プロフィール詳細

プロジェクトを作成

★★★★★

☆☆☆☆☆

★★★★★

☆☆☆☆☆

David O.に依頼

United States

Bioinformatician & Biostatistician | NGS, single-cell, survival & Bayesian analysis | R/Shiny tools | M.S. JHU, 8 pubs

プロフィール概要

I'm a bioinformatician and biostatistician with 15+ years of experience turning complex biological and clinical data into rigorous, publishable results and tools that scientists can use without writing code. I hold an M.S. in Bioinformatics from Johns Hopkins University and a B.S. in Biochemistry, and I'm a co-author on 8 peer-reviewed papers in neurogenetics, ALS, retinal biology, and cancer biology, serving as the statistical or computational collaborator on each. What I can help you with: Next-generation sequencing analysis: RNA-seq, miRNA-seq, and TRAP-seq, from QC (FastQC, Picard) through alignment (STAR), quantification, and differential expression (DESeq2, edgeR, limma), plus single-cell analysis (Seurat) including clustering, dimensionality reduction, and gene set enrichment. Biostatistics: study design consultation, survival analysis, Bayesian hierarchical modeling, causal inference (TMLE, Super Learner, propensity scores), missing-data handling, regression modeling, and meta-analysis (meta, metafor) with publication-quality forest plots. Custom analysis tools: interactive R Shiny applications, reproducible pipelines, and R packages, so your lab can re-run and explore analyses independently. Survey and behavioral data: hierarchical Bayesian MaxDiff, survey design and analysis, and clear reporting for mixed audiences. Background: I began at the bench, spending seven years in molecular and cellular biology research at Johns Hopkins (breast cancer metastasis, retinal biology) before moving fully into computation. As a bioinformatician in the Psychiatry and Genetics departments at Washington University, I analyzed NGS experiments in close collaboration with bench scientists, co-developed the CSEA cell type-specific expression analysis methodology, and helped release its R package (pSI) on CRAN. I then applied statistics and machine learning to electronic health records across a ~40-hospital system before moving into independent consulting. Selected recent projects: Co-developed a modular single-cell omics analysis platform (20+ R packages) that lets research institutions upload their own data and run clustering, differential expression, pseudotime, spatial transcriptomics, and cell-cell communication analyses in the browser. Built a laboratory information management system (48-module R Shiny application with a serverless cloud API) for a genomics sequencing lab, covering sample tracking through sequencing runs. Built a no-code causal-inference platform (TMLE, Super Learner) used by pharmaceutical scientists. Conducted a random-effects meta-analysis on a psychiatric epidemiology question with subgroup analyses and publication-ready figures. Contributor to the FAO's GLEAM-X livestock environmental assessment R package. How I work: I ask about the biological question and the intended publication or decision before touching the data, I document assumptions and methods so a reviewer can follow them, and I explain results in plain language. Most of my consulting work comes from repeat clients: as an independent consultant I've completed 66 contracts with a ~4.9/5 average rating. I work in R (expert level), Python, SQL, and Bash, on Linux, HPC clusters (Slurm, SGE), and cloud platforms (AWS, Google Cloud).

専門分野

• ★ Machine Learning
• ★ Bioinformatics
• ★ R
• ☆ Computational Biology
• ☆ Biostatistics
• ☆ Mathematical Biology
• ☆ Molecular Biology
• ☆ Genetics
• ☆ Microarrays
• ☆ Omics
• ☆ Transcriptomics
• ☆ Comparative Genomics
• ☆ Genomics
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ DNA Sequencing
• ☆ Gene Expression Analysis
• ☆ Genome Sequencing
• ☆ Exome Sequencing
• ☆ RNA Sequencing
• ☆ ChIP-Seq
• ☆ Cell Biology
• ☆ Gene Regulation
• ☆ Neuroscience
• ☆ Molecular Neuroscience
• ☆ Data Analysis
• ☆ Statistics
• ☆ Applied Statistics
• ☆ Comparative Analysis
• ☆ Meta-Analysis
• ☆ Regression Analysis
• ☆ Bayesian Statistics
• ☆ Correlation Analysis
• ☆ Statistical Computing
• ☆ Mathematical Statistics
• ☆ Survey Design
• ☆ Study Design
• ☆ Health Data Analysis
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Structural Bioinformatics
• ☆ Risk Assessment & Actuarial Science
• ☆ Information & Knowledge Management
• ☆ Data Storage
• ☆ Python
• ☆ Matlab
• ☆ SQL
• ☆ Excel
• ☆ Tensorflow
• ☆ LaTex
• ☆ Scikit-learn
• ☆ Markup Languages
• ☆ Drug Discovery
• ☆ High Throughput Screening (HTS)
• ☆ User Research
• ☆ Quantitative User Research
• ☆ Qualitative User Research
• ☆ Statistical Finance
• ☆ Financial Technology
• ☆ Mathematical Finance
• ☆ Investment Management

サービス

• Research
• Consulting
• Data & AI

Research Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Image Analysis, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics

職務経験

Contract Data Scientist

Freelancer

1月 2016 - 現在

Senior Data Scientist

Zenabi

1月 2018 - 1月 2022

Statistican

Mercy Hospital and Medical Center

1月 2015 - 1月 2016

BIoinformatician

Washington University in St. Louis

1月 2013 - 1月 2015

BIoinformatician

Johns Hopkins University

1月 2012 - 1月 2013

Research Technician

Johns Hopkins University

1月 2005 - 1月 2012

学歴

Bioinformatics

Johns Hopkins University

1月 2010 - 1月 2012

Biochemistry B.S.

State University of New York at Geneseo

1月 2001 - 1月 2005

認定資格

• 認定資格の詳細は未入力です。

出版物

JOURNAL ARTICLE

Mariah L. Hoye, Erica D. Koval, Amy J. Wegener, Theodore S. Hyman, Chengran Yang, David R. O'Brien, Rebecca L. Miller, Tracy Cole, Kathleen M. Schoch, Tao Shen, et al. (2017). MicroRNA Profiling Reveals Marker of Motor Neuron Disease in ALS Models . The Journal of Neuroscience.

Dalal JS, Yang C, Sapkota D, Lake AM, O'Brien DR, Dougherty JD (2017). Quantitative Nucleotide Level Analysis of Regulation of Translation in Response to Depolarization of Cultured Neural Cells . Frontiers in molecular neuroscience.

Reddy AS, O'Brien D, Pisat N, Weichselbaum CT, Sakers K, Lisci M, Dalal JS, Dougherty JD (2016). A Comprehensive Analysis of Cell Type-Specific Nuclear RNA From Neurons and Glia of the Brain . Biological psychiatry.

Wells A, Kopp N, Xu X, O'Brien DR, Yang W, Nehorai A, Adair-Kirk TL, Kopan R, Dougherty JD (2015). The anatomical distribution of genetic associations . Nucleic acids research.

Xu X, Wells AB, O'Brien DR, Nehorai A, Dougherty JD (2014). Cell type-specific expression analysis to identify putative cellular mechanisms for neurogenetic disorders . The Journal of neuroscience : the official journal of the Society for Neuroscience.

M. Natalia Vergara, Christian Gutierrez, David R. O'Brien, M. Valeria Canto-Soler (2013). Ex vivo electroporation of retinal cells: A novel, high efficiency method for functional studies in primary retinal cultures . Experimental Eye Research.

Stasinopoulos I, O'Brien DR, Bhujwalla ZM (2009). Inflammation, but not hypoxia, mediated HIF-1alpha activation depends on COX-2 . Cancer biology & therapy.

Ioannis Stasinopoulos, David R. O'Brien, Flonne Wildes, Kristine Glunde, Zaver M. Bhujwalla (2007). Silencing of Cyclooxygenase-2 Inhibits Metastasis and Delays Tumor Onset of Poorly Differentiated Metastatic Breast Cancer Cells . Molecular Cancer Research.

Stasinopoulos I, O'Brien DR, Wildes F, Glunde K, Bhujwalla ZM (2007). Silencing of cyclooxygenase-2 inhibits metastasis and delays tumor onset of poorly differentiated metastatic breast cancer cells . Molecular cancer research : MCR.