Publications by authors named "Adam A Margolin"

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Blueprints for Better Drugs: The Structural Revolution in Nanomedicine.
Chad A Mirkin, Robert Langer, Milan Mrksich, Adam A Margolin, Sarah Hurst Petrosko

ACS Nano· May 2025

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An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.
Burcu Gurun, Wesley Horton, Dhaarini Murugan, Biqing Zhu, Patrick Leyshock, Adam A Margolin

BMC Genomics· June 2023

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An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.
Burcu Gurun, Wesley Horton, Dhaarini Murugan, Biqing Zhu, Patrick Leyshock, Adam A Margolin

Res Sq· February 2023

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svpluscnv: analysis and visualization of complex structural variation data.
Gonzalo Lopez, Laura E Egolf, Federico M Giorgi, Sharon J Diskin, Adam A Margolin

Bioinformatics· July 2021

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Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A Margolin

Nature· January 2019

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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Anna Y Lee, Adam D Ewing, Kyle Ellrott, Yin Hu, Kathleen E Houlahan, Adam A Margolin

Genome Biol· November 2018

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Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy.
Terry R Medler, Dhaarini Murugan, Wesley Horton, Sushil Kumar, Tiziana Cotechini, Adam A Margolin

Cancer Cell· October 2018

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Valection: design optimization for validation and verification studies.
Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P'ng, Adam A Margolin

BMC Bioinformatics· September 2018

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Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer.
Chang Xu, Olga Nikolova, Ryan S Basom, Ryan M Mitchell, Reid Shaw, Adam A Margolin

Clin Cancer Res· June 2018

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Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism.
Ryan J Davis, Mehmet Gönen, Daciana H Margineantu, Shlomo Handeli, Jherek Swanger, Adam A Margolin

Proc Natl Acad Sci U S A· May 2018

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SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks.
Erik A Burlingame, Adam A Margolin, Joe W Gray, Young Hwan Chang

Proc SPIE Int Soc Opt Eng· February 2018

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Germline contamination and leakage in whole genome somatic single nucleotide variant detection.
Dorota H Sendorek, Cristian Caloian, Kyle Ellrott, J Christopher Bare, Takafumi N Yamaguchi, Adam A Margolin

BMC Bioinformatics· January 2018

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A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Mehmet Gönen, Barbara A Weir, Glenn S Cowley, Francisca Vazquez, Yuanfang Guan, Adam A Margolin

Cell Syst· November 2017

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Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies.
Olga Nikolova, Russell Moser, Christopher Kemp, Mehmet Gönen, Adam A Margolin

Bioinformatics· May 2017

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Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis.
Takahiro Tsujikawa, Sushil Kumar, Rohan N Borkar, Vahid Azimi, Guillaume Thibault, Adam A Margolin

Cell Rep· April 2017

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CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman, Adam A Margolin

Nat Genet· January 2017

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Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors.
In Sock Jang, Rodrigo Dienstmann, Adam A Margolin, Justin Guinney

Pac Symp Biocomput· April 2016

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The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition.
Henrik Sperber, Julie Mathieu, Yuliang Wang, Amy Ferreccio, Jennifer Hesson, Adam A Margolin

Nat Cell Biol· December 2015

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The NIH BD2K center for big data in translational genomics.
Benedict Paten, Mark Diekhans, Brian J Druker, Stephen Friend, Justin Guinney, Adam A Margolin

J Am Med Inform Assoc· November 2015

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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
Adam D Ewing, Kathleen E Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, Adam A Margolin

Nat Methods· July 2015

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Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting.
Elias Chaibub Neto, J Christopher Bare, Adam A Margolin

PLoS One· June 2015

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Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning.
Mehmet Gönen, Adam A Margolin

Bioinformatics· September 2014

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Toward better benchmarking: challenge-based methods assessment in cancer genomics.
Paul C Boutros, Adam A Margolin, Joshua M Stuart, Andrea Califano, Gustavo Stolovitzky

Genome Biol· September 2014

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Functional kinomics identifies candidate therapeutic targets in head and neck cancer.
Russell Moser, Chang Xu, Michael Kao, James Annis, Luisa Angelica Lerma, Adam A Margolin

Clin Cancer Res· August 2014

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