Multiple genome rearrangement: a general approach via the evolutionary genome graph. - Dmitry Korkin; Lev Goldfarb (ISMB, 2002)

Structural Modeling of Protein Interactions by Analogy: Application to PSD-95. - Dmitry Korkin; Fred P. Davis; Frank Alber; Tinh Luong; Min-Yi Shen; Vladan Lucic; Mary B. Kennedy; Andrej Sali (PLoS Comput. Biol., 2006)

An Efficient Parallel Algorithm for the Multiple Longest Common Subsequence (MLCS) Problem. - Dmitry Korkin; Qingguo Wang; Yi Shang (ICPP, 2008)

Efficient Dominant Point Algorithms for the Multiple Longest Common Subsequence (MLCS) Problem. - Qingguo Wang; Dmitry Korkin; Yi Shang (IJCAI, 2009)

Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments. - Pin-Hao Chi; Bin Pang 001; Dmitry Korkin; Chi-Ren Shyu (Bioinform., 2009)

A Fast Heuristic Search Algorithm for Finding the Longest Common Subsequence of Multiple Strings. - Qingguo Wang; Mian Pan; Yi Shang; Dmitry Korkin (AAAI, 2010)

An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches. - Nan Zhao 002; Bin Pang 001; Chi-Ren Shyu; Dmitry Korkin (BIBM, 2010)

ProteinDBS v2.0: a web server for global and local protein structure search. - Chi-Ren Shyu; Bin Pang 001; Pin-Hao Chi; Nan Zhao 002; Dmitry Korkin; Dong Xu 002 (Nucleic Acids Res., 2010)

A Fast Multiple Longest Common Subsequence (MLCS) Algorithm. - Qingguo Wang; Dmitry Korkin; Yi Shang (IEEE Trans. Knowl. Data Eng., 2011)

Fast protein binding site comparisons using visual words representation. - Bin Pang 001; Nan Zhao 002; Dmitry Korkin; Chi-Ren Shyu (Bioinform., 2012)

Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches. - Thanh Thieu; Sneha Joshi; Samantha Warren; Dmitry Korkin (Bioinform., 2012)

DOMMINO: a database of macromolecular interactions. - Xingyan Kuang; Jing Ginger Han; Nan Zhao 002; Bin Pang 001; Chi-Ren Shyu; Dmitry Korkin (Nucleic Acids Res., 2012)

PBSword: a web server for searching similar protein-protein binding sites. - Bin Pang 001; Xingyan Kuang; Nan Zhao 002; Dmitry Korkin; Chi-Ren Shyu (Nucleic Acids Res., 2012)

PBSalign: Sequence-independent local alignment of protein binding sites. - Bin Pang 001; David Schlessman; Xingyan Kuang; Nan Zhao 002; Daniel Shyu; Dmitry Korkin; Chi-Ren Shyu (BIBM, 2013)

Uncovering influence links in molecular knowledge networks to streamline personalized medicine. - Dmitriy Shin; Gerald C. Arthur; Mihail Popescu; Dmitry Korkin; Chi-Ren Shyu (J. Biomed. Informatics, 2014)

Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning. - Nan Zhao 002; Jing Ginger Han; Chi-Ren Shyu; Dmitry Korkin (PLoS Comput. Biol., 2014)

An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites. - Bin Pang 001; David Schlessman; Xingyan Kuang; Nan Zhao 002; Daniel Shyu; Dmitry Korkin; Chi-Ren Shyu (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Effect-specific analysis of pathogenic SNVs in human interactome: Leveraging edge-based network robustness. - Hongzhu Cui; Dmitry Korkin (EMBC, 2016)

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. - Xingyan Kuang; Andi Dhroso; Jing Ginger Han; Chi-Ren Shyu; Dmitry Korkin (Database J. Biol. Databases Curation, 2016)

Patterns of amino acid conservation in human and animal immunodeficiency viruses. - Olga S. Voitenko; Andi Dhroso; Anna Feldmann 001; Dmitry Korkin; Olga V. Kalinina (Bioinform., 2016)

DISPOT: a simple knowledge-based protein domain interaction statistical potential. - Oleksandr Narykov; Dmytro Bogatov; Dmitry Korkin (Bioinform., 2019)

An Exploratory Study of Social Media Analysis for Rare Diseases Using Machine Learning Algorithms: A Case Study of Trigeminal Neuralgia. - Haadi Mombini; Ruojun Li; Yixin Zhang; Dmitry Korkin; Bengisu Tulu (HICSS, 2020)

Boosting gene expression clustering with system-wide biological information: a robust autoencoder approach. - Hongzhu Cui; Chong Zhou; Xinyu Dai; Yuting Liang; Randy C. Paffenroth; Dmitry Korkin (Int. J. Comput. Biol. Drug Des., 2020)

A high-throughput, online tool for investigating host-pathogen macromolecular interactions buried in scientific literature. - Tuan-Dung Le; Phuong D. Nguyen; Dmitry Korkin; Thanh Thieu (CHASE, 2021)

PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. - Tuan-Dung Le; Phuong D. Nguyen; Dmitry Korkin; Thanh Thieu (Database J. Biol. Databases Curation, 2022)

Finding shortest and nearly shortest path nodes in large substantially incomplete networks. - Maksim Kitsak; Alexander A. Ganin; Ahmed Elmokashfi; Hongzhu Cui; Daniel A. Eisenberg; David L. Alderson; Dmitry Korkin; Igor Linkov (CoRR, 2022)