Search Results - "Goldman, Mary"

Reviewers: intercept weaponization of genetics by Goldman, Mary J.

“…Letter to the Editor…”
Get full text

Visualizing and interpreting cancer genomics data via the Xena platform by Goldman, Mary J., Craft, Brian, Hastie, Mim, Repečka, Kristupas, McDade, Fran, Kamath, Akhil, Banerjee, Ayan, Luo, Yunhai, Rogers, Dave, Brooks, Angela N., Zhu, Jingchun, Haussler, David

Get full text

The UCSC Cancer Genomics Browser: update 2015 by Goldman, Mary, Craft, Brian, Swatloski, Teresa, Cline, Melissa, Morozova, Olena, Diekhans, Mark, Haussler, David, Zhu, Jingchun

“…The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization,…”
Get full text

Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser by Cline, Melissa S., Craft, Brian, Swatloski, Teresa, Goldman, Mary, Ma, Singer, Haussler, David, Zhu, Jingchun

“…The UCSC Cancer Genomics Browser ( https://genome-cancer.ucsc.edu ) offers interactive visualization and exploration of TCGA genomic, phenotypic and clinical…”
Get full text

The UCSC Genome Browser database: extensions and updates 2013 by Meyer, Laurence R, Zweig, Ann S, Hinrichs, Angie S, Karolchik, Donna, Kuhn, Robert M, Wong, Matthew, Sloan, Cricket A, Rosenbloom, Kate R, Roe, Greg, Rhead, Brooke, Raney, Brian J, Pohl, Andy, Malladi, Venkat S, Li, Chin H, Lee, Brian T, Learned, Katrina, Kirkup, Vanessa, Hsu, Fan, Heitner, Steve, Harte, Rachel A, Haeussler, Maximilian, Guruvadoo, Luvina, Goldman, Mary, Giardine, Belinda M, Fujita, Pauline A, Dreszer, Timothy R, Diekhans, Mark, Cline, Melissa S, Clawson, Hiram, Barber, Galt P, Haussler, David, Kent, W James

“…The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence…”
Get full text

The UCSC Cancer Genomics Browser: update 2013 by Goldman, Mary, Craft, Brian, Swatloski, Teresa, Ellrott, Kyle, Cline, Melissa, Diekhans, Mark, Ma, Singer, Wilks, Chris, Stuart, Josh, Haussler, David, Zhu, Jingchun

“…The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its…”
Get full text

A user guide for the online exploration and visualization of PCAWG data by Goldman, Mary J., Zhang, Junjun, Fonseca, Nuno A., Cortés-Ciriano, Isidro, Xiang, Qian, Craft, Brian, Piñeiro-Yáñez, Elena, O’Connor, Brian D., Bazant, Wojciech, Barrera, Elisabet, Muñoz-Pomer, Alfonso, Petryszak, Robert, Füllgrabe, Anja, Al-Shahrour, Fatima, Keays, Maria, Haussler, David, Weinstein, John N., Huber, Wolfgang, Valencia, Alfonso, Park, Peter J., Papatheodorou, Irene, Zhu, Jingchun, Ferretti, Vincent, Vazquez, Miguel

“…The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the…”
Get full text

Best practices to evaluate the impact of biomedical research software—metric collection beyond citations by Afiaz, Awan, Ivanov, Andrey A, Chamberlin, John, Hanauer, David, Savonen, Candace L, Goldman, Mary J, Morgan, Martin, Reich, Michael, Getka, Alexander, Holmes, Aaron, Pati, Sarthak, Knight, Dan, Boutros, Paul C, Bakas, Spyridon, Caporaso, J Gregory, Del Fiol, Guilherme, Hochheiser, Harry, Haas, Brian, Schloss, Patrick D, Eddy, James A, Albrecht, Jake, Fedorov, Andrey, Waldron, Levi, Hoffman, Ava M, Bradshaw, Richard L, Leek, Jeffrey T, Wright, Carrie

“…Abstract Motivation Software is vital for the advancement of biology and medicine. Impact evaluations of scientific software have primarily emphasized…”
Get full text

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2 by Cline, Melissa S, Liao, Rachel G, Parsons, Michael T, Paten, Benedict, Alquaddoomi, Faisal, Antoniou, Antonis, Baxter, Samantha, Brody, Larry, Cook-Deegan, Robert, Coffin, Amy, Couch, Fergus J, Craft, Brian, Currie, Robert, Dlott, Chloe C, Dolman, Lena, den Dunnen, Johan T, Dyke, Stephanie O M, Domchek, Susan M, Easton, Douglas, Fischmann, Zachary, Foulkes, William D, Garber, Judy, Goldgar, David, Goldman, Mary J, Goodhand, Peter, Harrison, Steven, Haussler, David, Kato, Kazuto, Knoppers, Bartha, Markello, Charles, Nussbaum, Robert, Offit, Kenneth, Plon, Sharon E, Rashbass, Jem, Rehm, Heidi L, Robson, Mark, Rubinstein, Wendy S, Stoppa-Lyonnet, Dominique, Tavtigian, Sean, Thorogood, Adrian, Zhang, Can, Zimmermann, Marc, Burn, John, Chanock, Stephen, Rätsch, Gunnar, Spurdle, Amanda B

“…The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data…”
Get full text

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway by Carrot-Zhang, Jian, Yao, Xiaotong, Devarakonda, Siddhartha, Deshpande, Aditya, Damrauer, Jeffrey S., Silva, Tiago Chedraoui, Wong, Christopher K., Choi, Hyo Young, Felau, Ina, Robertson, A. Gordon, Castro, Mauro A.A., Bao, Lisui, Rheinbay, Esther, Liu, Eric Minwei, Trieu, Tuan, Haan, David, Yau, Christina, Hinoue, Toshinori, Liu, Yuexin, Shapira, Ofer, Kumar, Kiran, Mungall, Karen L., Zhang, Hailei, Lee, Jake June-Koo, Berger, Ashton, Gao, Galen F., Zhitomirsky, Binyamin, Liang, Wen-Wei, Zhou, Meng, Moorthi, Sitapriya, Berger, Alice H., Collisson, Eric A., Zody, Michael C., Ding, Li, Cherniack, Andrew D., Getz, Gad, Elemento, Olivier, Benz, Christopher C., Stuart, Josh, Zenklusen, J.C., Beroukhim, Rameen, Chang, Jason C., Campbell, Joshua D., Hayes, D. Neil, Yang, Lixing, Laird, Peter W., Weinstein, John N., Kwiatkowski, David J., Tsao, Ming S., Travis, William D., Khurana, Ekta, Berman, Benjamin P., Hoadley, Katherine A., Robine, Nicolas, Arora, Kanika, Shah, Minita, Shelton, Jennifer, Bowlby, Reanne, Friedl, Verena, Goldman, Mary, Craft, Brian, Heiman, David I., Hajirasouliha, Iman, Ricketts, Camir, Anur, Pavana, Chiotti, Kami E., Caesar-Johnson, Samantha J., Demchok, John A., Ferguson, Martin L., Kemal, Anab, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Spellman, Paul T., Raphael, Benjamin, Akbani, Rehan, Zhu, Jingchun, Jones, Steven J.M., Shen, Hui, Meyerson, Matthew, Govindan, Ramaswamy, Imielinski, Marcin

“…RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to…”
Get full text

UCSC cancer genomics browser: update 2011 by Sanborn, J. Zachary, Benz, Stephen C, Craft, Brian, Szeto, Christopher, Kober, Kord M, Meyer, Laurence, Vaske, Charles J, Goldman, Mary, Smith, Kayla E, Kuhn, Robert M, Karolchik, Donna, Kent, W. James, Stuart, Joshua M, Haussler, David, Zhu, Jingchun

“…The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and…”
Get full text

Discovery and antibacterial activity of glabramycin A–C from Neosartorya glabra by an antisense strategy by Jayasuriya, Hiranthi, Zink, Deborah, Basilio, Angela, Vicente, Francisca, Collado, Javier, Bills, Gerald, Goldman, Mary Lee, Motyl, Mary, Huber, Joann, Dezeny, Gabe, Byrne, Kevin, Singh, Sheo B

“…Treatment of drug-resistant bacteria is a significant unmet medical need. This challenge can be met only by the discovery and development of new antibiotics…”
Get full text

Making Tools that People Will Use: User-Centered Design in Computational Biology Research by Goldman, Mary, Gehlenborg, Nils

“…User-Centered Design (UCD) focuses on deeply understanding the needs of users and ensuring these needs are met by tools and software. UCD methodology aims to…”
Get more information

Toil enables reproducible, open source, big biomedical data analyses by Vivian, John, Rao, Arjun Arkal, Nothaft, Frank Austin, Ketchum, Christopher, Armstrong, Joel, Novak, Adam, Pfeil, Jacob, Narkizian, Jake, Deran, Alden D, Musselman-Brown, Audrey, Schmidt, Hannes, Amstutz, Peter, Craft, Brian, Goldman, Mary, Rosenbloom, Kate, Cline, Melissa, O'Connor, Brian, Hanna, Megan, Birger, Chet, Kent, W James, Patterson, David A, Joseph, Anthony D, Zhu, Jingchun, Zaranek, Sasha, Getz, Gad, Haussler, David, Paten, Benedict

Get full text

Abstract 911: UCSC Xena for cancer genomics visualization and interpretation by Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David

“…Abstract UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic…”
Get full text

Abstract 2274: Cancer genomics visualization and interpretation using UCSC Xena by Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David

“…Abstract The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize functional genomics data. Our…”
Get full text

Abstract 7406: Visualization and analysis of cancer genomics data using UCSC Xena by Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David

“…Abstract UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic…”
Get full text

Abstract 2584: The UCSC Xena system for cancer genomics data visualization and interpretation by Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David

“…Abstract The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize their private functional…”
Get full text

Abstract 2066: Visualization and analysis of cancer genomics data using UCSC Xena by Goldman, Mary, Craft, Brian, Zhu, Jingchun, Haussler, David

“…Abstract UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic…”
Get full text

UCSC Genome Browser database: update 2011 by Fujita, Pauline A, Rhead, Brooke, Zweig, Ann S, Hinrichs, Angie S, Karolchik, Donna, Cline, Melissa S, Goldman, Mary, Barber, Galt P, Clawson, Hiram, Coelho, Antonio, Diekhans, Mark, Dreszer, Timothy R, Giardine, Belinda M, Harte, Rachel A, Hillman-Jackson, Jennifer, Hsu, Fan, Kirkup, Vanessa, Kuhn, Robert M, Learned, Katrina, Li, Chin H, Meyer, Laurence R, Pohl, Andy, Raney, Brian J, Rosenbloom, Kate R, Smith, Kayla E, Haussler, David, Kent, W. James

“…The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for…”
Get full text