Faculty
Faculty members involved with the Bioinformatics and Genomics graduate program are at the vanguard of research in the biological sciences. Hailing from more than a dozen departments across Penn State, these faculty advisers collaborate to conduct research and to train graduate students. The community they have created provides a positive, collaborative environment that helps to position graduate students for career success.
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.
Naomi Altman
Professor Emeritus of Statistics Bioinformatics, gene expression analysis, functional genomics and gene clustering, experimental design, multiple testing, functional data analysis and nonparametric smoothing.
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.
Michael Axtell
Professor of Biology 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
Le Bao
Associate 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…
Terrence Bell
Assistant Professor of Phytobiomes Soil and root-associated microbiomes, microbiome assembly, microbiome manipulation, disturbance.
Arthur Berg
Associate Professor of Public Health Sciences and Statistics 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 F Boni
Associate 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…
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…
John Carlson
Professor of Molecular Genetics; 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 Genetic, epigenetic, and genomic regulation of expression on the mammalian X chromosome.
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.
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.
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.
Santhosh Girirajan
Associate Professor of Biochemistry & Molecular Biology; Associate 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…
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…
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
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
Yifei Huang
Assistant Professor of Biology Developing novel bioinformatic methods and using them to address fundamental questions in evolutionary genomics and medical genomics.
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 for Strategic Initiatives, 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.
Tae Hyun Kim
Huck Early Career Chair; Assistant Professor of Avian Biology
David Koslicki
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; Assistant 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.
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
Lynn Lin
Assistant Professor of Statistics
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…
Dajiang Liu
Associate Professor of Public Health Science 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.
Manuel Llinas
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.
Hong Ma
Huck Distinguished Research Professor of Plant Molecular Biology; 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
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.
Paul Medvedev
Director of the Center for Computational Biology and Bioinformatics; 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.
Edward O’Brien
Associate 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
Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Anthropology and Biology Anthropological genomics, paleogenomics, human body size evolution, parasite evolution, and evolutionary medicine.
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.
Tanya Renner
Assistant Professor of Entomology Evolution of chemical and structural defense. Molecular evolution, evolutionary genomics, and transcriptomics. Origins and evolution of carnivorous plants.
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
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)
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
David Vandenbergh
Professor of Biobehavioral Health Genetics of addiction in human populations and its neurobiological basis in animal models.
James Wang
Professor of Information Science and Technology Modeling
of objects, concepts, aesthetics, and emotions in big visual data from various
domains.
Rongling Wu
Director of the Center for Statistical Genetics; Professor of Public Health Sciences