People: 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
Associate Professor of Bioinformatics Bioinformatics, large scale biological data analysis, microarrays and sequence analysis. Scientific programming, algorithm development. Database-driven web development.
Reka Albert
Professor of Physics and Biology Biological physics and network modeling.
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
Assistant Professor of Biology Evolutionary genomics, molecular evolution, and bioinformatics. Particularly interested in how new functions evolve after gene duplication.
Sarah 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
Assistant Professor of Statistics Bayesian methods, data mining, computational methods, applications in health, environmental and social sciences.
Colin Barnstable
Co-Chair, Intercollege Graduate Degree Program in Neuroscience; 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
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 Biochemistry & Molecular Biology Roles of RNA-binding proteins in plant physiology. Plant ribonomics. Identification and characterization of functional RNAs in plants.
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…
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
Chromosome structure and function
Genome organization
Long-range control of gene expression
Heterochromatin formation
Epigenetic role in human disease
Genetics and genomics of X chromosome inactivation in human and mouse
Keith Cheng
Distinguished Professor of Pathology; Professor of Biochemistry & Molecular Biology; Professor of Pharmacology
Francesca Chiaromonte
Director of the Genome Sciences Institute; 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.
Michael DeGiorgio
Assistant Professor of Biology Development and application of mathematical models, statistical methods, and algorithms to uncover genomic footprints of past evolutionary events.
Claude dePamphilis
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
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
Associate Professor of Pediatric Hematology and Oncology 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 Biochemistry and Molecular Biology Mechanisms of human cell mutagenesis and repetitive DNA replication in relation to genome evolution.
David Geiser
Professor of Plant Pathology Molecular evolutionary genetics of pathogenic and toxigenic fungi.
Santhosh Girirajan
Associate Professor of Biochemistry & Molecular Biology; Associate Professor of Anthropology To understand the genetic basis of neurodevelopmental disorders
Suzanne Gonzalez
Assistant Professor of Psychiatry
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. Research focuses on identification of key genes for disease resistance and important traits in the tree crop Theoboma cacao, the Chocolate tree. We collaborated with other labs at Penn State…
Molly Hall
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
Assistant Professor, Biology and Entomology Genetics of adaptive mimetic color pattern variation in butterflies and bumble bees
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
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.
Daniel Kifer
Associate Professor (James L. Henderson Memorial Professorship) of Computer Science & Engineering
Jesse Lasky
Assistant Professor of Biology Ecological & evolutionary genomics, genetic and ecophysiological basis of adaptation to environmental stress, evolutionary ecology of biological complexity.
Qunhua Li
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…
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
Professor of Biology; Huck Distinguished Research Professor of Plant Molecular Biology Plant development under favorable and stressful conditions; phylogeny and evolutionary biology of plant groups containing major crops and ecologically important species.
Sally Mackenzie
Lloyd and Dottie Huck Chair for Functional Genomics; Professor of Biology; Professor 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
Assistant Professor of Biochemistry & Molecular Biology Computational biology and regulatory genomics
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…
Anton Nekrutenko
Professor of Biochemistry and Molecular Biology Evolution of overlapping reading frames in eukaryotic genomes.
Edward O’Brien
Assistant 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.
Andrew Patterson
Associate Professor of Molecular Toxicology The Patterson lab is focused on understanding the host-metabolite-microbiome axis
George Perry
Harry J. and Elissa M. Sichi Early Career Professor of Anthropology; Associate Professor, Departments of Anthropology and Biology Human and non-human primate evolutionary ecology, parasite evolutionary biology as a proxy for studying human evolution, genomics, and paleogenomics (ancient DNA).
Elizabeth Proctor
Assistant Professor of Neurosurgery, Pharmacology, and Biomedical Engineering Systems biology of complex disease. Integration of heterogeneous data types across length scales.
B. Franklin Pugh
Director of the Center for Eukaryotic Gene Regulation; Willaman Professor in Molecular Biology Biochemistry and genomics of eukaryotic transcription regulation.
Marilyn Roossinck
Professor of Plant Pathology and Biology Virus-plant interactions, virus evolution and ecology and evolution of disease
Howard Salis
Assistant Professor of Chemical Engineering; Assistant Professor of Agricultural and Biological 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,…
Cooduvalli Shashikant
Assistant Director for Graduate Training Initiatives, Huck Institutes of the Life Sciences; Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Molecular and Developmental Biology Developmental and evolutionary aspects of regulation of patterning genes.
Mark Shriver
Professor of Biological Anthropology Human population genomics and complex disease mapping.
Moriah L Szpara
Assistant Professor of Biochemistry & Molecular Biology Neurovirology, genomics of pathogen variation, neuron-virus relationships
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
Feng Yue
Assistant Professor of Biochemistry & Molecular Biology Using a combination of experimental and bioinformatics approaches, we study 3D genome structure and epigenomic regulation in human cancer.
Yu Zhang
Associate Professor of Statistics Statistical and computational methods development for solving problems in molecular biology and human health.