Informatics and Systems Biology of Complex Disease. The computational challenges of studying complex diseases, such as cancer, neurological disorders, diabetes, and deadly infections, are diverse and range from gathering biomedical data to determining the key molecular mechanisms behind the disease, from understanding the dynamics of the molecular system during the disease onset to making accurate predictions on the clinical outcomes. Our research in this area integrates the next-generation sequencing, structural genomics, and interactomics data and leverages state-of-the-art computational paradigms, such as deep learning, semi-supervised learning and agent-based systems. We are also working in collaboration with experimental labs to study specific diseases in human, animals, and plants.
Biomedical Data Analytics. We are developing computational methods for fast collection and processing of the large-scale biomedical datasets. Current projects include mining macromolecular interaction and genetic variation data and organizing it into a comprehensive database, text mining of host-pathogen interaction data using automated and crowd-sourcing approaches and mining eye-tracking movements to test basic cognitive hypothesis about learning.
Computational Genomics. Advances in computational genomics have the potential to greatly benefit evolutionary and regulatory genomics. We employ algorithms driven by biological phenomena to determine important functional and structural elements of the genome and trace their evolutionary origins. Current projects include discovering and analyzing genomic regions of extreme conservation in eukaryotic genomes and studying genome rearrangement in higher eukaryotes.
Cui H, Dhroso A, Johnson N, Korkin D. "The variation game: Cracking complex genetic disorders with NGS and omics data"; Methods (2016)
Zhao N, Han JG, Shyu CR, Korkin D, "Determining effects of non-synonymous SNPs on protein-protein interactions using supervised and semi-supervised learning", PLoS Comput. Biol.(2014)
T Liu S, Kandoth P, Warren S, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale P, Hill J, Baum T, Cianzio S, Whitham S, Korkin D, Meksem K, and Mitchum M. "A Soybean Cyst Nematode Resistance Gene Points to a New Mechanism of Plant Resistance to Pathogens"; Nature (2012)
Renecker J, Lyons E, Conant G, Pires C, Freeling M, Shyu CR, Korkin D. "Long Identical Multispecies Elements in Plant Genomes"; Proc Natl Acad Sci USA (2012)
August, 2016: The Lab welcomes its new member: Pavel Terentiev, who joined us as a postdoc.
May, 2016: Katie Hughes has successfully defended her Masters thesis, She is our first WPI alum! Katie will start her dream job at Moderna Therapeutics.
December, 2015: Thanh Thieu has successfully defended his Ph.D. He will join National Institute of Health as a postdoc
May, 2015: Samantha Warren has successfully defended her Ph.D. She will join Fontbonne University as an Assistant Professor
October, 2014: Xingyan Kuang has successfully defended her Ph.D. She will join Ohio State University's Comprehensive Cancer Center as a postdoc
September, 2014: Korkin Lab has moved to Worcester Polytechnic Institute (WPI)