Some Interdisciplinary Collaborations within QBMI

Arnosti, David	Quantitative Modeling and Analysis of Transcriptional Cis Regulatory Grammar - David Arnosti (Biochemistry, to identify and develop quantitative models of the “cis regulatory grammar” that controls gene expression) - Chichia Chiu (Mathematics, and colleagues have launched a collaborative research project that will map quantitative gene activity surfaces for highly defined transcriptional switches in Drosophila) - Walid Fakhouri (Plant Pathology, has joined the project to initiate the experimental side of the project, including capturing quantitative fluorescence from quantum dot probes) - Jiali Miao (Statistics, will focus on modeling efforts to develop numerical predictions of the activity of novel elements)
Chan, Christina	Identifying gene groups using shape space and corpula correlation - Sarat Dass, Department of Statistics and Probability Text-mining and integrating gene expression and metabolite profiles - Rong Jin, Department of Computer Science and Karim Oweiss, Department of Electrical Engineering Predicting Histological Changes Elicited by Estrogenic Endocrine Disruptor from Gene Expression Data - Tim Zacharewski, Department of Biochemistry
Feig, Michael	Detailed mechanism of RNA polymerase II - Zachary Burton (Biochemistry, fast kinetic experiments) - Michael Feig (Biochemistry, computational modeling) - Maria Zavodszky (Biochemistry, computational modeling) Higher-order Poisson Solver for Biomolecules - Guowei Wei (Mathematics, development of Poisson solver) - Shan Zhao (Mathematics, development of Poisson solver) - Michael Feig (Biochemistry, testing and application to biomolecules) Development of Biomolecular Simulation Database - Michael Feig (Biochemistry, database implementation and application) - Li Xiao (Computer science, distributed computing aspects) Protein Structure Refinement - Michael Feig (Biochemistry, force field based scoring, reduced model sampling) - Bob Cukier (Chemistry, enhanced sampling through re-weighting) - Leslie Kuhn (Biochemistry, knowledge-based scoring functions) - Guowei Wei (Mathematics, improved implicit solvent methods) - Bill Wedemeyer (Biochemistry, incorporation of experimental restraints)
Ferguson-Miller, Shelagh	Mechanism of Energy Transduction in Cytochrome Oxidase - John McCracken, Professor & Chair Chemistry Department. EPR expert: real-time analysis of water and ion movement in Cytochrome Oxidase by EPR/freeze-quench stopped flow - Gavin Reid, Ass. Professor, Chemistry Department, Mass Spec expert: analysis of membrane protein lipid content in native and crystalline state and in lipid mutant forms
Hausinger, Robert	Characterization of the structure and mechanism of Fe(II)- and alpha-ketoglutarate-dependent hydroxylases involved in DNA repair, herbicide degradation, sulfonate metabolism, and other processes. - Robert Hausinger (MMG/BMB; hausinge@msu.edu) - enzymology, molecular biology, steady-state and transient kinetic analyses, inhibitor characterization - John McCracken (Chemistry; mccracke@msu.edu) - pulsed electron paramagnetic resonance spectroscopic characterization of enzyme metallocenters - Michael Feig (BMB/Chemistry; feig@msu.edu) - computational methods for protein structure prediction - Leslie Kuhn (BMB; kuhnL@msu.edu) - computational structure-based screening and optimization of inhibitors - William Lanzilotta (Univ. Georgia) - crystallography of metalloproteins
Huebner, Marianne	Dynamics of the host-parasite system Daphnia dentifera-Metschnikowia - Alan Tessier, National Science Foundation - Meghan Duffy, Kellogg Biological Station and Department of Zoology(graduate student) - Carla Caceres, Department of Animal Biology, University of Illinois at Urbana Champaign - Sally MacIntyre, Marine Science Institute, University of California at Santa Barbara - Spencer Hall, Kellogg Biological Station and University of Illinois at Urbana Champaign (post doc) Mining of large genomic data sets to discover novel gene functions - Andreas Weber, Department of Plant Biology, Michigan State University - Dong-Yun Kim, Department of Statistics and Probability, Michigan State University and Illinois State University - Vince Melfi, Department of Statistics and Probability, Michigan State University VCA-PGR Triticeae -Fusarium graminearum: Plant Response to Fungal Pathogenesis - Frances Trail, Department of Plant Biology, Michigan State University - Corby Kistler, University of Minnesota - Gary Muehlbauer, University of Minnesota - Jin Rong Xu, Purdue University - Tom Clemente, UNL - Cari Soderlund, University of Arizona Genetic association study for asthma and allergy - Susan Ewart, Department of Large Animal Clinical Sciences, Michigan State University - Wilfried Karmaus, Department of Epidemiology, Michigan State University - Syed Hasan Arshad, Asthma and Allergy Research Centre, St. Mary's Hospital, Isle of Wight, and University of Southampton Neuroprotective factors in hypothalamic dopamine neurons - John Goudreau, Department of Nerurology and Ophtalmology, Michigan State University
Kuhn, Leslie	- Michael Kron (Medicine), David Wenkert (Physiology) Morten Grøtli (Göteborg Univ., Sweden), Jonathan Morris (Univ. Adelaide, Australia), and Stephen Cusack (EMBL) – structure-based screening and design of inhibitors against human parasites - Michael Feig (Biochemistry, Chemistry), Bob Cukier (Chemistry), Guowei Wei (Math), and Bill Wedemeyer (Biochemistry, Physics) – development of scoring functions for high-accuracy protein structural modeling and refinement - Honggao Yan (Biochemistry) and Bob Cukier (Chemistry) - flexibility modeling and structure-based antibiotic design for folate biosynthetic enzymes - Nihar Mahapatra (ECE) – optimization of ligand flexibility sampling and scoring for protein-ligand docking - Bob Hausinger (Microbiology, Biochemistry) - elucidating the structural basis for substrate specificity in herbicide degrading enzymes
Lapidus, Lisa	Measurement of fast protein folding processes using a microfluidic mixer. Current targets include Cholera EPS-G and scrapie protein. - Lisa Lapidus- Physics and Astonomy- optical spectroscopy - Bill Wedemeyer-Biochemistry-protein mutagenesis - Olgica Bakajin-Lawrence Livermore National Lab – microfabrication Conformational flexibility of Proteins L and G during folding - Lisa Lapidus -Physics and Astronomy -optical spectroscopy - Bill Wedemeyer - Biochemistry- protein mutagenesis
Pennock, Rob	Teaching Evolution and the Nature of Science using Digital Organisms - Robert T. Pennock (Lyman Briggs School of Science & Dept. of Philosophy); - Philosophy of Science, Evolutionary computation - Charles Ofria (Computer Science & Engineering); ofria@msu.edu - Evolutionary computation - Richard Lenski (Zoology); lenski@msu.edu - Evolutionary biology - Diane Ebert-May (Plant Biology & Division of Science and Math Education); - Science education assessment
Shachar-Hill, Yair	Metabolic flux analysis in developing plant seeds. - John Ohlrogge, Plant Biology, ohlrogge@msu.edu Professor Ohlrogge is a world-renowned expert in the Physiology and Biochemistry of oilseed metabolism. - Yair Shachar-Hill, Plant Biology, yairhill@msu.edu Our group contributes expertise in spectroscopy and computer-assisted metabolic modeling.
Torng, Eric	Evaluating Phylogeny Reconstruction using Digital Organisms - Eric Torng (Computer Science and Engineering) - Charles Ofria (Computer Science and Engineering) - Tom Schmidt (Microbiology and Molecular Genetics) Reconstructing Bacterial Tree of Life - Tom Schmidt (Microbiology and Molecular Genetics) - Rong Jin (Computer Science and Engineering) - Charles Ofria (Computer Science and Engineering) - Eric Torng (Computer Science and Engineering)
Vieille, Claire	Metabolic flux analysis in a succinate-producing bacterium - Claire Vieille (BMB; vieille@msu.edu) - microbiology, metabolism, molecular biology - Yair Shachar-Hill (Plant Biology; yairhill@msu.edu) - spectroscopy and computer-assisted metabolic modeling. Dynamics in thermostable proteins - Claire Vieille – protein biochemistry, molecular biology, enzyme kinetics - Honggao Yan (BMB; yanh@msu.edu) - NMR spectroscopy - Bob I. Cukier (Chemistry; cukier@cem.msu.edu) - Molecular dynamic simulations