A Comprehensive Comparison of Normalization Methods for Loading Control and Variance Stabilization of Reverse-Phase Protein Array Data

por Liu, Wenbin, Ju, Zhenlin, Lu, Yiling, Mills, Gordon B, Akbani, Rehan
Publicado 2014

Personalized Network Modeling of the Pan-Cancer Patient and Cell Line Interactome

por Bhattacharyya, Rupam, Ha, Min Jin, Liu, Qingzhi, Akbani, Rehan, Liang, Han, Baladandayuthapani, Veerabhadran
Publicado 2020

Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study

por Städler, Nicolas, Dondelinger, Frank, Hill, Steven M, Akbani, Rehan, Lu, Yiling, Mills, Gordon B, Mukherjee, Sach
Publicado 2017

TCGASpliceSeq a compendium of alternative mRNA splicing in cancer

por Ryan, Michael, Wong, Wing Chung, Brown, Robert, Akbani, Rehan, Su, Xiaoping, Broom, Bradley, Melott, James, Weinstein, John
Publicado 2016

Personalized Integrated Network Modeling of the Cancer Proteome Atlas

por Ha, Min Jin, Banerjee, Sayantan, Akbani, Rehan, Liang, Han, Mills, Gordon B., Do, Kim-Anh, Baladandayuthapani, Veerabhadran
Publicado 2018

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps

por Ryan, Michael C., Stucky, Mark, Wakefield, Chris, Melott, James M., Akbani, Rehan, Weinstein, John N., Broom, Bradley M.
Publicado 2020

Multiplatform-based Molecular Subtypes of Non-Small Cell Lung Cancer

por Chen, Fengju, Zhang, Yiqun, Parra, Edwin, Rodriguez, Jaime, Behrens, Carmen, Akbani, Rehan, Lu, Yiling, Kurie, Jonathan, Gibbons, Don L., Mills, Gordon B., Wistuba, Ignacio I., Creighton, Chad J.
Publicado 2016

RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data

por Shehwana, Huma, Kumar, Shwetha V, Melott, James M, Rohrdanz, Mary A, Wakefield, Chris, Ju, Zhenlin, Siwak, Doris R, Lu, Yiling, Broom, Bradley M, Weinstein, John N, Mills, Gordon B, Akbani, Rehan
Publicado 2022

TCPA: a resource for cancer functional proteomics data

por Li, Jun, Lu, Yiling, Akbani, Rehan, Ju, Zhenlin, Roebuck, Paul L, Liu, Wenbin, Yang, Ji-Yeon, Broom, Bradley M, Verhaak, Roeland G W, Kane, David W, Wakefield, Chris, Weinstein, John N, Mills, Gordon B, Liang, Han
Publicado 2013

Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer

por Mistretta, Brandon, Rankothgedera, Sakuni, Castillo, Micah, Rao, Mitchell, Holloway, Kimberly, Bhardwaj, Anjana, El Noafal, Maha, Albarracin, Constance, El-Zein, Randa, Rezaei, Hengameh, Su, Xiaoping, Akbani, Rehan, Shao, Xiaoshan M., Czerniecki, Brian J., Karchin, Rachel, Bedrosian, Isabelle, Gunaratne, Preethi H.
Publicado 2023

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

por Hoadley, Katherine A., Yau, Christina, Hinoue, Toshinori, Wolf, Denise M., Lazar, Alexander J., Drill, Esther, Shen, Ronglai, Taylor, Alison M., Cherniack, Andrew D., Thorsson, Vésteinn, Akbani, Rehan, Bowlby, Reanne, Wong, Christopher K., Wiznerowicz, Maciej, Sanchez-Vega, Francisco, Robertson, A. Gordon, Schneider, Barbara G., Lawrence, Michael S., Noushmehr, Houtan, Malta, Tathiane M., Stuart, Joshua M., Benz, Christopher C., Laird, Peter W.
Publicado 2018

A pan-cancer proteomic perspective on The Cancer Genome Atlas

por Akbani, Rehan, Ng, Patrick Kwok Shing, Werner, Henrica M.J., Shahmoradgoli, Maria, Zhang, Fan, Ju, Zhenlin, Liu, Wenbin, Yang, Ji-Yeon, Yoshihara, Kosuke, Li, Jun, Ling, Shiyun, Seviour, Elena G., Ram, Prahlad T., Minna, John D., Diao, Lixia, Tong, Pan, Heymach, John V., Hill, Steven M., Dondelinger, Frank, Städler, Nicolas, Byers, Lauren A., Meric-Bernstam, Funda, Weinstein, John N., Broom, Bradley M., Verhaak, Roeland G.W., Liang, Han, Mukherjee, Sach, Lu, Yiling, Mills, Gordon B.
Publicado 2014

Mutational Profiles Reveal an Aberrant TGF-β-CEA Regulated Pathway in Colon Adenomas

por Chen, Jian, Raju, Gottumukkala S., Jogunoori, Wilma, Menon, Vipin, Majumdar, Avijit, Chen, Jiun-Sheng, Gi, Young Jin, Jeong, Yun Seong, Phan, Liem, Belkin, Mitchell, Gu, Shoujun, Kundra, Suchin, Mistry, Nipun A., Zhang, Jianping, Su, Xiaoping, Li, Shulin, Lin, Sue-Hwa, Javle, Milind, McMurray, John S., Rahlfs, Thomas F., Mishra, Bibhuti, White, Jon, Rashid, Asif, Beauchemin, Nicole, Weston, Brian R., Shafi, Mehnaz A., Stroehlein, John R., Davila, Marta, Akbani, Rehan, Weinstein, John N., Wu, Xifeng, Mishra, Lopa
Publicado 2016

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

por Campbell, Joshua D., Alexandrov, Anton, Kim, Jaegil, Wala, Jeremiah, Berger, Alice H., Pedamallu, Chandra Sekhar, Shukla, Sachet A., Guo, Guangwu, Brooks, Angela N., Murray, Bradley A., Imielinski, Marcin, Hu, Xin, Ling, Shiyun, Akbani, Rehan, Rosenberg, Mara, Cibulskis, Carrie, Ramachandran, Aruna, Collisson, Eric A., Kwiatkowski, David J., Lawrence, Michael S., Weinstein, John N., Verhaak, Roel G. W., Wu, Catherine J., Hammerman, Peter S., Cherniack, Andrew D., Getz, Gad, Artyomov, Maxim N., Schreiber, Robert, Govindan, Ramaswamy, Meyerson, Matthew
Publicado 2016

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

por Knijnenburg, Theo A., Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N., Li, Lei, Ding, Li, Mills, Gordon B., Laird, Peter W., Wheeler, David A., Shmulevich, Ilya, Monnat, Raymond J, Xiao, Yonghong, Wang, Chen
Publicado 2018

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

por Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Zhu, Andrew X., Stuart, Josh M., Sander, Chris, Akbani, Rehan, Cherniack, Andrew D., Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael S., Kleiner, David E., Laird, Peter W., Wheeler, David A., McRee, Autumn J., Bathe, Oliver F., Andersen, Jesper B., Bardeesy, Nabeel, Roberts, Lewis R., Kwong, Lawrence N.
Publicado 2017

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

por Ricketts, Christopher J., De Cubas, Aguirre A., Fan, Huihui, Smith, Christof C., Lang, Martin, Reznik, Ed, Bowlby, Reanne, Gibb, Ewan A., Akbani, Rehan, Beroukhim, Rameen, Bottaro, Donald P., Choueiri, Toni K., Gibbs, Richard A., Godwin, Andrew K., Haake, Scott, Hakimi, A. Ari, Henske, Elizabeth P., Hsieh, James J., Ho, Thai H., Kanchi, Rupa S., Krishnan, Bhavani, Kwaitkowski, David J., Lui, Wembin, Merino, Maria J., Mills, Gordon B., Myers, Jerome, Nickerson, Michael L., Reuter, Victor E., Schmidt, Laura S., Shelley, C. Simon, Shen, Hui, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Vincent, Benjamin G., Vocke, Cathy D., Wheeler, David A., Yang, Lixing, Kim, William T., Robertson, A. Gordon, Spellman, Paul T., Rathmell, W. Kimryn, Linehan, W. Marston
Publicado 2018

Integrated Molecular Characterization of Testicular Germ Cell Tumors

por Shen, Hui, Shih, Juliann, Hollern, Daniel P., Wang, Linghua, Bowlby, Reanne, Tickoo, Satish K., Thorsson, Vésteinn, Mungall, Andrew J., Newton, Yulia, Hegde, Apurva M., Armenia, Joshua, Sánchez-Vega, Francisco, Pluta, John, Pyle, Louise C., Mehra, Rohit, Reuter, Victor E., Godoy, Guilherme, Jones, Jeffrey, Shelley, Carl S., Feldman, Darren R., Vidal, Daniel O., Lessel, Davor, Kulis, Tomislav, Cárcano, Flavio M., Leraas, Kristen M., Lichtenberg, Tara M., Brooks, Denise, Cherniack, Andrew D., Cho, Juok, Heiman, David I., Kasaian, Katayoon, Liu, Minwei, Noble, Michael S., Xi, Liu, Zhang, Hailei, Zhou, Wanding, ZenKlusen, Jean C., Hutter, Carolyn M., Felau, Ina, Zhang, Jiashan, Schultz, Nikolaus, Getz, Gad, Meyerson, Matthew, Stuart, Joshua M., Akbani, Rehan, Wheeler, David A., Laird, Peter W., Nathanson, Katherine L., Cortessis, Victoria K., Hoadley, Katherine A.
Publicado 2018