A photo of Alexey Porollo.

Member, Center for Autoimmune Genomics and Etiology

Member, Division of Biomedical Informatics

Associate Professor, UC Department of Pediatrics


Biography & Affiliation


The research areas that I find interesting include structural and functional annotation of proteins, assessment of the functional and medical effects of missense mutations, and investigation of biological pathways. I’m also interested in studying metal-binding proteins, antimicrobial resistance, discovery of novel drug targets, comparative genomic analysis and a microbiome assessment.

The goals for our lab include developing prediction and annotation approaches that enable us to annotate the impact of mutations in proteins, finding the processes of copper tolerance in human fungal pathogens, assessing host-pathogen interactions and expanding novel drug treatment.

A few notable discoveries we have made in our research studies are:

  • Accurately predicting protein-protein interaction sites (SPPIDER)
  • Using a co-evolution assessment in proteins that ensure the identification of functional sites (CoeViz)
  • Showing the reliance on myo-inositol in the obligate pathogens from the Pneumocystis species
  • Developing a tool for correctly forecasting antimicrobial resistance in Gram-negative bacteria from whole-genome sequencing data (WGS2AMR)

The web servers that include these methodological projects are POLYVIEW-2D/3D/MM, SABLE and SPPIDER. In addition, from 2013 to 2019, I pursued research related to direct culturing of Pneumocystis using metatranscriptomics. This project was meant to find essential nutrients with metatranscriptomics and distinguish the best system to maintain Pneumocystis growth outside of the mammalian lungs. This would then enable research to produce significant improvements in diagnosing and treating Pneumocystis pneumonia (PCP).

Starting in 2019, my colleagues and I engaged in research related to copper tolerance and homeostasis in Pneumocystis species. This project's objective was to describe the molecular mechanisms behind copper tolerance and homeostasis in Pneumocystis murina that allows the fungus to offset the host Cu-driven cytotoxicity.

I was led to these research interests by observing a need for greater knowledge regarding the adaptation processes among human pathogens as well as the design of new diagnostic tools and novel drug treatments for multiple infections.

I received the Team Science Award from the University of Cincinnati College of Medicine in 2019. This award was given in recognition of the achievements of our interdisciplinary team that includes the University of Cincinnati Internal Medicine, Pediatrics and Chemistry departments.

I have more than 15 years of biomedical informatics experience and first started working at the Cincinnati Children's Hospital Medical Center in 2002. My research has been published in multiple journals, such as Frontiers in Microbiology, mBio, Microbiome, Antimicrobial Agents and Chemotherapy, Bioinformatics, BMC Bioinformatics, Proteins: Structure, Function, and Bioinformatics and BMC Medical Genomics.

Academic Affiliation

Associate Professor, UC Department of Pediatrics

Research Divisions

Biomedical Informatics


MSc: Mari State University, Yoshkar-Ola, Russia, 1995.

PhD: Tver State University, Tver and Mari State University, Yoshkar-Ola, Russia, 1999.

Post-doc: Children’s Hospital Medical Center, Cincinnati, OH, 2006.


Selected Publication

Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation. Cushion, MT; Ashbaugh, A; Hendrix, K; Linke, MJ; Tisdale, N; Sayson, SG; Porollo, A. Antimicrobial Agents and Chemotherapy. 2018; 62.

A fast and robust protocol for metataxonomic analysis using RNAseq data. Cox, JW; Ballweg, RA; Taft, DH; Velayutham, P; Haslam, DB; Porollo, A. Microbiome. 2017; 5.

A quantitative model to estimate drug resistance in pathogens. Baker, FN; Cushion, MT; Porollo, A. Journal of Fungi. 2016; 2:30-30.

CoeViz: a web-based tool for coevolution analysis of protein residues. Baker, FN; Porollo, A. BMC Bioinformatics. 2016; 17.

MutaCYP: Classification of missense mutations in human cytochromes P450. Fechter, K; Porollo, A. BMC Medical Genomics. 2014; 7.

EC2KEGG: A command line tool for comparison of metabolic pathways. Porollo, A. Source Code for Biology and Medicine. 2014; 9.

Comparative Genomics of Pneumocystis Species Suggests the Absence of Genes for myo-Inositol Synthesis and Reliance on Inositol Transport and Metabolism. Porollo, A; Sesterhenn, TM; Collins, MS; Welge, JA; Cushion, MT. mBio. 2014; 5.

Rational engineering of the fungal P450 monooxygenase CYP5136A3 to improve its oxidizing activity toward polycyclic aromatic hydrocarbons. Syed, K; Porollo, A; Miller, D; Yadav, JS. Protein Engineering, Design and Selection. 2013; 26:553-557.

Prediction-based fingerprints of protein-protein interactions. Porollo, A; Meller, J. Proteins: Structure, Function, and Bioinformatics. 2007; 66:630-645.

Accurate prediction of solvent accessibility using neural networks-based regression. Adamczak, R; Porollo, A; Meller, J. Proteins: Structure, Function, and Bioinformatics. 2004; 56:753-767.