Current Lab Members

Graduate Students

Nam Nguyen (

I joined the Cirino lab in 2017 during my undergraduate junior year and was accepted into the Chemical and Biomolecular Engineering PhD program upon the completion of my BS degree here at the University of Houston. I have had experience in heterologous protein expression and purification, cloning strategies, directed evolution, data analysis, and mass spectrometry.  

My research focus is on cloning and achieving functional, anaerobic expression of multiple sets of iron-sulfur cluster-containing enzymes known as alkylsuccinate synthases, along with their respective partner activases. I am using E. coli as a host because it is easy to culture, clone, genetically engineer, and grow at large-scale in industrial bioreactors. I am using a variety of strategies to improve enzyme activity / production of alkylsuccinates: co-expression of additional proteins (e.g. chaperones), optimizing essential nutrients, genetic modifications, and protein engineering/ directed evolution. In collaboration with Dr. Ramon Gonzalez at USF, we aim to assemble a full metabolic pathway in E. coli to directly convert short-chain alkanes into butanol or other high value chemicals. The envisioned overall conversion process is shown here.


Ehsan Bahrami Moghadam (ebahrami@CougarNet.UH.EDU)

I received my bachelor’s degree from the Chemical Engineering Department of Sharif University of Technology in 2019. I’m currently a second-year graduate student in the Department of Chemical and Biomolecular Engineering at the University of Houston. My research focuses on the design of novel, genetically-encoded molecular biosensor/reporter systems, based on the ItcR repressor protein from Yersinia pseudotuberculosis. This repressor is natively induced by itaconic acid, but also shows response to methylsuccinate (Hanko, Minton & Malys, ACS Synthetic Biology 2018, 7). I am using protein engineering techniques to alter substrate specificity and sensitivity of ItcR, and implementing the resulting variants as reporters of alkylsuccinate synthase activity, for high-throughput biocatalyst screening. Research activities relating to this project include X-ray crystal structure determination, combinatorial methods, and FACS sorting.

ItcR Homology Model


Udayanidhi Ramesh Kumar (urameshk@CougarNet.UH.EDU)

Various types of bacteria are appealing as components in a novel class of “active emulsions”. Such living active emulsions represent a potentially transformative advance in biomaterials, as they provide a route to incorporate desirable properties of living systems into engineered materials that can be readily flowed, printed, or shaped. My project is part of a collaborative effort between Dr. Cirino and Dr. Conrad. We aim to develop the tools needed to program the mechanical properties of active, living emulsions by engineering and modeling the motility and adhesiveness of bacteria. These properties will be related to the ability of bacteria to drive the motion of individual droplets, to generate large-scale correlated motion in many droplets, and ultimately to control the “flowability” of bulk emulsions. The results from this project are expected to advance the design of feedstocks for advanced materials processing and 3-D printing applications.




Isaac Tidwell

Recent PhD Graduates

Yixi Wang

I am a fourth-year graduate student in the Chemical and Biomolecular Engineering department at the University of Houston. I graduated from Beijing University of Chemical technology with his B.S. in Chemical Engineering in 2015 and obtained an M.S. in Chemical and Biomolecular Engineering from the University of Irvine in 2017. At UH, my main research project is a contribution to the broader effort of converting short-chain alkanes, and ultimately methane, into “alkylsuccinate” intermediate metabolites, for subsequent conversion to biofuels. I have achieved functional expression of the “Mas” enzyme system in E. coli, capable of adding fumarate to C3 to C6 alkanes. I am using protein modeling and various mutagenesis techniques to probe the substrate binding pocket of the MasD catalytic subunit. I am also working to enhance functional expression, purify active enzyme, and developing / using assays to measure and quantify enzyme activity.

Aarti Doshi

I am working on the microbial production of orsellinic acid (OSA), which is an important platform chemical and has use as a precursor for production of a potent anti-HIV agent, naturally derived from plants. I am designing gene expression libraries to possibly increase the OSA production in E. coli. I am also interested in engineering the AraC transcriptional factor to develop a sensor for detecting OSA and use it to enable high throughput, continuous monitoring of OSA production in bacteria.

In collaboration with Dr. Navin V. and Dr. Dmitry N. (UT-MD Anderson), we are interested in using optimized E. coli transcriptional factors for developing an inducible gene expression system for mammalian cells.

Current Undergraduate Students

Joshua Nwose

Casie Denton


Former Cirino Lab Members


Former Postdocs

Dr. Joseph Gredell; Senior Scientist at Novozymes (Link)

Dr. Shuang-Yan Tang; Professor at Chinese Academy of Sciences, Institute of Microbiology (Link)

Dr. Hui Li


Former Graduate Students

Yixi Wang, PhD 2022; Postdoc at Rice University

Arti Doshi, PhD 2020; Research Scientist at Tessera Therapeutics

Zhiqing Wang, PhD 2019; Research Scientist at Mascoma, LLC.

Shuai Qian, PhD 2018; Senior Scientist at Solugen

Ye Li, PhD 2017; Assistant Professor at Jiangnan University

Shaza Abnouf (PhD student of N. Varadarajan (primary advisor))

Christopher Frei, PhD 2016; Senior Scientist at Manus Biosynthesis

Balakrishnan Ramesh (PhD student of N. Varadarajan (primary advisor)); Scientist at Muufri, Inc.

Olubolaji Akinterinwa, PhD 2010; Scientist at Procter & Gamble

Jonathan Chin, PhD 2010; Senior Scientist at Algenol Biofuels

Reza Khankal, PhD 2010; Chevron

Hossein Fazelinia, PhD 2009 (co-advised by C. Maranas); Children’s Hospital, Philadelphia

Lexan Lhu, MS, Now at Joule Biotechnologies

Francesca Luziatelli (visiting PhD student from the University of Tuscia, Italy)

Ryan McLay, co-advised MS student

Lois Eppihimer, Lab Manager


Former Undergraduate Students

  • Tania Pena Reyes (visiting from U. Chicago, Rowley Scholar)
  • Tasnuva Haider (volunteer)
  • Ibrahim Hassan (volunteer)
  • Anthara Krishnan (volunteer)
  • Carson Bush – SURF
  • Nam Nguyen – SURF
  • Priya Patel – SURF
  • Zheng You (volunteer)
  • Diep Nguyen – SURF
  • Jennie Nguyen – SURF
  • Aya Elsaadi – SURF
  • Rachel Dunn – PURS
  • Justin Hood (volunteer)
  • Danielle Valcourt (REU, Notre Dame)
  • Katy Norman (REU, Trinity)
  • Wayne Andrade (UH, volunteer)
  • Chelsea Kraynak (University of MD, REU summer 2012)
  • Oliver Chou (U Colorado Boulder) REU
  • Kyle Schutter (Brown University REU; now CEO of Takamoto Biogas Ltd.)
  • Nicholas Linn (NC State) – REU
  • Ajay Padaki
  • Berook T. Alemayehu (U Maryland: Baltimore County) REU
  • Audrey Leung (University of Iowa) REU
  • Alex Teng (UC Berkeley) – REU
  • Caroline Monroe (Penn State)
  • Anthony Tascone (Penn State)
  • Renae Patch (Penn State)
  • Garrett Tobin (Penn State)
  • Jeremy Sargent (Penn State)
  • J. Lane Weaver (Penn State)
  • Jon P. Badalamenti (Penn State)
  • Lucien E Weiss (Penn State)
  • Julie Sawlsville (Penn State)
  • Geoff Geise (Penn State) – REU
  • Doug Haag (Penn State)
  • Megan Rex (Penn State)
  • Chris Cottle (Penn State)
  • Panagiotis A Papadopoulos (Penn State)
  • Matthew Zapadka (Penn State)
  • Galen Lynch (PSU)
  • Noah Johnson (PSU)
  • Chris Frei (PSU)
  • Trevor Wiley
  • Erica Trump (West Virginia U) – REU
  • Nimrah Ahmed
  • Shariful Alam
  • Aubrey Dolly
  • Daniel Seong

Work-Study Students

  • Joshua Nwose
  • Ana Alvarez
  • Hiba Ahmed
  • Chiemela Ubani
  • Marilu Serna
  • Arlene Sanchez
  • Ghazal Nemati
  • Christian Miles
  • Mulbah Kallen
  • Louis Avila
  • Zeal Patel
  • Areeba Ahmed
  • Sana Basheer
  • Ryan Noraas
  • Tiffany Veet
  • Khai Van
  • Jon Ajak