Curriculum vitae


Education

Ph.D, Biomedical Engineering, University of California, Davis
2021

B.S., Bioengineering, University of Maryland
2015


Technical Expertise

Core Competencies:
  • Statistical modeling and machine learning for biological data
  • Bioinformatics pipeline development and high-throughput sequence analysis
  • Molecular virology and phylogenetics, virus population genetics
  • Molecular biology, cell culture, protein purification, next-generation sequencing
  • Big data analysis and integrative multi-omics data research
Programming Languages: Python, R, shell scripting

Specialized Tools & Methods:
  • Next-generation sequencing analysis (PacBio, Illumina, ONT)
  • Phylogenetics and evolutionary analyses
  • Bayesian inference and artificial intelligence
  • Protein and RNA structure prediction
  • High-performance computing (Slurm, UGE)
Additional: Git, \LaTeX, web development (Flask, Django, Java, JavaScript, SQL)



Experience

Postdoctoral Fellow (2021-Present)

Viral Persistence and Dynamics Section (Dr. Eli Boritz)
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health
  • Developed novel machine learning-based approaches for accurate, single-genome virus sequencing via long-read technologies
  • Developed SHUMI, a command-line tool for simulating single-genome sequencing datasets via mechanistic models of reverse transcription, PCR, and sequencing
  • Led bioinformatics analyses for study on intra-host evolution of SARS-CoV-2 via single-genome sequencing in clinical samples from immunocompromised individuals, leading to co-first authored publication in Nature Communications
  • Facilitated collaborations with diverse research groups both within and external to NIH, enabling complementary research studies that extended and enhanced original findings
  • Led immunology study group to facilitate team-building and enhanced understanding of immunological concepts, as directly related to on-going research projects
  • Communicated scientific advancements via research presentations at numerous international conferences, departmental meetings, and seminars
  • Developed novel, scalable pipelines for evolutionary analyses on large NGS datasets related to SARS-CoV-2, HIV, SHIV, and seasonal coronaviruses

Graduate Researcher (2015-2021)

Computational RNA Genomics Lab (Dr. Sharon Aviran)
Biomedical Engineering Graduate Group, UC Davis

Dissertation title: "Accurate, Automated, and Scalable Identification of RNA Structure Motifs in Structurome Profiling Data"

  • Theme: studied the role of RNA structure in cellular systems using computational, data-driven approaches
  • Applied state-of-the-art computational tools and custom in-house pipelines on genomic and transcriptomic data in cluster computing environments
  • Comprehensively benchmarked unsupervised statistical models in the context of RNA structure prediction and mining
  • Improved structure-mining algorithm via a novel normalization scheme, reformulated training procedure, and machine-learned structure motif classifier
  • Project culminated in release of patteRNA 2.0, a rapid, accurate, and automated algorithm for mining local RNA structures
  • Mentored three undergraduate students towards achieving technical independence and producing publishable results

Computational Consultant (March 2021-September 2021)

International Genetically Engineered Machine (iGEM) Competition Team, UC Davis BioInnovation Group
  • Developed Python tool for automating structural analyses of large batches of RNA sequences (fold-fastalike)
  • Guided team of undergraduates in using computational approaches to assess RNA structure in mRNA transcripts
  • Structural assessments were used to design an optimized synthetic mRNA for vaccine applications
  • Contributed to computational training, experimental design, and data analysis related to transcript/structure optimization

Undergraduate Researcher (October 2014-May 2015)

Control of Miniaturized Systems Lab (Dr. Benjamin Shapiro)
Fischell Department of Bioengineering, University of Maryland
  • Designed simulation platform for magnetic nanoparticle drug-delivery research
  • Implemented discrete-element model (DEM) of particles in MATLAB based on a first-principles approach accounting for magnetism, magnetic coupling, and fluid dynamics
  • Leveraged simulation platform to optimize properties of nanoparticles for speed and control under applied magnetic fields

Junior Software Engineer (April 2014-August 2014)

BrainScope, Inc., Bethesda, MD
  • Assisted in the development of an Android-based application for the real-time diagnosis of brain trauma via EEG, including user interface design, deployment, and verification
  • Designed and performed software test procedures using MATLAB
  • Developed an automated build server using Bash and Java
  • Composed and executed verification processes for FDA-regulated medical device

Research Assistant (Summers 2012 & 2013)

Medical Virology Section (Dr. Jeffrey Cohen)
National Institutes of Health (NIH), Bethesda, MD
  • Assisted in development of vaccine for Epstein-Barr virus (EBV) within the National Institute of Allergy and Infectious Diseases (NIAID)
  • Executed complex research tasks, including cell transfections, neutralization assays, FACS, genomic analyses, sequencing, and visualizations
  • Utilized innovative high-throughput laboratory procedures to profile array of antibodies within human serum samples
  • Research project concluded with two publications, including a clinical trial (see Communications below)

Awards

  • VRC Poster Session Honorable Mention (VRC Scientific Retreat, 2025)
  • NIH Director's Award (NIH Office of the Director, 2023)
  • RNA Society Poster Award (RNA, 2021)
  • Dr. Ronald J. Smith Distinguished Teaching Fellow in Quantitative Biology (College of Biological Sciences, UC Davis, June 2020)
    • Awarded for contributions to computational curriculum development in MAT 107


Communications

Publications

Radecki P, Ko SH, Lucas M, Boritz E. "SHUMI: Simulating high-throughput single-genome amplification and sequencing datasets." (in preparation)

Ko SH*, Radecki P*, Belinky F, Bhiman J, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong P, Wolter N, von Gottberg A, Cohen C, Boritz E. "Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection." Nature Communications. 2024 August 22; 15(1):7240.
doi: 10.1038/s41467-024-51539-8 [Press release]

Dias J, ..., Radecki P, ..., et al.. "Administration of anti-HIV-1 broadly neutralizing monoclonal antibodies with increased affinity to Fc gamma receptors during acute SHIV-AD8-EO infection." Nature Communications. 2024 August 29; 18(1):7461.
doi: 10.1038/s41467-024-51848-y [Press release]

Radecki P, Uppuluri R, Deshpande K, and Aviran S. "Accurate Detection of RNA Stem-Loops in Structurome Data Reveals Widespread Association with Protein Binding Sites." RNA Biology. 2021 October 15; 18(1):521-536.
doi: 10.1080/15476286.2021.1971382

Radecki P, Uppuluri R, and Aviran S. "Rapid Structure-Function Insights via Hairpin-Centric Analysis of Big RNA Structure Probing Datasets." NAR Genomics and Bioinformatics. 2021 August 24; 3(3).
doi: 10.1093/nargab/lqab073

Radecki P, Ledda M, and Aviran S. "Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures." Genes. 2018 June 14; 9(6):300.
doi: 10:3390/genes9060300

Cohen JI, ..., Radecki P, ..., et al.. "Hydroa vacciniforme-like lymphoproliferative disorder: an EBV disease with a low risk of systemic illness in whites." Blood. 2019 June 27; 133(26):2753-2764.
doi: 10.1182/blood.2018893750

Bu W, Hayes GM, Liu H, Gemmell L, Schmeling D, Radecki P, Aguilar F, Burbelo P, Woo J, Balfour H, Cohen JI. "Kinetics of Epstein-Barr Virus (EBV) Neutralizing and Virus-Specific Antibodies after Primary Infection with EBV." Clin Vaccine Immunol. 2016 April 4; 23(4):369-9.
doi: 10.1128/CVI.00674-15


Presentations

† Radecki P, Ko SH, Boritz E "SHUMI: Simulating High-Throughput UMI-based Single-Genome Amplification and Sequencing Data." VRC Scientific Retreat, June 3 2025. Bethesda, MD

Radecki P, Ko SH, Boritz E "SHUMI: Simulating High-Throughput UMI-based Single-Genome Amplification and Sequencing Data." 32nd International Dynamics and Evolution of Human Viruses, May 6 2025. Asnières-sur-Oise, France

Radecki P "It's all in the details: making sense of single-genome measurements of virus populations." HIV env Structure-Function-Sequence (SFS) Meeting, October 21 2024. Bethesda, MD

Radecki P, Ko SH, Belinky F, Guerra Canedo V, Lucas M, Bhiman J, Wolter N, von Gottberg A, Cohen C, Boritz E "High-throughput single-genome sequencing coupled to high-fidelity haplotype determination facilitates detailed investigation of SARS-CoV-2 evolution in immunocompromised individuals." 31st International Dynamics and Evolution of Human Viruses, June 20 2024. Squamish, BC, Canada

Radecki P, Ko SH, Boritz E "Intra-host evolution of Spike in people living with HIV assessed with high-throughput, single-genome sequencing." NIH SARS-CoV-2 Assessment of Viral Evolution (SAVE) Program, Early Detection and Analysis (EDA) Meeting, August 7 2023. Bethesda, MD

Radecki P "Intra-host Spike variants revealed by single-molecule sequencing: implications for SARS-CoV-2 mutation rates, evolutionary dynamics, and new VOCs." NIH-FDA COVID Workshop, 2022. Bethesda, MD

Radecki P "Towards low-frequency haplotype reconstruction via high-throughput single-genome sequencing." VRC Emerging Infectious Diseases Meeting, 2022. Bethesda, MD

† Radecki P, Aviran S "Rapid Structure-Function Insights from Mining Stem-Loops in Structurome Profiling Data." RNA Conference, 2021. (online)

Radecki P, Aviran S "Machine-Learning Approaches for Identifying RNA Structures in Massive Genomic Data." UC Davis BME Advisory Board Meeting, 2019. Davis, CA

Radecki P, Savageau M "Cognate Amino Acid Bias in Human Microbiomes." International Conference on Molecular Systems Biology (ICMSB), 2017. Burghausen, DE

Radecki P, Savageau M "Understanding Microbial Communities through Amino Acid Bias." BME Student Research Symposium, 2017. Davis, CA

Han W, Kim B, Radecki P, Runsewe P, Vinson R "Low-Cost Ankle Rehabilitation Robot for Children with Cerebral Palsy." University of Maryland Fischell Department of Bioengineering Capstone Showcase, 2015. College Park, MD

Bu W, Schmeling D, Burbelo P, Radecki P, Balfour H, Cohen JI "Neutralizing Antibody Titers Increase Over Many Months to Years After Epstein-Barr Virus Infectious Mononucleosis." International Herpesvirus Workshop, 2012. Calgary, AB

† Presentation received award or honorable mention



Service

  • VRC Scientific Retreat 2025, Poster Session Subcommittee (2025)
  • NIH ChIRP ("Chatbox for the Intramural Research Program") Advocate (since 2025)
  • Peer reviewer: Computational and Structural Biotechnology Journal (CSBJ), Scientific Reports, Virology, Virus Evolution, Viruses