Alla Karnovsky, PhD

 Alla Karnovsky
Program Director
Bioinformatics Master's Program
Associate Professor of Computational Medicine and Bioinformatics
Medical School
[email protected]
Available to mentor
Alla Karnovsky, PhD
Alla Karnovsky
Associate Professor
  • About
  • Center Memberships
  • Research Overview
  • Recent Publications

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    • About

    My background includes Ph.D. in cell and developmental biology (Russian Academy of Sciences), postdoctoral work at the University of Colorado at Boulder and nine years of bioinformatics work in Pharmaceutical industry (at Pharmacia and at Pfizer). I have broad experience in identification and validation of therapeutic targets in variety of disease areas including antibacterials, CNS and dermatology. I am also interested in structural aspects of drug/target interactions and the integration of chemical and genomic domains.

    Center Memberships
    • Center Member
      Caswell Diabetes Institute

    Research Overview

    My research interests involve the analysis of high throughout omics data, focusing primarily on metabolomics, and the development of computational methods and tools for the analysis and integration of metabolomics data with other types of genomic data. I am also interested in biomedical ontologies and one of my current projects involves the development of Informed Consent Ontology.

    Recent Publications

     See All Publications
    • Preprint
      LipidAnalyst; A Comprehensive Tool for Lipidomic Data Visualization and Analysis
      Liu X, Karnovsky A, Pennathur S, Afshinnia F. 2026 May 31; Preprints.org, DOI:10.20944/preprints202605.1883.v1
    • Journal Article
      Lipidomic Predictors of Paclitaxel-Induced Peripheral Neuropathy.
      Liu Y, Chen C-S, Nguyen-Hoang N, Karnovsky A, Henry NL, Stringer KA, Hertz DL. JCO Precis Oncol, 2026 Apr; 10 (4): e2501196 DOI:10.1200/PO-25-01196
      PMID: 42060862
    • Journal Article
      Gene expression signatures from whole blood predict amyotrophic lateral sclerosis case status and survival
      Zhao Y, Savelieff MG, Li X, Guo K, Wang K, Li M, Li B, Iyer G, Sakowski SA, Zhao L, Teener SJ, Bakulski KM, Dou JF, Traynor BJ, Karnovsky A, Batterman SA, Hur J, Goutman SA, Sartor MA, Feldman EL. Nature Communications, 2025 Dec 1; 16 (1): DOI:10.1038/s41467-025-64622-5
      PMID: 41173979
    • Journal Article
      DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data
      Patsalis C, Iyer G, Brandenburg M, Karnovsky A, Michailidis G. BMC Bioinformatics, 2024 Dec 1; 25 (1): DOI:10.1186/s12859-024-05994-1
      PMID: 39695921
    • Journal Article
      Epigenetic age acceleration is associated with occupational exposures, sex, and survival in amyotrophic lateral sclerosis
      Zhao Y, Li X, Wang K, Iyer G, Sakowski SA, Zhao L, Teener S, Bakulski KM, Dou JF, Traynor BJ, Karnovsky A, Batterman SA, Feldman EL, Sartor MA, Goutman SA. Ebiomedicine, 2024 Nov 1; 109: DOI:10.1016/j.ebiom.2024.105383
      PMID: 39369616
    • Journal Article
      Metabolomic Alterations Associated with Phthalate Exposures among Pregnant Women in Puerto Rico
      Siwakoti RC, Iyer G, Banker M, Rosario Z, Vélez-Vega CM, Alshawabkeh A, Cordero JF, Karnovsky A, Meeker JD, Watkins DJ. Environmental Science and Technology, 2024 Oct 15; 58 (41): 18076 - 18087. DOI:10.1021/acs.est.4c03006
      PMID: 39353139
    • Journal Article
      metabCombiner 2.0: Disparate Multi-Dataset Feature Alignment for LC-MS Metabolomics
      Habra H, Meijer JL, Shen T, Fiehn O, Gaul DA, Fernández FM, Rempfert KR, Metz TO, Peterson KE, Evans CR, Karnovsky A. Metabolites, 2024 Feb 1; 14 (2): DOI:10.3390/metabo14020125
    • Journal Article
      CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data
      Iyer G, Brandenburg M, Patsalis C, Michailidis G, Karnovsky A. Journal of Visualized Experiments, 2023 Nov 1; 2023 (201): DOI:10.3791/65512
      PMID: 38009735

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