David E. Condon, Ph.D.
Renner, SD 57055
Email-id :-Mobile No.:-
OrcID:-
LinkedIn Profile
Google Scholar
GitHub
Education
Degree
Ph.D.
M.S.
B.S.
University
University of Rochester
University of Rochester
Pennsylvania State University
Major
Chemistry
Chemistry
Chemistry
Location
Rochester, NY
Rochester, NY
State College, PA
Year-
Skills
• Genomics & Bioinformatics (9 years experience)
◦ Next-Generation Sequencing: Developed my own epigenetics pipeline in bisulfite-seq/methyl seq, using machine learning/AI to make polygenic risk scores for Covid using electronic health record (EHR),
protein target identification for antimicrobials, and for the global screening array (GSA). Developed,
optimized, and deployed data analysis pipelines for genomics, transcriptomics, proteomics, and clinical
data.
◦ Performed differential expression analysis RNA-Seq in mice, and again at Sanford with cancer patients.
◦ Used Survival GWAS for statistical genetics analysis for Diabetes & CVD, using electronic health record
(EHR) phenotypic data from Sanford BioBank
◦ created polygenic risk score (PRS) for COVID-19, and used previous PRS for prostate cancer
◦ Two years experience with RNA-Seq and Bisulfite sequencing/epigenetics at the University of Pennsylvania.
◦ 5 years of experience with microarray and whole-genome NGS data at Sanford Health. I have experience using survival genome-wide association studies, imputation, polygenic risk scores, delivering
analysis of patient HIPAA-protected biomedical data from the electronic medical record (EMR)
◦ experience in leadership while supervising undergrade and graduate students,
◦ Experience with clinical biomarker datasets for prostate cancer
◦ Familiarity with the management, design, and/or development of publicly accessible databases such
as NCBI, Saccharomyces Genome Database, PomBase, and FungiDB and data quality assurange
◦ have previously done single-cell sequencing on kidney disease,
◦ experience with bioinformatics programming tools and databases such as Conda, Git, Bioconductor,
BLAST, BWA, SAMtools, BedTools, DeepTools, GATK, UCSC Genome Browser, and STAR among
others
◦ I also have experience writing three proposals
• Programming (14 years experience)
◦ Python 5 years experience, used for scripting, but matplotlib for visualization, numpy, scipy, pandas,
scikit-learn, biopython, and xgboost classifier and regressor for machine learning/artificial intelligence.
Created repository AI.tester for testing various learning methods.
◦ R 5 years experience, used for statistics and plotting. I’ve used many packages, including EdgeR,
DESeq2, ggplot2, and gwasurvivr
◦ C 3 years experience, used for writing the Defiant, which identifies differentially methylated regions in
bisulfite-sequencing data. Used OpenMP for parallel programming
◦ SQL Beginner proficiency
◦ Perl 14 years experience, used for regular scripting and parsing many types of files. Publicly available
projects include PDB stacker, rotate.xyz and HitList
◦ BASH 14 years experience as a graduate student, postdoctoral researcher, lead analyst, and research
scientist
◦ HTML Beginner proficiency
• Computational Chemistry (5 years experience). Used AMBER Molecular Dynamics package to simulate
LNA oligonucleotide CAAU and RNA oligonucleotides CAAU, GACC, AAAA, and UUUU to test molecular
dynamics torsion reparametrizations and compare with NMR measurements. Have used Gaussian09 and
NWChem 6 for calculations with RNAs.
• Artificial Intelligence/Machine Learning I used clinical data to attempt to build predictive models of COVID
susceptibility using XGBoost.
• Linux & AWS (15 years experience) 4 years experience with IBM Blue Hive and Blue Gene P and Q
supercomputing Linux clusters. 14 years experience with Ubuntu and RedHat Linux. Used AWS for storage
of HIPAA-protected data.
• Cheminformatics Used RDKit for visualization of SMILES strings and chemprop for property prediction
using AI
Work Experience
University of Idaho,Research Scientist II; duration: 06/06/2023-01/23/2025
• Developed HitList: a bioinformatics pipeline to automate drug discovery, originally used for agricultural crops
• Discovered eight new novel anti-fungal drug targets in fungi
• Interpreted AlphaFold structures
Sanford Health, Lead Computational Bioinformatics Analyst; 11/27/2017-12/31/2022
• Developed concordance pipeline for Sanford Chip (Global Screening Array), benchmarking with WholeGenome Sequencing data (WGS)
• Learned Apache Spark (PySpark)
• Developed computational pipeline for clinical application of RNA-Seq
• Used RNA-Seq public TCGA dataset to link different types of cancers
• Learned Survival GWAS for statistical genetics analysis for Diabetes & CVD Project
• Used Machine Learning / artificial intelligence (AI) with XGBoost (gradient boosting library) in Python to
study patient data with covid-19 non-interventional health and patient data (electronic health record) research. I performed complex data extraction, manipulation, and summarization of large databases to support research activities. I took the lead role in design, testing, validation, analysis, and merging of complicated data structures from electronic health records
• Experience with polygenic risk scores in prostate cancer and pre-eclampsia
• Led & managed Imagenetics Journal Club
• Briefly worked with single-cell RNA-Seq and Whole-Exome Sequencing (WES)
• Used patient genetic data to enhance precision medicine, including pharmacogenetics
University of Pennsylvania, Postdoctoral Researcher; 1/15/2015-11/15/2017
• Used RNA-Seq for studying placental changes from obesity
• Used Bisulfite-Seq to study epigenetic changes in iron-deficient pregnancy in the rat hippocampus
• learned the R programming language
• Developed Defiant: a program designed to identify and annotate differentially methylated regions from
bisulfite-sequencing experiments; using output from epigenetic preprocessing
Publications
• Discovery of Novel Targets for Important Human and Plant Fungal Pathogens via Automated Computational
Pipeline HitList BioRxiv, David E Condon, Brenda K Schroeder, Paul Andrew Rowley, F Marty Ytreberg
• Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People with Type
2 Diabetes Mellitus Diabetes Soo Heon Kwak, Ryan B. Hernandez-Cancela, Daniel A DiCorpo, David E.
Condon, et al.
• Stacking in RNA: NMR of four tetramers benchmark molecular dynamics DE Condon, SD Kennedy, BC
Mort, R Kierzek, I Yildirim, DH Turner
• The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for
AMBER force field torsions improve structural predictions from molecular dynamics Biochemistry JD Tubbs,
DE Condon, SD Kennedy, M Hauser, PC Bevilacqua, DH Turner
• Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouseBiology of Reproduction TJ Stuart, K O’Neill, D Condon, I Sasson, P Sen, Y
Xia, RA Simmons
• Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L
(CAAU) J. Phys. Chem. B DE Condon, I Yildirim, SD Kennedy, BC Mort, R Kierzek, DH Turner
• Predicting the kinetics of RNA oligonucleotides using Markov state modelsJ. Chem. Theory Comput. G
Pinamonti, J Zhao, DE Condon, F Paul, F Noé, DH Turner, G Bussi
• Defiant:(DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from
iron-deficient rat hippocampus BMC Bioinformatics DE Condon, PV Tran, YC Lien, J Schug, MK Georgieff,
RA Simmons
• Dysregulation of neuronal genes by fetal-neonatal iron deficiency anemia is associated with altered DNA
methylation in the rat hippocampus Nutrients YC Lien, DE Condon, MK Georgieff, RA Simmons, PV Tran
• In utero bisphenol A exposure is linked with sex specific changes in the transcriptome and methylome of
human amniocytes J. Clin. Endocrinol. Metab. A Bansal, N Robles-Matos, PZ Wang, DE Condon, A Joshi,
SE Pinney105 (2), 453-467
• Exposure to gestational diabetes enriches immune-related pathways in the transcriptome and methylome of
human amniocytes J. Clin. Endocrinol. Metab. SE Pinney, A Joshi, V Yin, SW Min, C Rashid, DE Condon,
PZ Wang The Journal of Clinical Endocrinology & Metabolism 105 (10),-
• Establishing analytical validity of BeadChip array genotype data by comparison to whole-genome sequence
and standard benchmark datasets BMC Medical Genomics PF Cherukuri, MM Soe, DE Condon, S Bartaria,
K Meis, S Gu, FG Frost
Awards
• Teas Scholarship for Undergraduate Research, Penn State, Summer 2008
• Moses Passer Memorial Fellowship,-
• Sanford Health Quarterly Hero Award 2021
Foreign Languages
• Russian, B2-C1 fluency
• Spanish, 6 years experience-
