Search Results - "Ketchum, Karen A"

The CPTAC Data Portal: A Resource for Cancer Proteomics Research by Edwards, Nathan J., Oberti, Mauricio, Thangudu, Ratna R., Cai, Shuang, McGarvey, Peter B., Jacob, Shine, Madhavan, Subha, Ketchum, Karen A.

“…The Clinical Proteomic Tumor Analysis Consortium (CPTAC), under the auspices of the National Cancer Institute’s Office of Cancer Clinical Proteomics Research,…”
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A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline by Rudnick, Paul A, Markey, Sanford P, Roth, Jeri, Mirokhin, Yuri, Yan, Xinjian, Tchekhovskoi, Dmitrii V, Edwards, Nathan J, Thangudu, Ratna R, Ketchum, Karen A, Kinsinger, Christopher R, Mesri, Mehdi, Rodriguez, Henry, Stein, Stephen E

“…The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples…”
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Li-Fraumeni Exploration Consortium Data Coordinating Center: Building an Interactive Web-Based Resource for Collaborative International Cancer Epidemiology Research for a Rare Condition by Mai, Phuong L, Sand, Sharon R, Saha, Neiladri, Oberti, Mauricio, Dolafi, Tom, DiGianni, Lisa, Root, Elizabeth J, Kong, Xianhua, Bremer, Renee C, Santiago, Karina M, Bojadzieva, Jasmina, Barley, Derek, Novokmet, Ana, Ketchum, Karen A, Nguyen, Ngoc, Jacob, Shine, Nichols, Kim E, Kratz, Christian P, Schiffman, Joshua D, Evans, D Gareth, Achatz, Maria Isabel, Strong, Louise C, Garber, Judy E, Ladwa, Sweta A, Malkin, David, Weitzel, Jeffrey N

“…The success of multisite collaborative research relies on effective data collection, harmonization, and aggregation strategies. Data Coordination Centers (DCC)…”
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Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts by Tabb, David L, Wang, Xia, Carr, Steven A, Clauser, Karl R, Mertins, Philipp, Chambers, Matthew C, Holman, Jerry D, Wang, Jing, Zhang, Bing, Zimmerman, Lisa J, Chen, Xian, Gunawardena, Harsha P, Davies, Sherri R, Ellis, Matthew J. C, Li, Shunqiang, Townsend, R. Reid, Boja, Emily S, Ketchum, Karen A, Kinsinger, Christopher R, Mesri, Mehdi, Rodriguez, Henry, Liu, Tao, Kim, Sangtae, McDermott, Jason E, Payne, Samuel H, Petyuk, Vladislav A, Rodland, Karin D, Smith, Richard D, Yang, Feng, Chan, Daniel W, Zhang, Bai, Zhang, Hui, Zhang, Zhen, Zhou, Jian-Ying, Liebler, Daniel C

“…The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing…”
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Comparative genomics and understanding of microbial biology by Fraser, C M, Eisen, J, Fleischmann, R D, Ketchum, K A, Peterson, S

“…The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in…”
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The first genome from the third domain of life by Clayton, Rebecca A, White, Owen, Ketchum, Karen A, Venter, J. Craig

“…Life-forms on earth are divided into three domains, Eubacteria, Archaea and Eukarya. A complete genomic sequence of the first two was published in 1995 and…”
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NCI's Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data by Thangudu, Ratna R, Holck, Michael, Singhal, Deepak, Pilozzi, Alexander, Edwards, Nathan, Rudnick, Paul A, Domagalski, Marcin J, Chilappagari, Padmini, Ma, Lei, Xin, Yi, Le, Toan, Nyce, Kristen, Chaudhary, Rekha, Ketchum, Karen A, Maurais, Aaron, Connolly, Brian, Riffle, Michael, Chambers, Matthew C, MacLean, Brendan, MacCoss, Michael J, McGarvey, Peter B, Basu, Anand, Otridge, John, Casas-Silva, Esmeralda, Venkatachari, Sudha, Rodriguez, Henry, Zhang, Xu

“…Proteomics has emerged as a powerful tool for studying cancer biology, developing diagnostics, and therapies. With the continuous improvement and widespread…”
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A new family of outwardly rectifying potassium channel proteins with two pore domains in tandem by Ketchum, Karen A, Joiner, William J, Sellers, Andrew J, Kaczmarek, Leonard K, Goldstein, Steve A. N

“…Potassium channels catalyse the permeation of K+ ions across cellular membranes and are identified by a common structural motif, a highly conserved signature…”
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Isolation of an ion channel gene from Arabidopsis thaliana using the H5 signature sequence from voltage-dependent K + channels by Ketchum, Karen A., Slayman, Carolyn W.

“…A degenerate oligonucleotide corresponding to the K + channel signature sequence (TMTTVGYGD) was used to isolate the genomic and cDNA forms of a new channel…”
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Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma by Satpathy, Shankha, Cao, Song, Dhanasekaran, Saravana M., Vasaikar, Suhas V., Petralia, Francesca, Liang, Wen-Wei, Krek, Azra, Hong, Runyu, Blumenberg, Lili, Wendl, Michael C., Wen, Bo, Tang, Lauren C., MacMullan, Melanie A., Kane, M. Harry, Newton, Chelsea J., Cornwell, MacIntosh, Yoo, Seungyeul, Mannan, Rahul, Vats, Pankaj, Kumar-Sinha, Chandan, Colaprico, Antonio, Geffen, Yifat, Wiznerowicz, Maciej, Gümüş, Zeynep H., Veluswamy, Rajwanth R., Hostetter, Galen, Mesri, Mehdi, Boja, Emily S., Omenn, Gilbert S., Thiagarajan, Mathangi, Getz, Gad, Cieslik, Marcin P., Govindan, Ramaswamy, Wang, Pei, Nesvizhskii, Alexey I., Ding, Li, Mani, D.R., Francis, Alicia, Charamut, Alyssa, Paulovich, Amanda G., Karnuta, Andrii, Hindenach, Barbara, Druker, Brian J., Birger, Chet, Jones, Corbin D., Rohrer, Daniel C., Zhou, Daniel Cui, Chan, Daniel W., Chesla, David, Clark, David J., Tan, Donghui, Duffy, Elizabeth, Bergstrom, Erik J., Wilson, George D., Chen, Hai-Quan, Sun, Hua, Whiteaker, Jeffrey R., Rodland, Karin D., Hoadley, Katherine A., Elburn, Kim, Hannick, Linda, Qi, Liqun, Sokoll, Lori J., Wojtyś, Małgorzata, Domagalski, Marcin J., Beasley, Mary B., Monroe, Matthew E., Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Schnaubelt, Michael, Chaikin, Michelle, Selvan, Myvizhi Esai, McGarvey, Peter B., Thangudu, Ratna R., Smith, Richard D., Welsh, Robert J., Zelt, Robert, Mehra, Rohit, Matteotti, Ronald, Mareedu, Sailaja, Payne, Samuel H., Cottingham, Sandra, Chugh, Seema, Smith, Shaleigh, Tsang, Shirley, Cai, Shuang, Boca, Simina M., Stein, Stephen E., Krubit, Tanya, Skelly, Tara, Bauer, Thomas, Velvulou, Uma, Petyuk, Vladislav A., Bocik, William E., Maggio, William W., Chen, Xi, Wu, Yige, Shi, Zhiao

“…To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of…”
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Characterization of a hyperthermophilic P-type ATPase from Methanococcus jannaschii expressed in yeast by Morsomme, Pierre, Chami, Mohamed, Marco, Sergio, Nader, Joseph, Ketchum, Karen A, Goffeau, André, Rigaud, Jean-Louis

“…We report on the biochemical and structural properties of a putative P-type H(+)-ATPase, MJ1226p, from the anaerobic hyperthermophilic Archaea Methanococcus…”
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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Pan, Jianbo, Hu, Yingwei, Krek, Azra, Li, Yize, Chen, Lin S., Vasaikar, Suhas, Wu, Yige, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Ruggles, Kelly, Kawaler, Emily, Wen, Bo, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Pavlovich, Christian P., Brominski, Gabriel, Hsieh, James J., Lubinski, Jan, Wiznerowicz, Maciej, Kinsinger, Christopher R., Thiagarajan, Mathangi, Mesri, Mehdi, Hiltke, Tara, Ding, Li, Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Nesvizhskii, Alexey I., Zhang, Hui, Hashimi, Abdul Samad, Charamut, Alyssa, Druker, Brian J., Tognon, Cristina, Mani, D.R., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Chan, Doug, Demir, Emek, Wilson, George D., Liu, Hongwei, Zhou, Hua, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, Chen, Jin, Ketchum, Karen A., Rodland, Karin D., Krug, Karsten, Holloway, Kimberly, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Anderson, Matthew, Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Smith, Michael, Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Piehowski, Paul, McGarvey, Peter B., Hariharan, Pushpa, Gao, Qingsong, Thangudu, Ratna R., Montgomery, Rebecca, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Payne, Samuel H., Patel, Shalin, Satpathy, Shankha, Davies, Sherri R., Patil, Snehal, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., Carr, Steven A., Skelly, Tara, Borate, Uma, Maruvka, Yosef, Li, Zhi

“…To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic,…”
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Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy by Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., Gillette, Michael A., Avanessian, Shayan C., Cai, Shuang, Chan, Daniel, Chen, Xian, Edwards, Nathan J., Hoofnagle, Andrew N., Kane, M. Harry, Ketchum, Karen A., Kuhn, Eric, Levine, Douglas A., Li, Shunqiang, Liebler, Daniel C., Liu, Tao, Luo, Jingqin, Madhavan, Subha, Maher, Chris, McDermott, Jason E., McGarvey, Peter B., Oberti, Mauricio, Pandey, Akhilesh, Payne, Samuel H., Ransohoff, David F., Rivers, Robert C., Rodland, Karin D., Rudnick, Paul, Sanders, Melinda E., Shaw, Kenna M., Shih, Ie-Ming, Slebos, Robbert J.C., Smith, Richard D., Snyder, Michael, Stein, Stephen E., Tabb, David L., Thangudu, Ratna R., Thomas, Stefani, Wang, Yue, White, Forest M., Whiteaker, Jeffrey R., Whiteley, Gordon A., Zhang, Hui, Zhang, Zhen, Zhao, Yingming, Zhu, Heng, Zimmerman, Lisa J.

“…The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this…”
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Characterization of a Hyperthermophilic P-type ATPase fromMethanococcus jannaschii Expressed in Yeast by Morsomme, Pierre, Chami, Mohamed, Marco, Sergio, Nader, Joseph, Ketchum, Karen A., Goffeau, André, Rigaud, Jean-Louis

“…We report on the biochemical and structural properties of a putative P-type H+-ATPase, MJ1226p, from the anaerobic hyperthermophilic Archaea Methanococcus…”
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Abstract LB-242: Proteomic Data Commons: A resource for proteogenomic analysis by Thangudu, Ratna Rajesh, Rudnick, Paul A., Holck, Michael, Singhal, Deepak, MacCoss, Michael J., Edwards, Nathan J., Ketchum, Karen A., Kinsinger, Christopher R., Kim, Erika, Basu, Anand

“…Abstract The objective of the National Cancer Institutes' Proteomic Data Commons (PDC) is to make cancer-related proteomic datasets accessible to the public…”
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CPTAC Assay Portal: a repository of targeted proteomic assays by Whiteaker, Jeffrey R, Halusa, Goran N, Hoofnagle, Andrew N, Sharma, Vagisha, MacLean, Brendan, Yan, Ping, Wrobel, John A, Kennedy, Jacob, Mani, D R, Zimmerman, Lisa J, Meyer, Matthew R, Mesri, Mehdi, Rodriguez, Henry, Paulovich, Amanda G

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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Clark, David J., Petralia, Francesca, Pan, Jianbo, Hu, Yingwei, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Krek, Azra, Li, Yize, Ozbek, Umut, Wu, Yige, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Schnaubelt, Michael, Avtonomov, Dmitry M., Kalayci, Selim, Ma, Shiyong, Ruggles, Kelly, Gümüş, Zeynep H., Kawaler, Emily, Edwards, Nathan, Chen, Xi Steven, Antczak, Andrzej, Omelchenko, Tatiana, Kinsinger, Christopher R., Thiagarajan, Mathangi, Mesri, Mehdi, Robles, Ana I., Qian, Jiang, Fenyö, David, Zhang, Bing, Zhang, Zhen, Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Hashimi, Abdul Samad, Charamut, Alyssa, Druker, Brian J., Tognon, Cristina, Mani, D.R., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Chan, Doug, Demir, Emek, Modugno, Francesmary, Getz, Gaddy, Wilson, George D., Liu, Hongwei, Zhou, Hua, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, Chen, Jin, Ketchum, Karen A., Rodland, Karin D., Krug, Karsten, Holloway, Kimberly, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Anderson, Matthew, Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Smith, Michael, Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Grady, Pamela, Piehowski, Paul, McGarvey, Peter B., Hariharan, Pushpa, Gao, Qingsong, Thangudu, Ratna R., Montgomery, Rebecca, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Payne, Samuel H., Patel, Shalin, Satpathy, Shankha, Davies, Sherri R., Patil, Snehal, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., Carr, Steven A., Skelly, Tara, Borate, Uma, Maruvka, Yosef, Li, Zhi

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Characterization of potassium-dependent currents in protoplasts of corn suspension cells by Ketchum, K.A. (McGill University, Montreal, Quebec, Canada), Shrier, A, Poole, R.J

“…Protoplasts obtained from corn (Zea mays) suspension cells were studied using the whole cell patch-clamp technique. One time-independent current, as well as…”
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Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi by Fraser, Claire M, Casjens, Sherwood, Huang, Wai Mun, Sutton, Granger G, Clayton, Rebecca, Lathigra, Raju, White, Owen, Ketchum, Karen A, Dodson, Robert, Hickey, Erin K, Gwinn, Michelle, Dougherty, Brian, Tomb, Jean-Francois, Fleischmann, Robert D, Richardson, Delwood, Peterson, Jeremy, Kerlavage, Anthony R, Quackenbush, John, Salzberg, Steven, Hanson, Mark, van Vugt, Rene, Palmer, Nanette, Adams, Mark D, Gocayne, Jeannine, Weidman, Janice, Utterback, Teresa, Watthey, Larry, McDonald, Lisa, Artiach, Patricia, Bowman, Cheryl, Garland, Stacey, Fujii, Claire, Cotton, Matthew D, Horst, Kurt, Roberts, Kevin, Hatch, Bonnie, Smith, Hamilton O, Venter, J. Craig

“…The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17…”
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Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete by Fraser, Claire M., Norris, Steven J., Weinstock, George M., White, Owen, Sutton, Granger G., Dodson, Robert, Gwinn, Michelle, Hickey, Erin K., Clayton, Rebecca, Ketchum, Karen A., Sodergren, Erica, Hardham, John M., McLeod, Michael P., Salzberg, Steven, Peterson, Jeremy, Khalak, Hanif, Richardson, Delwood, Howell, Jerrilyn K., Chidambaram, Monjula, Utterback, Teresa, McDonald, Lisa, Artiach, Patricia, Bowman, Cheryl, Cotton, Matthew D., Fujii, Claire, Garland, Stacey, Hatch, Bonnie, Horst, Kurt, Roberts, Kevin, Sandusky, Mina, Weidman, Janice, Smith, Hamilton O., Venter, J. Craig

“…The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading…”
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