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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

A cost-effective two-step approach for multi-cancer early detection in high-risk populations

Shuaipeng Geng, Shiyong Li, Wei Wu, Yinyin Chang, Mao Mao
Journal: Cancer Research Communications
Cancer Research Communications (2024)
https://doi.org/10.1158/2767-9764.CRC-24-0508
Published: 31 December 2024
View article titled, A cost-effective two-step approach for multi-cancer early detection in high-risk populations
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Includes: Supplementary data
Journal Articles

Tumor Expression of CD83 Reduces Glioma Progression and Is Associated with Reduced Immunosuppression

Malcolm F. McDonald, Rachel Naomi Curry, Isabella O’Reilly, Brittney Lozzi, Alexis Cervantes, Zhung-Fu Lee, Anna Rosenbaum, Peihao He, Carrie Mohila, Arif O. Harmanci, Akdes Serin Harmanci, Benjamin Deneen, Ganesh Rao
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (12): 3209–3223.
https://doi.org/10.1158/2767-9764.CRC-24-0281
Published: 30 December 2024
View article titled, Tumor Expression of CD83 Reduces Glioma Progression and Is Associated with Reduced Immunosuppression
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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

SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors

Theron Palmer, Michael D. Kessler, Xiaoshan M. Shao, Archana Balan, Mark Yarchoan, Neeha Zaidi, Tamara Y. Lopez-Vidal, Ali M. Saeed, Jessica Gore, Nilofer S. Azad, Elizabeth M. Jaffee, Alexander V. Favorov, Valsamo Anagnostou, Rachel Karchin, Daria A. Gaykalova, Elana J. Fertig, Ludmila Danilova
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (12): 3137–3150.
https://doi.org/10.1158/2767-9764.CRC-23-0309
Published: 16 December 2024
View article titled, SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors
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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

Mathematical Modeling Unveils Optimization Strategies for Targeted Radionuclide Therapy of Blood Cancers

Maxim Kuznetsov, Vikram Adhikarla, Enrico Caserta, Xiuli Wang, John E. Shively, Flavia Pichiorri, Russell C. Rockne
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (11): 2955–2967.
https://doi.org/10.1158/2767-9764.CRC-24-0306
Published: 14 November 2024
View article titled, Mathematical Modeling Unveils Optimization Strategies for Targeted Radionuclide Therapy of Blood Cancers
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Includes: Supplementary data
Journal Articles

Transcriptome Deconvolution Reveals Absence of Cancer Cell Expression Signature in Immune Checkpoint Blockade Response

Yu Amanda Guo, Tanmay Kulshrestha, Mei Mei Chang, Irfahan Kassam, Egor Revkov, Simone Rizzetto, Aaron C. Tan, Daniel S.W. Tan, Iain Beehuat Tan, Anders J. Skanderup
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (6): 1581–1596.
https://doi.org/10.1158/2767-9764.CRC-23-0442
Published: 26 June 2024
View article titled, Transcriptome Deconvolution Reveals Absence of Cancer Cell Expression Signature in Immune Checkpoint Blockade Response
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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

Spectral Flow Cytometry Methods and Pipelines for Comprehensive Immunoprofiling of Human Peripheral Blood and Bone Marrow

Milos Spasic, Esther R. Ogayo, Adrienne M. Parsons, Elizabeth A. Mittendorf, Peter van Galen, Sandra S. McAllister
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (3): 895–910.
https://doi.org/10.1158/2767-9764.CRC-23-0357
Published: 25 March 2024
View article titled, Spectral Flow Cytometry Methods and Pipelines for Comprehensive Immunoprofiling of Human Peripheral Blood and Bone Marrow
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Includes: Supplementary data
Journal Articles

A Pilot Study on Patient-specific Computational Forecasting of Prostate Cancer Growth during Active Surveillance Using an Imaging-informed Biomechanistic Model

Guillermo Lorenzo, Jon S. Heiselman, Michael A. Liss, Michael I. Miga, Hector Gomez, Thomas E. Yankeelov, Alessandro Reali, Thomas J.R. Hughes
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (3): 617–633.
https://doi.org/10.1158/2767-9764.CRC-23-0449
Published: 01 March 2024
View article titled, A Pilot Study on Patient-specific Computational Forecasting of Prostate Cancer Growth during Active Surveillance Using an Imaging-informed Biomechanistic Model
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Includes: Supplementary data
Journal Articles

Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell–intrinsic Stemness or Mesenchymality Characteristics

Julian Kreis, Bogac Aybey, Felix Geist, Benedikt Brors, Eike Staub
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (2): 516–529.
https://doi.org/10.1158/2767-9764.CRC-23-0383
Published: 23 February 2024
View article titled, Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell–intrinsic Stemness or Mesenchymality Characteristics
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Includes: Supplementary data
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

Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Nilesh Gardi, Rohan Chaubal, Pallavi Parab, Sunil Pachakar, Suyash Kulkarni, Tanuja Shet, Shalaka Joshi, Yogesh Kembhavi, Pratik Chandrani, Jelmar Quist, Pradnya Kowtal, Anita Grigoriadis, Rajiv Sarin, Raman Govindarajan, Sudeep Gupta
Journal: Cancer Research Communications
Cancer Research Communications (2024) 4 (2): 404–417.
https://doi.org/10.1158/2767-9764.CRC-23-0277
Published: 14 February 2024
View article titled, Natural History of Germline <em>BRCA1</em> Mutated and <em>BRCA</em> Wild-type Triple-negative 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

Clinical Outcomes and Evolution of Clonal Hematopoiesis in Patients with Newly Diagnosed Multiple Myeloma

Tarek H. Mouhieddine, Chidimma Nzerem, Robert Redd, Andrew Dunford, Matthew Leventhal, Romanos Sklavenitis-Pistofidis, Sabrin Tahri, Habib El-Khoury, David P. Steensma, Benjamin L. Ebert, Robert J. Soiffer, Jonathan J. Keats, Shaadi Mehr, Daniel Auclair, Irene M. Ghobrial, Adam S. Sperling, Chip Stewart, Gad Getz
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (12): 2560–2571.
https://doi.org/10.1158/2767-9764.CRC-23-0093
Published: 18 December 2023
View article titled, Clinical Outcomes and Evolution of Clonal Hematopoiesis in Patients with Newly Diagnosed Multiple Myeloma
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Includes: Supplementary data
Journal Articles

Exogenous Sequences in Tumors and Immune Cells (Exotic): A Tool for Estimating the Microbe Abundances in Tumor RNA-seq Data

Rebecca Hoyd, Caroline E. Wheeler, YunZhou Liu, Malvenderjit S. Jagjit Singh, Mitchell Muniak, Ning Jin, Nicholas C. Denko, David P. Carbone, Xiaokui Mo, Daniel J. Spakowicz
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (11): 2375–2385.
https://doi.org/10.1158/2767-9764.CRC-22-0435
Published: 21 November 2023
View article titled, Exogenous Sequences in Tumors and Immune Cells (Exotic): A Tool for Estimating the Microbe Abundances in Tumor RNA-seq Data
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Includes: Supplementary data
Journal Articles

Mathematical Modeling Identifies Optimum Palbociclib-fulvestrant Dose Administration Schedules for the Treatment of Patients with Estrogen Receptor–positive Breast Cancer

Yu-Chen Cheng, Shayna Stein, Agostina Nardone, Weihan Liu, Wen Ma, Gabriella Cohen, Cristina Guarducci, Thomas O. McDonald, Rinath Jeselsohn, Franziska Michor
Journal: Cancer Research Communications
Cancer Research Communications (2023) 3 (11): 2331–2344.
https://doi.org/10.1158/2767-9764.CRC-23-0257
Published: 16 November 2023
View article titled, Mathematical Modeling Identifies Optimum Palbociclib-fulvestrant Dose Administration Schedules for the Treatment of Patients with Estrogen Receptor–positive Breast Cancer
Open the PDF for Mathematical Modeling Identifies Optimum Palbociclib-fulvestrant Dose Administration Schedules for the Treatment of Patients with Estrogen Receptor–positive Breast Cancer in another window
Includes: Supplementary data