³, Calabretta, Eleonora ¹, Shimono, Joji ³, Van Seters, Samantha ⁴, Wisemann, Sam ⁴, Belkin, Saveliy ⁴, Heimann, David ⁴, Redd, Robert ⁵, Shipp, Margaret A. ^{1, 2, ∗∗}, Getz, Gad ^{2, 4, 6, ∗∗∗}

Source: In Blood December 2024

Optimizing Event Selection with the Random Grid Search

Authors: Bhat, Pushpalatha C., Prosper, Harrison B., Sekmen, Sezen, Stewart, Chip

Source: Published in Comput.Phys.Commun. 228 (2018) 245-257

Subject Terms: High Energy Physics - Phenomenology

Access URL: http://arxiv.org/abs/1706.09907

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

Authors: Yizhak, Keren, Aguet, François, Kim, Jaegil, Hess, Julian M., Kübler, Kirsten, Grimsby, Jonna, Frazer, Ruslana, Zhang, Hailei, Haradhvala, Nicholas J., Rosebrock, Daniel, Livitz, Dimitri, Li, Xiao, Arich-Landkof, Eila, Shoresh, Noam, Stewart, Chip, Segrè, Ayellet V., Branton, Philip A., Polak, Paz, Ardlie, Kristin G., Getz, Gad

Source: Science, 2019 Jun 01. 364(6444), 970-970.

Access URL: https://www.jstor.org/stable/26681536

MOSAIK: A hash-based algorithm for accurate next-generation sequencing read mapping

Authors: Lee, Wan-Ping, Stromberg, Michael, Ward, Alistair, Stewart, Chip, Garrison, Erik, Marth, Gabor T.

Subject Terms: Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1309.1149

Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade

Authors: Chapuy, Bjoern ^{1, 2, *}, Stewart, Chip ^{3, *}, Dunford, Andrew J. ^{3, *}, Kim, Jaegil ³, Wienand, Kirsty ¹, Kamburov, Atanas ³, Griffin, Gabriel K. ⁴, Chen, Pei-Hsuan ⁴, Lako, Ana ⁴, Redd, Robert A. ⁵, Cote, Claire M. ¹, Ducar, Matthew D. ⁶, Thorner, Aaron R. ⁶, Rodig, Scott J. ⁴, Getz, Gad ^{3, 7, 8, †}, Shipp, Margaret A. ^{1, †}

Source: In Blood 26 December 2019 134(26):2369-2382

Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion

Authors: Wienand, Kirsty ^*, Chapuy, Bjoern ^*, Stewart, Chip ^*, Dunford, Andrew J. ^*, Wu, David ^*, Kim, Jaegil, Kamburov, Atanas, Wood, Timothy R., Cader, Fathima Zumla, Ducar, Matthew D., Thorner, Aaron R., Nag, Anwesha, Heubeck, Alexander T., Buonopane, Michael J., Redd, Robert A., Bojarczuk, Kamil, Lawton, Lee N., Armand, Philippe, Rodig, Scott J., Fromm, Jonathan R., Getz, Gad, Shipp, Margaret A.

Source: In Blood Advances 10 December 2019 3(23):4065-4080

Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma

Authors: Gopal, Raj K., Kübler, Kirsten, Calvo, Sarah E., Polak, Paz, Livitz, Dimitri, Rosebrock, Daniel, Sadow, Peter M., Campbell, Braidie, Donovan, Samuel E., Amin, Salma, Gigliotti, Benjamin J., Grabarek, Zenon, Hess, Julian M., Stewart, Chip, Braunstein, Lior Z., Arndt, Peter F., Mordecai, Scott, Shih, Angela R., Chaves, Frances, Zhan, Tiannan, Lubitz, Carrie C., Kim, Jiwoong, Iafrate, A. John, Wirth, Lori, Parangi, Sareh, Leshchiner, Ignaty, Daniels, Gilbert H., Mootha, Vamsi K., Dias-Santagata, Dora, Getz, Gad, McFadden, David G.

Source: In Cancer Cell 13 August 2018 34(2):242-255

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

Authors: Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Angulo Gonzalez, Ana Maria, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Mora Pinero, Edna M., Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Jr., Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Ellrott, Kyle, Bailey, Matthew H., Covington, Kyle R., Stewart, Chip, Ma, Singer, Chiotti, Kami E., McLellan, Michael, Hutter, Carolyn, Wheeler, David

Source: In Cell Systems 28 March 2018 6(3):271-281

A (fire)cloud-based DNA methylation data preprocessing and quality control platform

Authors: Kangeyan, Divy, Dunford, Andrew, Iyer, Sowmya, Stewart, Chip, Hanna, Megan, Getz, Gad, Aryee, Martin

Source: BMC bioinformatics. 20(1):1-5

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100186579156.0x000001&indx=1&recIds=ETOCvdc_100186579156.0x000001

Growth dynamics in naturally progressing chronic lymphocytic leukaemia

Authors: Gruber, Michaela, Bozic, Ivana, Leshchiner, Ignaty, Livitz, Dimitri, Stevenson, Kristen, Rassenti, Laura, Rosebrock, Daniel, Taylor-Weiner, Amaro, Olive, Oriol, Goyetche, Reaha, Fernandes, Stacey, Sun, Jing, Stewart, Chip, Wong, Alicia, Cibulskis, Carrie, Zhang, Wandi, Reiter, Johannes, Gerold, Jeffrey, Gribben, John, Rai, Kanti, Keating, Michael, Brown, Jennifer, Neuberg, Donna, Kipps, Thomas, Nowak, Martin, Getz, Gad, Wu, Catherine

Source: Nature. 570(7762):474-479

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181255693.0x000001&indx=1&recIds=ETOCvdc_100181255693.0x000001

Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma

Authors: Raphael, Benjamin J., Hruban, Ralph H., Aguirre, Andrew J., Moffitt, Richard A., Yeh, Jen Jen, Stewart, Chip, Robertson, A. Gordon, Cherniack, Andrew D., Gupta, Manaswi, Getz, Gad, Gabriel, Stacey B., Meyerson, Matthew, Cibulskis, Carrie, Fei, Suzanne S., Hinoue, Toshinori, Shen, Hui, Laird, Peter W., Ling, Shiyun, Lu, Yiling, Mills, Gordon B., Akbani, Rehan, Loher, Phillipe, Londin, Eric R., Rigoutsos, Isidore, Telonis, Aristeidis G., Gibb, Ewan A., Goldenberg, Anna, Mezlini, Aziz M., Hoadley, Katherine A., Collisson, Eric, Lander, Eric, Murray, Bradley A., Hess, Julian, Rosenberg, Mara, Bergelson, Louis, Zhang, Hailei, Cho, Juok, Tiao, Grace, Kim, Jaegil, Livitz, Dimitri, Leshchiner, Ignaty, Reardon, Brendan, Van Allen, Eliezer, Kamburov, Atanas, Beroukhim, Rameen, Saksena, Gordon, Schumacher, Steven E., Noble, Michael S., Heiman, David I., Gehlenborg, Nils, Lawrence, Michael S., Adsay, Volkan, Petersen, Gloria, Klimstra, David, Bardeesy, Nabeel, Leiserson, Mark D.M., Bowlby, Reanne, Kasaian, Katayoon, Birol, Inanc, Mungall, Karen L., Sadeghi, Sara, Weinstein, John N., Spellman, Paul T., Liu, Yuexin, Amundadottir, Laufey T., Tepper, Joel, Singhi, Aatur D., Dhir, Rajiv, Paul, Drwiega, Smyrk, Thomas, Zhang, Lizhi, Kim, Paula, Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Gerken, Mark, Lau, Kevin, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Renkel, Jeremy, Sherman, Mark, Wise, Lisa, Yena, Peggy, Zmuda, Erik, Shih, Juliann, Ally, Adrian, Balasundaram, Miruna, Carlsen, Rebecca, Chu, Andy, Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Holt, Robert A., Jones, Steven J.M., Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Brooks, Denise, Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Hayes, D. Neil, Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Charles M., Perou, Amy H., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Parker, Joel S., Wilkerson, Matthew D., Korkut, Anil, Senbabaoglu, Yasin, Burch, Patrick, McWilliams, Robert, Chaffee, Kari, Oberg, Ann, Zhang, Wei, Gingras, Marie-Claude, Wheeler, David A., Xi, Liu, Albert, Monique, Bartlett, John, Sekhon, Harman, Stephen, Yeager, Howard, Zaren, Judy, Miller, Breggia, Anne, Shroff, Rachna T., Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Jennifer, Smith, Roggin, Kevin, Becker, Karl-Friedrich, Behera, Madhusmita, Bennett, Joseph, Boice, Lori, Burks, Eric, Carlotti Junior, Carlos Gilberto, Chabot, John, Pretti da Cunha Tirapelli, Daniela, Sebastião dos Santos, Jose, Dubina, Michael, Eschbacher, Jennifer, Huang, Mei, Huelsenbeck-Dill, Lori, Jenkins, Roger, Karpov, Alexey, Kemp, Rafael, Lyadov, Vladimir, Maithel, Shishir, Manikhas, Georgy, Montgomery, Eric, Noushmehr, Houtan, Osunkoya, Adeboye, Owonikoko, Taofeek, Paklina, Oxana, Potapova, Olga, Ramalingam, Suresh, Rathmell, W. Kimryn, Rieger-Christ, Kimberly, Saller, Charles, Setdikova, Galiya, Shabunin, Alexey, Sica, Gabriel, Su, Tao, Sullivan, Travis, Swanson, Pat, Tarvin, Katherine, Tavobilov, Michael, Thorne, Leigh B., Urbanski, Stefan, Voronina, Olga, Wang, Timothy, Crain, Daniel, Curley, Erin, Gardner, Johanna, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Janssen, Klaus-Peter, Bathe, Oliver, Bahary, Nathan, Slotta-Huspenina, Julia, Johns, Amber, Hibshoosh, Hanina, Hwang, Rosa F., Sepulveda, Antonia, Radenbaugh, Amie, Baylin, Stephen B., Berrios, Mario, Bootwalla, Moiz S., Holbrook, Andrea, Lai, Phillip H., Maglinte, Dennis T., Mahurkar, Swapna, Triche, Timothy J., Jr., Van Den Berg, David J., Weisenberger, Daniel J., Chin, Lynda, Kucherlapati, Raju, Kucherlapati, Melanie, Pantazi, Angeliki, Park, Peter, Voet, Doug, Lin, Pei, Frazer, Scott, Defreitas, Timothy, Meier, Sam, Kwon, Sun Young, Kim, Yong Hoon, Park, Sang-Jae, Han, Sung-Sik, Kim, Seong Hoon, Kim, Hark, Furth, Emma, Tempero, Margaret, Sander, Chris, Biankin, Andrew, Chang, David, Bailey, Peter, Gill, Anthony, Kench, James, Grimmond, Sean, Cancer Genome Initiative (APGI, Australian Pancreatic, Postier, Russell, Zuna, Rosemary, Sicotte, Hugues, Demchok, John A., Ferguson, Martin L., Hutter, Carolyn M., Mills Shaw, Kenna R., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zhang, Jiashan (Julia), Felau, Ina, Zenklusen, Jean C.

Source: In Cancer Cell 14 August 2017 32(2):185-203

Sporadic Early-Onset Diffuse Gastric Cancers Have High Frequency of Somatic CDH1 Alterations, but Low Frequency of Somatic RHOA Mutations Compared With Late-Onset Cancers

Authors: Cho, Soo Young, Park, Jun Won, Liu, Yang, Park, Young Soo, Kim, Ju Hee, Yang, Hanna, Um, Hyejin, Ko, Woo Ri, Lee, Byung Il, Kwon, Sun Young, Ryu, Seung Wan, Kwon, Chae Hwa, Park, Do Youn, Lee, Jae-Hyuk, Lee, Sang Il, Song, Kyu Sang, Hur, Hoon, Han, Sang-Uk, Chang, Heekyung, Kim, Su-Jin, Kim, Byung-Sik, Yook, Jeong-Hwan, Yoo, Moon-Won, Kim, Beom-Su, Lee, In-Seob, Kook, Myeong-Cherl, Thiessen, Nina, He, An, Stewart, Chip, Dunford, Andrew, Kim, Jaegil, Shih, Juliann, Saksena, Gordon, Cherniack, Andrew D., Schumacher, Steven, Weiner, Amaro-Taylor, Rosenberg, Mara, Getz, Gad, Yang, Eun Gyeong, Ryu, Min-Hee, Bass, Adam J., Kim, Hark Kyun

Source: In Gastroenterology August 2017 153(2):536-549

Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident.

Authors: Morton, Lindsay M., Lee, Olivia W., Karyadi, Danielle M., Bogdanova, Tetiana I., Stewart, Chip, Hartley, Stephen W., Breeze, Charles E., Schonfeld, Sara J., Cahoon, Elizabeth K., Drozdovitch, Vladimir, Masiuk, Sergii, Chepurny, Mykola, Zurnadzhy, Liudmyla Yu, Dai, Jieqiong, Krznaric, Marko, Yeager, Meredith, Hutchinson, Amy, Hicks, Belynda D., Dagnall, Casey L., Steinberg, Mia K.

Source: Nature Communications; 6/13/2024, Vol. 15 Issue 1, p1-18, 18p

Subject Terms: IODINE isotopes, LYMPHATIC metastasis, PAPILLARY carcinoma, THYROID cancer, GENETIC profile, GENOMICS

Integrated Molecular Characterization of Uterine Carcinosarcoma

Authors: Akbani, Rehan, Ally, Adrian, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Beroukhim, Rameen, Bodenheimer, Tom, Bogomolniy, Faina, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Broaddus, Russell, Brooks, Denise, Carlsen, Rebecca, Cherniack, Andrew D., Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Kristian, Cline, Melissa, Dao, Fanny, David, Mutch, Demchok, John A., Dhalla, Noreen, Dowdy, Sean, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Frick, Jessica, Gabriel, Stacey, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gupta, Manaswi, Haussler, David, Hayes, D. Neil, Heiman, David I., Hess, Julian, Hoadley, Katherine A., Hoffmann, Robert, Holt, Robert A., Hoyle, Alan P., Hu, Xin, Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Jones, Corbin D., Kanchi, Rupa S., Kandoth, Cyriac, Kasaian, Katayoon, Kerr, Sarah, Kim, Jaegil, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Leraas, Kristen M., Leshchiner, Ignaty, Levine, Douglas A., Lichtenberg, Tara M., Lin, Pei, Ling, Shiyun, Liu, Jia, Liu, Wenbin, Liu, Yuexin, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., Olvera, Narciso, Parker, Joel S., Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Salvesen, Helga B., Schein, Jacqueline E., Schumacher, Steven E., Shen, Hui, Sheth, Margi, Shi, Yan, Shih, Juliann, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Soslow, Robert A., Sougnez, Carrie, Stewart, Chip, Sun, Charlie, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Tse, Kane, Tseng, Jill, Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, von Bismarck, Amanda, Walter, Vonn, Wan, Yunhu, Wang, Zhining, Wang, Chen, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Winterhoff, Boris, Wise, Lisa, Wong, Tina, Wu, Ye, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Hailei, Zhang, Wei, Zhu, Jing-chun, Zmuda, Erik, Zuna, Rosemary E., Broaddus, Russell R., Robertson, Gordon, Kucherlapati, Raju, Zhang, Jiashan

Source: In Cancer Cell 13 March 2017 31(3):411-423

Optimizing event selection with the random grid search

Authors: Bhat, Pushpalatha C., Prosper, Harrison B., Sekmen, Sezen, Stewart, Chip

Source: Computer physics communications. 228:245-257

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100076714787.0x000001&indx=1&recIds=ETOCvdc_100076714787.0x000001

SvABA: genome-wide detection of structural variants and indels by local assembly

Authors: Wala, Jeremiah A., Bandopadhayay, Pratiti, Greenwald, Noah F., O Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong

Source: Genome research. 28(4):581-591

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN615549137&indx=1&recIds=ETOCRN615549137

DeTiN: overcoming tumor-in-normal contamination

Authors: Taylor-Weiner, Amaro, Stewart, Chip, Giordano, Thomas, Miller, Mendy, Rosenberg, Mara, Macbeth, Alyssa, Lennon, Niall, Rheinbay, Esther, Landau, Dan-Avi, Wu, Catherine, Getz, Gad

Source: Nature methods. 15(7):531-534

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100171361081.0x000001&indx=1&recIds=ETOCvdc_100171361081.0x000001

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

Authors: Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Lander, Eric S., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A.

Source: In Cell Reports 26 April 2016 15(4):857-865

Targetable genetic features of primary testicular and primary central nervous system lymphomas

Authors: Chapuy, Bjoern ^*, Roemer, Margaretha G.M. ^*, Stewart, Chip, Tan, Yuxiang, Abo, Ryan P., Zhang, Liye, Dunford, Andrew J., Meredith, David M., Thorner, Aaron R., Jordanova, Ekaterina S., Liu, Gang, Feuerhake, Friedrich, Ducar, Matthew D., Illerhaus, Gerald, Gusenleitner, Daniel, Linden, Erica A., Sun, Heather H., Homer, Heather, Aono, Miyuki, Pinkus, Geraldine S., Ligon, Azra H., Ligon, Keith L., Ferry, Judith A., Freeman, Gordon J., van Hummelen, Paul, Golub, Todd R., Getz, Gad, Rodig, Scott J., de Jong, Daphne, Monti, Stefano, Shipp, Margaret A. ^*

Source: In Blood 16 February 2016 127(7):869-881