Recent Faculty Publications

Our contributions to the scholarly literature demonstrate our commitment to advancing the field of biomedical informatics.

Handelmann CR, Tsompana M, Samudrala R, Buck MJ. (2023) The impact of nucleosome structure on CRISPR/Cas9 fidelity. Nucleic acids research (Mar), 51(5): 2333-2344. doi:10.1093/nar/gkad021
Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S. (2023) Antiviral Approaches against Influenza Virus. Clinical microbiology reviews (Jan)e0004022.
Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S. (2023) Antiviral Approaches against Influenza Virus. Clinical microbiology reviews (Jan)e0004022.
Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R. (2023) Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer. International journal of molecular sciences (Jan), 24(2) doi:10.3390/ijms24020997
Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R. (2023) Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer. International journal of molecular sciences (Jan), 24(2). doi:10.3390/ijms24020997
Mangione W, Falls Z, Samudrala R. (2023) Effective holistic characterization of small molecule effects using heterogeneous biological networks. Frontiers in pharmacology (Jan), 14: 1113007. doi:10.3389/fphar.2023.1113007
Jacobs DM, Tober R, Yu C, Gibson W, Dunn T, Lu CH, Bednzarczyk E, Jette G, Lape-Newman B, Falls Z, Elkin PL, Leonard KE. (2022) Trends in Prescribing Opioids, Benzodiazepines, and Both Among Adults with Alcohol Use Disorder in New York State. Journal of general internal medicine (Jun)
Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao M, Samudrala R. (2022) Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology. Molecules (Basel, Switzerland) (May), 27(9) doi:10.3390/molecules27093021
Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao M, Samudrala R. (2022) Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology. Molecules (Basel, Switzerland) (May), 27(9) doi:10.3390/molecules27093021
Falls Z, Brown SH, Shah N, LeHouillier F, Badwal R, Hall K, Franklin G, Kelly WH, Holdaway A, Montella D, Wedemeyer L, Keni S, Rose E, Nebeker JR, Elkin PL. (2022) CDS-Compare: A Web Application for Machine Learning Assisted Curation of Clinical Order Sets. Studies in health technology and informatics (May), 294: 465-469.
Falls Z, Brown SH, Shah N, LeHouillier F, Badwal R, Hall K, Franklin G, Kelly WH, Holdaway A, Montella D, Wedemeyer L, Keni S, Rose E, Nebeker JR, Elkin PL. (2022) CDS-Compare: A Web Application for Machine Learning Assisted Curation of Clinical Order Sets. Studies in health technology and informatics (May), 294: 465-469.
Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R. (2022) Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease. Pharmaceuticals (Basel, Switzerland) (May), 15(5) doi:10.3390/ph15050566
Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R. (2022) Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease. Pharmaceuticals (Basel, Switzerland) (May), 15(5) doi:10.3390/ph15050566
Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R. (2022) Evaluating the performance of drug-repurposing technologies. Drug discovery today (Jan), 27(1): 49-64.
Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R. (2022) Evaluating the performance of drug-repurposing technologies. Drug discovery today (Jan), 27(1): 49-64.
Mangione W, Falls Z, Samudrala R. (2022) Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Frontiers in pharmacology (Jan), 13: 970494. doi:10.3389/fphar.2022.970494
Mangione W, Falls Z, Samudrala R. (2022) Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Frontiers in pharmacology (Jan), 13: 970494. doi:10.3389/fphar.2022.970494
Overhoff B, Falls Z, Mangione W, Samudrala R. (2021) A Deep-Learning Proteomic-Scale Approach for Drug Design. Pharmaceuticals (Basel, Switzerland) (Dec), 14(12) doi:10.3390/ph14121277
Overhoff B, Falls Z, Mangione W, Samudrala R. (2021) A Deep-Learning Proteomic-Scale Approach for Drug Design. Pharmaceuticals (Basel, Switzerland) (Dec), 14(12) doi:10.3390/ph14121277
Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R, Stavrou S, Melendy T. (2021) A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition. Antiviral research (Nov), 195: 105183. doi:10.1016/j.antiviral.2021.105183

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