Publications by authors named "Alexander Baras"

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Context-dependent MAN1A1 protein expression in metastatic breast cancer progression predicts patient survival.
Nicole M Jenkinson, Sarah Hughes, Alexander Baras, Alan Meeker, Pedram Argani

BMC Cancer· December 2025

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Atypical intraductal proliferation (AIP) of the prostate: Findings in repeat biopsy or radical prostatectomy in patients who met pathologic criteria for active surveillance.
Ruihe Lin, Huili Li, Ezra Baraban, Tamara Lotan, Angelo DeMarzo, Alexander Baras

Hum Pathol· June 2025

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WITHDRAWN: Atypical Intraductal Proliferation (AIP) of the Prostate: Findings in Repeat Biopsy or Radical Prostatectomy in Patients who Met Pathologic Criteria for Active Surveillance.
Ruihe Lin, Huili Li, Ezra Baraban, Tamara Lotan, Angelo DeMarzo, Alexander Baras

Hum Pathol· June 2025

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Evaluation of a Task-Specific Self-Supervised Learning Framework in Digital Pathology Relative to Transfer Learning Approaches and Existing Foundation Models.
Tawsifur Rahman, Alexander S Baras, Rama Chellappa

Mod Pathol· January 2025

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Concordance of Whole-Slide Imaging and Conventional Light Microscopy for Assessment of Pathologic Response Following Neoadjuvant Therapy for Lung Cancer.
Julie S Deutsch, Daphne Wang, Krista Y Chen, Ashley Cimino-Mathews, Elizabeth D Thompson, Alexander S Baras

Lab Invest· January 2025

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The Journey to Improve the College of American Pathologists Cancer Biomarker Reporting Protocols.
Brett Baskovich, Alexander Baras, Raja R Seethala, Patrick L Fitzgibbons, Frank Schneider

Arch Pathol Lab Med· October 2024

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Characterization of Non-Monotonic Relationships between Tumor Mutational Burden and Clinical Outcomes.
Jordan Anaya, Julia Kung, Alexander S Baras

Cancer Res Commun· July 2024

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Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology.
Haoyang Mi, Shamilene Sivagnanam, Won Jin Ho, Shuming Zhang, Daniel Bergman, Alexander S Baras

Brief Bioinform· July 2024

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Analysis of 3D pathology samples using weakly supervised AI.
Andrew H Song, Mane Williams, Drew F K Williamson, Sarah S L Chow, Guillaume Jaume, Alexander S Baras

Cell· May 2024

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Multiple-instance learning of somatic mutations for the classification of tumour type and the prediction of microsatellite status.
Jordan Anaya, John-William Sidhom, Faisal Mahmood, Alexander S Baras

Nat Biomed Eng· January 2024

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A deep learning model to triage and predict adenocarcinoma on pancreas cytology whole slide imaging.
Andrew Sohn, Daniel Miller, Efrain Ribeiro, Nakul Shankar, Syed Ali, Alexander Baras

Sci Rep· October 2023

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Precision Oncology Core Data Model to Support Clinical Genomics Decision Making.
Taxiarchis Botsis, Joseph C Murray, Paola Ghanem, Archana Balan, Alexander Kernagis, Alexander S Baras

JCO Clin Cancer Inform· April 2023

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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,

Cancer Res Commun· March 2023

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Placental bands on MRI in the setting of placenta accreta spectrum: Case report with radiologic-pathologic correlation.
Robert Weinstein, Arthur Vaught, Alexander Baras, Erin Gomez

Radiol Case Rep· February 2023

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Genomic Landscapes and Hallmarks of Mutant RAS in Human Cancers.
Robert B Scharpf, Archana Balan, Biagio Ricciuti, Jacob Fiksel, Christopher Cherry, Alexander S Baras

Cancer Res· November 2022

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Deep learning reveals predictive sequence concepts within immune repertoires to immunotherapy.
John-William Sidhom, Giacomo Oliveira, Petra Ross-MacDonald, Megan Wind-Rotolo, Catherine J Wu, Alexander S Baras

Sci Adv· September 2022

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Spatial UMAP and Image Cytometry for Topographic Immuno-oncology Biomarker Discovery.
Nicolas A Giraldo, Sneha Berry, Etienne Becht, Deniz Ates, Kara M Schenk, Alexander S Baras

Cancer Immunol Res· November 2021

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Predictive models of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer using nuclear morphology and tissue architecture.
Haoyang Mi, Trinity J Bivalacqua, Max Kates, Roland Seiler, Peter C Black, Alexander S Baras

Cell Rep Med· September 2021

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Deep learning identifies antigenic determinants of severe SARS-CoV-2 infection within T-cell repertoires.
John-William Sidhom, Alexander S Baras

Sci Rep· July 2021

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Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade.
Sneha Berry, Nicolas A Giraldo, Benjamin F Green, Tricia R Cottrell, Julie E Stein, Alexander Baras

Science· June 2021

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Deep learning for diagnosis of acute promyelocytic leukemia via recognition of genomically imprinted morphologic features.
John-William Sidhom, Ingharan J Siddarthan, Bo-Shiun Lai, Adam Luo, Bryan C Hambley, Alexander S Baras

NPJ Precis Oncol· May 2021

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Author Correction: DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires.
John-William Sidhom, H Benjamin Larman, Drew M Pardoll, Alexander S Baras

Nat Commun· April 2021

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DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires.
John-William Sidhom, H Benjamin Larman, Drew M Pardoll, Alexander S Baras

Nat Commun· March 2021

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Identification of BXDC2 as a Key Downstream Effector of the Androgen Receptor in Modulating Cisplatin Sensitivity in Bladder Cancer.
Guiyang Jiang, Yuki Teramoto, Takuro Goto, Taichi Mizushima, Satoshi Inoue, Alexander S Baras

Cancers (Basel)· February 2021

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College of American Pathologists Cancer Protocols: From Optimizing Cancer Patient Care to Facilitating Interoperable Reporting and Downstream Data Use.
Vanda F Torous, Ross W Simpson, Jyoti P Balani, Alexander S Baras, Michael A Berman

JCO Clin Cancer Inform· January 2021

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