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Jeremy L. Warner
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Journal Articles

Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal

Ino de Bruijn, Ritika Kundra, Brooke Mastrogiacomo, Thinh Ngoc Tran, Luke Sikina, Tali Mazor, Xiang Li, Angelica Ochoa, Gaofei Zhao, Bryan Lai, Adam Abeshouse, Diana Baiceanu, Ersin Ciftci, Ugur Dogrusoz, Andrew Dufilie, Ziya Erkoc, Elena Garcia Lara, Zhaoyuan Fu, Benjamin Gross, Charles Haynes, Allison Heath, David Higgins, Prasanna Jagannathan, Karthik Kalletla, Priti Kumari, James Lindsay, Aaron Lisman, Bas Leenknegt, Pieter Lukasse, Divya Madela, Ramyasree Madupuri, Pim van Nierop, Oleguer Plantalech, Joyce Quach, Adam C. Resnick, Sander Y.A. Rodenburg, Baby A. Satravada, Fedde Schaeffer, Robert Sheridan, Jessica Singh, Rajat Sirohi, Selcuk Onur Sumer, Sjoerd van Hagen, Avery Wang, Manda Wilson, Hongxin Zhang, Kelsey Zhu, Nicole Rusk, Samantha Brown, Jessica A. Lavery, Katherine S. Panageas, Julia E. Rudolph, Michele L. LeNoue-Newton, Jeremy L. Warner, Xindi Guo, Haley Hunter-Zinck, Thomas V. Yu, Shirin Pilai, Chelsea Nichols, Stuart M. Gardos, John Philip, AACR Project GENIE BPC Core Team, AACR Project GENIE Consortium, Kenneth L. Kehl, Gregory J. Riely, Deborah Schrag, Jocelyn Lee, Michael V. Fiandalo, Shawn M. Sweeney, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2023) 83 (23): 3861–3867.
https://doi.org/10.1158/0008-5472.CAN-23-0816
Published: 01 December 2023
View article titled, Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal
Open the PDF for Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal in another window
Includes: Supplementary data
Journal Articles

Abstract 1177: Genomic characteristics and clinical outcomes of early onset colorectal cancer (EOCRC): Findings from AACR Project GENIE Biopharma Collaborative registry

Enrique Sanz Garcia, Eric Chen, Marios Giannakis, Gregory J. Riely, Jeremy L. Warner, Michele L. LeNoue-Newton, Jessica Weiss, Katrina Hueniken, Kenneth L. Kehl, Deborah Schrag, Andrea Cercek, Kimmie Ng, AACR GENIE BPC Core Team
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 1177.
https://doi.org/10.1158/1538-7445.AM2023-1177
Published: 04 April 2023
View article titled, Abstract 1177: Genomic characteristics and clinical outcomes of early onset colorectal cancer (EOCRC): Findings from AACR Project GENIE Biopharma Collaborative registry
Journal Articles

Abstract 2620: Ignoring left truncation in overall survival within real-world genomic-phenomic data leads to inflated survival estimates

Samantha Brown, Jessica A. Lavery, Eva M. Lepisto, Caroline McCarthy, Hira Rizvi, Celeste Yu, Kenneth L. Kehl, Shawn M. Sweeney, Julia E. Rudolph, Nikolaus Schultz, Ritika Kundra, Brooke Mastrogiacomo, Phillipe Bedard, Jeremy L. Warner, Gregory J. Riely, Deborah Schrag, Katherine S. Panageas, The AACR Project GENIE Consortium
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 2620.
https://doi.org/10.1158/1538-7445.AM2021-2620
Published: 01 July 2021
View article titled, Abstract 2620: Ignoring left truncation in overall survival within real-world genomic-phenomic data leads to inflated survival estimates
Journal Articles

Abstract PS7-01: Characteristics and outcomes of SARS-CoV-2 infection in patients with invasive breast cancer (BC) from the COVID-19 and cancer consortium (CCC19) cohort study

Ali Raza Khaki, Dimpy P Shah, Maryam B Lustberg, Melissa K Accordino, Daniel G Stover, Gayathri Nagaraj, Donna R Rivera, Edith A Perez, Sara M Tolaney, Jeffrey Peppercorn, Petros Grivas, Jeremy L Warner, Corrie A Painter, Gilberto de Lima Lopes, Jr, Solange Peters, Michael A Thompson, Toni K Choueiri, Brian I Rini, Gary H Lyman, Nicole M Kuderer, Shaveta Vinayak
Journal: Cancer Research
Cancer Res (2021) 81 (4_Supplement): PS7-01.
https://doi.org/10.1158/1538-7445.SABCS20-PS7-01
Published: 15 February 2021
View article titled, Abstract PS7-01: Characteristics and outcomes of SARS-CoV-2 infection in patients with invasive breast cancer (BC) from the COVID-19 and cancer consortium (CCC19) cohort study
Journal Articles

Abstract 3222: The Virtual Molecular Tumor Board of the Variant Interpretation for Cancer Consortium: A systematic gateway connecting cancer genome interpretation and progress in genomic knowledgebases in cancer

Beth A. Pitel, Shruti Rao, Catherine Del Vecchio Fitz, Subha Madhavan, Rodrigo Dientsmann, Peter Horak, Ian King, Susan M. Mockus, Gordana Raca, Damian T. Rieke, Peter Rogan, Dmitriy Sonkin, David Tamborero, Ioannis S. Vlachos, Brian Walsh, Jeremy L. Warner, Malachi Griffith, Obi L. Griffith, Debyani Chakravarty, Alex H. Wagner
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 3222.
https://doi.org/10.1158/1538-7445.AM2020-3222
Published: 15 August 2020
View article titled, Abstract 3222: The Virtual Molecular Tumor Board of the Variant Interpretation for Cancer Consortium: A systematic gateway connecting cancer genome interpretation and progress in genomic knowledgebases in cancer
Journal Articles

Abstract 3215: ClinGen somatic cancer working group: Disseminating standardized cancer molecular diagnostic data and evidence through global collaboration and expert curation

Shruti Rao, Deborah Ritter, Arpad Danos, Gordana Raca, Angshumoy Roy, Kilannin Krysiak, Wan-Hsin Lin, Erica Barnell, Matthew McCoy, Beth Pitel, Dmitriy Sonkin, Jue Wang, Seyed Ali Hosseini, Shamini Selvarajah, Ian King, Rashmi Kanagal-Shamana, Xinjie Xu, Jeremy L. Warner, Funda Meric-Bernstam, Jason D. Merker, Marilyn Li, Alex H. Wagner, Malachi Griffith, Obi L. Griffith, Shashikant Kulkarni, Subha Madhavan
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 3215.
https://doi.org/10.1158/1538-7445.AM2020-3215
Published: 15 August 2020
View article titled, Abstract 3215: ClinGen somatic cancer working group: Disseminating standardized cancer molecular diagnostic data and evidence through global collaboration and expert curation
Journal Articles

Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records

Guergana K. Savova, Ioana Danciu, Folami Alamudun, Timothy Miller, Chen Lin, Danielle S. Bitterman, Georgia Tourassi, Jeremy L. Warner
Journal: Cancer Research
Cancer Res (2019) 79 (21): 5463–5470.
https://doi.org/10.1158/0008-5472.CAN-19-0579
Published: 01 November 2019
View article titled, Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records
Open the PDF for Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records in another window
Journal Articles

Abstract 3363: Mapping cancer: Employing geographic information systems (GIS) to explore co-authorship networks

Monica A. Gallagher, Jeremy L. Warner
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): 3363.
https://doi.org/10.1158/1538-7445.AM2019-3363
Published: 01 July 2019
View article titled, Abstract 3363: Mapping cancer: Employing geographic information systems (GIS) to explore co-authorship networks
Journal Articles

Abstract 5114: Deep phenotype extraction to facilitate cancer research: Extending DeepPhe to ovarian cancer

Alicia Beeghly-Fadiel, Jeremy L. Warner, Sean Finan, James Masanz, Harry Hochheiser, Guergana Savova
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): 5114.
https://doi.org/10.1158/1538-7445.AM2019-5114
Published: 01 July 2019
View article titled, Abstract 5114: Deep phenotype extraction to facilitate cancer research: Extending DeepPhe to ovarian cancer
Journal Articles

Abstract 1025: Clinical outcomes and differential tumor immune microenvironment in patients with small cell lung cancer and paraneoplastic syndromes

Wade T. Iams, Eileen Shiuan, Catherine B. Meador, Marc Roth, Jennifer Bordeaux, Christine Vaupel, Lucy L. Wang, Joseph T. Schneider, Jeremy L. Warner, Zhiguo Zhao, Christine M. Lovly
Journal: Cancer Research
Cancer Res (2018) 78 (13_Supplement): 1025.
https://doi.org/10.1158/1538-7445.AM2018-1025
Published: 01 July 2018
View article titled, Abstract 1025: Clinical outcomes and differential tumor immune microenvironment in patients with small cell lung cancer and paraneoplastic syndromes