Some Interdisciplinary Collaborations within QBI
Structural Biology
Feig, Michael
Detailed mechanism of RNA polymerase II
- Zachary Burton (Biochemistry and Molecular Biology) - fast kinetic experiments
- Michael Feig (Biochemistry and Molecular Biology/Chemistry) - computational modeling
- Maria Zavodszky (Biochemistry and Molecular Biology) - computational modeling
- Guowei Wei (Mathematics) - development of Poisson solver
- Shan Zhao (Mathematics) - development of Poisson solver
- Michael Feig (Biochemistry and Molecular Biology/Chemistry) - testing and application to biomolecules
- Michael Feig (Biochemistry and Molecular Biology/Chemistry) - database implementation and application
- Li Xiao (Computer Science and Engineering) - distributed computing aspects
- Michael Feig (Biochemistry/Chemistry) - force field based scoring, reduced model sampling
- Bob Cukier (Chemistry) - enhanced sampling through re-weighting
- Leslie Kuhn (Biochemistry and Molecular Biology) - knowledge-based scoring functions
- Guowei Wei (Mathematics) - improved implicit solvent methods
- Bill Wedemeyer (Biochemistry and Molecular Biology/Physics and Astronomy) - incorporation of experimental restraints
Ferguson-Miller, Shelagh
Mechanism of Energy Transduction in Cytochrome Oxidase
- John McCracken (Chemistry) - real-time analysis of water and ion movement in Cytochrome Oxidase by EPR/freeze-quench stopped flow
- Gavin Reid (Chemistry) - 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 (Microbiology and Molecular Genetics/Biochemistry and Molecular Biology) - enzymology, molecular biology, steady-state and transient kinetic analyses, inhibitor characterization
- John McCracken (Chemistry) - pulsed electron paramagnetic resonance spectroscopic characterization of enzyme metallocenters
- Michael Feig (Biochemistry and Molecular Biology/Chemistry) - computational methods for protein structure prediction
- Leslie Kuhn (Biochemistry and Molecular Biology) - computational structure-based screening and optimization of inhibitors
- William Lanzilotta (University of Georgia) - crystallography of metalloproteins
Kuhn, Leslie
- Michael Kron (Medical College of Wisconsin), David Wenkert (Physiology), Morten Grřtli (Göteborg Univ., Sweden), Jonathan Morris (Univ. Adelaide, Australia), and Stephen Cusack (EMBL) – structure-based screening and design of inhibitors against human parasites
- Honggao Yan (Biochemistry and Molecular Biology) and Bob Cukier (Chemistry) - identifying conformationally selective inhibitors of folate biosynthetic enzymes
- Maria Zavodszky (Biochemistry and Molecular Biology) – scoring function optimization for docking and high-throughput screening
- Michael Thomashow and Donatella Canella (Plant Research Laboratory) - structural analysis of DNA binding by cold response proteins
- Mark Gerstein and Kevin Keating (Yale) - hinge prediction in protein structures
Lapidus, Lisa
Protein Folding
- Steven Waldauer, graduate student, Lapidus Lab
- Michael King, graduate student, Lapidus Lab
- Kai-Chun Chen, graduate student, Wedemeyer Lab
- William Wedemeyer, Departments of Biochemistry and Molecular Biology and Physics and Astronomy, MSU
- Olgica Bakajin, Lawrence Livermore National Lab
- Shimon Weiss, University of California Los Angeles
- Vijay Singh, graduate student, Lapidus Lab
- Yujie Chen, graduate student, Lapidus Lab
- William Wedemeyer, Departments of Biochemistry and Molecular Biology and Physics and Astronomy, MSU
- Shimon Weiss, University of California Los Angeles
Vieille, Claire
Dynamics in thermostable proteins
- Claire Vieille (Biochemistry and Molecular Biology) – protein biochemistry, molecular biology, enzyme kinetics
- Honggao Yan (Biochemistry and Molecular Biology) - NMR spectroscopy
- Bob I. Cukier (Chemistry) - Molecular dynamic simulations
Evolutionary Modeling
Pennock, Rob
Teaching Evolution and the Nature of Science using Digital Organisms
- Robert T. Pennock (Lyman Briggs School of Science/Philosophy) - Philosophy of Science, Evolutionary Computation
- Charles Ofria (Computer Science & Engineering) - Evolutionary Computation
- Richard Lenski (Zoology) - Evolutionary Biology
- Diane Ebert-May (Plant Biology & Division of Science and Math Education) - Science education assessment
Torng, Eric
Evaluating Phylogeny Reconstruction using Digital Organisms
- Eric Torng, Computer Science and Engineering, Michigan State University
- Charles Ofria, Computer Science and Engineering, Michigan State University
- Tom Schmidt, Microbiology and Molecular Genetics, Michigan State University
- Tom Schmidt, Microbiology and Molecular Genetics, Michigan State University
- Rong Jin, Computer Science and Engineering, Michigan State University
- Charles Ofria, Computer Science and Engineering, Michigan State University
- Eric Torng, Computer Science and Engineering, Michigan State University
Systems Biology
Arnosti, David
Giant-in-situ-hybridization
- Walid Fakhouri, (post-doc, Arnosti lab)
- Ahmet Ay, (Ph.D. student, Mathematics)
- Evan Dayringer, (undergraduate participant in the NSF UBM training grant program, Mathematics)
Chan, Christina
Identifying gene groups using shape space and corpula correlation
- Sarat Dass, Statistics and Probability, Michigan State University
- Rong Jin, Computer Science and Engineering, Michigan State University
- Karim Oweiss, Electrical Engineering, Michigan State University
- Tim Zacharewski, Biochemistry and Molecular Biology, Michigan State University
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, 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)
- Andreas Weber, Plant Biology, Michigan State University
- Dong-Yun Kim, Statistics and Probability, Michigan State University and Illinois State University
- Vince Melfi, Statistics and Probability, Michigan State University
- 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
- Susan Ewart, Large Animal Clinical Sciences, Michigan State University
- Wilfried Karmaus, Epidemiology, Michigan State University
- Syed Hasan Arshad, Asthma and Allergy Research Centre, St. Mary's Hospital, Isle of Wight, and University of Southampton
- John Goudreau, Department of Nerurology and Ophtalmology, Michigan State University
Shachar-Hill, Yair
Metabolic flux analysis in developing plant seeds
- John Ohlrogge (Plant Biology) - Professor Ohlrogge is a world-renowned expert in the Physiology and Biochemistry of oilseed metabolism.
- Yair Shachar-Hill (Plant Biology) - Our group contributes expertise in spectroscopy and computer-assisted metabolic modeling.
Tang, Moxun
Functional roles of transcriptional factors in human cancer cells
- Justin McCormick, Biochemistry and Molecular Biology/Microbiology and Molecular Genetics, Michigan State University
Vieille, Claire
Metabolic flux analysis in a succinate-producing bacterium
- Claire Vieille (Biochemistry and Molecular Biology) - microbiology, metabolism, molecular biology
- Yair Shachar-Hill (Plant Biology) - spectroscopy and computer-assisted metabolic modeling
Bioinformatics and Functional Genomics
Arnosti, David
Giant-in-situ-hybridization
- Walid Fakhouri, (post-doc, Arnosti lab)
- Ahmet Ay, (Ph.D. student, Mathematics)
- Evan Dayringer, (undergraduate participant in the NSF UBM training grant program, Mathematics)
Duxbury, Phillip
Selective control of signaling in cell populations
- Carlo Piermarocchi, Biochemistry, Michigan State University
- Giovanni Paternostro, Burnham Institute, La Jolla, California
Hausinger, Robert
Identification of Functions of Putative Fe(II)/alpha-Ketoglutatarate Dioxygenases
- Bob Hausinger (Microbiology and Molecular Genetics/ Biochemistry and Molecular Biology) - purify gene products with putative Fe(II)/alpha-ketoglutarate dioxygenase-type activities, and test for activity with potential substrates
- Michael Feig (Biochemistry and Molecular Biology/ Chemistry) - create homology models of the target proteins.
- Donna Koslowsky (Microbiology and Molecular Genetics) - assist with in vivo analyses of gene products from Trypanosomes.
- Dan Jones (Biochemistry and Molecular Biology/ Chemistry) - carry out metabolomics studies of wild-type cells and knockout variants missing the target protein
Huebner, Marianne
Dynamics of the host-parasite system Daphnia Dentifera-Metschnikowia
- Alan Tessier, National Science Foundation
- Carla Caceres, Animal Biology, University of Illinois at Urbana Champaign
- Spencer Hall, Biology, Indiana University, Mining of large genomic data sets of Arabidopsis Thaliana to discover novel gene functions
- Andreas Weber, Plant Biology, Michigan State University
- Bill Swindell, Pathology, University of Michigan, VCA-PGR Triticeae -Fusarium graminearum: Plant Response to Fungal Pathogenesis
- Frances Trail, Plant Biology, Michigan State University
- Shin-Han Shiu, Plant Biology, Michigan State University
- Ulrich Gueldener,Munich Information Center for Protein Sequences, Genetic association study for asthma and allergy
- Susan Ewart, Large Animal Clinical Sciences, Michigan State University
- Wilfried Karmaus, School of Public Health, University of South Carolina
- Syed Hasan Arshad, Asthma and Allergy Research Centre, St. Mary's Hospital, Isle of Wight, and University of Southampton
- Alireza Sadeghnejad, School of Medicine, Wake Forest University, Neuroprotective factors in hypothalamic dopamine neurons
- John Goudreau, Department of Neurology and Ophtalmology, Michigan State University
Lenski, Richard
Functional Genomics in Evolving Microbial and Digital Systems
- Prof. Chris Adami, Keck Graduate Institute of Applied Life Sciences, Claremont, California
- Dr. Jeff Barrick, Department of Microbiology and Molecular Genetics, Michigan State University
- Dr. Jihyun Kim, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Prof. Charles Ofria, Department of Computer Science, Michigan State University
- Prof. Rob Pennock, Department of Philosophy, Michigan State University
- Prof. Dom Schneider, Université Joseph Fourier, Grenoble, France
Shiu, Shinhan
Bioinformatics and comparative genomics. Gene family and cis-regulatory evolution
- Ning Jiang (Horticulture) - on genome evolution and gene duplication through transposition.
- Rong Jin (Computer Science and Engineering) - on uncovering plant cis-regulatory logic under stress conditions using macine learning techniques.
- Pan-Ning Tang (Computer Science and Engineering) - on using data mining to uncover genome parameters important for regulation of stress responsive genes.