David Nicholson

David Nicholson

dnicholson329@gmail.com • 412-607-6313 • 11291 Chatterly Loop Apt 104, Manassas VA 20109

Summary

Data Scientist with 13+ years of programming experience and 5+ years of experience in data analytics and visualization. Most of my data analytics experience has utilized language models and document embeddings to gain further insight into biomedical research.

Skills & Proficiency

Github • Python • R • SQL • Data Visualization • Machine Learning • Deep Learning • Transformers • Auto Encoders • Clustering • Natural Language Processing • Topic Modeling • Bayesian Modeling • Data Structures • Data Engineering • GCP Data Engineering • Databases • Vector Databases • Embeddings • Algorithms • Parallel Processing • XML Parsing • Web Development

Education

Doctor of Philosophy (Ph.D.), Genomics and Computational Biology; University of Pennsylvania (Philadelphia, PA) Postbaccalaureate Program (Penn Prep); University of Pennsylvania (Philadelphia, PA) Bachelor of Science, Computer Science; University of Maryland Baltimore County (Baltimore, MD) Winchester Thurston School: Pittsburgh, PA St. Edmunds Academy: Pittsburgh, PA

Publications

• Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published PapersOn Biomedical Preprints And Published Papers
  Nicholson, D. N. (2022)
• Changing Word Meanings in Biomedical Literature Reveal Pandemics and New Technologies
  Nicholson, D. N. Alquaddoomi, F., Rubinetti, V., Greene, C. S. (2023)
• Characterization of the Genome and Silk-gland Transcriptomes of Darwin’s Bark Spider (Caerostris darwini)
  Babb, P. L., Gregorič, M., Lahens, N. F.,Nicholson, D. N., Hayashi, C. Y., Higgins, L., Kuntner, M., Agnarsson, I., Voight, B. F. (2022)
• Examining Linguistic Shifts between Preprints and Publications
  Nicholson, D. N., Rubinetti, V., Hu, D., Thielk, M., Hunter, L. E., Greene, C. S. (2022)
• Expanding a Database-derived Biomedical Knowledge Graph via Multi- Relation Extraction from Biomedical Abstracts
  Nicholson, D. N., Himmelstein, D. S., Greene, C. S. (2022)
• Constructing Knowledge Graphs and Their Biomedical Applications
  Nicholson, D. N., Greene, C. S. (2020)
• The Nephila Clavipes Genome Highlights the Diversity of Spider Silk Genes and their Complex Expression
  Babb, P. L., Lahens, N. F., Correa-Garhwal, S. M., Nicholson, D. N., Kim, E.J., Hogenesch, J.B., Kuntner, M., Higgins, L., Hayashi, C. Y., Agnarsson, I., Voight, B.F. (2017)

Professional Experience

Data Scientist
Digital Science & Research Solutions, Ltd.
June 2022 - Present

• Constructed a software package to enable fast clustering of document sets, cluster hierarchy generation, and cluster metadata (labels from LLMs, various metrics such as Growth Rate, etc.).
• Constructed software packages for calculating cluster metrics using bigquery, but can be extended to other databasees like Redshift and Postgres.
• Maintained an ETL pipeline design to extract and update over 100GB of document data for the National Institute of Health (NIH) clientele.
• Designed and implemented a data analysis pipeline designed to cluster an 818k+ document set centered on women’s health for a ARPA-H (HHS affiliated).
• Constructed an ETL pipeline designed to detect cancer drug treatments using a 64k+ biomedical document set for a pharmaceutical client.
• Back-tested vector databases were used to determine which database is most optimal for handling 10M+ document embedding vectors.
• Constructed a pipeline that used deep learning and dimensionality reduction models to uncover research topics and trends within a 20M+ document set for government clients.
• Hackathon where we worked on citation sentiment for predicting how citaitons were used in full text. Gemini was the model, but really should be for Ollama and open source models (cheaper).
• Created pipeline for a dashboard that categorizes arpa-h data into gropus defined by Field Of Research categories (SPACE/PACE). Do not put acronym in resume.

Graduate Researcher Scientist
University of Pennsylvania
August 2016 - June 2022

• Designed and implemented parallel processing pipelines that achieved a 3x speed-up when analyzing terabytes of biomedical text.
• Used weak supervision for a 1.5x speed-up when training deep learning models (recurrent neural networks and transformers) to extract biomedical relationships from biomedical text.
• Applied a k-nearest-neighbor model to provide scientists with a web service that lists journals linguistically similar to a preprint of interest.
• Applied a time series analysis to discover over 20,000 different time points where words have changed their semantic meaning.

Postbaccalaureate Researcher
University of Pennsylvania
June 2015 - June 2016

• Used hypothesis testing (hyper geometric test) to discover over 1000 protein domains that are easily targetable by small molecules and drugs.
• Constructed a bioinformatics pipeline that efficiently discovers novel motifs in the Golden Orb-weaver spider genome.

Undergrad Researcher
University of Maryland Baltimore County (UMBC)
September 2013 - May 2015

• Characterized population-level transcriptional regulation by assisting with the creation of a bioinformatic pipeline that quantifies transcription factor enrichment in metagenomic data.

Summer Research Intern University of Pennsylvania (SUIP) June 2014

• Created a Perl pipeline that utilized Mendelian Randomization and Approximate Bayesian Computation to discover if having an elevated level of triglycerides causes heart disease.

Summer Research Intern
Bioinformatics and Integrative Genomics (BIG)
Harvard University and Massachusetts Institute of Technology
June 2013

• Explored a more efficient measure to track DNA samples. Researched the use of SNP (single nucleotide polymorphisms) information to act as a DNA barcode to keep track of patient samples that have undergone different gene sequencing workflows.

Summer Research Intern University of Pittsburgh and Carnegie Mellon University (TecBio) June 2012

• Conducted machine learning to assess algorithms to determine the best strategies to identify lung cancer in patients as early as possible.

Teaching Experience

Advisor for a rotation student for Research Lab
University of Pennsylvania (Genomics and Computational Biology Program)
Sept 2020 - Dec 2020

• Guided rotation student on conducting and executing a research project that analyzed biomedical abstracts to model disease-gene trajectories through time.

Student Advisor for 1st and 2nd Year Ph.D. Students University of Pennsylvania (Genomics and Computational Biology Program) August 2018 - August 2020

• Advised first and second year Ph.D. students on which classes to take for the fall and spring semester
• Advised first year Ph.D. students about the mechanics of lab rotations

Python BootCamp/Teaching Assistant
University of Pennsylvania (Genomics and Computational Biology Program)
August 2019

• Assisted in teaching Ph.D. students how to program in python.

Advanced Computational Biology/Tutor
University of Pennsylvania (Genomics and Computational Biology Program)
April 2019 - May 2019

• Assisted a Ph.D. student in learning advanced computational biology topics.
• Topics ranged from machine learning algorithms to various statistical algorithms

Python BootCamp/Teaching Assistant
University of Pennsylvania (Genomics and Computational Biology Program)
September 2017

• Assisted in teaching Ph.D. students how to program in python.

Data Structures/Tutor
University of Maryland Baltimore County (UMBC)
Sept 2013 - May 2014

• Tutored and assisted students in studying/programming various data structures such as binary search trees to hash tables.

Math Tutor University of Maryland Baltimore County (UMBC) Sept 2012 - May 2013

• Worked in walk-in tutoring sessions for university services.
• Tutored students in math classes from Algebra I to Calculus II

Calculus I and II/Learning Assistant University of Maryland Baltimore County (UMBC) Sept 2012 - May 2013

• Helped professor assist students in homework during office hours

Honors

Appointed trainee on T32 Computational Genetics, June 2019 - August 2021

• National Human Genome Research Institute (NHGRI)

Meyerhoff Scholar (M23), August 2011 - June 2015

• University of Maryland Baltimore County

Marc U*Star Scholar, Sept 2014 -June 2015

• University of Maryland Baltimore County

National Security Agency (NSA) Scholar, Sept 2012 - June 2014

• University of Maryland Baltimore County

Thomson Reuters Award HackMIT, October 2014

ABRCMS Poster Presentation Award, November 2013

Presentations

Changing Word Meanings in Biomedical Literature Reveal Pandemics and New Technologies (ISCB Rocky), December 2022

• 1 hour talk

Elsevier’s Labs Online Lecture services, October 2021

• 30 Minute Talk

Institute for Biomedical Informatics (IBI) Annual Retreat, December 2020

• Poster Presentation

Cold Spring Harbor Biological Data Science Symposium, November 2020

• Lightning Talk and Poster Presentation

National Human Genome Research Institute National Trainee Meeting, March 2020

• Poster Presentation

Seminar at Elsevier, December 2019

• Invited Speaker

International Society of Computational Biology (ISCB) Rocky, December 2019

• Poster Presentation

Institute for Biomedical Informatics (IBI) Annual Retreat, June 2019

• Poster Presentation

International Society of Computational Biology (ISCB) Rocky, December 2018

• Poster Presentation

Computational Systems for Integrative Genomics (CSIG), July 2017

• Lightning Talk

UMBC’s Undergraduate Research and Creative Achievement Day, Spring 2014

• Poster Presentation

Attended Harvard’s Biomedical Science Careers Student Conference, April 2014

Participated in MIT’s Quantitative Biology Workshop,, Jan 2014

Annual Biomedical Research Conference for Minority Students, November 2013