Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling

por Riordan, Daniel P., Varma, Sushama, West, Robert B., Brown, Patrick O.
Publicado 2015

Self-Organizing Maps for Cellular In Silico Staining and Cell Substate Classification

por Yuan, Edwin, Matusiak, Magdalena, Sirinukunwattana, Korsuk, Varma, Sushama, Kidziński, Łukasz, West, Robert
Publicado 2021

Discovery of recurrent structural variants in nasopharyngeal carcinoma

por Valouev, Anton, Weng, Ziming, Sweeney, Robert T., Varma, Sushama, Le, Quynh-Thu, Kong, Christina, Sidow, Arend, West, Robert B.
Publicado 2014

CD142 Identifies Neoplastic Desmoid Tumor Cells, Uncovering Interactions Between Neoplastic and Stromal Cells That Drive Proliferation

por Al-Jazrawe, Mushriq, Xu, Steven, Poon, Raymond, Wei, Qingxia, Przybyl, Joanna, Varma, Sushama, van de Rijn, Matt, Alman, Benjamin A.
Publicado 2023

A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions

por Brunner, Alayne L, Li, Jun, Guo, Xiangqian, Sweeney, Robert T, Varma, Sushama, Zhu, Shirley X, Li, Rui, Tibshirani, Robert, West, Robert B
Publicado 2014

Prognostic relevance of the hexosamine biosynthesis pathway activation in leiomyosarcoma

por Tolwani, Angela, Matusiak, Magdalena, Bui, Nam, Forgó, Erna, Varma, Sushama, Baratto, Lucia, Iagaru, Andrei, Lazar, Alexander J., van de Rijn, Matt, Przybyl, Joanna
Publicado 2021

YAP-independent mechanotransduction drives breast cancer progression

por Lee, Joanna Y., Chang, Jessica K., Dominguez, Antonia A., Lee, Hong-pyo, Nam, Sungmin, Chang, Julie, Varma, Sushama, Qi, Lei S., West, Robert B., Chaudhuri, Ovijit
Publicado 2019

Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma

por Barasch, Nicholas, Gong, Xue, Kwei, Kevin A., Varma, Sushama, Biscocho, Jewison, Qu, Kunbin, Xiao, Nan, Lipsick, Joseph S., Pelham, Robert J., West, Robert B., Pollack, Jonathan R.
Publicado 2017

Cell cycle progression in confining microenvironments is regulated by a growth-responsive TRPV4-PI3K/Akt-p27(Kip1) signaling axis

por Nam, Sungmin, Gupta, Vivek Kumar, Lee, Hong-pyo, Lee, Joanna Y., Wisdom, Katrina M., Varma, Sushama, Flaum, Eliott Marie, Davis, Ciara, West, Robert B., Chaudhuri, Ovijit
Publicado 2019

Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas

por Przybyl, Joanna, Spans, Lien, Lum, Deirdre A., Zhu, Shirley, Vennam, Sujay, Forgó, Erna, Varma, Sushama, Ganjoo, Kristen, Hastie, Trevor, Bowen, Raffick, Debiec-Rychter, Maria, van de Rijn, Matt
Publicado 2019

Transcriptome and genome evolution during HER2-amplified breast neoplasia

por Lu, Peipei, Foley, Joseph, Zhu, Chunfang, McNamara, Katherine, Sirinukunwattana, Korsuk, Vennam, Sujay, Varma, Sushama, Fehri, Hamid, Srivastava, Arunima, Zhu, Shirley, Rittscher, Jens, Mallick, Parag, Curtis, Christina, West, Robert
Publicado 2021

Genome evolution during progression to breast cancer

por Newburger, Daniel E., Kashef-Haghighi, Dorna, Weng, Ziming, Salari, Raheleh, Sweeney, Robert T., Brunner, Alayne L., Zhu, Shirley X., Guo, Xiangqian, Varma, Sushama, Troxell, Megan L., West, Robert B., Batzoglou, Serafim, Sidow, Arend
Publicado 2013

Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer

por Afghahi, Anosheh, Forgó, Erna, Mitani, Aya A., Desai, Manisha, Varma, Sushama, Seto, Tina, Rigdon, Joseph, Jensen, Kristin C., Troxell, Megan L., Gomez, Scarlett Lin, Das, Amar K., Beck, Andrew H., Kurian, Allison W., West, Robert B.
Publicado 2015

The microdissected gene expression landscape of nasopharyngeal cancer reveals vulnerabilities in FGF and noncanonical NF-κB signaling

por Tay, Joshua K., Zhu, Chunfang, Shin, June Ho, Zhu, Shirley X., Varma, Sushama, Foley, Joseph W., Vennam, Sujay, Yip, Yim Ling, Goh, Chuan Keng, Wang, De Yun, Loh, Kwok Seng, Tsao, Sai Wah, Le, Quynh-Thu, Sunwoo, John B., West, Robert B.
Publicado 2022

Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types

por Giacomini, Craig P., Sun, Steven, Varma, Sushama, Shain, A. Hunter, Giacomini, Marilyn M., Balagtas, Jay, Sweeney, Robert T., Lai, Everett, Del Vecchio, Catherine A., Forster, Andrew D., Clarke, Nicole, Montgomery, Kelli D., Zhu, Shirley, Wong, Albert J., van de Rijn, Matt, West, Robert B., Pollack, Jonathan R.
Publicado 2013

A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk

por Gentles, Andrew J., Hui, Angela Bik-Yu, Feng, Weiguo, Azizi, Armon, Nair, Ramesh V., Bouchard, Gina, Knowles, David A., Yu, Alice, Jeong, Youngtae, Bejnood, Alborz, Forgó, Erna, Varma, Sushama, Xu, Yue, Kuong, Amanda, Nair, Viswam S., West, Rob, van de Rijn, Matt, Hoang, Chuong D., Diehn, Maximilian, Plevritis, Sylvia K.
Publicado 2020

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

por Brunner, Alayne L, Beck, Andrew H, Edris, Badreddin, Sweeney, Robert T, Zhu, Shirley X, Li, Rui, Montgomery, Kelli, Varma, Sushama, Gilks, Thea, Guo, Xiangqian, Foley, Joseph W, Witten, Daniela M, Giacomini, Craig P, Flynn, Ryan A, Pollack, Jonathan R, Tibshirani, Robert, Chang, Howard Y, van de Rijn, Matt, West, Robert B
Publicado 2012

Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors

por van IJzendoorn, David G.P., Matusiak, Magdalena, Charville, Gregory W., Spierenburg, Geert, Varma, Sushama, Colburg, Deana R.C., van de Sande, Michiel A.J., van Langevelde, Kirsten, Mohler, David G., Ganjoo, Kristen N., Bui, Nam Q., Avedian, Raffi S., Bovée, Judith V.M.G., Steffner, Robert, West, Robert B., van de Rijn, Matt
Publicado 2022

Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma

por Risom, Tyler, Glass, David R., Averbukh, Inna, Liu, Candace C., Baranski, Alex, Kagel, Adam, McCaffrey, Erin F., Greenwald, Noah F., Rivero-Gutiérrez, Belén, Strand, Siri H., Varma, Sushama, Kong, Alex, Keren, Leeat, Srivastava, Sucheta, Zhu, Chunfang, Khair, Zumana, Veis, Deborah J., Deschryver, Katherine, Vennam, Sujay, Maley, Carlo, Hwang, E. Shelley, Marks, Jeffrey R., Bendall, Sean C., Colditz, Graham A., West, Robert B., Angelo, Michael
Publicado 2022

Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

por Strand, Siri H., Rivero-Gutiérrez, Belén, Houlahan, Kathleen E., Seoane, Jose A., King, Lorraine M., Risom, Tyler, Simpson, Lunden A., Vennam, Sujay, Khan, Aziz, Cisneros, Luis, Hardman, Timothy, Harmon, Bryan, Couch, Fergus, Gallagher, Kristalyn, Kilgore, Mark, We, Shi, DeMichele, Angela, King, Tari, McAuliffe, Priscilla F., Nangia, Julie, Lee, Joanna, Tseng, Jennifer, Storniolo, Anna Maria, Thompson, Alastair M., Gupta, Gaorav P., Burns, Robyn, Veis, Deborah J., DeSchryver, Katherine, Zhu, Chunfang, Matusiak, Magdalena, Wang, Jason, Zhu, Shirley X., Tappenden, Jen, Ding, Daisy Yi, Zhang, Dadong, Luo, Jingqin, Jiang, Shu, Varma, Sushama, Anderson, Lauren, Straub, Cody, Srivastava, Sucheta, Curtis, Christina, Tibshirani, Rob, Angelo, Robert Michael, Hall, Allison, Owzar, Kouros, Polyak, Kornelia, Maley, Carlo, Marks, Jeffrey R., Colditz, Graham A., Shelley Hwang, E., West, Robert B.
Publicado 2023