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Benjamin Haibe-Kains
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Journal Articles

Genomic, Epigenomic, and Transcriptomic Inter- and Intratumor Heterogeneity in Desmoid Tumors

Chelsea De Bellis, Sujay Vennam, Christopher Eeles, Pegah Rahimizadeh, Justin Cates, Thomas Stricker, Jenny Hoffman, Kristen Ganjoo, Gregory W. Charville, Benjamin Haibe-Kains, Matt van de Rijn, Joanna Przybyl
Journal: Clinical Cancer Research
Clin Cancer Res (2025) 31 (1): 205–216.
https://doi.org/10.1158/1078-0432.CCR-24-1240
Published: 06 January 2025
View article titled, Genomic, Epigenomic, and Transcriptomic Inter- and Intratumor Heterogeneity in Desmoid Tumors
Open the PDF for Genomic, Epigenomic, and Transcriptomic Inter- and Intratumor Heterogeneity in Desmoid Tumors in another window
Includes: Supplementary data
Journal Articles

Safety, Immunologic, and Clinical Activity of Durvalumab in Combination with Olaparib or Cediranib in Advanced Leiomyosarcoma: Results of the DAPPER Clinical Trial.

Abdulazeez Salawu, Ben X. Wang, Ming Han, Caryn Geady, Alya Heirali, Hal K. Berman, Thomas D. Pfister, Alberto Hernando-Calvo, Esmail Mutahar Al-Ezzi, Lee-Anne Stayner, Abha A. Gupta, Olubukola Ayodele, Bernard Lam, Aaron R. Hansen, Anna Spreafico, Philippe L. Bedard, Marcus O. Butler, Lisa Avery, Bryan Coburn, Benjamin Haibe-Kains, Lillian L. Siu, Albiruni R. Abdul Razak
Journal: Clinical Cancer Research
Clin Cancer Res (2023) 29 (20): 4128–4138.
https://doi.org/10.1158/1078-0432.CCR-23-1137
Published: 13 October 2023
View article titled, Safety, Immunologic, and Clinical Activity of Durvalumab in Combination with Olaparib or Cediranib in Advanced Leiomyosarcoma: Results of the DAPPER Clinical Trial.
Open the PDF for Safety, Immunologic, and Clinical Activity of Durvalumab in Combination with Olaparib or Cediranib in Advanced Leiomyosarcoma: Results of the DAPPER Clinical Trial. in another window
Includes: Supplementary data
Journal Articles

Abstract PO-071: Characterizing transcriptomic indicators of radiosensitivity in cancer and identifying sensitizing therapeutic agents

Ian Smith, Rachel Bell, Meghan Lambie, Benjamin Haibe-Kains, Scott Bratman
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (8_Supplement): PO-071.
https://doi.org/10.1158/1557-3265.RADSCI21-PO-071
Published: 15 April 2021
View article titled, Abstract PO-071: Characterizing transcriptomic indicators of radiosensitivity in cancer and identifying sensitizing therapeutic agents
Journal Articles

Abstract IA-15: Platforms to improve reproducibility in artificial intelligence research

Benjamin Haibe-Kains, Anthony Mammoliti, Minoru Nakano
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): IA-15.
https://doi.org/10.1158/1557-3265.ADI21-IA-15
Published: 01 March 2021
View article titled, Abstract IA-15: Platforms to improve reproducibility in artificial intelligence research
Journal Articles

Abstract PO-031: Evaluating clinical utility of organs-at-risk segmentation in head & neck cancer by simple open-source 3D CNNs

Joseph Marsilla, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-031.
https://doi.org/10.1158/1557-3265.ADI21-PO-031
Published: 01 March 2021
View article titled, Abstract PO-031: Evaluating clinical utility of organs-at-risk segmentation in head & neck cancer by simple open-source 3D CNNs
Journal Articles

Abstract PO-030: Radiomics for head and neck cancer prognostication: results from the RADCURE machine learning challenge

Michal Kazmierski, Mattea Welch, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-030.
https://doi.org/10.1158/1557-3265.ADI21-PO-030
Published: 01 March 2021
View article titled, Abstract PO-030: Radiomics for head and neck cancer prognostication: results from the RADCURE machine learning challenge
Journal Articles

Abstract PR-07: ORCESTRA: A platform for orchestrating and sharing high-throughput multimodal data analyses

Anthony Mammoliti, Petr Smirnov, Minoru Nakano, Zhaleh Safikhani, Sisira Nair, Arvind Singh Mer, Chantal Ho, Gangesh Beri, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PR-07.
https://doi.org/10.1158/1557-3265.ADI21-PR-07
Published: 01 March 2021
View article titled, Abstract PR-07: ORCESTRA: A platform for orchestrating and sharing high-throughput multimodal data analyses
Journal Articles

Abstract PO-034: The prediction of mandibular osteoradionecrosis in head and neck cancer patients using CT-derived radiomics features

Reza Reiazi, Mattea Welch, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-034.
https://doi.org/10.1158/1557-3265.ADI21-PO-034
Published: 01 March 2021
View article titled, Abstract PO-034: The prediction of mandibular osteoradionecrosis in head and neck cancer patients using CT-derived radiomics features
Journal Articles

Abstract PO-033: The impact of the variation of CT scanner on the prediction of HPV status in head & neck cancer patients

Reza Reiazi, Collin Arrowsmith, Farnoosh Abbas-Aghababazadeh, Christopher Eles, Aria Rezaie, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-033.
https://doi.org/10.1158/1557-3265.ADI21-PO-033
Published: 01 March 2021
View article titled, Abstract PO-033: The impact of the variation of CT scanner on the prediction of HPV status in head & neck cancer patients
Journal Articles

Abstract PO-066: Data standardization, integration and meta-analysis of preclinical pharmacogenomics studies for gene expression biomarker discovery

Petr Smirnov, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-066.
https://doi.org/10.1158/1557-3265.ADI21-PO-066
Published: 01 March 2021
View article titled, Abstract PO-066: Data standardization, integration and meta-analysis of preclinical pharmacogenomics studies for gene expression biomarker discovery
Journal Articles

Abstract PO-049: Pseudo-alignment resolution in discriminating mouse reads

Soheil Jahangiri-Tazehkand, Farnoosh Agha-Babazadeh, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-049.
https://doi.org/10.1158/1557-3265.ADI21-PO-049
Published: 01 March 2021
View article titled, Abstract PO-049: Pseudo-alignment resolution in discriminating mouse reads
Journal Articles

Abstract PO-070: Bimodality of gene expression in cancer patient tumors as interpretable biomarkers for drug sensitivity

Wail Ba-alawi, Sisira Kadambat Nair, Bo Li, Anthony Mammoliti, Petr Smirnov, Arvind Singh Mer, Linda Penn, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-070.
https://doi.org/10.1158/1557-3265.ADI21-PO-070
Published: 01 March 2021
View article titled, Abstract PO-070: Bimodality of gene expression in cancer patient tumors as interpretable biomarkers for drug sensitivity
Journal Articles

Abstract PO-051: Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: Quality evaluation of nasopharyngeal carcinoma

Jun Won Kim, Joseph Marsilla, Michal Kazmierski, Denis Tkachuk, Benjamin Haibe-Kains, Andrew Hope
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-051.
https://doi.org/10.1158/1557-3265.ADI21-PO-051
Published: 01 March 2021
View article titled, Abstract PO-051: Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: Quality evaluation of nasopharyngeal carcinoma
Journal Articles

Abstract PO-052: Exploring patient derived xenografts based pharmacogenomic data for precision oncology

Arvind Singh Mer, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2021) 27 (5_Supplement): PO-052.
https://doi.org/10.1158/1557-3265.ADI21-PO-052
Published: 01 March 2021
View article titled, Abstract PO-052: Exploring patient derived xenografts based pharmacogenomic data for precision oncology
Journal Articles

Abstract B13: Utilizing metabolic reprogramming to regulate fibroblast phenotype and reduce radiation fibrosis

Xiao Zhao, Pamela Psarianos, David Goldstein, Ralph Gilbert, Ian Witterick, Laurie Ailles, Benjamin Haibe-Kains, Fei-Fei Liu
Journal: Clinical Cancer Research
Clin Cancer Res (2020) 26 (12_Supplement_2): B13.
https://doi.org/10.1158/1557-3265.AACRAHNS19-B13
Published: 15 June 2020
View article titled, Abstract B13: Utilizing metabolic reprogramming to regulate fibroblast phenotype and reduce radiation fibrosis
Journal Articles

Abstract 33: Drug sensitivity prediction modeling from genomics, transcriptomics and inferred protein activity

Hassan Mahmoud, Benjamin Haibe-Kains
Journal: Clinical Cancer Research
Clin Cancer Res (2020) 26 (12_Supplement_1): 33.
https://doi.org/10.1158/1557-3265.ADVPRECMED20-33
Published: 15 June 2020
View article titled, Abstract 33: Drug sensitivity prediction modeling from genomics, transcriptomics and inferred protein activity
Journal Articles

Organoid Cultures as Preclinical Models of Non–Small Cell Lung Cancer

Ruoshi Shi, Nikolina Radulovich, Christine Ng, Ni Liu, Hirotsugu Notsuda, Michael Cabanero, Sebastiao N. Martins-Filho, Vibha Raghavan, Quan Li, Arvind Singh Mer, Joshua C. Rosen, Ming Li, Yu-Hui Wang, Laura Tamblyn, Nhu-An Pham, Benjamin Haibe-Kains, Geoffrey Liu, Nadeem Moghal, Ming-Sound Tsao
Journal: Clinical Cancer Research
Clin Cancer Res (2020) 26 (5): 1162–1174.
https://doi.org/10.1158/1078-0432.CCR-19-1376
Published: 02 March 2020
View article titled, Organoid Cultures as Preclinical Models of Non–Small Cell Lung Cancer
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Includes: Supplementary data
Journal Articles

Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma

Gregory M. Chen, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Zhaleh Safikhani, Deena M.A. Gendoo, Giovanni Parmigiani, Michael Birrer, Benjamin Haibe-Kains, Levi Waldron
Journal: Clinical Cancer Research
Clin Cancer Res (2018) 24 (20): 5037–5047.
https://doi.org/10.1158/1078-0432.CCR-18-0784
Published: 15 October 2018
View article titled, Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma
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Includes: Supplementary data
Journal Articles

Administration of Hypoxia-Activated Prodrug Evofosfamide after Conventional Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Preclinical Models of Colorectal Cancer

Jennifer Haynes, Trevor D. McKee, Andrew Haller, Yadong Wang, Cherry Leung, Deena M.A. Gendoo, Evelyne Lima-Fernandes, Antonija Kreso, Robin Wolman, Eva Szentgyorgyi, Douglass C. Vines, Benjamin Haibe-Kains, Bradly G. Wouters, Ur Metser, David A. Jaffray, Myles Smith, Catherine A. O'Brien
Journal: Clinical Cancer Research
Series: Author Choice
Clin Cancer Res (2018) 24 (9): 2116–2127.
https://doi.org/10.1158/1078-0432.CCR-17-1715
Published: 30 April 2018
View article titled, Administration of Hypoxia-Activated Prodrug Evofosfamide after Conventional Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Preclinical Models of Colorectal Cancer
Open the PDF for Administration of Hypoxia-Activated Prodrug Evofosfamide after Conventional Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Preclinical Models of Colorectal Cancer in another window
Includes: Supplementary data
Journal Articles

A Genome-Wide Aberrant RNA Splicing in Patients with Acute Myeloid Leukemia Identifies Novel Potential Disease Markers and Therapeutic Targets

Sophia Adamia, Benjamin Haibe-Kains, Patrick M. Pilarski, Michal Bar-Natan, Samuel Pevzner, Herve Avet-Loiseau, Laurence Lode, Sigitas Verselis, Edward A. Fox, John Burke, Ilene Galinsky, Ibiayi Dagogo-Jack, Martha Wadleigh, David P. Steensma, Gabriela Motyckova, Daniel J. Deangelo, John Quackenbush, Richard Stone, James D. Griffin
Journal: Clinical Cancer Research
Clin Cancer Res (2014) 20 (5): 1135–1145.
https://doi.org/10.1158/1078-0432.CCR-13-0956
Published: 02 March 2014
View article titled, A Genome-Wide Aberrant RNA Splicing in Patients with Acute Myeloid Leukemia Identifies Novel Potential Disease Markers and Therapeutic Targets
Open the PDF for A Genome-Wide Aberrant RNA Splicing in Patients with Acute Myeloid Leukemia Identifies Novel Potential Disease Markers and Therapeutic Targets in another window
Includes: Supplementary data