The Huck Institutes of the Life Sciences

People

Faculty involved in the Bioinformatics and Genomics graduate program, and a summary of their research interests

Faculty are listed in alphabetical order by last name. To see more information about a faculty member, click on his/her name.

Reka Albert
Professor of Physics and Biology

Biological physics and network modeling.
Istvan Albert
Associate Professor of Bioinformatics

Large scale biological data analysis, microarrays and sequence analysis.
Naomi Altman
Professor of Statistics

Bioinformatics: the design and analysis of microarray studies, functional genomics and gene clustering. Functional data analysis and nonparametric smoothing.
Raquel Assis
Asst. Professor, Biology

Evolutionary genomics, molecular evolution, and bioinformatics. Particularly interested in how new functions evolve after gene duplication.
Sarah Assmann
Waller Professor of Biology

Molecular genetic elucidation of role of G-proteins in plant growth and development.
Michael Axtell
Professor of Biology

Genomics and bioinformatics of microRNAs, siRNAs, and their targets.
Le Bao
Assistant Professor of Statistics

Bayesian methods, mixture models, stochastic modeling, networks, computational methods, and applications in health, environmental and social sciences.
Colin Barnstable
Professor and Chair, Neural & Behavioral Sciences
Co-Chair of the Graduate Program in Neuroscience

How interacting networks of transcription factors and signal transduction molecules guide the development of precursor/stem cells into mature neurons. Role of these networks in neurodegenerative diseases. Factors that can act as neuroprotective agents.
Arthur Berg
Associate Professor of Public Health Sciences and Statistics

Clinical Informatics Electronic Health Record Research
Philip Bevilacqua
Professor of Chemistry
Professor of Biochemistry and Molecular Biology
Co-Director, Center for RNA Molecular Biology

Roles of RNA-binding proteins in plant physiology. Plant ribonomics. Identification and characterization of functional RNAs in plants.
James Broach
Professor and Chair, Biochemistry
Co-director, Bioinformatics and Genomics Graduate Program

Regulation of metabolism through signaling networks Cellular stress response Quiescence—the essence of chronological aging
John Carlson
Professor of Molecular Genetics, Department of Ecosystem Science and Management
Director, Schatz Center for Tree Molecular Genetics

Genome mapping, including genetic linkage mapping, molecular cytogenetics; studies of genetic diversity in forests.
Laura Carrel
Associate Professor of Biochemistry and Molecular Biology

Keith Cheng
Professor of Pathology, Biochemistry and Molecular Biology, and Pharmacology
Director of Experimental Pathology

Francesca Chiaromonte
Professor of Statistics and Public Health Sciences

Analysis and modelling of large-scale genomic data.
Surinder Chopra
Professor of Maize Genetics, Department of Plant Science

Regulation of flavonoid biosynthesis during plant development and plant-pathogen interaction. Epigenetic regulation and allele specific patterns.
Michael DeGiorgio
Assistant Professor of Biology

Population genetics, phylogenetics, human evolutionary genomics, and bioinformatics.
Sinisa Dovat
Staff Physician

Biology and Treatment of Leukemia Molecular Mechanisms of Cellular Immortalization and Senescence Accelerated Drug Discovery
David Geiser
Professor of Plant Pathology
Director, Fusarium Research Center

Molecular evolutionary genetics of pathogenic and toxigenic fungi.
Santhosh Girirajan
Assistant Professor of Biochemistry & Molecular Biology
Assistant Professor of Anthropology

The primary focus of my research is to discover and characterize genetic changes including genomic deletions and duplications and single nucleotide mutations contributing to neurodevelopmental disorders such as autism, developmental delay and congenital malformation.
Mark Guiltinan
Professor of Plant Molecular Biology, Department of Plant Science
Director, Endowed Program in the Molecular Biology of Cocoa

Plant molecular and developmental biology. Starch biosynthesis. Tropical plant biotechnology. Plant-pathogen interactions. Biofuel feedstock production.
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology

Functional genomics of non-coding DNA.
Heather Hines
Assistant Professor, Biology

* Genetics of adaptive mimetic color pattern variation in butterflies and bumble bees
Vasant Gajanan Honavar
Professor and Edward Frymoyer Chair of Information Sciences and Technology

Statistical machine learning algorithms for predictive modeling from big data (large, distributed, semantically disparate data, partially specified data, richly structured (sequence, relational, network) data); Causal inference from experimental and observational data; Information Integration (logical, probabilistic, and network-based approaches); Characterization and prediction of protein-protein, protein-RNA, and protein-DNA interactions, protein sub-cellular localization, B-cell and T-cell epitopes, and other functionally important sites of protein; Automated protein structure and function annotation; Modeling and inference of biological networks; Comparative analyses of biological networks (network alignment); Biomedical Ontologies; Integrative modeling of patients from electronic medical records, genetic, physiological, environmental and lifestyle data for personalized interventions.
Judie Howrylak
Assistant Professor of Medicine, Public Health Sciences, and Biochemistry and Molecular Biology

Seogchan Kang
Professor, Department of Plant Pathology and Environmental Microbiology

Molecular genetics and genomics of plant-pathogen interactions.
Sagarika Kanjilal
Associate Professor of Veterinary Science

Molecular, genomic, and proteomic investigation of cancer pathways, biomarkers, and targeted therapeutics.
Vivek Kapur
Associate Director for Strategic Initiatives, Huck Institutes of the Life Sciences
Professor of Veterinary and Biomedical Sciences

Research in my Laboratory seeks to define the basic mechanisms by which pathogenic microbes successfully infect, colonize, and cause disease in their hosts. The research effort is organized along two thematic lines:
Daniel Kifer
Assistant Professor (James L. Henderson Memorial Professorship)
Department of Computer Science & Engineering

Machine learning applications in various areas such as statistical privacy, security, databases, streaming data processing, and text modeling.
Jesse Lasky
Assistant Professor of Biology

Ecological & evolutionary genomics, genetic and ecophysiological basis of adaptation to environmental stress, evolutionary ecology of biological complexity.
Arthur Lesk
Professor of Biochemistry and Molecular Biology

Protein evolution. Conformations of antigen-binding sites of immunoglobulins and related proteins.
Qunhua Li
Assistant Professor of Statistics

My primary research interests concern developing statistical methods for uncovering complicated patterns in large and complex biological data. I have been developing latent variable models (e.g. mixture models, copula models) and machine learning techniques (e.g. clustering or classification) to identify and infer scientifically meaningful structures from high-throughput genomic and proteomic data.
Lynn Lin
Asst. Professor, Statistics

My research interests include a range of related problems in Bayesian mixture model development for classification, variable selection, design and model selection, structured and hierarchical non-parametric Bayesian methods, rare event detection, and statistical computation involving simulation and optimization.
Dajiang Liu
Assistant Professor

My field is statistical genomics and genetic epidemiology. Much of my research is focused on developing and applying statistical methods and computational tools for mapping complex trait and analyzing sequence data.
Yanxi Liu
Professor of Computer Science and Engineering and Electrical Engineering

Computational Symmetry Group Theory and Applications, Machine Learning (particularly low-dimensional subspace learning from very large, multi-modality feature set), Computer-Aided Diagnosis, Computer Vision, Computer Graphics.
Wansheng Liu
Associate Professor of Genomics

Structural, functional and comparative genomics of the mammalian Y‐chromosome; characterization of Y-chromosome variations and their application in male health, fertility, and reproduction in cattle and other livestock species; function of the PRAME/PRAMEY gene family during spermatogenesis in cattle and mice
Manuel Llinas
Associate Professor, Biochemistry and Molecular Biology

Understanding the molecular mechanisms of gene regulation and metabolism in the malaria parasite Plasmodium falciparum using functional genomics and metabolomics.
Hong Ma
Professor of Biology
Huck Distinguished Research Professor of Plant Molecular Biology

Kamesh Madduri
Assistant Professor of Computer Science and Engineering

Next generation sequencing data analysis, metagenomics, biological network analysis, parallel algorithms.
Shaun Mahony
Assistant Professor, Biochemistry & Molecular Biology

Computational biology and regulatory genomics
Kateryna Makova
Professor of Biology
Director, Center for Medical Genomics

Molecular evolution, population genetics, evolutionary genomics, bioinformatics, and human genetics
Costas Maranas
Donald B. Broughton Professor of Chemical Engineering

Development of algorithmic and optimization techniques to support the analysis and redesign of systems at different scales.
James Marden
Professor of Biology
Director of Operations, Huck Institutes of the Life Sciences

Physiological ecology. Causes and consequences of flight performance in insects.
Monica Medina
Associate Professor of Biology

Our group has been studying coral-algal-microbial interactions for several years. We use a combination of ecological, physiological, and genomic techniques to understand these interactions.
Paul Medvedev
Assistant Professor of Computer Science and Engineering
Assistant Professor of Biochemistry and Molecular Biology

Developing rigorous algorithms and analysis for problems in the biological sciences. Genome assembly, variation detection, cancer genomics, phylogenetics, graph theory, computational complexity, on-line algorithms, and networking.
Anton Nekrutenko
Professor of Biochemistry and Molecular Biology

Evolution of overlapping reading frames in eukaryotic genomes.
William Noid
Associate Professor of Chemistry

Theories of statistical mechanics applied to investigate structural biology and, in particular, the physical properties of unfolded and intrinsically disordered proteins; theories for coarse-grained modeling of peptides.
Edward O'Brien
Asst. Professor, Chemistry and of the Institute for CyberScience

Theory and computation of molecular and cellular processes
Andrew Patterson
Director/Faculty Oversight, Metabolomics Core Facility (University Park)
Associate Professor of Molecular Toxicology

The Patterson lab is focused on understanding the host-metabolite-microbiome axis
George Perry
Assistant Professor of Anthropology and Biology

Human and non-human primate evolutionary ecology and genomics.
Mary Poss
Professor in Biology and in Veterinary and Biomedical Sciences

Molecular mechanisms of virus and host adaptation at scales that span protein and structure to population dynamics.
B. Franklin Pugh
Willaman Professor in Molecular Biology

Biochemistry and genomics of eukaryotic transcription regulation.
Matthew Reimherr
Assistant Professor of Statistics

Joan Richtsmeier
Professsor of Anthropology

Analysis of craniofacial phenotypes.
Marylyn Deriggi Ritchie
Professor, Biochemistry and Molecular Biology

Bioinformatics, Computational Genomics, Pharmacogenomics, Genetic Architecture of Complex Human Traits.
Marilyn J Roossinck
Professor of Plant Pathology and Biology

Virus-plant interactions, virus evolution and ecology and evolution of disease
James Rosenberger
Professor of Statistics

The design of experiments. Statistical computing methodology and algorithms.
Howard Salis
Assistant Professor of Chemical Engineering
Assistant Professor of Agricultural and Biological Engineering

Stephen Schaeffer
Professor of Biology

Molecular population genetics and genomics.
Cooduvalli Shashikant
Associate Professor of Molecular and Developmental Biology
Co-director, Bioinformatics and Genomics graduate program
Assistant Director for Graduate Training Initiatives

Developmental and evolutionary aspects of regulation of patterning genes.
Mark Shriver
Professor of Biological Anthropology

Moriah L Szpara
Assistant Professor of Biochemistry & Molecular Biology

Neurovirology, genomics of pathogen variation, neuron-virus relationships
James Wang
Professor of Information Sciences and Technology

Visual database search and retrieval; retrieval from large-scale genome databases through pattern recognition.
Rongling Wu
Professor, Division of Biostatistics
Director, Center for Statistical Genetics

He is particularly interested in integrating the idea and principle of systems biology into statistical genetic research, ultimately elucidating a comprehensive atlas of the genetic control network of complex biology.
Feng Yue
Assistant Professor, Biochemistry & Molecular Biology

Study the function of non-coding variant in the human genome and how they contribute to diseases such as cancer Cancer epigenomics: investigate epigenetic marks for certain types of cancer with a hope that it may eventually contribute to drug discovery Study the 3D structure of the genome organization by 5C/Hi-C, in particular the interactions between enhancers and their target gene promoters Comparative genomics: investigate the evolutionary landscape of cis-regulatory elements in the mammalian genome
Yu Zhang
Associate Professor of Statistics

My current research interest is to develop computational methods to solve problems in molecular biology. I have been working on DNA sequence analysis, gene evolution, and genetics.