Faculty Advisors

Edgar A. Arriaga

Chemistry

Subcellular Analysis, Mitochondria, Doxorubicin Metabolism

phone: 612-624-8024
email: arriaga@umn.edu
Edgar A. Arriaga

Samira Azarin

Chemical Engineering and Materials Science

Engineering the Cell Microenvironment, Regulation of Cellular Dormancy and Activation, Stem Cell-based models of Barrier Function

Phone: (612) 301-3488
email: azarin@umn.edu
Samira Azarin

Victor Barocas

Biomedical Engineering

Computational Biomechanics and Transport

Phone: 612-626-5572
email: baroc001@umn.edu
Victor Barocas

David Bernlohr

Biochemistry, Molecular Biology and Biophysics

Metabolic Control and Regulation in Adipocytes, Obesity/Insulin Action, Lipid Metabolism, Protein-lipid Association, Lipid Oxidation, Proteomics

Phone: 612-624-0839
email: bates001@umn.edu
David Bernlohr

Erin Carlson

Chemistry

Bacterial Communication Mechanisms and Antibiotics. Advancing the Analysis of Biological Systems, Designing and Synthesizing Molecules.

Phone: 612-625-2580
email: carlsone@umn.edu
Erin Carlson

Mark D. Distefano

Chemistry/BTI

Physiology of Anaerobes, Electricity Generation by Electrode-attached Bacteria

Phone: 612-624-0544
email: diste001@umn.edu
Mark D. Distefano

Kevin Dorfman

Chemical Engineering and Materials Science

Microfluidics, DNA Technologies, Biophysics

Phone: (612) 624-5560
email: dorfman@umn.edu
Kevin Dorfman

Gary M. Dunny

Microbiology

Cell-cell Communication and Gene Regulation in Bacteria, Novel RNA Regulators of Gene Expression, Genetic Determinants of Biofilm Formation

Phone: (612) 625-9930
email: dunny001@umn.edu
Gary M. Dunny

Mikael Elias

Biochemistry, Molecular Biology, and Biophysics

Cellular phosphate uptake and bacterial virulence, Molecular engineering of enzymes and biotechnological applications

Phone: (612) 626-1915
email: mhelias@umn.edu
Mikael Elias

Jeffrey A. Gralnick

Microbiology/BTI

Physiology and synthetic biology of environmental bacteria

Phone: (612) 626-6496
email: gralnick@umn.edu
Jeffrey A. Gralnick

Timothy Griffin

Biochemistry, Molecular Biology, and Biophysics

Proteomics, Mass Spectrometry, Bioinformatics

Phone: (612) 624-5249
email: tgriffin@umn.edu
Timothy Griffin

Ben Hackel

Chemical Engineering and Materials Science

Engineering Principles Applied to Chemistry, Biology, and Physiology. Disease Detection, Non-invasive in Vivo Molecular Imaging of Tumors

Phone: (612) 624-7102
email: hackel@umn.edu
Ben Hackel

Christine Haynes

Chemistry

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

Phone: (612) 626-1096
email: chaynes@umn.edu
Christine Haynes

Adrian Hegeman

Horticultural Science

Plant Metabolomics

Phone: (612) 626 3650
email: hegem007@umn.edu
Adrian Hegeman

Wei-Shou Hu

Chemical Engineering and Materials Science/BTI

Genomic Cell Engineering, Tissue Engineering, Bioreaction Engineering

Phone: (612) 625-0546
email: wshu@umn.edu
Wei-Shou Hu

George Karypis

Computer Science and Engineering/BTI

Bioinformatics, Parallel Computing, Data Mining

Phone: (612) 626 7524
email: karypis@cs.umn.edu
George Karypis

Fumiaki Katagiri

Plant Biology

Systems Biology of Plant Disease Resistance

Phone: (612) 624-5195
email: katagiri@umn.edu
Fumiaki Katagiri

Romas Kazlauskas

Biochemistry, Molecular Biology, Biophysics/BTI

Enantioselective Synthesis, Protein Engineering, Catalytic Plasticity, Evolution of Enzymes, Dynamic Combinatorial Chemistry

Phone: (612) 624-5904
email: rjk@umn.edu
Romas Kazlauskas

Yiannis Kaznessis

Chemical Engineering and Materials Science/BTI

Computational biology, bioinformatics, statistical mechanics, protein fold recognition, antimicrobial peptides, multiscale modeling

Phone: (612) 624-4197
email: Yiannis@cems.umn.edu
Yiannis Kaznessis

Dan Knights

Computer Science

Computational Biology

Phone: (612) 626- 7502
email: knights@cs.umn.edu
Dan Knights

Efrosini Kokkoli

Chemical Engineering and Materials Science

DNA Nanotechnology, Biomolecular Engineering, Targeted Drug & Gene Delivery, Peptide Hydrogels, Biopolymers

Phone: (612) 626-1185
email: kokko002@umn.edu
Efrosini Kokkoli

John D. Lipscomb

Biochemistry, Molecular Biology, and Biophysics

Oxygenase Mechanisms, Metalloproteins, Magnetic Resonance Techniques, Kinetics

Phone: (612) 625-6454
email: lipsc001@umn.edu
John D. Lipscomb

Chad Myer

Computer Science and Engineering

Bioinformatics and Computational Biology

Phone: (612) 624 8306
email: cmyers@cs.umn.edu
Chad Myer

Michael O’Connor

Genetics, Cell Biology and Development

Molecular Genetics of Development, Growth Factor Signaling, Gene Regulation

Phone: 612-626-0642
email: moconnor@umn.edu
Michael O’Connor

Brenda Ogle

Biomedical Engineering

Cardiovascular Tissue Engineering

Phone: (612) 624-5948
email: ogle@umn.edu
 Brenda Ogle

Will Pomerantz

Chemistry

Protein Engineering for Chemical Modulation of Transcription Factor Function

Phone: (612) 624-9091
email: wcp@umn.edu
Will Pomerantz

Michael J. Sadowsky

Soil, Water, and Climate/BTI

Biocatalysis/Biodegradation of Chlorocarbon Compounds, Bioremediation, Plant-microbe Interactions with Bradurhizobiujm and Rhizobium, Ecophysiology of E. coli, Methods to Determine Sources of Bacteria in the Environment

Phone: 612-624-2706
email: sadowsky@umn.edu
Michael J. Sadowsky

Casim Sarkar

Biomedical Engineering

Biomolecular Engineering, Synthetic Biology, Systems Biology

Phone: (612) 626 0525
email: csarkar@umn.edu
Casim Sarkar

Claudia Schmidt-Dannert

Biochemistry, Molecular Biology, Biophysics/BTI

Metabolic Pathway Engineering, Combinatorial Biosynthesis, Directed Evolution, Natural Products

Phone: 612-625-5782
email: schmi232@umn.edu
Claudia Schmidt-Dannert

Daniel Schmidt

Genetics, Cell biology, and Development

Protein Engineering, Cellular Engineering

Phone: (612) 625-1180
email: schmida@umn.edu
Daniel Schmidt

Burckhard Seelig

Biochemistry, Molecular Biology, Biophysics/BTI

Biocatalysis, Directed Evolution, Protein Engineering, Artificial Enzymes

Phone: (612) 626-6281
email: seelig@umn.edu
Burckhard Seelig

Wei Shen

Biomedical Engineering Engineering of Biomaterials and Cellular

Microenvironments, Cell-environment Interactions, Biomolecular Engineering

Phone: (612) 624-3771
email: shenx104@umn.edu
Wei Shen

Mike Smanski

Biochemistry, Molecular Biology, and Biophysics

Synthetic Biology, Natural Product Biosynthesis, Engineering Multigene Systems

Phone: (612) 624.9752
email: smanski@umn.edu
Mike Smanski

Robert T. Tranquillo

Biomedical Engineering

Cardiovascular Tissue Engineering, Neural Tissue Engineering

Phone: 612-625-6868
email: tranquillo@umn.edu
Robert T. Tranquillo

Daniel Voytas

Genetics, Cell Biology and Development

Plant Genome Engineering Through Homologous Recombination; Retrotransposable Elements and Genome Organization

email: voytas@umn.edu
Daniel Voytas

Lawrence P. Wackett

Biochemistry, Molecular Biology, Biophysics/BTI

Biodegradation, Microbial Genomics, Metabolic Engineering

Phone: 612-625-3785
email: wacke003@umn.edu
Lawrence P. Wackett

Chun Wang

Biomedical Engineering

Biomaterials, Nonviral Delivery of Genes and Vaccines, Tissue Engineering

Phone: (612) 626-3990
email: wangx504@umn.edu
Chun Wang

Kechun Zhang

Chemical Engineering

Principles of Chemistry, Biology and Engineering to Achieve Biosynthesis Beyond Nature

Phone: (612) 626-0635
email: kzhang@umn.edu

 

Program Theme

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

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.


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.


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.


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)


Brenda Ogle

Cardiovascular Tissue Engineering

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


Wei Shen

Biomedical Engineering

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


Robert T. Tranquillo

Biomedical Engineering

Cardiovacular tissue engineering, neural tissue engineering


Chun Wang

Biomedical Engineering

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


Victor Barocas

Biomedical Engineering

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

BMBB (Biochemistry, Molecular Biology and Biophysics)


David Bernlohr

BMBB

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


Timothy Griffin

BMBB

Proteomics, mass spectrometry, bioinformatics


John D. Lipscomb

BMBB

Oxygenase mechanisms, metalloproteins, magnetic resonance techniques, kinetics


Romas Kazlauskas

BMBB, BTI

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


Do-Hyung Kim

BMBB

Biological networks that coordinate metabolism and growth


Claudia Schmidt-Dannert

BMBB; BTI

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


Burckhard Seelig

BMBB; BTI

Biocatalysis, directed evolution, protein engineering, artificial enzymes


Lawrence P. Wackett

BMBB; BTI

Biodegradation, microbial genomics, metabolic engineering


Kylie Walters

BMBB

Targeted protein degradation; Protein quality control; NMR spectroscopy

BTI (Biotechnology Training Institute)


Daniel Bond

Microbiology; BTI

Physiology of anaerobes, electricity generation by electrode-attached bacteria


Mark D. Distefano

Chemistry; BTI

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


Jeffrey A. Gralnick

Microbiology; BTI

Physiology and genetic engineering of environmental bacteria


Wei-Shou Hu

Chemical Eng. & Mats. Sci.; BTI

Genomic cell engineering, tissue engineering, bioreaction engineering


Romas Kazlauskas

BMBB, BTI

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


Yiannis Kaznessis

Chemical Eng. & Mats. Sci.; BTI

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


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


Claudia Schmidt-Dannert

BMBB; BTI

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


Burckhard Seelig

BMBB; BTI

Biocatalysis, Directed Evolution, Protein Engineering, Artificial Enzymes


Friedrich Srienc

Chemical Eng. & Mats. Sci.; BTI

Population dynamics and biopolymers


Lawrence P. Wackett

BMBB; BTI

Biodegradation, microbial genomics, metabolic engineering

Chemistry


Edgar A. Arriaga

Chemistry

Subcellular analysis, mitochondria, doxorubicin metabolism


Erin Carlson

Chemistry

Bacterial communication mechanisms and antibiotics


Mark D. Distefano

Chemistry; BTI

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


Christy Haynes

Chemistry

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


Will Pomerantz

Chemistry

Protein engineering for chemical modulation of transcription factor function

CEMS (Chemical Engineering & Materials Science)


Kevin Dorfman

Chemical Eng. & Mats. Sci.

Microfluidics, DNA electrophoresis, biophysics


Benjamin Hackel

Chemical Eng. & Mats. Sci.

Molecular imaging, engineering proteins, tumor targeting


Wei-Shou Hu

Chemical Eng. & Mats. Sci.; BTI

Genomic cell engineering, tissue engineering, bioreaction engineering


Yiannis Kaznessis

Chemical Eng. & Mats. Sci.; BTI

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


Efrosini Kokkoli

Chemical Eng. & Mats. Sci.

Biotechnology and bioengineering polymers


Friedrich Srienc

Chemical Eng. & Mats. Sci.; BTI

Population dynamics and biopolymers


Kechun Zhang

Chemical Engineering & Mats. Sci.

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

CSE (Computer Science & Engineering)


George Karypis

Computer Science and Engineering

Bioinformatics, parallel computing, data mining


Dan Knights

Computer Science and Engineering

Computational biology


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)


Judith Berman

Genetics, Cell Biology and Development

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


Scott R. McIvor

Genetics, Cell Biology and Development

Gene therapy for genetic diseases and cancer


Michael O’Connor

Genetics, Cell Biology and Development

Molecular genetics of development, growth factor signaling, gene regulation


Daniel Schmidt

Genetics, Cell Biology and Development

Protein engineering, cellular engineering


Daniel Voytas

Genetics, Cell Biology and Development

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

Horticultural Science


Adrian Hegeman

Horticultural Science

Plant metabolomics

ECE (Electrical & Computer Engineering)


Mark Riedel

Electrical and Computer Engineering

Logic synthesis and synthetic biology

Mathematics


Hans Othmer

Mathematics

Modeling of complex systems, mathematical biology, morphogenesis

Microbiology


Daniel Bond

Microbiology; BTI

Physiology of anaerobes, electricity generation by electrode-attached bacteria


Gary M. Dunny

Microbiology

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


Jeffrey A. Gralnick

Microbiology; BTI

Physiology and genetic engineering of environmental bacteria

Plant Biology


Fumiaki Katagiri

Plant Biology

Systems biology of plant disease resistance

SWAC (Soil, Water, and Climate)


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