Alexey A Porollo

Computational Biology | Biomedical AI | Structural Bioinformatics | Infectious Disease Research

Master: Mari State University Yoshkar-Ola, Russia, 1995 (Chemistry)

Doctoral Degree: Tver State University Tver, Russia, 1999 (Chemistry)

Postdoctorate: Cincinnati Children’s Hospital Medical Center Cincinnati, OH, USA, 2006 (Computational biology and bioinformatics)

My research lies at the intersection of computational biology, artificial intelligence, and biomedical data science, with a focus on developing computational methods to advance our understanding of protein structure and function, molecular interactions, and mechanisms of human disease. Building on my interdisciplinary background in chemistry, structural bioinformatics, and molecular biology, I have developed widely used methods and software tools for protein structure prediction, functional annotation, and visualization, including SABLE, SPPIDER, and POLYVIEW. My group has also developed computational approaches for predicting antimicrobial resistance from whole-genome and metagenomic sequencing data (WGS2AMR and MGS2AMR). More recently, my research has expanded to deep learning and protein language models, including the development of SPPIDER-seq, a partner-aware predictor of protein–protein interaction interfaces. My current methodological interests include contrastive learning, retrieval-augmented generation, and AI-driven integration of molecular and multi-omics data.

My translational research involves interdisciplinary collaborations aimed at understanding host–pathogen interactions, fungal metabolism, and pathogenesis. A major focus is on opportunistic fungal infections, particularly Pneumocystis pneumonia, where we integrate comparative genomics, transcriptomics, single-cell RNA sequencing, metabolomics, and metabolic modeling to investigate pathogen biology, host immune responses, and potential therapeutic targets.

My research has resulted in numerous peer-reviewed publications, widely used bioinformatics resources, and sustained NIH funding as a principal investigator, multiple principal investigator, and co-investigator. I am actively involved in interdisciplinary research collaborations, graduate education, scientific mentorship, and professional service, including journal editorial activities, grant peer review, and international conference organization. My long-term goal is to advance AI-driven biomedical research by developing computational approaches that connect molecular mechanisms with clinically relevant discoveries. For a complete list of publications and citation metrics, please visit my Google Scholar profile.

Grant: #1R01HL119190 Investigators:Cushion MT, Porollo A 05-22-2013 -02-28-2019 NHLBI Directed Culturing of Pneumocystis Using Metatranscriptomics Role:Co-PI Completed Type:Grant

Grant: #1R21AI143467 Investigators:Porollo A 07-05-2019 -06-30-2023 NIAID Copper tolerance and homeostasis in Pneumocystis species Role:PI Completed

Grant: #1R61AI187113 Investigators:Smulian AG, Molestina R, Porollo A 12-20-2024 -11-30-2027 NIAID Alveolar organoids and metabolomic-driven cultivation of Pneumocystis species Role:Co-PI Active

Grant: #1R01HL176858 Investigators:Smulian AG, Cushion MT, Porollo A 08-01-2025 -05-31-2029 NHLBI Elucidating the Sexual Cycle of HIV/AIDS-Related Pneumocystis Pneumonia Role:Co-PI Active

Peer Reviewed Publications

Porollo, Aleksey; Jadhav, Om; Alvarez, Aaron; Chen, Jichao (2026. ) SPPIDER-seq: sequence-based partner-aware predictor of protein-protein interaction sites.Bioinformatics (Oxford, England), , 42 (7 ) , More Information

Albee, Aaron W; Sayson, Steven G; Ashbaugh, Alan; Wolf, Nicholas J; Porollo, Aleksey; Smulian, George; Cushion, Melanie T (2025. ) Single-cell RNA sequencing defines developmental progression and reproductive transitions of Pneumocystis carinii.Microbiology spectrum, , 13 (10 ) ,e0127725 More Information

Porollo, Aleksey; Sayson, Steven G; Ashbaugh, Alan; Rebholz, Sandra; Landero Figueroa, Julio A; Cushion, Melanie T (2024. ) Insights into copper sensing and tolerance in Pneumocystis species.Frontiers in microbiology, , 15 ,1383737 More Information

Van Camp, Pieter-Jan; Prasath, V B Surya; Haslam, David B; Porollo, Aleksey (2023. ) MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile.Microbiome, , 11 (1 ) ,223 More Information

Tran, Chau; Khadkikar, Siddharth; Porollo, Aleksey (2023. ) Survey of Protein Sequence Embedding Models.International journal of molecular sciences, , 24 (4 ) , More Information

Van Camp, Pieter-Jan; Haslam, David B; Porollo, Aleksey (2020. ) Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.Frontiers in microbiology, , 11 ,1013 More Information

Baker, Frazier N; Porollo, Aleksey (2016. ) CoeViz: a web-based tool for coevolution analysis of protein residues.BMC bioinformatics, , 17 ,119 More Information

Porollo, Aleksey; Sesterhenn, Thomas M; Collins, Margaret S; Welge, Jeffrey A; Cushion, Melanie T (2014. ) Comparative genomics of pneumocystis species suggests the absence of genes for myo-inositol synthesis and reliance on inositol transport and metabolism.mBio, , 5 (6 ) ,e01834 More Information

Syed K, Porollo A, Miller D, Yadav JS. (2013. ) Rational engineering of the fungal P450 monooxygenase CYP5136A3 to improve its oxidizing activity toward polycyclic aromatic hydrocarbons.Protein Eng Des Sel., , 26 (9 ) ,553 More Information

Porollo, Aleksey; Meller, Jarosław (2007. ) Prediction-based fingerprints of protein-protein interactions.Proteins, , 66 (3 ) ,630-45 More Information

Academic - Biostatistics, Health Informatics and Data Sciences
260 Stetson Street
Cincinnati  Ohio, 45219
alexey.porollo@uc.edu