Research — Genetics

(M20 900)
Cross-listed with L41 (Bio 590)

Barak Cohen, PhD
SMRB – Scott McKinley Research Building, room 4308
Functional Genomics in Yeast. Gene regulatory networks, complex trait genetics, synthetic biology studies of cis-regulation.

Don Conrad, PhD
SMRB – Scott McKinley Research Building, room 6213
Our group has a long-standing interest in developing new methods for characterizing the origin and functional impact of human genetic variation. Recently completed projects have covered the following topics: mapping of copy number variants, measurement of sex-specific mutation rate and variation in mutation rate among decomposing the relative impact of different types of mutation (SNPs, indels, CNVs, etc.) on gene expression variation and disease susceptibility. Currently, we have a number of active projects that address fundamental unsolved problems related to human reproduction. First (1) we are trying to unravel the genetic basis for a common form of male infertility, non-obstructive azoospermia, using oligonucleotide arrays and exome sequencing. The short-term goal of this project is to define causal mutations in the >400 cases in which we have access. Our ultimate goal is to provide an unbiased view of the genetic architecture of the disease and establish a definitive reference panel of causal mutations that clinicians can use to facilitate diagnosis of spermatogenic failure. Second (2) we are using sperm DNA from a longitudinal cohort of semen donors to study the processes of mutation and selection within the population of germ cells of individuals. There are a number of other potential projects ranging from topics of medical relevance such as the biology of the placenta and maternal-fetal compatibility to more basic questions regarding genome biology and evolution. Training in this elective will be primarily computational, and can cover skills such as population genetic analysis, rare-variant association study methodology and other aspects of statistical genetics. However, parties interested in using other approaches to address the topics discussed here are welcome.

Joseph Dougherty, PhD
SMRB – Scott McKinley Research Building, room 6316
Our laboratory utilizes a variety of techniques spanning from human molecular genetics and informatics to mouse behavioral neuroscience and neuroanatomy. We develop and employ mouse models of psychiatric disorder, particularly those that mimic genetic variations we’ve identified from human patient populations, with the goal of trying to understand the cellular and molecular underpinnings of these disorders.

Susan K. Dutcher, PhD
SMRB – Scott McKinley Research Building, room 5301
Studies on the role of centrioles and basal bodies in ciliary signaling, assembly, and motility using molecular genetics, computational, and biochemical approaches.

Justin Fay, PhD
SMRB – Scott McKinley Research Building, room 4305
Population and evolutionary genetics, evolution of gene regulation in yeast, human evolution.

Stephen L. Johnson, PhD
711 McDonnell Science Building
Growth control and morphogenesis in vertebrate development. Focus on genes and mechanisms affecting proportionate fin growth, fin regeneration and pigment stripe patterning in zebrafish.

Heather Lawson, PhD
SMRB – Scott McKinley Research Building, room 6312
This research focuses on molecular mechanisms underlying parent-of-origin effects on metabolic traits. Parent-of-origin effects are epigenetic phenomena that appear as phenotypic differences between reciprocal heterozygotes depending on the allelic parent of origin. Genomic imprinting is a parent-of-origin effect that results in two alleles at a locus being functionally non-equivalent. Imprinted genes can be important contributors to phenotypic variation and imprinting patterns can be complex. We integrate whole-genome sequence data with transcriptome data and correlate this with variation in multiple metabolic traits under different dietary conditions. This discovery research uses a mouse model and our two main goals are to 1) identify molecular patterns that may have predictive power and 2) translate these patterns to human data.

Elaine Mardis, PhD
Room 4122, 4444 Forest Park Building
Technology development for second-generation DNA sequencing with an emphasis on methods and applications development. Non-human primate genomics.

Jeffrey Milbrandt, MD, PhD
SMRB – Scott McKinley Research Building, room 6306
Studies of metabolic control of glial/axonalinteractions necessary for proper nerve function. The use of high throughput genetic and pharmacologic screens using primary neurons and induced pluripotent stem cells to identify molecular mechanisms of axonal degeneration in neuropathy and neurodegenerative disease.

Rob Mitra, PhD
SMRB – Scott McKinley Research Building, room 4301
Systems Biology and Technology Development.  We are developing tools to make quantitative biological measurements and applying these tools to build mathematical models of biological processes.

Samantha Morris, PhD
SMRB – Scott McKinley Research Building, room 3316
Engineering cell fate to generate clinically valuable cell populations: Stem Cell and Developmental Biology. Our research focuses on dissecting the gene regulatory networks that define cell identity, using the developing embryo and tissue regeneration as a guide to engineer fate in vitro. We apply insight from these analyses to generate clinically relevant populations by differentiating cells from a pluripotent state, or by directly converting cells between mature fates. We employ a combination of computational, single cell transcriptomics, cell and developmental biology approaches.

Zachary Pincus, PhD
SMRB – Scott McKinley Research Building, room 5304
Inter-individual variability in aging and lifespan. Developmental origins of longevity and adult health. Quantitative microscope and image analysis of C. elegans.

Michael A. Province, PhD
Suite 6318, 4444 Forest Park Building
Development and evaluation of novel statistical genetics methodology, especially as applied to genomic identification and validation of variants for human complex quantitative traits, such as heart disease, cancer, pulmonary function, diabetes, and human longevity.

Nancy L. Saccone, PhD
308 Biotechnology Building
Statistical genetics and psychiatric genetics. Development and application of analysis methods for studying the genetics of human disease and complex traits.

Tim Schedl, PhD
SMRB – Scott McKinley Research Building, room 5305
Germ cell development in the model organism Caenorhabditis elegans. The major focuses are: control of the decision to proliferate or enter the meiotic pathway, control and coordination of meiotic prophase progression and gametogenesis, and control of meiotic maturation and ovulation.

James Skeath, PhD
SMRB – Scott McKinley Research Building, room 6315
Identification of the genes and the elucidation of the molecular mechanisms that regulate the early events of Drosophila central neurogenesis; illumination of the mechanisms that form, pattern and specify the individual identities of the progenitor cells of the Drosophila embryonic CNS.

Gary D. Stormo, PhD
SMRB – Scott McKinley Research Building, room 4208
Computational biology of protein-DNA interactions, RNA folding, gene and promoter finding. Biochemical analysis of DNA-protein interactions and gene regulation.

Ting Wang, PhD
SMRB – Scott McKinley Research Building, room 5211
We work in the general field of computational genomics and epigenomics. We study the evolution of human regulatory networks, with a focus on mobile elements (or transposable elements) and their impact on gene regulation, their genetic and epigenetic control, and their roles in human biology and diseases.

Richard K. Wilson, PhD
Room 4122, 4444 Forest Park Building
Genome research. Large-scale DNA sequence analysis of genomes and expressed genes (cDNAs) from humans, non-human primates, mammals, invertebrates, plants and various bacterial species.  Targeted genomic analysis of genes and regulatory elements in human cancers and other hereditary diseases. Development of novel technology for large-scale DNA sequence analysis and genetic analysis.