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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Faculty

Costas D. Maranas

Costas D. Maranas

Donald B. Broughton Professor, Department of Chemical Engineering
The Pennsylvania State University

Dr. Costas D. Maranas (b. 1967) is the Donald B. Broughton Professor in the Department of Chemical Engineering at The Pennsylvania State University. He received his Diploma in Chemical Engineering  from the Aristotle University, Greece  in 1990 and a Ph.D. in Chemical Engineering from Princeton University in 1995. He has been in the faculty of the department of Chemical Engineering at Penn State since 1995. He is the recipient of the Allan P. Colburn Award for Excellence in Publications by a Young Member of AIChE (2002), the Outstanding Young Investigator Award of the Computing and Systems Technology AIChE Division (2006), the S.V. Sotirchos Lectureship at 6th Panhellenic Chemical Engineering Conference (2007), the Penn State Engineering Alumni Society (PSEAS) Premier Research Award (2016) and Outstanding Research Award in (2012). He is a member of a number of journal Editorial Boards including  PLOS Computational Biology, BMC Systems Biology, Biotechnology Journal and Metabolic Engineering. He is a Fellow of the American Institute of Medical and Biological Engineering (AIMBE). He is a member of advisory/steering committees for PNNL/EMSL and EcoCyc and the “Use Inspired Research” Lead in the Center for Bioenergy Innovation (CBI) DOE center.

The C. Maranas group develops and deploys computational framework informed by systems engineering and mathematical optimization to understand, analyze and redesign metabolism and proteins.  Research interests include: Computational protein design; enzyme and antibody engineering; reconstruction, curation and analysis of metabolic networks; computational strain design and synthetic biology; metabolism of photosynthetic organisms; metabolism of obligatory anaerobes; modeling of microbial communities; optimization theory and algorithms. He has co-authored over 160 refereed journal publications including a textbook on “Optimization Methods in Metabolic Networks” (2016). He has supervised 29 PhD theses with many group alumni occupying leading positions in industry and academia. He lives in State College, PA with his wife and children. Contact Dr. Wühr.

 
Joshua D. Rabinowitz

Joshua D. Rabinowitz

Professor of Chemistry and the Lewis-Sigler Institute for Integrative Genomics
Princeton University

Our lab aims to achieve a quantitative, comprehensive understanding of cellular metabolism. Our motivation for studying metabolism is two-fold. From a basic science perspective, the molecular connections involved in metabolism are the best understood of any major biochemical network. Accordingly, metabolism provides a unique opportunity for quantitative analysis. From a practical perspective, derangements of metabolism are a major cause of disease, and small molecules that inhibit metabolism are the basis of many important pharmaceuticals. Accordingly, systems-level analysis of metabolism is likely to yield discoveries of medical significance. Contact Dr. Rabinowitz.

 

Chris Rao

Christopher V. Rao

Professor, Department of Chemical and Biomolecular Engineering
University of Illinois at Urbana-Champaign

Our work focuses on engineering intracellular protein networks. We are investigating how cells process chemical signals, communicate with one another, and adapt to their environment. We're also utilizing this information to genetically reprogram cellular behavior for biotechnology applications. Contact Dr. Rao.

 

 

Martin Wuhr

Martin Wühr

Assistant Professor of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics
Princeton University

Martin obtained his PhD in Systems Biology from Harvard. Together with Tim Mitchison, he studied how the cell division machinery adapts to the drastically changing cell size in early vertebrate embryos. They proposed a model in which dynein pulling on bulk cytoplasm centers nascent spindles and orients them along the long axis of the cell, thereby explaining the canonical embryonic cleavage patterns. For his Postdoc, Martin joined the laboratories of Steven Gygi, a leader in quantitative proteomics, and Marc Kirschner, who is interested in the description of cellular and developmental processes on the systems level. Martin developed new methods for quantitative proteomics and applied them to investigate nucleocytoplasmic segregation and developmental processes in the early embryo. The proteome scale perspective provided new insight into the partitioning of proteins between nucleus and cytoplasm and overall strategy for RNA and protein regulation in the embryo. Contact Dr. Wühr.

 
Yasuo Yoshikuni

Yasuo Yoshikuni

Biologist Staff Scientist
Joint Genome Institute

Prior to joining at the DOE JGI, Yasuo was a co-founder and Chief Science Officer at a clean technology start-up, Bio Architecture Lab, Inc. (BAL) where his significant achievement was using synthetic biology to develop the first microbial platform technologies enabling to unlock the potential of macroalgae as highly environmentally sustainable and cost-effective biomass for the production of renewable fuels and chemicals. The development of this technology allowed the company to raise $40 million from private funding sources, receive prestigious national grants and build a commercial partnership with leading companies in the oil and chemical industries. The work also led to several high impact scientific publications.  Yasuo’s research focus is to discover novel secondary metabolites and to study their roles in microbial-microbial and plant-microbial communications in various environments. He is currently developing design principles, tools, and methodologies to mine and characterize novel secondary metabolite biosynthetic pathways and component enzymes by leveraging on the DOE JGI’s unique resources and capabilities. Contact Dr. Yoshikuni.

 
Huimin Zhao

Huimin Zhao

Steven L. Miller Chair, Chemical and Biomolecular Engineering
Professor of Chemistry, Biochemistry, Biophysics, and Bioengineering
University of Illinois at Urbana-Champaign

Dr. Huimin Zhao is the Steven L. Miller Chair of chemical and biomolecular engineering, and professor of chemistry, biochemistry, biophysics, and bioengineering at the University of Illinois at Urbana-Champaign (UIUC). He received his B.S. degree in Biology from the University of Science and Technology of China in 1992 and his Ph.D. degree in Chemistry from the California Institute of Technology in 1998 under the guidance of Dr. Frances Arnold. Prior to joining UIUC in 2000, he was a project leader at the Industrial Biotechnology Laboratory of the Dow Chemical Company. He was promoted to full professor in 2008. Dr. Zhao has authored and co-authored over 260 research articles and over 20 issued and pending patent applications with several being licensed by industry. In addition, he has given plenary, keynote or invited lectures in over 300 international meetings, universities, industries, and research institutes. Fifteen (15) of his former graduate students and postdocs became professors in the United States (7), China (5), Korea (2), and Egypt (1). Read short bio and full CV. Contact Dr. Zhao.

 

Students and Staff

Joshua Chan

Siu Hung (Joshua) Chan

Postdoctoral Scholar, Maranas Lab
The Pennsylvania State University

Ph.D., Biological Systems Engineering, Technical University of Denmark, Denmark
M.Phil., Computational Systems Biology, The Hong Kong Polytechnic University, Hong Kong, 2011 B.Sc., Mathematics and Physics, The University of Hong Kong, Hong Kong, 2008. Contact Dr. Chan.

 
Anshu Deewan

Anshu Deewan

Graduate Student, Rao Lab
University of Illinois at Urbana-Champaign

B.Tech., Chemical Engineering, Indian Institute of Technology Delhi, 2012. Contact Anshu.

 
Hoang Dinh

Hoang Dinh

Graduate Student, Maranas Lab
The Pennsylvania State University

MS, Bioengineering, UC San Diego, 2017
B.S. Chemical Engineering, Penn State, 2015. Contact Hoang

 
Saratram Gopalakrishnan

Saratram Gopalakrishnan

Graduate Student, Maranas Lab
The Pennsylvania State University

B.E. Biotechnology, Manipal University, 2011
M.S.E. Chemical and Biomolecular Engineering, Johns Hopkins University, 2013. Contact Saratram.

 
Meera Gupta

Meera Gupta

Graduate Student, Wühr lab
Princeton University

Meera earned her BS in Chemical Engineering at the Indian Institute of Technology (IIT)-Delhi. As an undergrad, she worked on multi-phase flow model development and drug delivery. Contact Meera.

 
hsiehph@berkeley.edu

Ping-Hung Hsieh

Graduate Student, Fischer and Zilberman Labs
University of California, Berkeley

Martin obtained his PhD in Systems Biology from Harvard. Together with Tim Mitchison, he studied how the cell division machinery adapts to the drastically changing cell size in early vertebrate embryos. They proposed a model in which dynein pulling on bulk cytoplasm centers nascent spindles and orients them along the long axis of the cell, thereby explaining the canonical embryonic cleavage patterns. For his Postdoc, Martin joined the laboratories of Steven Gygi, a leader in quantitative proteomics, and Marc Kirschner, who is interested in the description of cellular and developmental processes on the systems level. Martin developed new methods for quantitative proteomics and applied them to investigate nucleocytoplasmic segregation and developmental processes in the early embryo. The proteome scale perspective provided new insight into the partitioning of proteins between nucleus and cytoplasm and overall strategy for RNA and protein regulation in the embryo. Contact Ping-Hung.

 
Jing Ke

Jing Ke

R&D Project Scientist
Joint Genome Institute

Bioprocess design, fermentation of bio-active natural product, biomolecules & protein characterization. Contact Dr. Ke.

 
 
Shekhar Mishra

Shekhar Mishra

Graduate Student, Zhao Lab
University of Illinois at Urbana-Champaign

B.Tech in Chemical Engineering, IIT Bombay 2014
M.Tech in Chemical Engineering, IIT Bombay 2014
I am interested in exploring the design principles of biological systems for the purpose of improved metabolic engineering strategies using a combination of mathematical models and experimental techniques. Contact Mishra.

 
Carl Schultz

Carl Schultz

Graduate Student, Zhao Lab
University of Illinois at Urbana-Champaign

B.S., Cornell University, 2015
I am developing genetic tools for the genome-scale metabolic engineering of yeasts for biofuel and biochemical production. Contact Carl.

 
Arjuna Subramanian

Arjuna Subramanian

Graduate Student, Wuhr Lab
Princeton University

Arjuna is an undergraduate in the Department of Chemistry. He is interested in mathematical modeling of biochemistry and in how physical and chemical principles influence protein structure and organization within cells. Contact Arjuna.

 
 
 

Tianxia Xiao

Graduate Student, Rabinowitz Lab
Princeton University

Contact Tianxiao.

 

Xi Xing

Staff Scientist, Rabinowitz Lab
Princeton University

Contact Xi.

 

Zhiying Zhao

Research Associate
Joint Genome Institute

Contact Dr. Zhiying.