Bioinformatics Ph.D. Program Alumni

The alumni list below may be filtered by last name.

Name Current Title Employer Chair Dissertation
Subramanian Shankar Ajay Subramanian Shankar Ajay

Senior Bioinformatics Scientist

Illumina, Inc.

Brian Athey, Inhan Lee

Novel Bioinformatics Approaches for MicroRNA Detection and Target Prediction
Raquel Assis Raquel Assis

Assistant Professor of Biology

Eberly College of Science, Pennsylvania State University

Alexey Kondrashov

Origin and Evolution of Novel Sequences by Gene Duplication
Oscar Alejandro Balbin Oscar Alejandro Balbin

Investigator I in Bioinformatics

Novartis Institutes for Biomedical Research

Arul Chinnaiyan

Identifying Novel Targetable Genes and Pathways in Cancer by Integrating Diverse Omics Data
Mark Benson Mark Benson

NCBI Contractor

TAJ Technologies, Inc.

Heather Carlson

Binding MOAD (Mother of All Databases)
Stewart Chang Stewart Chang

Computational Biologist

Intellectual Ventures

Denise Kirschner, Jennifer Linderman

Multi-Scale Modeling of Antigen Presentation With Applications to Tuberculosis
Ji Chen Ji Chen

Business Analytics Manager

eBay, Inc.

David States

Identification of Global and Specific Gene Expression Patterns Based on Microarray
Yili Chen Yili Chen

Data Scientist (Manager)

Pfizer, Inc.

Jessica Schwartz, David States

Integrative Analysis of Transcriptional Regulation Using Computational Approaches
Yu Chen Yu Chen

Software Engineer

Google, Inc.

Gordon Crippen

Protein Structural Alignment and Application for Fold Recognition
Shanshan Cheng Shanshan Cheng

Charles Brooks III

Delineating Structural Characteristics of Viral Capsid Proteins Critical for their Functional Assembly
Chad Creighton Chad Creighton

Asst. Professor of Medicine

Baylor College of Medicine

Arul Chinnaiyan, Kerby Shedden

Comparing Gene Expression Profiles of Cell Culture Models with Profiles of Tumor Xenografts and Patient Tumors : Implications for Lung and Breast Cancers
Lan Dai Lan Dai

Associate Scientist

Genentech, Inc.

David Lubman

The Application of Mass Spectrometry-Based Label-Free Quantitative Proteomic Strategies in Cancer Stem Cell Research
Michael DeGiorgio Michael DeGiorgio

Assistant Professor of Biology

Eberly College of Science, Pennsylvania State University

Noah Rosenberg

Genetic Variation and Modern Human Origins
Casey Diekman Casey Diekman

Assistant Professor

New Jersey Institute of Technology (Newark)

Daniel Forger; Vijayan Nair, KP Unnikrishnan

Modeling and Analysis of Electrical Network Activity in Neuronal Systems
Joseph Donohoe Joseph Donohoe

Informatics & Special Projects Lead

Mountain Pacific Quality Health

Rajesh Balkrishnan

Evaluating the Methodology and Clinical Utility of Spatial Access to Health Care Measures in Appalachia
Jayson Falkner Jayson Falkner

Software Engineer

Counsyl, Inc.

Philip Andrews

Aggregation, Dissemination, and Analysis of High-throughput Scientific Data Sets in the Field of Proteomics
Damian Fermin Damian Fermin


Yale School of Medicine

Gil Omenn

Use of Proteomics as a Method of Enhancing Genome Annotation
Mallory Freeberg Mallory Freeberg

Postdoctoral Research Fellow

Dept. of Biology, Johns Hopkins University

John Kim

Computational Analysis of the Post-Transcriptional Gene Regulatory Network
Patrick Harrington Patrick Harrington

Team Lead & Director of Engineering


Alfred O. Hero, III

Inverse Problems in High Dimensional Stochastic Systems Under Uncertainty
Andrew Hodges Andrew Hodges

Bioinformatics Specialist

Sanford-Burnham Medical Research Institute

Yongqun He, Peter Woolf

Bayesian Network Approaches for Refining and Expanding Cellular and Immunological Pathways
Juichi (“Lucy”) Huang Juichi (“Lucy”) Huang


McKinsey & Co.

Noah Rosenberg

Integrative Statistical Learning with Applications to Predicting Features of Diseases and Health
Yongsheng Huang Yongsheng Huang

Research Staff

Merck, Inc.

Alfred Here III, Jay L Hess

Integrative Statistical Learning with Applications to Predicting Features of Diseases and Health
Junguk Hur Junguk Hur

Assistant Professor

University of North Dakota

Eva Feldman, Hosagrahar V Jagadish

Integration of Text Mining with Systems Biology Provides New Insight into the Pathogenesis of Diabetic Neuropathy
Matthew Iyer Matthew Iyer

MSTP Student

University of Michigan

Arul Chinnaiyan

Discovery and characterization of long non-coding RNAs in cancer transcriptomes
Doug Jacobsen Doug Jacobsen

NERSC Systems Engineer

Lawrence Berkeley National Lab

Charles Brooks III, Matthew Young

An Investigation of the Roles of Magnesium Ions in the Catalytic Cycle of the Protein Kinase CDK2: A Molecular Link between Allosteric Activation and Catalytic Activity
Reagan Kelly Reagan Kelly

Bioinformatics Scientist

SRA International

Sharon Kardia

The Development and Application of a Risk Index to Predict Individualized Chronic Disease Risk
Nickolay Khazanov Nickolay Khazanov

Bioinformatics Scientist III

Thermo Fisher Scientific, Inc.

Heather Carlson

Large-Scale Analysis of Protein-Ligand Binding Sites using the Binding MOAD Database
Jung Kim Jung Kim

Data Scientist

Progenity, Inc.

Arul Chinnaiyan, Kerby Shedden

Characterization of Copy Number Aberrations and Epigenetic Modifications in Prostate Cancer
Bo Li Bo Li

Postdoctoral Fellow

Dana Farber Cancer Center, Harvard Medical School

Jun Li

Development and Application of Novel Methods to Study Tumor Heterogeneity and Cancer Genome Evolution
Xing Li Xing Li

Bioinformatics Scientist

Mayo Clinic

Deborah Gumucio

Bioinformatic Analysis of Epithelial:Mesenchymal Crosstalk during Mouse Gut Development and Patterning
Yu-Hsuan Lin

Software Development Engineer

Microsoft, Inc.

James D. Engel, Maureen Sartor

Analysis of, and Software Development for, ChIP-Seq and RNA-Seq Data
Arun Manoharan Arun Manoharan

Senior Bioinformatics Analyst

Recombine, Inc.

John Kim

The Landscape of C. elegans 3'UTRs
Datta Mellacheruvu Datta Mellacheruvu

Postdoctoral Fellow

University of Michigan

Alexey Nesvizhskii

A Computational and Informatics Framework for the Analysis of Affinity Purification Mass Spectrometry Data and Reconstruction of Protein Interaction Networks
Arvind Rao Arvind Rao

Assistant Professor

University of Texas - MD Anderson Cancer Center

Doug Engel, Alfred O. Hero III, David States

Prospective Identification of Long-range Transcriptional Regulatory Regions via Integrative Genomics
Daniel Rhodes Daniel Rhodes

VP Oncology

ThermoFisher Scientific, Inc.

Eric Fearon

Development and integrative analysis of a cancer gene expression database
Lee Sam Lee Sam

Arul Chinnaiyan

Integrative bioinformatics in the age of massive throughput sequencing: from the transcriptome to the proteome in prostate cancer
Conner Iknokwayyo Sandefur Conner Iknokwayyo Sandefur

Postdoctoral Fellow

University of North Carolina

Santiago Schnell

Defining Chemical Reaction Mechanisms Associated with Threshold Phenomena in Conformational Diseases
Carlos Santos Carlos Santos


Retinapharma Technologies, Inc.

Brian Athey, David States

Automated Natural-Language Processing for Integration and Functional Annotation of Complex Biological Systems
Sirarat Sarntivijai Sirarat Sarntivijai

Bioinformatician – Ontologist

Biovest International, Inc.

Brian D. Athey and Yongqun He

Novel Integrative Bioinformatics Approaches to Biomedical Ontology Practice for Translational Informatics
Yasin Senbabaoglu Yasin Senbabaoglu

Postdoctoral Researcher

Memorial Sloan-Kettering Cancer Center

Jun Li, George Michailidis

Developing and Application of Statistical Algorithms for High-Demensional Biological Data Analysis
Abhik Shah Abhik Shah

Bioinformatics Scientist

Brian Athey, Peter Woolf, James Peter

Mechanistic Bayesian Networks for Integrating Knowledge and Data to Unravel Biological Complexity
Erin Shellman

Research Scientist II

Amazon Web Services

Charles Burant and Charles Burant

Network Motifs Provide Signatures That Characterize Metabolism and Produce Novel Insights into the Evolutionary History of the Eukaryotic Cell
Kraig Stevenson Kraig Stevenson

Data Scientist

Trinity Health

Patricia Wittkopp

The Evolution of Gene Regulation in Drosophila
Viktoriya Strumba Viktoriya Strumba

Margit Burmeister

Association Analyses of Known Genetic Variants with Gene Expression in Brain
Gang Su Gang Su

Data Mining Scientist and Consultant

Med Data Quest

Brian Athey, Fan Meng

Omics Data Exploration: Across Scales and Dimensions
Zachary Szpiech Zachary Szpiech

Postdoctoral Scholar

School of Pharmacy, University of CA-San Francisco

Noah Rosenberg

Human Migration, Population Divergence, and the Accumulation of Deleterious Alleles: Insights from Private Genetic Variation and Whole-exome Sequencing
Peter Ulintz Peter Ulintz

Bioinformatics Sr. Developer

University of Michigan

Philip Andrews

Mining Deeper into the Proteome: Computational Strategies for Improving Depth and Breadth of Coverage in High-Throughput Protein Identification Studies
Artur Veloso Artur Veloso

Oncology Bioinformatics Investigator I

Novartis Institutes for Biomedical Research

Mats Ljungman

Insights into Transcription through Nascent RNA Sequencing
Huy Vuong Huy Vuong

Bioinformatics Scientist

Ambry Genetics

David Lubman

Bioinformatics Analysis of Humoral Immune Response and Protein Microarray for Biomarker Discovery
Chaolong Wang Chaolong Wang

Senior Investigator

Genome Institute of Singapore

Noah Rosenberg

Statistical Methods for Analyzing Human Genetic Variation in Diverse Populations
Ryan Welch Ryan Welch

Research Associate Specialist Lead

University of Michigan

Michael Boehnke, Laura Scott

Bioinformatics Software and Methods for Genome-wide Association and ChIP-Seq Studies
Michelle Leigh Wynn  Michelle Leigh Wynn

James S. McDonnell Postdoctoral Fellow

University of Michigan

Sofia Merajver and Santiago Schnell

Unraveling the Complex Regulatory Relationships between Metabolism and Signal Transduction in Breast Cancer
Jinrui Xu Jinrui Xu

Jianzhi Zhang

Jianjun Yu Jianjun Yu

Investigator III

Novartis Oncology, Inc.

Arul Chinnaiyan

Bioinformatics Analysis of 'Omics' Data Towards Cancer Diagnosis and Prognosis
Chunchao Zhang Chunchao Zhang

Postdoctoral Fellow

MD Anderson Cancer Center

Phil Andrews

Analysis of Post-translational Modifications of Histones and Myelin Basic Protein: Crosstalk and Beyond
Peng Zhang

Statistical Geneticist

Center for Inherited Disease Research (CIDR), Johns Hopkins University: Baltimore, MD

Sebastian Zoellner

The Road to Identifying Disease Causing Genes: Association Tests, Genotype Imputations, and Sampling Strategies for Sequencing Studies
Yan Zhang Yan Zhang

Postdoctoral Fellow

Yale University

Phil Andrews

Network Discovery in Equilibrium-state and Dynamic Data: Applications to Phosphoproteomics and Kinetics
Dongxiao Zhu Dongxiao Zhu

Assistant Professor

Department of Computer Science, Wayne State University

Alfred O. Hero, III

Reconstructing Signaling Pathways from High Throughput Data
Daniel Zinder Daniel Zinder

Mercedes Pascual