Koffas Research Group

Network and Metabolic Engineering

Rensselaer Polytechnic Institute

Lab Members

Postdoctoral Fellows

Dr. Jian Zha
Email: zhaj@rpi.edu

Education
B.S. Chemical Engineering, Tianjin University, China, 2008
Ph.D. Chemical Engineering, Tianjin University, China, 2013

Project
My current project focuses on metabolic engineering of bacteria for overproduction of flavonoid compounds. My research involves the application of the prevailing technologies in metabolic engineering and synthetic biology, such as pathway assembly and pathway balancing.

Research Interests
I am interested in the development and application of cutting-edge technologies in metabolic engineering and synthetic biology. Especially, it is my prior interest to produce many natural products through microbial fermentation of engineered microorganisms instead of costly and environment-unfriendly methods such as extraction from plants.

Future Plans
I want to establish my own team and lab in the near future. I will keep moving towards that dream. I believe metabolic engineering and synthetic biology will make our future better!


Dr. Rufeng Wang
Email: rufengwang007@gmail.com

Education
B.S. Pharmaceutical Science, Qinghai University for Nationalities, 2009
M.S. Microbiology and Biochemical Pharmacy, Wuhan Polytechnic University, 2012
Ph.D. Pharmacognosy, China Pharmaceutical University, 2015

Project
My specific research is currently being performed to develop a method involves biosynthesis and metabolic engineering of Saccharomyces cerevisiae for the high titer production of bioactive flavonoids.

Research Interests
Biocatalysis, biosynthesis and metabolic engineering of microorganisms for the efficient and sustainable production of chemicals ranging from high-value pharmaceuticals and cosmetic ingredients.

I am looking into a synergism of specific enzymatic activities, bioprocess optimization and metabolic engineering promises a commercially viable alternative to the production of bioactive chemicals in virtue of the establishment and application of high-throughput screening method for the selection of best-performing cell factories.

Future Plans
My expectation is to achieve the industrial production for several kinds of rare traditional Chinese medicine-derived therapeutic compounds with the joint efforts of trustworthy partners.


Dr. Mamta Gupta
Email: mamtagupta2503@gmail.com

Education
B.S. Biology, Government College for Girls, Sector-11, Chandigarh, India, 2002
M.S. Environment Science, Panjab University, Chandigarh, India, 2005
Ph.D. Environment Science, Panjab University, Chandigarh, India, 2011

Project
I am working as an Indo-US postdoctoral fellow mentored by Dr. Mattheos Koffas. My research is focused on engineering metabolic pathways in E. coli for the expression of enzymes for converting C-1 carbon sources to biofuels.

Research Interests
My research interests are to develop expertise in the area of metabolic engineering and synthetic biology for the production of value added compounds such as biofuels and flavonoids from simple carbon sources in a sustainable manner.

Future Plans
My future goal is to start my own research in the area of metabolic engineering. I want to develop the value added products in a sustainable manner. I want to pass my knowledge to my research students.


Dr. Hulya Akdemir
Email: pinarakdemir@gmail.com

Education
B.S. Biology, Istanbul University, Turkey, 2002
M.S. Biology, Gebze Technical University, Turkey, 2006
Ph.D. Molecular Biology and Genetics, Gebze Technical University, Turkey, 2013

Project
My main project includes metabolic engineering of flavonoids in microorganisms.

Research Interests
I am interested in over-production of plant-based metabolites in different microbial hosts.

Future Plans
I pursue my career in the metabolic engineering area as a faculty member in academia.



Graduate Students

Karolina Kalbarczyk
Email: kalbak@rpi.edu

Education
B.S. Chemical Engineering (Biomolecular), California Institute of Technology, 2013
Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2018

Project
My research is focused on combining the work of Dr. Mattheos Koffas in glucose to fatty acid production with the work of Dr. Cynthia Collins in interspecies commutations systems. The project involves engineering of recombinant microbial communities for production of fatty acids from cellulose.

Research Interests
Protein engineering, metabolic engineering, directed evolution, systems biology, simulations, microbial communities, co-culture communications. Focused on production of valuable biofuels and pharmaceuticals with innovative methods.

In my research, I hope to combine existing ideas in metabolic engineering and microbial communities to develop innovative ways of fatty acid production, which can be adapted for a range of valuable end products. With this work, I would like to further incorporate systems biology and model simulations to create tools for more efficient future developments, bringing a rational and predictive component to current protein engineering innovations.

Future Plans
My goals are to stay at the forefront of protein engineering and systems biology, pursuing a post-doc in simulations modeling and finally a faculty position in a chemical and biological engineering department.


Cliff Morrison
Email: Clifford.S.Morrison@gmail.com

Education
B.S. Chemistry, Biochemistry, University of North Texas, 2014
Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2019

Project
I will investigate the ability to develop recombinant microorganisms that can potentially utilize methanol as a carbon source. Understanding how electron equivalents are transported into cellular organisms, and generating microorganisms that can grow on alternative carbon sources using tools from synthetic biology, holds great promise for the next generation of sustainable bio-fuel alternatives.

Research Interests
My primary interest is in the sustainable production of value-added products and energy using metabolic engineering and synthetic biology.

Future Plans
I intend to pursue a career in the biotechnology industry.


Kamil S. Gedeon
Email: gedeok@rpi.edu

Education
B.S. Chemical-Biological Engineering, MIT, 2011
Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2020

Project
My research project is focused on increasing fatty acid production for biofuels. I will be utilizing pathway balancing to optimize engineered microbes. Subsequently, I will use the engineered microbes in co-culture fermentation to improve volumetric production, yields, and production rates. I am co-advised by Dr. Mattheos Koffas and Dr. Cynthia Collins.

Research Interests
Creating novel biotechnology platforms for production of high-value and commodity compounds.

Future Plans
To return to industry and continue my career in the biotechnology industry.


Asher Williams
Email: willia9@rpi.edu

Education
B.S. Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, 2015
Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2020

Project
I am currently co-advised by Dr. Koffas and Dr. Linhardt. My research project will involve the biosynthesis of chondroitin/dermatan sulfate through metabolic engineering of Escherichia coli.

Research Interests
My research interests lie in the area of protein engineering and I aim to develop expertise in the area of metabolic engineering.


Abinaya Badri
Email: badria@rpi.edu

Education
B.Tech Industrial Biotechnology, SASTRA University, Thanjavur, India, 2013
M.S. Research in Biotechnology, Indian Institute of Technology, Madras, India, 2016
Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2020

Project
High value biomolecules are game-changers in several industries. However, efficient and controlled production of these biological molecules almost always involves the interplay of several metabolic and regulatory processes in the cell. My work (co-advised by Prof. Mattheos Koffas and Prof. Robert Linhardt) focuses on employing concepts from networks and control systems to improve the design of the cellular blueprint for glycosaminoglycan biosynthesis in E. coli.

Research Interests
My primary interests lie in engineering the metabolism of microorganisms for industrial purposes. More specifically, I am interested in transforming concepts from other fields of science and engineering and adapting them to biological systems to markedly improve the scope of their industrial capabilities.

Future Plans
I want to establish my base in translational research bridging basic to applied sciences. I plan to continue researching as a scientist in this interdisciplinary area of metabolic engineering, thereby accruing a wide base of expertise. In due course, I also want to play an active part in being able to actually start an industry based off of my research and successfully running it.


Matthew Wong
Email: wongm6@rpi.edu

Education
B.S. Chemical Engineering, University of Delaware, 2016
Ph.D. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2021

Project
My research project is the cell-free production of biofuels. The goal is to optimize an immobilized system of enzymes to convert a cellular intermediate to the alcohol, Isobutanol. I am also researching membrane pervaporation to take the reaction broth and separate out Isobutanol. For this project, I am being co-advised by Dr. Koffas and Dr. Belfort.

Research Interests
My research interests lie in the development of biofuels for a sustainable future.

Future Plans
To pursue a career in the biotechnology industry



Visiting Scholars

Dr. Guoqiang Xu
Email: xug5@rpi.edu, xgq908@gmail.com

Education
B.S. Biological Engineering, Huazhong Agricultural University, China, 2006
M.S. Fermentation engineering, Jiangnan University, China, 2008
Ph.D. Fermentation engineering, Jiangnan University, China, 2012

Project
My current project aims at metabolic engineering of bacteria for overproduction of fine chemicals such as amino acids as well as flavonoids. I am interested in using the advanced tools and technologies in metabolic engineering and synthetic biology such as CRISPR interference and protein engineering.

Research Interests
My interest includes the production of C4-dicarboylatic acids and bioethanol using S. cerevisiae as microbial cell factory, and the biosynthesis of amino acids in C. glutamicum with the strategies in metabolic engineering.

Future Plans
I want to be a successful professor in my field and enjoy my research. Meanwhile, I hope I can apply my technologies in industry and make our life better!


Ying Zang
Email: yingzangnjfu@gmail.com

Education
M.S. Department of Chemical Processing Engineering of Forest Products, Nanjing Forestry University, Sept 2012 - July 2014
Ph.D. Department of Chemical Processing Engineering of Forest Products, Nanjing Forestry University, Sept 2014 - present

Project
Research on anthocyanin production in C. glutamicum.

Research Interests
Produce the plant metabolites by metabolic engineering of microorganism.

Future Plans
Using C. glutamicum to produce anthocyanin and improve the production of anthocyanins through the metabolic engineering.



Undergraduate Students

James (JJ) Hu
Email: huj@rpi.edu

Education
B.S. Biology, Rensselaer Polytechnic Institute, Expected May 2017
M.S. Biochemistry/Biophysics, Rensselaer Polytechnic Institute, Expected May 2018

Research Interests
I am currently working on an electrochemical bioreactor, which is an intersection of a number of my research interests: biochemistry, microbiology, and metabolic engineering.

Future Plans
I plan on continuing my research on the electrochemical bioreactor, as well as pursing my Master's in Biochemistry/Biophysics at RPI. After graduation, I plan on applying to medical school.


Thomas Beusse
Email: beusst@rpi.edu

Education
B.S. Chemical Engineering, Rensselaer Polytechnic Institute, Expected May 2019

Research Interests
My interests include biofuel production, pharmaceutical production, and the optimization of an electrochemical bioreactor process for production of value-added products.

Future Plans
After graduating with my chemical engineering degree, I plan to pursue a career in industry. I potentially may pursue a masters or Ph.D. after receiving a few years of work experience.


Hunter Dalton
Email: daltoh@rpi.edu

Education
B.S. Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Expected May 2020

Research Interests
Molecular and Synthetic Biology.