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Dmitry Korkin, Ph.D. - Publications

Affiliations: 
2003 University of New Brunswick (Canada) 
Area:
Computer Science
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Narykov O, Johnson NT, Korkin D. Predicting protein interaction network perturbation by alternative splicing with semi-supervised learning. Cell Reports. 37: 110045. PMID 34818539 DOI: 10.1016/j.celrep.2021.110045  0.327
2020 Srinivasan S, Cui H, Gao Z, Liu M, Lu S, Mkandawire W, Narykov O, Sun M, Korkin D. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins. Viruses. 12. PMID 32218151 DOI: 10.3390/V12040360  0.331
2019 Cui H, Srinivasan S, Korkin D. Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases. Genes. 10. PMID 31731769 DOI: 10.3390/Genes10110933  0.341
2019 Narykov O, Bogatov D, Korkin D. DISPOT: A simple knowledge-based protein domain interaction statistical potential. Bioinformatics (Oxford, England). PMID 31350874 DOI: 10.1093/Bioinformatics/Btz587  0.404
2019 Masonbrink R, Maier TR, Muppirala U, Seetharam AS, Lord E, Juvale PS, Schmutz J, Johnson NT, Korkin D, Mitchum MG, Mimee B, den Akker SE, Hudson M, Severin AJ, Baum TJ. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. Bmc Genomics. 20: 119. PMID 30732586 DOI: 10.1186/S12864-019-5485-8  0.328
2018 Dhroso A, Eidson S, Korkin D. Genome-wide prediction of bacterial effector candidates across six secretion system types using a feature-based statistical framework. Scientific Reports. 8: 17209. PMID 30464223 DOI: 10.1038/S41598-018-33874-1  0.346
2018 Cui H, Zhao N, Korkin D. Multilayer View of Pathogenic SNVs in Human Interactome through in-silico Edgetic Profiling. Journal of Molecular Biology. PMID 30017919 DOI: 10.1016/J.Jmb.2018.07.012  0.335
2018 Gardner M, Dhroso A, Johnson N, Davis EL, Baum TJ, Korkin D, Mitchum MG. Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. Scientific Reports. 8: 2505. PMID 29410430 DOI: 10.1038/S41598-018-20536-5  0.371
2016 Zhang D, Cui H, Korkin D, Wu Z. Incorporation of protein binding effects into likelihood ratio test for exome sequencing data. Bmc Proceedings. 10: 275-281. PMID 27980649 DOI: 10.1186/S12919-016-0043-8  0.348
2016 Voitenko OS, Dhroso A, Feldmann A, Korkin D, Kalinina OV. Patterns of amino acid conservation in human and animal immunodeficiency viruses. Bioinformatics (Oxford, England). 32: i685-i692. PMID 27587690 DOI: 10.1093/Bioinformatics/Btw441  0.381
2016 Kuang X, Dhroso A, Han JG, Shyu CR, Korkin D. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. Database : the Journal of Biological Databases and Curation. 2016. PMID 26827237 DOI: 10.1093/Database/Bav114  0.404
2015 Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu CR. An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 298-308. PMID 26357218 DOI: 10.1109/Tcbb.2014.2355208  0.414
2015 Cui H, Dhroso A, Johnson N, Korkin D. The variation game: Cracking complex genetic disorders with NGS and omics data. Methods (San Diego, Calif.). 79: 18-31. PMID 25944472 DOI: 10.1016/J.Ymeth.2015.04.018  0.348
2014 Shin D, Arthur G, Popescu M, Korkin D, Shyu CR. Uncovering influence links in molecular knowledge networks to streamline personalized medicine. Journal of Biomedical Informatics. 52: 394-405. PMID 25150201 DOI: 10.1016/J.Jbi.2014.08.003  0.351
2014 Dhroso A, Korkin D, Conant GC. The yeast protein interaction network has a capacity for self-organization. The Febs Journal. 281: 3420-32. PMID 24924781 DOI: 10.1111/Febs.12870  0.4
2014 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 Computational Biology. 10: e1003592. PMID 24784581 DOI: 10.1371/Journal.Pcbi.1003592  0.374
2014 Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, ... ... Korkin D, et al. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nature Communications. 5: 3650. PMID 24722188 DOI: 10.1038/Ncomms4650  0.349
2014 Finch TM, Zhao N, Korkin D, Frederick KH, Eggert LS. Evidence of positive selection in mitochondrial complexes I and V of the African elephant. Plos One. 9: e92587. PMID 24695069 DOI: 10.1371/Journal.Pone.0092587  0.304
2013 Warren S, Wan XF, Conant G, Korkin D. Extreme evolutionary conservation of functionally important regions in H1N1 influenza proteome. Plos One. 8: e81027. PMID 24282564 DOI: 10.1371/Journal.Pone.0081027  0.34
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Korkin D, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.343
2013 Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu CR. PBSalign: Sequence-independent local alignment of protein binding sites Proceedings - 2013 Ieee International Conference On Bioinformatics and Biomedicine, Ieee Bibm 2013. 35-42. DOI: 10.1109/BIBM.2013.6732456  0.314
2012 Pang B, Kuang X, Zhao N, Korkin D, Shyu CR. PBSword: a web server for searching similar protein-protein binding sites. Nucleic Acids Research. 40: W428-34. PMID 22689645 DOI: 10.1093/Nar/Gks527  0.352
2012 Pang B, Zhao N, Korkin D, Shyu CR. Fast protein binding site comparisons using visual words representation. Bioinformatics (Oxford, England). 28: 1345-52. PMID 22492639 DOI: 10.1093/Bioinformatics/Bts138  0.394
2012 Pang B, Zhao N, Becchi M, Korkin D, Shyu CR. Accelerating large-scale protein structure alignments with graphics processing units. Bmc Research Notes. 5: 116. PMID 22357132 DOI: 10.1186/1756-0500-5-116  0.338
2012 Thieu T, Joshi S, Warren S, Korkin D. Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches. Bioinformatics (Oxford, England). 28: 867-75. PMID 22285561 DOI: 10.1093/Bioinformatics/Bts042  0.325
2012 Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D. DOMMINO: a database of macromolecular interactions. Nucleic Acids Research. 40: D501-6. PMID 22135305 DOI: 10.1093/Nar/Gkr1128  0.384
2011 Zhao N, Pang B, Shyu CR, Korkin D. Feature-based classification of native and non-native protein-protein interactions: Comparing supervised and semi-supervised learning approaches. Proteomics. 11: 4321-30. PMID 22002942 DOI: 10.1002/Pmic.201100217  0.418
2011 Zhao N, Pang B, Shyu CR, Korkin D. Structural similarity and classification of protein interaction interfaces. Plos One. 6: e19554. PMID 21589874 DOI: 10.1371/Journal.Pone.0019554  0.421
2011 Zhao N, Pang B, Shyu CR, Korkin D. Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence. Protein Science : a Publication of the Protein Society. 20: 1275-84. PMID 21563227 DOI: 10.1002/Pro.655  0.374
2010 Wang J, Joshi S, Korkin D, Mitchum MG. Variable domain I of nematode CLEs directs post-translational targeting of CLE peptides to the extracellular space. Plant Signaling & Behavior. 5: 1633-5. PMID 21150256 DOI: 10.4161/Psb.5.12.13774  0.328
2010 Shyu CR, Pang B, Chi PH, Zhao N, Korkin D, Xu D. ProteinDBS v2.0: a web server for global and local protein structure search. Nucleic Acids Research. 38: W53-8. PMID 20538653 DOI: 10.1093/Nar/Gkq522  0.398
2010 Wang J, Lee C, Replogle A, Joshi S, Korkin D, Hussey R, Baum TJ, Davis EL, Wang X, Mitchum MG. Dual roles for the variable domain in protein trafficking and host-specific recognition of Heterodera glycines CLE effector proteins. The New Phytologist. 187: 1003-17. PMID 20497349 DOI: 10.1111/J.1469-8137.2010.03300.X  0.363
2009 Chi PH, Pang B, Korkin D, Shyu CR. Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments. Bioinformatics (Oxford, England). 25: 2559-65. PMID 19667079 DOI: 10.1093/Bioinformatics/Btp474  0.396
2008 Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annual Review of Biochemistry. 77: 443-77. PMID 18318657 DOI: 10.1146/Annurev.Biochem.77.060407.135530  0.349
2006 Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. Structural modeling of protein interactions by analogy: application to PSD-95. Plos Computational Biology. 2: e153. PMID 17096593 DOI: 10.1371/Journal.Pcbi.0020153  0.416
2005 Korkin D, Davis FP, Sali A. Localization of protein-binding sites within families of proteins. Protein Science : a Publication of the Protein Society. 14: 2350-60. PMID 16081657 DOI: 10.1110/Ps.051571905  0.349
2004 Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Current Opinion in Structural Biology. 14: 313-24. PMID 15193311 DOI: 10.1016/J.Sbi.2004.04.006  0.402
2002 Korkin D, Goldfarb L. Multiple genome rearrangement: a general approach via the evolutionary genome graph. Bioinformatics (Oxford, England). 18: S303-11. PMID 12169560  0.451
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