Faculty | Bioinformatics and Genomics | The Huck Institutes (en-US)

Istvan Albert

Research Professor of Bioinformatics

Bioinformatics, large scale biological data analysis, microarrays and sequence analysis. Scientific programming, algorithm development. Database-driven web development.

Reka Albert

Distinguished Professor of Physics and Biology

Biological physics and network modeling.

Sally Assmann

Waller Professor of Biology

Molecular biology of plant G-proteins and kinases. Phytohormone regulation of signal transduction and RNA processing. Second messenger regulation of ion channels in plant cells.

Discovery and characterization of plant microRNAs and siRNAs. Functions of microRNAs and siRNAs in the evolution of plant development. Genomics and bioinformatics of microRNAs, siRNAs, and their targets

Lu Bai

Professor of Biochemistry and Molecular Biology; Professor of Physics

Single cell / single molecule study of chromatin and gene regulation.

Le Bao

Professor of Statistics

Bayesian methods, data mining, computational methods, applications in health, environmental and social sciences.

Colin Barnstable

Professor and Chair of Neural Behavioral Sciences
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…

Arthur Berg

Professor of Public Health Sciences, Statistics, Surgery, Neurosurgery, and Family & Community Medicine

Unlocking the mysteries of DNA and its connection to human health.

Philip Bevilacqua

Co-Director, Center for RNA Molecular Biology; Distinguished Professor of Chemistry and of Biochemistry and Molecular Biology

RNA folding in vivo and genome-wide; RNA regulation of gene expression; Ribozyme Mechanism; roles RNA may have played in the emergence of life on early earth

Maciej Boni

Professor of Biology
Human influenza epidemiology and evolution, evaluating population-level malaria treatment strategies with individual-based microsimulation models, phylogenetic analysis of avian influenza evolution in southern Vietnam, economic epidemiology of avian…

Seth Bordenstein

Director of the Microbiome Center; Huck Chair in Microbiome Sciences; Professor of Biology and Entomology

The evolutionary and genetic principles that shape symbiotic interactions between animals, microbes, and viruses and the major applications of these interactions to human health.

srb6251@psu.edu

James Broach

Distinguished Professor and Chair of Biochemistry and Molecular Biology

Liana Burghardt

Huck Early Career Chair of Root Biology and Rhizosphere Interactions; Assistant Professor of Plant Science
Plant-microbe-climate interactions; the evolution and ecology of legumes and nitrogen-fixing rhizobia; the genomic basis and environment dependence of root, nodule, and mutualism traits; GWAS/transcriptomics/evolve & resequence…

Stefan Canzar

Associate Professor of Computer Science and Engineering

Algorithmic bioinformatics, computational genomics. We develop algorithms and software for single-cell genomics and spatial transcriptomics data. We use techniques from combinatorial optimization, linear programming, and machine learning.

Laura Carrel

Professor of Biochemistry and Molecular Biology

Genetic, epigenetic, and genomic regulation of expression on the mammalian X chromosome.

luc3@psu.edu

Keith Cheng

Distinguished Professor of Pathology and Laboratory Medicine, of Biochemistry and Molecular Biology, and of Pharmacology

Computational phenomics, image informatics, and "Geometry of Life" based on x-ray histotomography, population, genomic, and functional genomic analyses of complex traits in human and zebrafish; web-based science resources.

Francesca Chiaromonte

Director of the Genome Sciences Institute; Huck Chair in Statistics for the Life Sciences; Professor of Statistics

Developing methods for the analysis of large, high-dimensional and complex data.

Surinder Chopra

Professor of Maize Genetics

Regulation of flavonoid biosynthesis during plant development and plant-pathogen interaction. Epigenetic regulation and allele specific patterns.

Eric Crandall

Assistant Research Professor of Biology

Applying population genomic methods to answer questions about ecology and evolution, particularly in marine species. Improving the accessibility of genomic data through metadata and capacity development

edc5240@psu.edu

Emily Davenport

Assistant Professor of Biology

Understanding the complex relationship humans have with our microbiomes, using high-throughput sequencing technologies and novel computational and statistical techniques.

exd44@psu.edu

Claude dePamphilis

Director of the Center for Parasitic and Carnivorous Plants; Huck Distinguished Chair in Plant Biology and Evolutionary Genomics; Professor of Biology
Genomics, bioinformatics, and molecular evolution. Origin and diversification of flowers and developmental pathways. Comparative genomics of plants, organelles, and plant gene families. Genomics, evolution, and functional biology of parasitic…

Nikolay Dokholyan

G. Thomas Passananti Professor of Pharmacology; Professor of Biochemistry and Molecular Biology
We are a translational systems research group in the Pharmacology at the Penn State College of Medicine. Our laboratory focuses on understanding etiologies of human diseases, such as cystic fibrosis (CF), amyotrophic lateral sclerosis (ALS), and pain…

Sinisa Dovat

Professor and Vice Chair for Basic Science Research, Department of Pediatrics; Professor of Biochemistry and Molecular Biology and of Pharmacology

Investigate the role of lymphoid master regulator, IKZF1/Ikaros, in the development of acute lymphoblastic leukemia (ALL); other transcriptional factors in leukemia; CK2 activity; chromatin remodeling; super-enhancers.

Kristin Eckert

Professor of Pathology and Laboratory Medicine and of Biochemistry and Molecular Biology

Mechanisms of human cell mutagenesis and repetitive DNA replication in relation to genome evolution.

Lindsay Fernandez-Rhodes

Assistant Professor of Biobehavioral Health

The genetic epidemiology of complex diseases in diverse human populations and contexts.

Erika Ganda

Assistant Professor of Food Animal Microbiomes

Developing practical ways to leverage the microbiome to improve food safety and improve food production animals' production efficiency.

David Geiser

Professor of Mycology

Molecular evolutionary genetics of pathogenic and toxigenic fungi.

Ilias Georgakopoulos-Soares

Assistant Professor
The development and implementation of new computational methods in genomics and molecular biology, with the aim of identifying genetic biomarkers for the diagnosis, monitoring, and treatment of human diseases, including bacterial and viral infections…

izg5139@psu.edu

Santhosh Girirajan

Professor of Genomics; Interim Department Head of Biochemistry and Molecular Biology; Professor of Anthropology

Understanding the genetic basis of neurodevelopmental disorders.

Suzanne Gonzalez

Assistant Professor of Psychiatry and Behavioral Health and of Pharmacology
My laboratory focuses on neuropsychiatric genetics in diverse populations. I am particularly interested in understanding how genetic polymorphisms within key physiological pathways translate into clinical phenotypes of psychiatric disorders, such…

szg550@psu.edu

Mark Guiltinan

J. Franklin Styer Professor of Horticultural Botany; Professor of Plant Molecular Biology; Director, Endowed Program in the Molecular Biology of Cocoa

Plant functional genomics, metabolomics and biotechnology. Identification of key genes for disease resistance and important traits in the tree crop Theoboma cacao, the Chocolate tree.

Molly Hall

Dr. Frances Keesler Graham Early Career Professor; Assistant Professor of Veterinary and Biomedical Sciences
Building tools to elucidate the complex genetic and environmental underpinnings of human disease. Integrating genetic (genotype, sequence, structural variation) and exposure (derived from surveys and metabolomics methods) big data to predict disease…

Wenrui Hao

Assistant Professor of Mathematics

Ross Hardison

Associate Director of the Genome Sciences Institute; T. Ming Chu Professor of Biochemistry and Molecular Biology

Regulation of gene expression during development.

Heather Hines

Associate Professor of Biology and Entomology
Applies genomic, transcriptomic, phylogenomic, and bioinformatic approaches to study the evolution and genetics of diverse traits in bees and wasps. This includes study of mimetic color diversification, plant gall induction, novel morphologies,…

Vasant Honavar

Huck Chair in Biomedical Data Sciences and AI; Professor and Edward Frymoyer Chair of Information Sciences and Technology

Statistical machine learning algorithms for predictive modeling; modeling and inference of biological networks; characterization and prediction of protein-protein, protein-RNA, and protein-DNA interactions.

Judie Howrylak

Assistant Professor of Medicine, Public Health Sciences, and Biochemistry and Molecular Biology

jhowrylak@hmc.psu.edu

Yifei Huang

Assistant Professor of Biology

Developing novel bioinformatic methods and using them to address fundamental questions in evolutionary genomics and medical genomics.

yuh371@psu.edu

Christian Huber

Assistant Professor of Biology

How evolutionary mechanisms such as mutation, recombination, and natural selection shape genetic diversity and the variability between individuals and species.

Seogchan Kang

Professor of Plant Pathology & Environmental Microbiology

Genetic and cellular mechanisms underpinning plant-fungal interactions with Arabidopsis thaliana and Fusarium oxysporum as a model system. Molecular genetics and comparative genomics of fungal plant pathogens. Bioinformatics.

Vivek Kapur

Associate Director, Huck Institutes of the Life Sciences; Huck Distinguished Chair in Global Health; Professor of Microbiology and Infectious Diseases

The basic mechanisms by which pathogenic microbes successfully infect, colonize, and cause disease in their hosts.

Deb Kelly

Director of the Center for Structural Oncology; Huck Chair in Molecular Biophysics; Professor of Biomedical Engineering

Engineering new molecular paradigms to create a world without cancer.

David Kennedy

Assistant Professor of Biology

Ecology and evolution of infectious diseases, with particular interest in how disease dynamics influence pathogen emergence, virulence evolution, and drug or vaccine resistance.

Daniel Kifer

Professor of Computer Science & Engineering

Tae Hyun Kim

Huck Early Career Chair; Assistant Professor of Avian Biology

Improving poultry health by applying modern genetic approaches including gene editing. Particular focus on identifying key genes and regulatory elements associated with improved economic traits.

David Koslicki

Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Computer Science and Engineering and Biology

Developing efficient algorithms to extract insight from high-throughput sequencing data.

Jasna Kovac

Lester Earl and Veronica Casida Career Development Professor of Food Safety; Associate Professor of Food Science

Integrating epidemiological, microbiological, molecular and omics methods to better understand microbial pathogenic potential, antimicrobial resistance, and epidemiology of foodborne pathogens.

Jesse Lasky

Associate Professor of Biology

Ecological and evolutionary genomics, genetic and ecophysiological basis of adaptation to environmental stress, evolutionary ecology of biological complexity.

Nicole Lazar

Professor of Statistics

Arthur Lesk

Professor of Biology and of Biochemistry & Molecular Biology

aml25@psu.edu

Qunhua Li

Associate Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Statistics

Developing statistical and computational methods for analyzing complex omics data and improving quality and reproducibility of high-throughout data

Dajiang Liu

Co-Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Professor of Public Health Sciences and Biochemistry and Molecular Biology

Developing novel methods to analyze very large scale datasets in order to identify genes that are responsible for disease, understand the disease mechanism, and gain clinical insights.

Wansheng Liu

Professor of Genomics

Functional annotation of farm animal genomes, structure and function of mammalian sex (X and Y) chromosome, spermatogenesis and male fertility.

Yanxi Liu

Associate Professor of Computational Science and Engineering

yul11@psu.edu

Manuel Llinas

Distinguished Professor of Biochemistry and Molecular Biology

Understanding the molecular mechanisms of gene regulation and metabolism in the malaria parasite Plasmodium falciparum using functional genomics and metabolomics.

Margarita Lopez-Uribe

Associate Professor of Entomology

How environmental change and human management shape bee health and long-term persistence of their populations in agricultural areas.

Hong Ma

Huck Chair in Plant Reproductive Development and Evolution; Professor of Biology

Plant development under favorable and stressful conditions; phylogeny and evolutionary biology of plant groups containing major crops and ecologically important species.

Sally Mackenzie

Director of the Plant Institute; Huck Chair of Functional Genomics; Professor of Biology and of Plant Science

Organelle biology and cellular specializations. Plant epigenetics, memory and phenotypic plasticity. Crop epigenetic breeding.

Kamesh Madduri

Associate Professor of Computer Science and Engineering

Computational biology, algorithms, and high-performance computing.

Shaun Mahony

Associate Professor of Biochemistry & Molecular Biology

We apply neural networks and other machine learning approaches to understand how transcription factors control cellular identity

Kateryna Makova

Director of the Center for Medical Genomics; Professor of Biology

Molecular evolution, population genetics, evolutionary genomics, bioinformatics, and human genetics.

Costas Maranas

Donald B. Broughton Professor of Chemical Engineering

Computational studies of metabolism and gene regulation.

James Marden

Associate Director of Operations, Huck Institutes of the Life Sciences; Professor of Biology

How physiological variation within species affects their ecology and evolution. Primarily with insects, but recently also with plants, and a particular interest in allelic variation in the pathogen resistance genes of tropical trees.

Monica Medina

Professor of Biology

Paul Medvedev

Director of the Center for Computational Biology and Bioinformatics; Professor of Electrical Engineering; Associate Professor of Computer Science and Engineering; Associate Professor of Biochemistry and Molecular Biology
Please see the researcher's homepage at…

Anton Nekrutenko

Professor of Biochemistry and Molecular Biology

Evolution of overlapping reading frames in eukaryotic genomes.

William Noid

Assistant Professor of Chemistry

wgn1@psu.edu

Edward O’Brien

Professor of Chemistry

Developing and applying Physical Bioinformatic techniques to measure rates of translation transcriptome-wide and their molecular origins as relates to fundamental biology and disease.

Denise Okafor

Assistant Professor of Biochemistry and Molecular Biology

Structural mechanisms of signaling and regulation in protein complexes.

Andrew Patterson

Professor and Huck Chair of Molecular Toxicology; Faculty Oversight, Metabolomics Core Facility

The Patterson lab is focused on understanding the host-metabolite-microbiome axis

George Perry

Professor of Anthropology and Biology

Anthropological genomics, paleogenomics, human body size evolution, parasite evolution, and evolutionary medicine.

ghp3@psu.edu

Elizabeth Proctor

Assistant Professor of Neurosurgery, Pharmacology, Biomedical Engineering, and Engineering Science & Mechanics

Systems biology of complex disease. Integration of heterogeneous data types across length scales.

Matthew Reimherr

Associate Professor of Statistics

Tanya Renner

Associate Professor of Entomology

Evolution of chemical and structural defense. Molecular evolution, evolutionary genomics, and transcriptomics. Origins and evolution of carnivorous plants.

Joan Richtsmeier

Professsor of Anthropology

Analysis of craniofacial phenotypes.

jta10@psu.edu

James Rosenberger

Professor of Statistics

Howard Salis

Associate Professor of Chemical Engineering; Associate Professor of Agricultural and Biological Engineering

Engineering microorganisms for applications in synthetic biology and metabolic engineering.

Stephen Schaeffer

Professor of Biology

Population Genetics and Genomics of Chromosomal Rearrangements in Drosophila

sws4@psu.edu

Mingfu Shao

Assistant Professor of Computer Science and Engineering
Our research interests are designing algorithms and developing methods for solving the various challenging problems in biology using combinatorial optimization and machine learning approaches. Current research topics include: transcript assembly,…

Mark Shriver

Professor of Biological Anthropology

Human population genomics and complex disease mapping.

Justin Silverman

Assistant Professor of Information Sciences and Technology

Statistical methods for the analysis of biomedical data (or any other interesting data/questions)

Aleksandra Slavkovic

Huck Chair in Data Privacy and Confidentiality; Professor of Statistics and of Public Health Sciences

Methodological developments in the area of data privacy and confidentiality in the context of small and large scale surveys, health, genomic, and network data.

Hyebin Song

Assistant Professor of Statistics

Moriah Szpara

Associate Professor of Biochemistry & Molecular Biology and Biology
How genetic variation influences the outcomes of viral infection, particularly for neurotropic viruses such as herpes simplex virus 1 (HSV-1) and HSV-2, using high-throughput sequencing, comparative genomics, neuronal cultures, and genetic…

Zachary Szpiech

Assistant Professor of Biology

Population and evolutionary genetics, with applications to medical genetics, anthropology, and conservation

zps5164@psu.edu

David Toews

Assistant Professor of Biology

Yasin Uzun

Assistant Professor of Pediatrics

Developing and applying systems biology approaches to better understand gene regulation at the molecular level in development and disease by using single-cell genomic sequencing data.

David Vandenbergh

Professor of Biobehavioral Health

Genetics of addiction in human populations and its neurobiological basis in animal models.

Yogasudha Veturi

Assistant Professor of Biobehavioral Health and of Statistics
Developing novel statistical and machine learning methods to better understand shared genetics between complex human diseases across the “phenome” and their connections with cognitive decline as well as genetic underpinnings of sex and ancestral…

yzv101@psu.edu

Jennifer Wagner

Assistant Professor of Law, Policy, and Engineering
Promoting the international human right to science in genetics/omics, precision medicine, and digital health technologies; conducting anthroengineering and ELSI (ethical, legal, and social issues) research (with an emphasis on nondiscrimination, data…

jkw131@psu.edu

rkz5110@psu.edu

Xiang Zhu

Assistant Professor of Statistics

Statistical Genetics and Genomics

xkz5224@psu.edu