Stephen Turner

I’m Head of Genomics Strategy at Colossal Biosciences working on species restoration and conservation using synthetic biology and genome engineering. I have a M.S. in statistics and Ph.D. in genetics, and did my postdoc in epidemiology. I was a professor in Public Health at the University of Virginia School of Medicine and founding director of UVA’s Bioinformatics Core from 2011-2019. I taught graduate courses in data science and bioinformatics, and wrote the Biological Data Science with R textbook to accompany the course. I left academia for consulting 2019-2023 to build bioinformatics and data science solutions for the US Government in public health, defense, and national security. I’ve been working in de-extinction and conservation genomics ever since. I love talking about genomics, bioinformatics, R, Docker, de-extinction, trail running, and homebrewing.

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Publications

tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets

Stephen D. Turner, Kathleen Morrill, Gregory L. Gedman, A. Titus

bioRxiv 2023

Stephen Turner

Publications

tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets

k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data

Quality Control Procedures for Genome‐Wide Association Studies

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

KGP: An R Package with Metadata from the 1000 Genomes Project

Relationship Inference with Low-Coverage Whole Genome Sequencing on Forensic Samples

Automated Infectious Disease Forecasting: Use-cases and Practical Considerations for Pipeline Implementation (preprint)

vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework

Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples

vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

Complex Genetic Interactions/Data Mining/Dimensionality Reduction

skater: an R package for SNP-based kinship analysis, testing, and evaluation

Sexually dimorphic crosstalk at the maternal-fetal interface.

Faculty Opinions recommendation of FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.

2157. Evaluation of the Utility of the MRSA Nasal PCR Assay in a Community Healthcare System

Faculty Opinions recommendation of InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines.

Faculty Opinions recommendation of Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Knowledge-Driven Genome-Wide Analysis of Multigenic Interactions Impacting HDL Cholesterol Level

Faculty Opinions recommendation of Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.

Faculty Opinions recommendation of Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Annotables: R data package for annotating/converting Gene IDs

Electronic medical records and genomics (eMERGE) network exploration in cataract: Several new potential susceptibility loci

qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Faculty Opinions recommendation of A genomic day in the life of a clinical microbiology laboratory.

Faculty Opinions recommendation of A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

Faculty Opinions recommendation of A comparative evaluation of sequence classification programs.

Faculty Opinions recommendation of [CONFERENCE POSTER]: DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

Faculty Opinions recommendation of Rapid identification of non-human sequences in high-throughput sequencing datasets.

Faculty Opinions recommendation of Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Faculty of 1000 evaluation for Ten years of pathway analysis: current approaches and outstanding challenges.

Faculty Opinions recommendation of Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

Faculty Opinions recommendation of Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease.

Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality

Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

Knowledge-Driven Multi-Locus Analysis Reveals Gene-Gene Interactions Influencing HDL Cholesterol Level in Two Independent EMR-Linked Biobanks

Faculty Opinions recommendation of A Database of Gene-Environment Interactions Pertaining to Blood Lipid Traits, Cardiovascular Disease and Type 2 Diabetes.

Association of haplotypes of inflammation‐related genes with gastric preneoplastic lesions in African Americans and Caucasians

Quality Control Procedures for Genome‐Wide Association Studies

Lack of Association between Single Nucleotide Polymorphism rs3811647 in the TF Gene and Iron Status in Patients with Iron Deficiency and Control Subjects

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci

Incorporating Domain Knowledge into Evolutionary Computing for Discovering Gene-Gene Interaction

Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of small main effects

Faculty Opinions recommendation of Genetic heterogeneity in human disease.

Genome-Wide Association Study of Cataract in the Emerge Consortium

Grammatical Evolution of Neural Networks for Discovering Epistasis among Quantitative Trait Loci

A General Framework for Formal Tests of Interaction after Exhaustive Search Methods with Applications to MDR and MDR-PDT

Methods for optimizing statistical analyses in pharmacogenomics research

Conquering the Needle-in-a-Haystack: How Correlated Input Variables Beneficially Alter the Fitness Landscape for Neural Networks

Abstract A10: IL1B haplotypes and risk of gastric precancerous lesions in African Americans and Caucasians in New Orleans

P3-240: Genome-wide analysis of gene-gene interaction in Alzheimer's disease

Generating Linkage Disequilibrium Patterns in Data Simulations Using genomeSIMLA

Multivariate Analysis of Regulatory Snps: Empowering Personal Genomics by Considering Cis-Epistasis and Heterogeneity

- 1-ATHENA : A Knowledge [ 1 ]-Based Hybrid Backpropagation-Grammatical Evolution Neural Network Algorithm for Discovering Epistasis among Quantitative Trait Loci

Differential Gene Expression during Placentation in Pregnancies Conceived with Different Fertility Treatments Compared to Spontaneous Pregnancies