Program Theme

From Genomes and Biological Systems via Discovery and Synthesis to Products and Processes

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Genome – Engineering, Regulation, Interaction

Voytas (Lead), Dunny, Wei-Shou Hu, Katagiri , Myers, O’Connor, Smanski

This group will give our trainees instructions in genome engineering, computational analysis and visualization of biological interaction networks.

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Systems – Analysis, Tools

Haynes (Lead), Arriaga, Bernlohr, Distefano,Griffin, Hegeman, John D. Lipscomb, Will Pomerantz, Dan Knights, Daniel Schmidt

Trainees will receive instruction from these trainers in omics approaches and the application of cutting-edge probes and tools.

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Discovery and Design – Synthesis, Fabrication

Burckhard Seelig (Lead), Samira Azarin, Erin Carlson, Mikael Elias, Ben Hackel, Romas Kazlauskas, Yiannis Kaznessis, Efrosini Kokkoli, Casim Sarkar, Claudia Schmidt-Dannert

Trainers in this group are interested in the discovery and design of new protein and metabolic pathways with the goal of generating new cellular or protein functions for biotechnological applications. They use synthetic biology and computational design methods to create emergent functions. They combine molecular engineering strategies with computational design, thereby exposing trainees to quantitative and rational molecular design.

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Processes and Product – Molecules, Biomaterials

Brenda Ogle (Lead), Victor Barocas, Kevin Dorfman, Jeffrey A. Gralnick, George Karypis, Michael J. Sadowsky, Wei Shen, Robert T. Tranquillo, Lawrence P. Wackett, Chun Wang, Kechun Zhang

This group of faculty is experienced at implementing scientific discoveries and developments into applied technologies and products. They will expose trainees to aspects lof entrepreneurship and innovation.

BME (Biomedical Engineering)

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Brenda Ogle

Cardiovascular Tissue Engineering

Engineering of biomaterials and cellular microenvironments, cell-environment interactions, biomolecular engineering

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Wei Shen

Biomedical Engineering

Engineering of biomaterials and cellular microenvironments, cell-environment interactions, biomolecular engineering

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Robert T. Tranquillo

Biomedical Engineering

Cardiovacular tissue engineering, neural tissue engineering

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Chun Wang

Biomedical Engineering

Biomaterials, non-viral delivery of genes and vaccines, tissue engineering

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Victor Barocas

Biomedical Engineering

Ocular biomechanics and transport, tissue- equivalent mechanics, microelectromechanical systems

BMBB (Biochemistry, Molecular Biology and Biophysics)

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David Bernlohr

BMBB

Metabolic control and regulation in adipocytes, obesity/insulin action, lipid metabolism, protein- lipid association, lipid oxidation, proteomics

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Timothy Griffin

BMBB

Proteomics, mass spectrometry, bioinformatics

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John D. Lipscomb

BMBB

Oxygenase mechanisms, metalloproteins, magnetic resonance techniques, kinetics

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Romas Kazlauskas

BMBB, BTI

Enantioselective synthesis, protein engineering, catalytic plasticity, evolution of enzymes, dynamic combinatorial chemistry

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Do-Hyung Kim

BMBB

Biological networks that coordinate metabolism and growth

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Claudia Schmidt-Dannert

BMBB; BTI

Metabolic pathway engineering, combinatorial biosynthesis, directed evolution, natural products

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Burckhard Seelig

BMBB; BTI

Biocatalysis, directed evolution, protein engineering, artificial enzymes

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Lawrence P. Wackett

BMBB; BTI

Biodegradation, microbial genomics, metabolic engineering

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Kylie Walters

BMBB

Targeted protein degradation; Protein quality control; NMR spectroscopy

BTI (Biotechnology Training Institute)

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Daniel Bond

Microbiology; BTI

Physiology of anaerobes, electricity generation by electrode-attached bacteria

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Mark D. Distefano

Chemistry; BTI

Protein engineering, biocatalysis, protein chemistry, enzymology, organic synthesis, protein prenylation

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Jeffrey A. Gralnick

Microbiology; BTI

Physiology and genetic engineering of environmental bacteria

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Wei-Shou Hu

Chemical Eng. & Mats. Sci.; BTI

Genomic cell engineering, tissue engineering, bioreaction engineering

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Romas Kazlauskas

BMBB, BTI

Enantioselective synthesis, protein engineering, catalytic plasticity, evolution of enzymes, dynamic combinatorial chemistry

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Yiannis Kaznessis

Chemical Eng. & Mats. Sci.; BTI

Computational biology, bioinformatics, statistical mechanics, protein fold recognition, antimicrobial peptides, multi-scale modeling

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Michael J. Sadowsky

Soil, Water and Climate; BTI

Biocatalysis/biodegradation of chlorocarbon compounds, bioremediation, plant-microbe interactions with bradurhizobiujm and rhizobium, exophysiology of E. coli, methods to determine sources of bacteria in the environment

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Claudia Schmidt-Dannert

BMBB; BTI

Metabolic pathway engineering, combinatorial biosynthesis, directed evolution, natural products

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Burckhard Seelig

BMBB; BTI

Biocatalysis, Directed Evolution, Protein Engineering, Artificial Enzymes

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Friedrich Srienc

Chemical Eng. & Mats. Sci.; BTI

Population dynamics and biopolymers

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Lawrence P. Wackett

BMBB; BTI

Biodegradation, microbial genomics, metabolic engineering

Chemistry

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Edgar A. Arriaga

Chemistry

Subcellular analysis, mitochondria, doxorubicin metabolism

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Erin Carlson

Chemistry

Bacterial communication mechanisms and antibiotics

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Mark D. Distefano

Chemistry; BTI

Protein engineering, biocatalysis, protein chemistry, enzymology, organic synthesis, protein prenylation

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Christy Haynes

Chemistry

Analytical chemistry, chemical biology, materials chemistry, environmental chemistry, chemical physics

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Will Pomerantz

Chemistry

Protein engineering for chemical modulation of transcription factor function

CEMS (Chemical Engineering & Materials Science)

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Kevin Dorfman

Chemical Eng. & Mats. Sci.

Microfluidics, DNA electrophoresis, biophysics

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Benjamin Hackel

Chemical Eng. & Mats. Sci.

Molecular imaging, engineering proteins, tumor targeting

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Wei-Shou Hu

Chemical Eng. & Mats. Sci.; BTI

Genomic cell engineering, tissue engineering, bioreaction engineering

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Yiannis Kaznessis

Chemical Eng. & Mats. Sci.; BTI

Computational biology, bioinformatics, statistical mechanics, protein fold recognition, antimicrobial peptides, multi-scale modeling

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Efrosini Kokkoli

Chemical Eng. & Mats. Sci.

Biotechnology and bioengineering polymers

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Friedrich Srienc

Chemical Eng. & Mats. Sci.; BTI

Population dynamics and biopolymers

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Kechun Zhang

Chemical Engineering & Mats. Sci.

Principles of chemistry, biology, and engineering to achieve biosynthesis beyond nature

CSE (Computer Science & Engineering)

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George Karypis

Computer Science and Engineering

Bioinformatics, parallel computing, data mining

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Dan Knights

Computer Science and Engineering

Computational biology

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Chad Myers

Computer Science and Engineering

Machine learning methods for integrating large- scale genomic datasets to understand gene function and biological networks

GCD (Genetics, Cell Biology and Development)

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Judith Berman

Genetics, Cell Biology and Development

Morphogenesis, cell cycle, chromosome function and genomic structure in yeasts

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Scott R. McIvor

Genetics, Cell Biology and Development

Gene therapy for genetic diseases and cancer

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Michael O’Connor

Genetics, Cell Biology and Development

Molecular genetics of development, growth factor signaling, gene regulation

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Daniel Schmidt

Genetics, Cell Biology and Development

Protein engineering, cellular engineering

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Daniel Voytas

Genetics, Cell Biology and Development

Plant genome engineering through homologous recombination; Retrotransposable elements and genome organization

Horticultural Science

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Adrian Hegeman

Horticultural Science

Plant metabolomics

ECE (Electrical & Computer Engineering)

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Mark Riedel

Electrical and Computer Engineering

Logic synthesis and synthetic biology

Mathematics

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Hans Othmer

Mathematics

Modeling of complex systems, mathematical biology, morphogenesis

Microbiology

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Daniel Bond

Microbiology; BTI

Physiology of anaerobes, electricity generation by electrode-attached bacteria

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Gary M. Dunny

Microbiology

Cell-cell communication and gene regulation in bacteria, novel RNA regulators of gene expression

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Jeffrey A. Gralnick

Microbiology; BTI

Physiology and genetic engineering of environmental bacteria

Plant Biology

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Fumiaki Katagiri

Plant Biology

Systems biology of plant disease resistance

SWAC (Soil, Water, and Climate)

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Michael J. Sadowsky

Soil, Water and Climate; BTI

Biocatalysis/biodegradation of chlorocarbon compounds, bioremediation, plant-microbe interactions with bradurhizobiujm and rhizobium, exophysiology of E. coli, methods to determine sources of bacteria in the environment