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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