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Indiana University Bloomington

THE FACULTY

Faculty from several departments participate in our program. They are listed below according to research area.

Biochemistry of Genes and Genomes

Carl Bauer: Oxygen and light regulation of gene expression; biosynthesis of heme and chlorophyll; prokaryotic development.

Stephen Bell: The study of the molecular and cellular biology of the Archaea, with particular interest in transcription, DNA replication and cell division.

Matthew L. Bochman: The maintenance of genomic integrity with a focus on DNA helicases and other factors involved in DNA replication, recombination, and repair; the evolution of DNA helicases.

Yves Brun: Cell cycle control, cell division, and cell differentiation in bacteria; bacterial adhesion and biofilm formation.

Brian Calvi: Cell cycle and epigenetic control of DNA replication and genome stability.

Patricia L. Foster: Mutagenesis, DNA repair, replication, and recombination.

Richard Hardy: Genome functions of RNA viruses and the roles of trans-acting factors.

Peter C Hollenhorst: Sequence specific interactions of DNA binding proteins with the genome.  The role of transcription factors in carcinogenesis.

Heather A. Hundley: Post-transcriptional gene regulation with a focus on the effects of RNA editing on normal and cancer gene expression programs, Biochemistry of RNA editing enzymes.

Cheng Kao: RNA virus replication; innate immunity; receptor-ligand recognition; viral nanotechnology

Scott Michaels: Regulation of chromatin structure and gene expression by epigenetic modifications.

Anirban Mitra:The role of microenvironment regulated microRNAs in promoting ovarian cancer metastasis.

Kenneth P. Nephew: Cancer epigenetics/epigenomics, ovarian and breast cancer; cancer systems biology; non-coding RNAs.

Hengyao Niu: Detection and Repair of DNA breaks with a focus on Homologous Recombination (HR) mediated DNA double-strand break (DSB) repair, interplay of DNA repair machinery and chromatin structures.

Martha G. Oakley: Bacterial chromosome segregation; coiled coil proteins; structure and function of condensins and other structural maintenance of chromosomes proteins.

Heather O'Hagan: The role of inflammation in initiating cancer-specific epigenetic changes. Oxidative damage-induced chromatin and epigenetic changes. DNA repair.

Craig S. Pikaard: Biochemistry of gene regulation; enzymes of RNA-mediated gene silencing pathwayss; biochemical analyses of chromatin modifying enzymes; structure and function of plant RNA polymerases IV and V.

Joe Pomerening: Signal transduction pathways governing early embryonic and somatic cell cycles, and understanding the integration of feedback loops and other signaling elements in their M-phase control systems.

Dean Rowe-Magnus: Bacterial adaptation and evolution via Integrons; biofilm formation; c-di-GMP signalling pathways and the regulation of gene expression.

Julia van Kessel: Bacterial cell-cell communication (quorum sensing); mechanisms of gene regulation in bacteria; regulation of bacterial stress response; dynamics of global transcriptional regulation.

Claire E. Walczak: Mechanisms of mitotic spindle assembly, chromosome alignment and segregation; error correction in mitosis; mechanisms of anueploidy.

Malcolm E. Winkler: Physiology, pathogenesis, molecular genetics, stress responses, and genomics of the gram-positive human respiratory pathogenic bacterium, Streptococcus pneumoniae.

Yuzhen Ye: Bioinformatics for Metagenomics, protein bioinformatics, protein structure prediction and comparison, comparison of protein domain organization, biochemical pathways reconstruction and analysis.

Miriam Zolan: Mechanisms of chromosome pairing and meiotic recombination.

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Microbial Biochemistry and Virology

Carl Bauer: Oxygen and light regulation of gene expression; biosynthesis of heme and chlorophyll; prokaryotic development.

Stephen Bell: The study of the molecular and cellular biology of the Archaea, with particular interest in transcription, DNA replication and cell division.

Matthew L. Bochman: The maintenance of genomic integrity with a focus on DNA helicases and other factors involved in DNA replication, recombination, and repair; the evolution of DNA helicases.

Yves Brun: Cell cycle control, cell division, and cell differentiation in bacteria; bacterial adhesion and biofilm formation.

Lingling Chen: Mechanistic understanding of molecular chaperone functions and bacterial infections.

Pranav Danthi: Viral and cellular determinants of virus-induced cell death and disease.

Bogdan Dragnea: Virus-based biomaterials; biophotonics; biophysical chemistry of virus self-assembly; methodologies for measuring microscopic dynamics in supramolecular complexes.

Patricia L. Foster: Mutagenesis, DNA repair, replication, and recombination.

Clay Fuqua: Multicellular interactions of bacteria.

David P. Giedroc: Metal sensor proteins in pathogenic bacteria; NMR structural studies of regulatory RNAs in mammalian RNA viruses.

Richard Hardy: Genome functions of RNA viruses and the roles of trans-acting factors.

Cheng Kao: RNA virus replication; innate immunity; receptor-ligand recognition; viral nanotechnology

David Kehoe: Environmental regulation of gene expression in bacteria.

Melanie Marketon: Molecular mechanisms of pathogenic microbe-host interactions.

James Mckinlay: Microbial metabolism; bioprocessing; biofuels; 13C-metabolic flux analysis.

Tuli Mukhopadhyay: Structure and assembly of enveloped, RNA viruses.

Martha G. Oakley: Bacterial chromosome segregation; coiled coil proteins; structure and function of condensins and other structural maintenance of chromosomes proteins.

Nikki Pohl: Glycobiology and glycochemistry (synthetic and analytical), carbohydrate active enzymes, carbohydrate-binding proteins (especially those related to immune responses), proteins from archaea and hyperthermophiles.

Dean Rowe-Magnus: Bacterial adaptation and evolution via Integrons; biofilm formation; c-di-GMP signalling pathways and the regulation of gene expression.

Julia van Kessel: Bacterial cell-cell communication (quorum sensing); mechanisms of gene regulation in bacteria; regulation of bacterial stress response; dynamics of global transcriptional regulation.

Malcolm E. Winkler: Physiology, pathogenesis, molecular genetics, stress responses, and genomics of the gram-positive human respiratory pathogenic bacterium, Streptococcus pneumoniae.

Michael VanNieuwenhze: Synthesis, study, and design of antibiotics that inhibit bacterial cell wall biosynthesis; peptidoglycan biosynthesis and bacterial cell morphology; development of HBV capsid-binding probes and assembly-directed antivirals; oxidized phospholipids in disease and diagnostics.

Adam Zlotnick: Physical and structural basis of virus self-assembly from the perspectives of biological activity, antiviral strategies, and nanotechnology.

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Structural Biology

Carl Bauer: Crystallographic analysis of bacterial transcription factors that respond to changes in cellular redox, light and heme.

Lingling Chen: Mechanistic understanding of molecular chaperone functions and bacterial infections.

Jared Cochran: Kinetic, thermodynamic, and structural investigations of unconventional cytoskeletal molecular motors.

Charles E. Dann III: Biochemical, mechanistic, and X-ray crystallographic analyses of regulatory RNAs; developing riboswitch-based molecular sensors.

David P. Giedroc: Metal sensor proteins in pathogenic bacteria; NMR structural studies of regulatory RNAs in mammalian RNA viruses.

Tuli Mukhopadhyay: Cryo-EM analysis of the structure and assembly of enveloped RNA viruses.

Yuzhen Ye: Bioinformatics for Metagenomics, protein bioinformatics, protein structure prediction and comparison, comparison of protein domain organization, biochemical pathways reconstruction and analysis.

Adam Zlotnick: Physical and structural basis of virus self-assembly from the perspectives of biological activity, antiviral strategies, and nanotechnology.

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Chemical Biology

David E. Clemmer: Conformational analysis of proteins and peptides; development of techniques for examining mixtures of biomolecules.

David L. Daleke: Membrane structure and function; regulation of lipid organization by “flippases” in normal and diabetic blood cells.

Richard D. DiMarchi: Structure-activity relationships of macromolecules.

Jim Drummond: Limited alphabet coding sequences and proteins: a minimalist approach to macromolecular structure and interactions.

Martha G. Oakley: Bacterial chromosome segregation; coiled coil proteins; structure and function of condensins and other structural maintenance of chromosomes proteins.

James P. Reilly: Bacteria fingerprinting and proteomics by mass spectrometry; analysis of bacterial ribosomes; development of novel mass spectrometric techniques.

Michael VanNieuwenhze: Synthesis, study, and design of antibiotics that inhibit bacterial cell wall biosynthesis; peptidoglycan biosynthesis and bacterial cell morphology; development of HBV capsid-binding probes and assembly-directed antivirals; oxidized phospholipids in disease and diagnostics.

Theodore S. Widlanski: Bioorganic methodology; enzyme reaction mechanisms; anti-breast tumor agents; DNA polymerization; new strategies for HIV inhibition; phosphotyrosine phosphatases; biomimetic catalysis.

Yan Yu: Biomaterials for quantitative study and control of immune cells; molecular interaction in biomembranes both in vitro and in vivo.

Jeffrey M. Zaleski: Probing metal ions and catalytic nucleic acids using various ground and excited state spectroscopic methods; Synthesis and mechanistic evaluation of metal-mediated therapeutic agents.

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Cellular and Medicinal Biochemistry

Stephen Bell: The study of the molecular and cellular biology of the Archaea, with particular interest in transcription, DNA replication and cell division.

Joseph A. Bonanno: Regulation of epithelial cell ION transport and fluid secretion; role of carbonic anhydrase in HCO3 transport; hypoxia pre-conditioning and protection from UV induced apoptosis.

Heather Bradshaw: Female reproductive neuroendocrinology and the neurochemistry of reproductive pain.

Yves Brun: Cell cycle control, cell division, and cell differentiation in bacteria; bacterial adhesion and biofilm formation.

Brian Calvi: Cell cycle control of DNA replication and genome stability.

Jared Cochran: Kinetic, thermodynamic, and structural investigations of unconventional cytoskeletal molecular motors.

David L. Daleke: Membrane structure and function; regulation of lipid organization by “flippases” in normal and diabetic blood cells.

Christina Dann: Mouse models for stem cell and gene therapy; molecular mechanisms of spermatogonial stem cell fate decisions.

John G. Foley: Epithelial-mesenchyme interactions in the repair and regeneration of specialized skin.

Andrea Hohmann: Functional roles of the brain's own cannabis-like (endocannabinoid) system in the nervous system; mechanisms of pain and analgesia; mechanisms of action of drugs of abuse; novel therapeutics of learning and memory

Peter C Hollenhorst: Sequence specific interactions of DNA binding proteins with the genome.  The role of transcription factors in carcinogenesis.

Heather A. Hundley: Post-transcriptional gene regulation with a focus on the effects of RNA editing on normal and cancer gene expression programs, Biochemistry of RNA editing enzymes.

Cheng Kao: RNA virus replication; innate immunity; receptor-ligand recognition; viral nanotechnology.

Cary Lai: Developmental neurobiology; the use of transgenic mouse models to study nervous system function.

Kenneth Mackie: Regulation of cannabinoid receptor signaling; regulation of endocannabinoid production; role of endocannabinoids in synaptic plasticity; novel cannabinoid receptors.

Scott Michaels: Regulation of chromatin structure and gene expression by epigenetic modifications.

Anirban Mitra:The role of microenvironment regulated microRNAs in promoting ovarian cancer metastasis.

Kenneth P. Nephew: Cancer epigenetics/epigenomics, ovarian and breast cancer;  cancer systems biology; non-coding RNAs.

Hengyao Niu: Detection and Repair of DNA breaks with a focus on Homologous Recombination (HR) mediated DNA double-strand break (DSB) repair, interplay of DNA repair machinery and chromatin structures.

Heather O'Hagan: The role of inflammation in initiating cancer-specific epigenetic changes. Oxidative damage-induced chromatin and epigenetic changes. DNA repair.

Craig S. Pikaard: Biochemistry of gene regulation; enzymes of RNA-mediated gene silencing pathwayss; biochemical analyses of chromatin modifying enzymes; structure and function of plant RNA polymerases IV and V.

Anne Prieto: Function and signaling of receptor tyrosine kinases and their ligands in the developing and mature nervous system.

Joe Pomerening: Signal transduction pathways governing early embryonic and somatic cell cycles, and understanding the integration of feedback loops and other signaling elements in their M-phase control systems.

Sidney L. Shaw: Microtubule dynamics and cellular morphogenesis in Arabidopsis .

Claire E. Walczak: Mechanisms of mitotic spindle assembly and chromosome segregation; regulation of microtubule dynamics during interphase and mitosis.

Michael VanNieuwenhze: Synthesis, study, and design of antibiotics that inhibit bacterial cell wall biosynthesis; peptidoglycan biosynthesis and bacterial cell morphology; development of HBV capsid-binding probes and assembly-directed antivirals; oxidized phospholipids in disease and diagnostics.

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Plant Biochemistry

Bogdan Dragnea: Virus-based biomaterials; biophotonics; biophysical chemistry of virus self-assembly; methodologies for measuring microscopic dynamics in supramolecular complexes.

Cheng Kao: RNA virus replication; innate immunity; receptor-ligand recognition; viral nanotechnology.

Scott Michaels: Regulation of chromatin structure and gene expression by epigenetic modifications.

Craig S. Pikaard: Biochemistry of gene regulation; enzymes of RNA-mediated gene silencing pathwayss; biochemical analyses of chromatin modifying enzymes; structure and function of plant RNA polymerases IV and V.

Sidney L. Shaw: Microtubule dynamics and cellular morphogenesis in Arabidopsis .

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