Curriculum vitae


Education

Doctor of Philosophy (Ph.D.), Biomedical Engineering
University of California, Davis
Awarded June 2021

Bachelor of Science (B.S.), Bioengineering
University of Maryland, College Park
Awarded May 2015


Technical Profile

Proficient in Python, MATLAB, nucleotide sequence data manipulation, bash scripting, bioinformatics pipeline development

Experienced in Java, Git, web application development, LaTeX

Familiar with C/C++, JavaScript, R, SQL



Experience

Postdoctoral Fellow (2021-Present)

Virus Persistence and Dynamics Section (Dr. Eli Boritz)
Vaccine Research Center, NIAID, NIH
  • Developed analysis pipeline for high-fidelity reconstruction of single-genome sequences from raw PacBio sequencing data (see UMI-pacbio-pipeline)
  • Led bioinformatics and computational biology analyses of a large cohort of sequencing data of SARS-CoV-2 evolution in immunocompromised individuals (see Ko & Radecki et al., 2024)
  • Developed Bayesian approaches for the inference of genuine full-length sequences (haplotypes) in error-prone high-throughput long read sequencing data (in preparation)
  • Managed multiple collaborations investigating the intra-host evolution of HIV-1, SHIV, SARS-CoV-2, and seasonal coronaviruses
  • Mentored and instructed multiple postdoctoral fellows and post baccalaureate fellows in computational methods and bioinformatics
  • Regularly presented research advances at international and institutional research conferences and symposiums

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 (Slurm)
  • Comprehensively benchmarked unsupervised statistical models in the context of RNA structure prediction and mining
  • Improved structure-mining algorithm via a novel normalization scheme, a 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 (Summer 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 (see fold-fastalike)
  • Guided team of undergraduates in using computational approaches to assess RNA structure in mRNA transcripts, in the context of mRNA vaccine optimization
  • Structural assessments were used to design an optimized synthetic mRNA transcript for vaccine applications
  • Contributed to computational training, experimental design, and data analysis related to transcript/structure optimization

Undergraduate Researcher (Oct. 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

Software Engineering Intern (Apr. 2014–Aug. 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

  • NIH Director's Award (NIH, 2023)
    • Awarded for contributions to the Early Detection and Analysis (EDA) team of the SARS-CoV-2 Assessment of Viral Evolution (SAVE) Program at NIH/NIAID
  • Grand Prize: Vaccine Research Center Annual Bake-off (VRC, 2023)
  • RNA 2021 Poster Award (RNA Society Meeting, 2021)
  • Dr. Ronald J. Smith Distinguished Teaching Fellow in Quantitative Biology (UC Davis College of Biological Sciences, 2020)
  • College Park Scholars Citation; Science, Discovery, and the Universe (University of Maryland, 2013)


Communications

Publications

Ko SH*, Radecki P*, Belinky F, Bhiman J, Meiring S, Kleynhans J, Amoako S, 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, and Boritz E. "Rapid Emergence and Evolution of SARS-CoV-2 Variants in Advanced HIV Infection." bioRxiv. 2024 Jan 6. (preprint)
doi: 10.1101/2024.01.05.574420

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 Oct 4; 18(1).
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 Aug 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 Jun 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 Jun 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 Apr 4; 23(4):369-9.
doi: 10.1128/CVI.00674-15


Presentations

Radecki P. "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, Uppuluri R, Deshpande K, Aviran S. "Rapid Structure-Function Insights from Mining Stem-Loops in Structurome Profiling Data." RNA Society Meeting, 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, Germany.

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, Canada.



Teaching Experience at UC Davis

Course Development

MAT/BIS 107: Probability and Statistics with Applications to Biology (Winter 2019)
  • Independently designed and wrote 10 interactive computer labs (MATLAB-based) to emphasize fundamentals of computational analysis and demonstrate practical applications in biology using real-world data
  • Served as lab instructor during Spring 2020 and Spring 2021 with exceptional departmental feedback
  • Success of labs culminated with Dr. Ronald J. Smith teaching award from the College of Biological Sciences (see Awards above)

Teaching Assistantships

BIM 20: Fundamentals of Bioengineering (Spring 2016, Spring 2017)
BIM 162: Introduction to the Biophysics of Molecules & Cells (Winter 2017)
BIM 105: Probability and Stat. for Biomedical Engineers (Fall 2018, Fall 2020)
MAT/BIS 107: Prob. and Stat. with App. to Biology (Spring 2020, Spring 2021)
BIM 152: Molecular Biosystems (Winter 2021)

Readerships

BIM 152: Molecular Biosystems (Winter 2020)