Anne E Kwitek Ph.D. [Former faculty]

Todd E Scheetz Ph.D.

Current
Todd
E
Scheetz
Ph.D.
Professor
Ophthalmology and Visual Sciences
Research area(s): 
Ophthalmology and Visual Sciences
Address
3185
MERF
3185
MERF
Research
Research Focus: 

Dr. Scheetz's research interests focus on bioinformatics, genomics, systems biology, and genetic analyses including genotype-phenotype correlation and genome-wide association studies. Much of his research is performed in collaboration with other faculty within the University of Iowa and other institutions. These collaborative projects include analysis of genomic integration patterns, analysis of expression, and identification of regulatory elements in the mammalian eye.

Faculty affiliations: 

Paul B McCray M.D.

Current
Paul
B
McCray
M.D.
Professor
Pediatrics
Research area(s): 
Human Genetics; Molecular and Biochemical Genetics
Address
6320
PBDB
6320
PBDB
Research
Research Focus: 

Dr. McCray has a long-standing interest in the pathogenesis and treatment of cystic fibrosis. His laboratory has two main areas of investigation: 1) innate mucosal immunity in the lung and how this is altered in disease states, and 2) gene transfer for the treatment of inherited diseases.

Studies of the anti-microbial properties of the airway surface liquid have stimulated interest in the anti-microbial proteins and peptides secreted by epithelia. Dr. McCray's lab is currently defining the tissue specific expression, regulation and anti-microbial activity of epithelial defensins and other proteins in model systems. These molecules may play a role in the innate mucosal immunity of the lung and other mucosal surfaces. A major effort is directed towards identifying novel host defense genes using genomics and large scale expression profiling.

Another area of investigation is the development of integrating viral vectors for the treatment of inherited diseases. Current projects include gene transfer to airway epithelia for cystic fibrosis and gene transfer to the hepatocytes for the treatment of hemophilia A. The focus of these studies is on the development and optimization of retrovirus-derived vectors. A long-term goal is to develop strategies with integrating vector systems that could be successfully used to treat genetic diseases.

Faculty affiliations: 

John Logsdon Ph.D.

Current
John
Logsdon
Ph.D.
Associate Professor
Biology
Research area(s): 
Computational Genetics; Molecular and Biochemical Genetics; Evolutionary Genetics
Address
310
BB
301
BB
Research
Research Focus: 

The Logsdon lab works on a variety of related topics in molecular evolutionary genetics:

SEX & MEIOSIS:

  1. Exploring the origin and evolution of meiotic genes in diverse eukaryotes.
  2. Molecular evolution and phylogeny of meiotic genes.
  3. Isolation of meiosis-related genes from protists and other eukaryotes.
  4. Functional studies of meiotic genes isolated from diverse eukaryotes.
  5. Bioinformatic studies of meiosis and recombination/repair genes.

TREES:

  1. Understanding the molecular phylogeny of eukaryotes.
  2. Using complex gene families to root the eukaryotic tree of life.
  3. Isolating new protein genes to address thorny issues in eukaryotic phylogeny.

LATERAL GENE TRANSFER:

  1. Developing a better understanding of the frequency, roles, distribution and phylogenetic impacts of LGT in prokaryotes.
  2. Comparative bioinformatics of bacterial genomes.
  3. Mathematical modeling/ computer simulation.

GENOMES:

  1. Discovery and analysis of genomic sequence from key protists.
  2. Comparative bioinformatics of protist genomes as grist for hypothesis-driven research in the lab.

INTRONS:

  1. Understanding of the origin and evolution of spliceosomal introns
  2. What are their roles in eukaryotic genome evolution? What is their phylogenetic distribution?

Bryant F McAllister Ph.D.

Current
Bryant
F
McAllister
Ph.D.
    Associate Professor
    Biology
    Research area(s): 
    Computational Genetics; Evolutionary Genetics
    Address
    Research
    Research Focus: 

    My research interests are in the field of evolutionary genetics, especially in processes occurring at or influenced by the genome. Active research projects in the lab are primarily concerned with using the fly species Drosophila americana to understand the factors influencing chromosomal change and the mechanisms involved in the differentiation of sex chromosomes. Changes in chromosomal arrangement are common, but their significance is unknown. We are currently examining a chromosomal rearrangement involving a centromeric fusion of the X chromosome and an autosome in D. americana. This derived arrangement exists as a polymorphism with the ancestral arrangement, showing a strong latitudinal cline in the central and eastern US. Population genetic analyses are used to examine the hypothesis that these alternative chromosomal arrangements coordinate adaptive genetic variation. Independently evolved pairs of sex chromosomes exhibit similar patterns of differentiation. The Y chromosome is genetically inert, and the X chromosome contains many active unique genes and often compensates for differences in dosage between genders. The X-4 centromeric fusion in D. americana provides a system for examining the earliest asymmetries between newly evolved sex chromosomes. We are testing models of sex chromosome evolution by examining patterns of sequence variation on this pair of neo-sex chromosomes.

    Faculty affiliations: 

    Anne E Kwitek Ph.D.

    Associate Professor, Pharmacology & Internal Medicine
    Associate Director, Iowa Institute of Human Genetics

    John H. Fingert M.D., PhD.

    Current
    John
    H.
    Fingert
    M.D., PhD.
    Professor
    Ophthalmology and Visual Sciences
    Research area(s): 
    Molecular Genetics of Glaucoma and other inherited eye diseases
    Address
    3125
    MERF
    3111B
    MERF
    Research
    Research Focus: 

    I am a board-certified ophthalmologist with fellowship training in glaucoma and I have a Ph.D. in ophthalmic genetics. My training and experience has provided me with broad clinical and laboratory expertise to investigate the genetic basis of optic nerve disease. My early research resulted in the detection of the first glaucoma gene, myocilin, and more recently my laboratory has discovered one of two known normal tension glaucoma genes, TBK1. My laboratory is currently investigating the mechanisms by which defects in genes in the autophagy pathway (TBK1, OPTN, and others) lead to normal tension glaucoma using transgenic mice, induced pluripotent stem cells, and other patient-based studies. Other major projects include genetic studies of pigmentary glaucoma, exfoliative glaucoma, dominant optic atrophy, and studies of the genetic basis of quantitative features of glaucoma (eye pressure, corneal thickness, and optic nerve cupping). These projects are part of an overall mission to investigate the genetic basis of optic nerve disease and develop sight-saving therapies for this common group of blinding diseases.

     

    Faculty affiliations: 

    Josep M Comeron Ph.D.

    Current
    Josep
    M
    Comeron
    Ph.D.
    Associate Professor
    Biology
    Research area(s): 
    Computational Genetics; Evolutionary Genetics
    Address
    Research
    Research Focus: 

    We apply a multidisciplinary approach-combining empirical work to obtain sequence data, large-scale genomic analyses, and the development of theoretical, analytical and computational tools-to investigate: 1) variation in the efficacy of natural selection among species and across genomes, 2) the evolution of recombination across genomes and among species, 3) the evolution of introns (presence and size) and genome structure in eukaryotes, 4) the evolutionary consequences of changes in population size, and 5) the genetic basis of speciation. Likely, many mutations important to evolution have much smaller selection coefficients than it is practicable to demonstrate in the laboratory. Population genetics and molecular evolution analyses-the study of nucleotide variability within and between species, respectively-are powerful tools that allow us to detect the action of selection on naturally-occurring mutations, even if the fitness effects of these mutations are extremely weak. We study the causes and consequences of changes in recombination rates among species and across genomes, focusing on the influence of meiotic recombination on the efficacy of selection in eukaryotes. To measure possible changes in the effectiveness of selection, we study weakly selected mutations such as synonymous mutations (changes in the coding sequence that do not alter protein sequence) and small insertion/deletions (indels). The same population genetics techniques that are commonly applied to nucleotide changes can be also applied to genomic features, allowing us to investigate the forces involved in the evolution of gene number, the origin of introns, the evolution of exon-intron structures, and ultimately genome size. This genomics-meets-population genetics approach (i.e., population genomics) can be implemented with computer simulations mimicking the evolutionary process (in silico evolution), a computationally-intensive technique that provides new and valuable insights into the expected outcome of complex evolutionary processes. We also apply molecular evolution and population genetics techniques to study recent speciation events. In particular, we investigate Drosophila species to gain insight into the evolutionary patterns of genes involved in phenotypic differentiation and reproductive isolation.

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