Search Results - "Shi, Zhiao"

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit by Wang, Jing, Vasaikar, Suhas, Shi, Zhiao, Greer, Michael, Zhang, Bing

“…Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web…”
Get full text

Fast network centrality analysis using GPUs by Shi, Zhiao, Zhang, Bing

“…With the exploding volume of data generated by continuously evolving high-throughput technologies, biological network analysis problems are growing larger in…”
Get full text

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 by Wang, Jing, Duncan, Dexter, Shi, Zhiao, Zhang, Bing

Get full text

Proteogenomic characterization of human colon and rectal cancer by Zhang, Bing, Wang, Jing, Wang, Xiaojing, Zhu, Jing, Liu, Qi, Shi, Zhiao, Chambers, Matthew C., Zimmerman, Lisa J., Shaddox, Kent F., Kim, Sangtae, Davies, Sherri R., Wang, Sean, Wang, Pei, Kinsinger, Christopher R., Rivers, Robert C., Rodriguez, Henry, Townsend, R. Reid, Ellis, Matthew J. C., Carr, Steven A., Tabb, David L., Coffey, Robert J., Slebos, Robbert J. C., Liebler, Daniel C.

“…Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem,…”
Get full text

Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis by Zhu, Jing, Wang, Jing, Shi, Zhiao, Franklin, Jeffrey L, Deane, Natasha G, Coffey, Robert J, Beauchamp, R Daniel, Zhang, Bing

“…Both transcriptional subtype and signaling network analyses have proved useful in cancer genomics research. However, these two approaches are usually applied…”
Get full text

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 by Wang, Jing, Duncan, Dexter, Shi, Zhiao, Zhang, Bing

“…Functional enrichment analysis is an essential task for the interpretation of gene lists derived from large-scale genetic, transcriptomic and proteomic…”
Get full text

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs by Liao, Yuxing, Wang, Jing, Jaehnig, Eric J, Shi, Zhiao, Zhang, Bing

“…WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12…”
Get full text

Robust task scheduling in non-deterministic heterogeneous computing systems by Zhiao Shi, Jeannot, E., Dongarra, J.J.

“…The paper addresses the problem of matching and scheduling of DAG-structured application to both minimize the makespan and maximize the robustness in a…”
Get full text

Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data by Shi, Zhiao, Wen, Bo, Gao, Qiang, Zhang, Bing

“…Untargeted mass spectrometry (MS)-based proteomics provides a powerful platform for protein biomarker discovery, but clinical translation depends on the…”
Get full text

Deep Learning in Proteomics by Wen, Bo, Zeng, Wen‐Feng, Liao, Yuxing, Shi, Zhiao, Savage, Sara R., Jiang, Wen, Zhang, Bing

“…Proteomics, the study of all the proteins in biological systems, is becoming a data‐rich science. Protein sequences and structures are comprehensively…”
Get full text

NetGestalt: integrating multidimensional omics data over biological networks by Shi, Zhiao, Wang, Jing, Zhang, Bing

Get full text

GLAD4U: deriving and prioritizing gene lists from PubMed literature by Jourquin, Jérôme, Duncan, Dexter, Shi, Zhiao, Zhang, Bing

“…Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine,…”
Get full text

Proteogenomic characterization of pancreatic ductal adenocarcinoma by Cao, Liwei, Huang, Chen, Cui Zhou, Daniel, Hu, Yingwei, Savage, Sara R., Krug, Karsten, Schnaubelt, Michael, Eguez, Rodrigo Vargas, Yang, Weiming, Pan, Jianbo, Wen, Bo, Jiang, Wen, Liao, Yuxing, Terekhanova, Nadezhda V., Cao, Song, Lu, Rita Jui-Hsien, Liu, Ruiyang, Zhu, Houxiang, Wu, Yige, Easwaran, Hariharan, Yoo, Seungyeul, Liu, Wenke, Haibe-Kains, Benjamin, Thiagarajan, Mathangi, Jewell, Scott D., Hostetter, Galen, Li, Qing Kay, Fenyö, David, Wang, Pei, Mani, D.R., Omenn, Gilbert S., Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Chan, Daniel W., Hruban, Ralph H., Ding, Li, Zhang, Hui, Amin, Mitual, An, Eunkyung, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Bocik, William, Borucki, Melissa, Carr, Steven A., Cerda, Sandra, Chen, Huan, Chen, Steven, Chesla, David, Chinnaiyan, Arul M., Colaprico, Antonio, Cottingham, Sandra, Derejska, Magdalena, Dhanasekaran, Saravana M., Domagalski, Marcin J., Edwards, Nathan J., Francis, Alicia, Francis, Jesse, Gabriel, Stacey, Gabrovski, Nikolay, Gardner, Johanna, Getz, Gad, Goldthwaite, Charles A., Grady, Pamela, Guo, Shuai, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Jones, Corbin D., Ketchum, Karen A., Kinsinger, Christopher R., Kusnierz, Katarzyna, Mallery, David, Matteotti, Ronald, McGarvey, Peter B., Minoo, Parham, Paklina, Oxana V., Paulovich, Amanda G., Payne, Samuel H., Potapova, Olga, Qi, Liqun, Roche, Nancy, Rodland, Karin D., Rohrer, Daniel C., Shabunin, Alexey V., Shelton, Troy, Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Smith, Richard D., Sokoll, Lori J., Suh, James, Thangudu, Ratna R., Valley, Dana R., Wang, Wenyi, Wilson, George D., Wiznerowicz, Maciej, Zhang, Zhen

“…Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations…”
Get full text

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma by Savage, Sara R., Eguez, Rodrigo Vargas, Li, Yize, Jaehnig, Eric J., Cieślik, Marcin, Chang, Hui-Yin, Li, Kai, Li, Qing Kay, Clark, David J., Hu, Yingwei, Cao, Liwei, Wang, Yuefan, Cho, Kyung-Cho, Liao, Yuxing, Anurag, Meenakshi, Ji, Jiayi, Zhou, Daniel Cui, Carr, Steven A., Zhang, Zhen, Chen, Xi S., Pico, Alexander R., Kinsinger, Christopher R., Robles, Ana I., An, Eunkyung, Hiltke, Tara, Mesri, Mehdi, Weaver, Alissa M., Sikora, Andrew G., Wierzbicka, Małgorzata, Wiznerowicz, Maciej, Satpathy, Shankha, Gillette, Michael A., Miles, George, Ellis, Matthew J., Omenn, Gilbert S., Boja, Emily S., Dhanasekaran, Saravana M., Agarwal, Anupriya, Avanessian, Shayan C., Bathe, Oliver F., Birger, Chet, Birrer, Michael J., Bocik, William E., Borate, Uma, Borucki, Melissa, Cai, Shuang, Charamut, Alyssa, Chen, Lin S., Chowdhury, Shrabanti, Clauser, Karl R., Culpepper, Houston, Czernicki, Tomasz, D'Angelo, Fulvio, Domagalski, Marcin J., Dyer, Maureen, Edwards, Nathan J., Ermakova, Tatiana S., Francis, Alicia, Goldthwaite, Charles A., Hannick, Linda I., Hayes, David N., Heiman, David, Jewell, Scott D., Jones, Corbin D., Krek, Azra, Liu, Tao, Ma, Weiping, Malc, Ewa, Malovannaya, Anna, Mareedu, Sailaja, Marrero-Oliveras, Annette, McGee, John, Mieczkowski, Piotr, Newton, Chelsea J., Ozbek, Umut, Payne, Samuel H., Pazardzhikliev, Dimitar Dimitrov, Petralia, Francesca, Piehowski, Paul D., Polonskaya, Larisa, Ponomareva, Elena V., Qu, Ning, Ramkissoon, Shakti, Reva, Boris, Richey, Shannon, Robinson, Karna, Roche, Nancy, Rodland, Karin, Shi, Yan, Shutack, Yvonne, Sokoll, Lori J., Stein, Stephen E., Szopa, Wojciech, Tyner, Jeffrey, Vasilev, Lyubomir Valkov, Whiteaker, Jeffrey R., Wu, Yige, Yi, Xinpei, Zakhartsev, Yuriy, Zhao, Grace

“…We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically…”
Get full text

WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics by Elizarraras, John M, Liao, Yuxing, Shi, Zhiao, Zhu, Qian, Pico, Alexander R, Zhang, Bing

“…Enrichment analysis, crucial for interpreting genomic, transcriptomic, and proteomic data, is expanding into metabolomics. Furthermore, there is a rising…”
Get full text

Mathematical model development and simulation of in situ stabilization in lead-contaminated soils by Shi, Zhiao, Erickson, Larry E.

“…Stabilization and remediation of lead-contaminated soils has received considerable attention recently. Amending Pb-contaminated soils with phosphate as an in…”
Get full text

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities by Vasaikar, Suhas, Huang, Chen, Wang, Xiaojing, Petyuk, Vladislav A., Savage, Sara R., Wen, Bo, Dou, Yongchao, Zhang, Yun, Shi, Zhiao, Arshad, Osama A., Gritsenko, Marina A., Zimmerman, Lisa J., McDermott, Jason E., Clauss, Therese R., Moore, Ronald J., Zhao, Rui, Monroe, Matthew E., Wang, Yi-Ting, Chambers, Matthew C., Slebos, Robbert J.C., Lau, Ken S., Mo, Qianxing, Ding, Li, Ellis, Matthew, Thiagarajan, Mathangi, Kinsinger, Christopher R., Rodriguez, Henry, Smith, Richard D., Rodland, Karin D., Liebler, Daniel C., Liu, Tao, Zhang, Bing, Pandey, Akhilesh, Paulovich, Amanda, Hoofnagle, Andrew, Mani, D.R., Chan, Daniel W., Ransohoff, David F., Fenyo, David, Tabb, David L., Levine, Douglas A., Boja, Emily S., Kuhn, Eric, White, Forest M., Whiteley, Gordon A., Zhu, Heng, Zhang, Hui, Shih, Ie-Ming, Bavarva, Jasmin, Whiteaker, Jeffrey, Ketchum, Karen A., Clauser, Karl R., Ruggles, Kelly, Elburn, Kimberly, Hannick, Linda, Watson, Mark, Oberti, Mauricio, Mesri, Mehdi, Sanders, Melinda E., Borucki, Melissa, Gillette, Michael A., Snyder, Michael, Edwards, Nathan J., Vatanian, Negin, Rudnick, Paul A., McGarvey, Peter B., Mertins, Philip, Townsend, R. Reid, Thangudu, Ratna R., Rivers, Robert C., Payne, Samuel H., Davies, Sherri R., Cai, Shuang, Stein, Stephen E., Carr, Steven A., Skates, Steven J., Madhavan, Subha, Hiltke, Tara, Chen, Xian, Zhao, Yingming, Wang, Yue, Zhang, Zhen

“…We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired…”
Get full text

Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results by Savage, Sara R., Shi, Zhiao, Liao, Yuxing, Zhang, Bing

“…Weighted set cover and affinity propagation algorithms are used to combine results from multiple enrichment analyses. Weighted set cover first condenses…”
Get full text

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…”
Get full text

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer by Zhang, Hui, Zhang, Zhen, Payne, Samuel H., Zhang, Bai, McDermott, Jason E., Zhou, Jian-Ying, Petyuk, Vladislav A., Chen, Li, Ray, Debjit, Sun, Shisheng, Yang, Feng, Chen, Lijun, Wang, Jing, Cha, Seong Won, Aiyetan, Paul, Woo, Sunghee, Tian, Yuan, Gritsenko, Marina A., Clauss, Therese R., Choi, Caitlin, Monroe, Matthew E., Thomas, Stefani, Nie, Song, Wu, Chaochao, Moore, Ronald J., Yu, Kun-Hsing, Tabb, David L., Fenyö, David, Bafna, Vineet, Wang, Yue, Rodriguez, Henry, Boja, Emily S., Hiltke, Tara, Rivers, Robert C., Sokoll, Lori, Zhu, Heng, Shih, Ie-Ming, Cope, Leslie, Pandey, Akhilesh, Zhang, Bing, Snyder, Michael P., Levine, Douglas A., Smith, Richard D., Chan, Daniel W., Rodland, Karin D., Carr, Steven A., Gillette, Michael A., Klauser, Karl R., Kuhn, Eric, Mani, D.R., Ketchum, Karen A., Thangudu, Ratna, Cai, Shuang, Oberti, Mauricio, Paulovich, Amanda G., Whiteaker, Jeffrey R., Edwards, Nathan J., McGarvey, Peter B., Madhavan, Subha, Wang, Pei, Chan, Daniel W., Pandey, Akhilesh, Shih, Ie-Ming, Zhang, Hui, Zhang, Zhen, Zhu, Heng, Cope, Leslie, Skates, Steven J., White, Forest M., Levine, Douglas A., Boja, Emily S., Kinsinger, Christopher R., Hiltke, Tara, Mesri, Mehdi, Rivers, Robert C., Rodriguez, Henry, Shaw, Kenna M., Stein, Stephen E., Fenyo, David, Liu, Tao, McDermott, Jason E., Payne, Samuel H., Rodland, Karin D., Smith, Richard D., Rudnick, Paul, Zhao, Yingming, Ransohoff, David F., Hoofnagle, Andrew N., Liebler, Daniel C., Sanders, Melinda E., Shi, Zhiao, Slebos, Robbert J.C., Tabb, David L., Zhang, Bing, Zimmerman, Lisa J., Wang, Yue, Davies, Sherri R., Ding, Li, Ellis, Matthew J.C., Townsend, R. Reid

“…To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive…”
Get full text