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Journal Articles

Autofluorescence Virtual Staining System for H&E Histology and Multiplex Immunofluorescence Applied to Immuno-Oncology Biomarkers in Lung Cancer

Jessica Loo, Marc Robbins, Carson McNeil, Tadayuki Yoshitake, Charles Santori, Chuanhe (Jay) Shan, Saurabh Vyawahare, Hardik Patel, Tzu Chien Wang, Robert Findlater, David F. Steiner, Sudha Rao, Michael Gutierrez, Yang Wang, Adrian C. Sanchez, Raymund Yin, Vanessa Velez, Julia S. Sigman, Patricia Coutinho de Souza, Hareesh Chandrupatla, Liam Scott, Shamira S. Weaver, Chung-Wein Lee, Ehud Rivlin, Roman Goldenberg, Suzana S. Couto, Peter Cimermancic, Pok Fai Wong
Journal: Cancer Research Communications
Cancer Research Communications (2025) 5 (1): 54–65.
https://doi.org/10.1158/2767-9764.CRC-24-0327
Published: 08 January 2025
View article titled, Autofluorescence Virtual Staining System for H&E Histology and Multiplex Immunofluorescence Applied to Immuno-Oncology Biomarkers in Lung Cancer
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Includes: Supplementary data
Journal Articles

DeePathNet: A Transformer-Based Deep Learning Model Integrating Multiomic Data with Cancer Pathways

Zhaoxiang Cai, Rebecca C. Poulos, Adel Aref, Phillip J. Robinson, Roger R. Reddel, Qing Zhong
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (12): 3151–3164.
https://doi.org/10.1158/2767-9764.CRC-24-0285
Published: 18 December 2024
View article titled, DeePathNet: A Transformer-Based Deep Learning Model Integrating Multiomic Data with Cancer Pathways
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Includes: Supplementary data
Journal Articles

Pan-Cancer Analysis of Homologous Recombination Deficiency in Cell Lines

Anne E. Dodson, Sol Shenker, Pamela Sullivan, Sumeet U. Nayak, Chris Middleton, Michael McGuire, Edmond Chipumuro, Yuji Mishina, Erica R. Tobin, Louise Cadzow, Andrew A. Wylie, Dipen Sangurdekar
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (12): 3084–3098.
https://doi.org/10.1158/2767-9764.CRC-24-0316
Published: 06 December 2024
View article titled, Pan-Cancer Analysis of Homologous Recombination Deficiency in Cell Lines
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Includes: Supplementary data
Journal Articles

Artificial Intelligence–Assisted Cancer Status Detection in Radiology Reports

Ankur Arya, Andrew Niederhausern, Nadia Bahadur, Neil J. Shah, Chelsea Nichols, Avijit Chatterjee, John Philip
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (4): 1041–1049.
https://doi.org/10.1158/2767-9764.CRC-24-0064
Published: 09 April 2024
View article titled, Artificial Intelligence–Assisted Cancer Status Detection in Radiology Reports
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Journal Articles

Estrogen Receptor Mutations as Novel Targets for Immunotherapy in Metastatic Estrogen Receptor–positive Breast Cancer

Jonathan Goldberg, Na Qiao, Jennifer L. Guerriero, Brett Gross, Yagiz Meneksedag, Yoshimi F. Lu, Anne V. Philips, Tasnim Rahman, Funda Meric-Bernstam, Jason Roszik, Ken Chen, Rinath Jeselsohn, Sara M. Tolaney, George E. Peoples, Gheath Alatrash, Elizabeth A. Mittendorf
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (2): 496–504.
https://doi.org/10.1158/2767-9764.CRC-23-0244
Published: 22 February 2024
View article titled, Estrogen Receptor Mutations as Novel Targets for Immunotherapy in Metastatic Estrogen Receptor–positive Breast Cancer
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Includes: Supplementary data
Journal Articles

A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Cankun Wang, Anjun Ma, Yingjie Li, Megan E. McNutt, Shiqi Zhang, Jiangjiang Zhu, Rebecca Hoyd, Caroline E. Wheeler, Lary A. Robinson, Carlos H.F. Chan, Yousef Zakharia, Rebecca D. Dodd, Cornelia M. Ulrich, Sheetal Hardikar, Michelle L. Churchman, Ahmad A. Tarhini, Eric A. Singer, Alexandra P. Ikeguchi, Martin D. McCarter, Nicholas Denko, Gabriel Tinoco, Marium Husain, Ning Jin, Afaf E.G. Osman, Islam Eljilany, Aik Choon Tan, Samuel S. Coleman, Louis Denko, Gregory Riedlinger, Bryan P. Schneider, Daniel Spakowicz, Qin Ma, the exORIEN Consortium
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (2): 293–302.
https://doi.org/10.1158/2767-9764.CRC-23-0213
Published: 05 February 2024
View article titled, A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset
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Includes: Supplementary data
Journal Articles

A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing

Chien-Wei Wang, Simon D. Weaver, Nicha Boonpattrawong, Naviya Schuster-Little, Manish Patankar, Rebecca J. Whelan
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (1): 253–263.
https://doi.org/10.1158/2767-9764.CRC-23-0327
Published: 31 January 2024
View article titled, A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing
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Includes: Supplementary data
Journal Articles

A Systems Biology Approach to Understand the Racial Disparities in Colorectal Cancer

Annabelle Nwaokorie, Walter Kolch, Dirk Fey
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (1): 103–117.
https://doi.org/10.1158/2767-9764.CRC-22-0464
Published: 12 January 2024
View article titled, A Systems Biology Approach to Understand the Racial Disparities in Colorectal Cancer
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Includes: Supplementary data
Journal Articles

Predicting Mammogram Screening Follow Through with Electronic Health Record and Geographically Linked Data

Matthew Davis, Kit Simpson, Leslie A. Lenert, Vanessa Diaz, Alexander V. Alekseyenko
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (10): 2126–2132.
https://doi.org/10.1158/2767-9764.CRC-23-0263
Published: 19 October 2023
View article titled, Predicting Mammogram Screening Follow Through with Electronic Health Record and Geographically Linked Data
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Includes: Supplementary data
Journal Articles

Accelerating Cancer Histopathology Workflows with Chemical Imaging and Machine Learning

Kianoush Falahkheirkhah, Sudipta S. Mukherjee, Sounak Gupta, Loren Herrera-Hernandez, Michael R. McCarthy, Rafael E. Jimenez, John C. Cheville, Rohit Bhargava
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (9): 1875–1887.
https://doi.org/10.1158/2767-9764.CRC-23-0226
Published: 18 September 2023
View article titled, Accelerating Cancer Histopathology Workflows with Chemical Imaging and Machine Learning
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Includes: Supplementary data
Journal Articles

Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness

Maria-Fernanda Senosain, Yong Zou, Khushbu Patel, Shilin Zhao, Alexis Coullomb, Dianna J. Rowe, Jonathan M. Lehman, Jonathan M. Irish, Fabien Maldonado, Michael N. Kammer, Vera Pancaldi, Carlos F. Lopez
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (7): 1350–1365.
https://doi.org/10.1158/2767-9764.CRC-22-0373
Published: 26 July 2023
View article titled, Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness
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Includes: Supplementary data
Journal Articles

Multi-institutional Prognostic Modeling in Head and Neck Cancer: Evaluating Impact and Generalizability of Deep Learning and Radiomics

Michal Kazmierski, Mattea Welch, Sejin Kim, Chris McIntosh, Katrina Rey-McIntyre, Shao Hui Huang, Tirth Patel, Tony Tadic, Michael Milosevic, Fei-Fei Liu, Adam Ryczkowski, Joanna Kazmierska, Zezhong Ye, Deborah Plana, Hugo J.W.L. Aerts, Benjamin H. Kann, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (6): 1140–1151.
https://doi.org/10.1158/2767-9764.CRC-22-0152
Published: 29 June 2023
View article titled, Multi-institutional Prognostic Modeling in Head and Neck Cancer: Evaluating Impact and Generalizability of Deep Learning and Radiomics
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Includes: Supplementary data
Journal Articles

Probabilistic Mixture Models Improve Calibration of Panel-derived Tumor Mutational Burden in the Context of both Tumor-normal and Tumor-only Sequencing

Jordan Anaya, John-William Sidhom, Craig A. Cummings, Alexander S. Baras, for AACR Project GENIE Consortium
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (3): 501–509.
https://doi.org/10.1158/2767-9764.CRC-22-0339
Published: 28 March 2023
View article titled, Probabilistic Mixture Models Improve Calibration of Panel-derived Tumor Mutational Burden in the Context of both Tumor-normal and Tumor-only Sequencing
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Includes: Supplementary data
Journal Articles

Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt, Stéphane Elie Grauzam, David Lewin, Peggi Angel, Lewis R. Roberts, Richard Drake, Anand S. Mehta
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (3): 383–394.
https://doi.org/10.1158/2767-9764.CRC-22-0422
Published: 06 March 2023
View article titled, Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma
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Includes: Supplementary data
Journal Articles

Brain Neural Progenitors are New Predictive Biomarkers for Breast Cancer Hormonotherapy

Agnes Basseville, Chiara Cordier, Fadoua Ben Azzouz, Wilfried Gouraud, Hamza Lasla, Fabien Panloup, Mario Campone, Pascal Jézéquel
Journal: Cancer Research Communications
Cancer Research Communications (2022) 2 (8): 857–869.
https://doi.org/10.1158/2767-9764.CRC-21-0090
Published: 24 August 2022
View article titled, Brain Neural Progenitors are New Predictive Biomarkers for Breast Cancer Hormonotherapy
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Includes: Supplementary data