Publications by authors named "Alejandro A Schaffer"

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Exonic Variation and Its Clinical Impact in 7221 Old Order Amish.
Braxton D Mitchell, Ebuka Onyenobi, Joshua P Lewis, Brady Gaynor, James A Perry

Am J Med Genet A· December 2025

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Hypoxia-induced EGR1 remodels neutrophils to suppress antitumor immunity.
Tian-Gen Chang, Jay Friedman, Paul E Clavijo, Yvette Robbins, Marco Craveiro

Sci Immunol· December 2025

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Re-evaluation of the contribution of variants to antibody deficiency.
Hassan Abolhassani, Andres Caballero-Oteyza, Mingyu Yang, Michele Proietti, Samaneh Delavari

J Hum Immun· November 2025

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A machine learning framework for supervised treatment response prediction from tumor transcriptomics: A large-scale pan-cancer study.
Lipika Ray Pal, Edward Michael Gertz, Nishanth Ulhas Nair, Sumit Mukherjee, Sumeet Patiyal, Alejandro A Schaffer

bioRxiv· November 2025

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Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer.
Xuan Cindy Li, Yuelin Liu, Alejandro A Schäffer, Stephen M Mount, S Cenk Sahinalp

Bioinformatics· July 2025

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A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment.
Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Padma Sheila Rajagopal, Gulzar N Daya

NAR Cancer· June 2025

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The effect of HLA genotype on disease onset and severity in CTLA-4 insufficiency.
Sara Posadas-Cantera, Noriko Mitsuiki, Florian Emmerich, Virginia Patiño, Hanns-Martin Lorenz

Front Immunol· May 2025

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Ancestral Differences in Anticancer Treatment Efficacy and Their Underlying Genomic and Molecular Alterations.
Mei Luo, Jingwen Yang, Alejandro A Schäffer, Chengxuan Chen, Yuan Liu

Cancer Discov· March 2025

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Hallmarks of artificial intelligence contributions to precision oncology.
Tian-Gen Chang, Seongyong Park, Alejandro A Schäffer, Peng Jiang, Eytan Ruppin

Nat Cancer· March 2025

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Finding Multiple Optimal Solutions to an Integer Linear Program by Random Perturbations of Its Objective Function.
Noah Schulhof, Pattara Sukprasert, Eytan Ruppin, Samir Khuller, Alejandro A Schäffer

Algorithms· March 2025

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Single-cell-guided identification of logic-gated antigen combinations for designing effective and safe CAR therapy.
Sanna Madan, Tian-Gen Chang, Alexandra R Harris, Huaitian Liu, Andrew Martinez

bioRxiv· March 2025

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Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma.
Sapir Cohen Shvefel, Joy A Pai, Yingying Cao, Lipika R Pal, Osnat Bartok

Cancer Discov· January 2025

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confers resistance to antiandrogens: mechanism and therapeutic implications.
Arunachalam Sekar, Rishita Chatterjee, Boobash Raj Selvadurai, Lipika R Pal, Aakanksha Verma, Alejändro A Schaffer

bioRxiv· January 2025

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Temporal genomic analysis of homogeneous tumor models reveals key regulators of immune evasion in melanoma.
Sapir Cohen Shvefel, Joy A Pai, Yingying Cao, Lipika R Pal, Osnat Bartok, Alejandro A Schaffer

Cancer Discov· November 2024

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Chromosome 7 Gain Compensates for Chromosome 10 Loss in Glioma.
Nishanth Ulhas Nair, Alejandro A Schäffer, E Michael Gertz, Kuoyuan Cheng, Johanna Zerbib

Cancer Res· October 2024

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Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes.
Welles Robinson, Joshua K Stone, Fiorella Schischlik, Billel Gasmi, Michael C Kelly

Sci Adv· July 2024

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PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors.
Sanju Sinha, Rahulsimham Vegesna, Sumit Mukherjee, Ashwin V Kammula, Saugato Rahman Dhruba

Nat Cancer· June 2024

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Outcome differences by sex in oncology clinical trials.
Ashwin V Kammula, Alejandro A Schäffer, Padma Sheila Rajagopal, Razelle Kurzrock, Eytan Ruppin

Nat Commun· March 2024

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ClinGen guidance for use of the PP1/BS4 co-segregation and PP4 phenotype specificity criteria for sequence variant pathogenicity classification.
Leslie G Biesecker, Alicia B Byrne, Steven M Harrison, Tina Pesaran, Alejandro A Schäffer

Am J Hum Genet· January 2024

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A systematic analysis of the landscape of synthetic lethality-driven precision oncology.
Alejandro A Schäffer, Youngmin Chung, Ashwin V Kammula, Eytan Ruppin, Joo Sang Lee

Med· January 2024

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Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas.
Nishanth Ulhas Nair, Alejandro A Schäffer, E Michael Gertz, Kuoyuan Cheng, Johanna Zerbib

bioRxiv· January 2024

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Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion.
Sapir Cohen Shvefel, Joy A Pai, Yingying Cao, Lipika R Pal, Ronen Levy

bioRxiv· November 2023

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Pan-Cancer Analysis of Patient Tumor Single-Cell Transcriptomes Identifies Promising Selective and Safe Chimeric Antigen Receptor Targets in Head and Neck Cancer.
Sanna Madan, Sanju Sinha, Tiangen Chang, J Silvio Gutkind, Ezra E W Cohen

Cancers (Basel)· October 2023

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Glucose-6-phosphate dehydrogenase deficiency and long-term risk of immune-related disorders.
Ariel Israel, Alejandro A Schäffer, Matitiahu Berkovitch, David J Ozeri, Eugene Merzon

Front Immunol· September 2023

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Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models.
Yuelin Liu, Xuan Cindy Li, Farid Rashidi Mehrabadi, Alejandro A Schäffer, Drew Pratt

Genome Res· July 2023

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