Yi Xing Ph.D. [Former faculty]

Michael J. Schnieders DSc

Current
Michael
J.
Schnieders
DSc
Associate Professor
Biochemistry, Biomedical Engineering (BME)
Research area(s): 
Molecular biophysics theory and high performance computational algorithms
Address
4-516
BSB
4-514
BSB
Research
Research Focus: 

Our lab is focused on molecular biophysics theory and high performance computational algorithms that are needed to reduce the time and cost of engineering drugs and organic biomaterials. A complementary goal is to help open the door to personalized medicine by developing tools to map genetic information onto molecular phenotypes.

Faculty affiliations: 

Ben Darbro M.D., Ph.D.

Current
Ben
Darbro
M.D., Ph.D.
Associate Professor, Director of the Shivanand R. Patil Cytogenetics and Molecular Laboratory
Pediatrics
Research area(s): 
Genetic Determinants of Intellectual Disability
Address
Research
Research Focus: 

My primary research interest is in the genetic determinants of intellectual disability (ID), formerly referred to as mental retardation (MR).  I specifically study the roles of copy number variation and somatic structural variation in the context of a “genomic mutational burden” hypothesis of ID.  This hypothesis is investigated using a combination of conventional cytogenetics methods (chromosome analysis and fluorescence in situ hybridization) and new molecular, high throughput, and high data volume, genomic technologies including single nucleotide polymorphism (SNP) arrays, gene expression microarrays, comparative genomic hybridization (CGH) arrays as well as custom targeted, whole exome, and whole genome massively parallel DNA sequencing.  We perform all our own bioinformatics and are actively engaged in the development of new analysis tools to better meet our needs and those of the scientific community.  Drosophila melanogaster and the well-established GAL4/UAS/RNAi system are used to evaluate candidate ID genes with the use of a validated olfaction learning technique (T-Maze).  Candidate genes are derived from our extensive clinical database of patients with ID that have already undergone diagnostic chromosomal microarray testing.

Albert J Erives PhD

Current
Albert
J
Erives
PhD
Associate Professor
Biology
Research area(s): 
Bioinformatics, Developmental Genetics, Evolutionary Genetics, Gene Expression and Regulation
Address
424A
BB
424
BB
Research
Research Focus: 

The Genetics of Eukaryotic Transcriptional Enhancers

Transcriptional enhancers are DNA sequences that specify inducible, spatiotemporal patterns of gene expression at most gene loci. Several complementary results from genomic studies have shown that the majority of functional sites in a genome correspond to transcriptional enhancer sequences, thus underscoring their importance for understanding basic physiology. However, while transcriptional enhancers represent a major class of regulatory DNAs in eukaryotic genomes, the entire set of sequences that are necessary and sufficient for constructing a complex eukaryotic enhancer are not yet known.

Our laboratory is focused on using molecular biology, genomics, bioinformatics, and transgenic model systems to understand enhancer biology. A major area of focus in our laboratory is the study of how different morphogen-concentration specific responses are encoded at different loci. We are also interested in understanding the sequence-function relationship well enough to understand the complex patterns of molecular evolution occurring at enhancer sequences.

Yi Xing Ph.D.

Associate Professor
Internal Medicine

Richard J Smith M.D.

Current
Richard
J
Smith
M.D.
Professor and Vice Chair
Otolaryngology
Research area(s): 
Human Genetics
Address
Research
Research Focus: 

My laboratory is studying the genetic basis of deafness and membranoproliferative glomerulonephritis type 2 (MPGN 2). Hereditary deafness is common. It affects 1:2,000 newborns and accounts for greater than 50% of severe-to-profound childhood deafness. It also affects the elderly. Nearly 50% of octogenarians have difficulty communicating without the use of amplification, and in many, the cause is genetic. Inherited hearing impairment can occur with other co-inherited clinical features to form a recognized phenotype (syndromic hearing loss) or appear in isolation (non-syndromic hearing loss). Non-syndromic hearing loss accounts for approximately 70% of genetic deafness. It is almost exclusively monogenic and is highly heterogeneous, with some estimates of the number of deafness-causing genes exceeding 100. We are studying both syndromic and non-syndromic types of deafness. Projects include gene localization by linkage analysis and homozygosity mapping, mutation screening and detection, a variety of functional studies, and hearing-related research on mouse mutants targeting specific genes by RNAi. Membranoproliferative glomerulonephritis type 2 is also called Dense Deposit Disease (MPGN II/DDD). It causes chronic renal dysfunction that leads to kidney failure and a retinal disease similar to age-related macular degeneration, which is the most common cause of blindness in the elderly. Deficiency of and mutations in complement Factor H (CFH) are associated with development of MPGN II/DDD. Changes in CFH are also associated with another renal disease, atypical hemolytic uremic syndrome, and with age-related macular degeneration. We are studying relationships between the alternative pathway of the complement cascade, the structure of the glomerular basement membrane, and MPGN II/DDD to better understanding the pathophysiology of this disease.

Faculty affiliations: 

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: 

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?

Deborah V Dawson Ph.D., Sc.M.

Current
Deborah
V
Dawson
Ph.D., Sc.M.
    Professor
    Pediatric Dentistry
    Research area(s): 
    Human Genetic Disorders, Statistical Genetics
    Address
    Research
    Research Focus: 

    My research interests focus on human genetic disorders, including both the development of new statistical methods for their investigation, and applied studies. My methodological research has included development of techniques in the areas of delayed onset disorders and correction for ascertainment bias, as well as approaches to problems in population immunogenetics, most recently as they relate to vaccine research. My applied work includes statistical genetic modeling of human disorders, and biostatistical modeling related to other clinical and epidemiologic studies. Modeling activities have focused on the genetics of the human major histocompatibility (HLA) complex, immune and inflammatory disorders (including autoimmune disorders and periodontal disease), and developmental disorders. The latter include studies of Fragile X syndrome, and genetic syndromes affecting teeth and bone. Other areas of application include studies related to craniofacial development, including longitudinal studies of normal development, and investigations of late onset disorders and of aging, including the genetics of longevity. More recent interests include the analysis of microarray data, meta-analytic assessment, and classification and risk assessment problems, particularly as they relate to genetic counseling.

    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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