Members

Qian Cong, PhD

Principal Investigator

I have been an assistant professor in the McDermott Center for Human Growth and Development at UT Southwestern since 2020. I focused on evolutionary genomics as a graduate student in the Grishin lab and worked on computational structure biology as a postdoctoral fellow in the Baker lab. Leveraging on my expertise in genomics, evolution and protein structure modeling, I work on predicting protein-protein interaction (PPI) and modeling protein complex structures on a proteome-wide scale based on coevolution signal between proteins. I have been applying the methods we developed and the knowledge we gained about genome and protein evolution to systems of biomedical importance. Going forward, through collaborations with other labs and establishing an experimental component in my lab, I want to develop a research program to combine evolutionary perspectives, large-scale data, Deep Learning methods, and experimental validations to make biological discoveries about the functional mechanisms of human proteins and pathogenetic factors of infectious bacteria and viruses.

Jimin Pei, PhD

Computational Biologist

I received my Ph.D. in Biophysics from UT Southwestern and B.S. from University of Science and Technology of China. I have worked on developing computational methods for protein sequence and structure analysis and the tools I developed include: PROMALS3D, PROMALS, MUMMALS, and PCMA for protein sequence alignment, AL2CO for estimation of sequence conservation, and SPEL for prediction of residues dictating functional specificity of protein families. In addition, I have made numerous discoveries of the evolutionary relationships between protein families. Recently I constructed the FlyXCDB for extracellular domains of fruit fly proteins and developed a measure (GTS) for quantifying the deleterious effects of mutations, which was used in the database of human single-amino-acid variations (DBSAV). I have collaborated with experimental biologists in applying computational methods to solve biological problems. Since joining the Cong lab in 2021, I am working on applying coevolution analysis and Deep Learning methods for protein-protein interaction predictions at the organelle or proteome levels and the analysis of disease-related human variations. Outside the lab, I enjoy watching sports and listening to classic music.

Jing Zhang, PhD

Postdoctoral Fellow

I received my bachelor’s degree in Biology from Wuhan University, China. I obtained my Ph.D. in UT Southwestern in the laboratory of Nick Grishin. I mainly focused on evolutionary genomics of butterflies as a graduate student. I am interested in mining large-scale biological data with computational tools to understand how diverse phenotypes, especially diseases, and complicated traits are generated through changes in DNA sequences. I joined the Cong lab in 2021, and I am currently working on protein-protein interaction prediction for human and human pathogens using coevolution signals in protein sequences and Deep Learning methods. In a longer term, I am expecting that these structural data will offer a solid basis to interpret how genetic variants contribute to diseases and phenotypes. Inside the lab, I enjoy collecting and digesting information for the subjects we work on and developing methods that are tailored to specific problems we meet in our studies. My advisor thinks that “information and knowledge is the food your brain craves for”. I guess she is right. Outside the lab, I also enjoy getting them through reading books and travelling.

Jesse Durham

Graduate Student

I am a 1st year graduate student in the Biochemistry Program. I obtained both my bachelor’s and master’s degrees from Texas State University, in Biology and Biochemistry, respectively. I used to study proteins using experimental approaches, but I got interested in learning how computational tools can help us to understand complex biological problems. I am fascinated by how artificial intelligence can learn from the large amounts of experimental data accumulated over decades by the scientific community and make predictions that illuminate future studies. I joined the Cong lab in 2022 because of her outstanding work in protein-protein interaction prediction and modeling with Deep Learning methods. I worked in the pharmaceutical industry for 10 years before pursuing my advanced degrees. With the skills I will gain from my graduate study, I hope to prepare myself to start my own biotechnology company in the future. Outside the lab, I challenge my minds and hands by becoming a Master Chess Player and rebuilding my 1990 Ford Bronco. I enjoy watching sports, listening to live music, and traveling in every state of the US.