People

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.

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 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.

Chalam received his Ph.D in computer science from The University of Texas at Dallas in 2007 specializing in algorithm design and analysis. Specifically, he studied transformation of strings with different  operations such as prefix reversals and prefix transpositions. Currently he is working on a project to (a) computationally generate compact motifs of protein structures, and (b) perform frequency analysis on such motifs. This project attempts to bring out abnormalities with respect to the frequency of occurrence of different motifs. His areas of research include algorithm analysis and design, computational biology, and medical informatics.

Bong-Hyun received his undergraduate degree from Handong University, Po-Hang, Republic of Korea (South) in Life and Food Science with a minor in Computer Science. Bong-Hyun is interested in building evolutionary classification of proteins that describes the genealogy of all proteins. Currently, he is working on improving evolutionary distance estimates by combining both sequence and structural information, as sequence and structural information are complementary. The combination procedure is based on the reduction of errors in capturing naturally existing protein families. This procedure is a generalized algorithm used in COG (Clusters of Orthologous Groups) database at NCBI. The preliminary results show that the combination helps us to make a better evolutionary classification than sequence or structural information alone as measured by the agreement with SCOP (Structural Classification of Proteins) database, and Bong-Hyun hopes to see the final outcome soon.

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.

Indraneel received his formal education in India. His MSc is in Marine Biotechnology and BSc in Zoology. His primary interest for the last seven years has been software development in the field of bioinformatics. He has successfully installed and managed a computer cluster for two years. His past and current projects involve the study of protein structures for secondary structure and domain definition. He is interested in structure visualization using tools like PyMOL, development of the visualization strategies, manual domain definition in proteins, and developing and implementing algorithms for automatic definition of structural domain.

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 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.

Ruslan holds a Ph.D. in Biophysics from the Department of Physics, Moscow State University, Russia. His research career spans several fields, including neurophysiology, molecular biology, and computational biology. His postdoctoral research of proteins expressed in individual neurons and their role in animal behavior got him interested in general relations between protein sequence, structure, and function. His current work in the Grishin lab is focused on sensitive methods for the detection of protein similarities and their applications; prediction of protein structure and function, protein classification, and evolutionary analysis

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.

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.

Prior to coming to the United States, Dorothee attended Law School in Germany. She holds a Bachelor in Administrative Managment, and has many years of experiences as an administrator as well as lab manager. Her responsibilities are the management of the office, investigator, and whoever would like to be organized! And all is done with a smile!

Ming hold a Bachelor's degree in Physics from Nankai University, Tianjin, China. In 1992 he received a Masters in Mechanics from the same 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. In his free time, Ming enjoys reading history books, and playing tennis.

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.