Grishin Lab Members

  Nick V. Grishin

Born and educated in Russia, Nick received a Diplom (the Russian equivalent of a master's degree) in biochemistry from the Moscow State University (1993). His doctoral research in molecular biophysics was done with Margaret Phillips at the University of Texas Southwestern Medical Center (1998). After a postdoctoral year with Eugene Koonin at the National Institutes of Health, he joined the faculty at UT Southwestern. Nick is interested in most projects in the lab.

Raquel Bromberg  Graduate Student    

Raquel received her Masters in computer science from the University of Texas at Dallas. Her focus was in algorithms and her thesis was a statistical analysis of the pancake problem, a problem involving prefix reversals. She is now a student of the Division of Basic Sciences at UT Southwestern.  She is interested in the evolution of proteins and is currently working on determining phylogenetic distances between prokaryotic organisms.  Her work is a collaboration between the labs of Prof. Nick Grishin and Prof. Zbyszek Otwinowski.

 Hua Cheng  Postdoc

Hua received her Ph.D. from the Molecular Biophysics Program at UT Southwestern in August, 2007. Her research interests include using computational and manual expert methods to study protein structures in an evolutionary context, detecting distant evolutionary relationships between proteins, and predicting protein structure and function based on its experimentally-characterized evolutionary relatives (= homologs).

Qian Cong  Graduate Student  

Qian received B.S. in Biological Sciences from Peking University and entered the Division of Basic Sciences at UT Southwestern Medical Center in 2009. Qian is studying evolution of protein spatial structures and the reasons behind significant structural differences between proteins with highly similar sequences. She is also developing software to predict nuclear export signals in proteins.

 Adam Haraburda  Graduate Student  

Adam received his B.S. in Chemistry from the University of Texas at Dallas in 2010, where he did research synthesizing macrocyclic molecules designed with the intent to detect explosives and/or carbon nanotubes. He joined the Division of Basic Sciences at UT Southwestern in 2011 and is working on developing a protein sequence to structure prediction tool.

Lisa N. Kinch  Bioinformatics Scientist  

Lisa received her Ph.D degree in Molecular Biophysics from the University of Texas Southwestern Medical Center at Dallas, where she studied enzymes of Trypanosoma polyamine biosynthetic pathways under the guidance of Margaret Phillips. She also carried out postdoctoral work in the lab of Elliott Ross examining the complex kinetics of G-protein signaling systems. Her experience relating enzyme structure to function attracted her to the bioinformatics field, where she developed an expertise in using sequence and structure analysis tools to classify proteins. Her current research interests include prediction of protein structure and function from sequence and exploration of fold changes in protein evolution.

Wenlin Li Graduate Student 

Wenlin comes from Tsinghua University, with BS degree in biological science. As a graduate student in UTsouthwestern, he is currently involved in data mining projects about presenting biological meaningful data to understand the protein functions and investigating the effect of clinical mutations on protein structures.

Yuxing Liao Graduate Student    

Yuxing received a B.S. degree in Biosciences from University of Science and Technology of China in 2010. In rotation works, he participated in the assessment of CASP9. Now as a graduate student, he is trying to develop a pipeline for automatic domain assignment to help achieve weekly updates of the ECOD structural classification database.

   Erik D. Nelson  Bioinformatics Scientist 

Erik received his Ph. D. in condensed matter physics from the University of Massachusetts, Amherst. His research interests include protein folding kinetics, energy landscape theory and the influence of biological function requirements on protein self assembly. Erik is currently using explicit chain Langevin and Monte Carlo models to describe the effects of water and cooperative interactions on the folding of small, fast folding proteins. One of his goals is to develop a simple statistical model of protein free energy landscapes that can provide a quick and qualitatively accurate method of inference from kinetics and thermodynamics measurements.

Jimin Pei  Bioinformatics Scientist  

Jimin Pei received his Ph.D. in biophysics from UT Southwestern Medical Center in 2004. His research is about the development and application of computational methods for analysis of biological sequences and structures. He has developed methods in multiple sequence alignment, protein design, functional site prediction, and evolutionary analysis. His computational work has facilitated annotation, classification, and structure/function prediction of protein families.

  Sasha Safronova  Graduate Student  

Sasha received her M.Sc. in Applied Mathematics from Moscow State University, Russia in 2001. Her focus was the study of the ill-posed problems in Mathematical Physics. She joined the Grishin lab as a student in 2007, and is working on ab initio protein structure prediction algorithms.

Dustin Schaeffer  Postdoc  

Dustin Schaeffer received his B.S. in molecular biology from the University of California, San Diego and his Ph.D. in biochemistry from the University of Washington, Seattle. He joined the Grishin lab in 2010. His thesis work focused on methods for high-throughput molecular dynamics simulations of protein folding and the study of the folding pathways of DNA/RNA-binding three-helix bundle homeodomains. His research focuses on the partition of protein structure and the quantitative classification of protein folds.

  Jeremy Semeiks  Graduate Student  

Jeremy is an MD/PhD student at UT Southwestern. He is from Albany NY, where he received a BS in Biology and Computer Science (double major) from SUNY Albany in 2002. Then he did bioinformatics and microarray work at Lawrence Berkeley National Lab in California, before moving to UT Southwestern in 2007 and joining the Grishin lab as a PhD student in the Biophysics program in 2010. His main interest is gerontology, the study of organismal aging. In particular, he is interested in the relationship of aging to metabolism and DNA repair. In his rotation project, he compared the longevity of several animal species to the sequence and structure of their conserved DNA repair proteins.

Shuoyong Shi  Postdoc    

Shuoyong completed my Ph.D. degree in Biochemistry from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, where he worked on detecting evolutionary events which occurred in the history of the genome evolution including gene duplication, gene loss and horizontal gene transfer. He joined the Grishin Lab as a postdoctoral fellow in 2006. His research interest is investigating the evolutionary history in the protein universe via statistical analysis, computational approaches and software development. His current research projects focus on structure pattern search, protein domain parsing, protein structure superposition algorithm development and domain-based sequence and structure evolutionary analysis of proteins sharing a particular fold.

  Ming Tang System Administrator  

Ming hold a Bachelor's degree in Physics from Nankai University, Tianjin, China. In 1992 he received a Masters in Mechanics from Tianjin University. Between 1992 and 2000, Ming worked as a computer engineer. In the Grishin lab Ming makes sure all computers are in tip top shape, software is running and the databases are timely updated.

  Jing Tong Graduate Student   

Jing received her Master's degree (2008) and Bachelor's degree (2005) in Biomedical Engineering from Southeast University, Nanjing, China. And now, she is persuing her Ph.D. in the Division of Basic Science at UTSouthwestern. During her rotation period, she focused on the evaluation of protein structure prediction by contact methods. She is interested in protein structure-function prediction and is currently working on multiple sequence alignment methods.

  Darui Xu Postdoc 

Darui received her MS in computer science in 2002 and her Ph.D. in chemistry in 2007, both from Florida State University. Her graduate work focused on the electrostatics and molecular dynamics of nucleic acids. Now she is a postdoc in Yuh-Min Chook's lab collaborating with us on the analysis and prediction of nuclear export signals.

Previous Lab Members

Name Position Year
Ning Zhang Rotation Student 2013
Fangzhou Zhao Rotation Student 2013
Renkai Ji Graduate Student 2012-2013
Ivan Huang Undergraduate Intern Summer 2011&2012
Tao Wang Rotation Student 2012
Bong-Hyun Kim Postdoctoral researcher 2003-2012
Chalam Chitturi Postdoctoral researcher 2007-2011
Adam Coster Rotation Student 2010
Deng Mao Rotation Student 2010
Dorothee Staber Lab Manager 2007-2010
Ruslan I. Sadreyev Bioinformatics Scientist 2001-2010
Indraneel Majumdar Research Associate 2001-2010
Yong Wang Graduate Student 2005-2009
Dhriti Pandya Undergraduate Intern Summer 2008
Jamie O Wrabl Bioinformatics Scientist 2000-2008
Daniel Parente Undergraduate Intern Summer 2007
Yi Zhong Scientific Programmer 2003-2006
Yuan Qi Graduate Student 2001-2006
Anthony Yeh Undergraduate Intern Summer 2005
Mingzhu Zheng Graduate Student 2004-2005
Krzysztof Ginalski Visiting Assistant Professor 2004-2005
Nathan Holladay Medical PhD Student 2003-2005
Sara Cheek Graduate Student 2001-2005
S. Sri Krishna Postdoctoral researcher 2000-2005
Wei Cai Scientific Programmer 2002-2004
David Mittelman Scientific Programmer 2002-2002
Shunming Fang Research Associate 2001-2002
Shide Liang Postdoctoral researcher 2000-2002
Lakshmi Iyer Postdoctoral researcher 2000-2001
Xuguang Shao Postdoctoral researcher 2000-2000
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