Dmitry Korkin, Ph.D. - Publications

Affiliations: 
2003 University of New Brunswick (Canada) 
Area:
Computer Science

37 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
2016 Williams M, Hoffman MD, Daniel JJ, Madren SM, Dhroso A, Korkin D, Givan SA, Jacobson SC, Brown PJ. Short-stalked Prosthecomicrobium hirschii cells have a Caulobacter-like cell cycle. Journal of Bacteriology. PMID 26833409 DOI: 10.1128/JB.00896-15  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2014 Chen Z, Shin D, Chen S, Mikhail K, Hadass O, Tomlison BN, Korkin D, Shyu CR, Cui J, Anthony DC, Gu Z. Histological quantitation of brain injury using whole slide imaging: a pilot validation study in mice. Plos One. 9: e92133. PMID 24637518 DOI: 10.1371/journal.pone.0092133  0.96
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  0.96
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  0.96
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  0.96
2012 Liu S, Kandoth PK, Warren SD, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale PS, Hill J, Baum TJ, Cianzio S, Whitham SA, Korkin D, et al. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature. 492: 256-60. PMID 23235880 DOI: 10.1038/nature11651  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2011 Wang Q, Korkin D, Shang Y. A fast multiple longest common subsequence (MLCS) algorithm Ieee Transactions On Knowledge and Data Engineering. 23: 321-334. DOI: 10.1109/TKDE.2010.123  0.96
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: 10.1111/j.1469-8137.2010.03300  0.96
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  0.96
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  0.96
2010 Zhao N, Pang B, Shyu CR, Korkin D. An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches Proceedings - 2010 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2010. 185-189. DOI: 10.1109/BIBM.2010.5706560  0.96
2010 Wang Q, Pan M, Shang Y, Korkin D. A fast heuristic search algorithm for finding the longest common subsequence of multiple strings Proceedings of the National Conference On Artificial Intelligence. 3: 1287-1292.  0.96
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  0.96
2009 Ahuja N, Korkin D, Chaba R, Cezairliyan BO, Sauer RT, Kim KK, Gross CA. Analyzing the interaction of RseA and RseB, the two negative regulators of the sigmaE envelope stress response, using a combined bioinformatic and experimental strategy. The Journal of Biological Chemistry. 284: 5403-13. PMID 19103591 DOI: 10.1074/jbc.M806012200  0.96
2009 Wang Q, Korkin D, Shang Y. Efficient dominant point algorithms for the multiple longest common subsequence (MLCS) problem Ijcai International Joint Conference On Artificial Intelligence. 1494-1499.  0.96
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  0.96
2008 Korkin D, Wang Q, Shang Y. An efficient parallel algorithm for the multiple longest common subsequence (MLCS) problem Proceedings of the International Conference On Parallel Processing. 354-363. DOI: 10.1109/ICPP.2008.79  0.96
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  0.96
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  0.96
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  0.96
2002 Korkin D, Goldfarb L. Multiple genome rearrangement: a general approach via the evolutionary genome graph. Bioinformatics (Oxford, England). 18: S303-11. PMID 12169560  0.96
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