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Dariusz Plewczynski - Publications

Affiliations: 
Interdisciplinary Centre for Mathematical and Computational Modeling University of Warsaw, Poland 
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59 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
2020 Halder AK, Bandyopadhyay SS, Chatterjee P, Nasipuri M, Plewczynski D, Basu S. JUPPI: A multi-level feature based method for PPI prediction and a refined strategy for performance assessment. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32750875 DOI: 10.1109/Tcbb.2020.3004970  0.341
2020 Dawson W, Lazniewski M, Plewczynski D. Free energy-based model of CTCF-mediated chromatin looping in the human genome. Methods (San Diego, Calif.). PMID 32645447 DOI: 10.1016/J.Ymeth.2020.05.025  0.357
2020 Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D. 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. Nucleic Acids Research. PMID 32442297 DOI: 10.1093/Nar/Gkaa388  0.336
2020 Xu H, Zhang S, Yi X, Plewczynski D, Li MJ. Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction. Computational and Structural Biotechnology Journal. 18: 558-570. PMID 32226593 DOI: 10.1016/J.Csbj.2020.02.013  0.305
2019 Kadlof M, Rozycka J, Plewczynski D. Spring Model - chromatin modeling tool based on OpenMM. Methods. PMID 31790732 DOI: 10.1016/J.Ymeth.2019.11.014  0.342
2019 Halder AK, Denkiewicz M, Sengupta K, Basu S, Plewczynski D. Aggregated Network Centrality Shows Non-Random Structure of Genomic and Proteomic Networks. Methods (San Diego, Calif.). PMID 31740366 DOI: 10.1016/J.Ymeth.2019.11.006  0.306
2019 Saha S, Chatterjee P, Basu S, Nasipuri M, Plewczynski D. FunPred 3.0: improved protein function prediction using protein interaction network. Peerj. 7: e6830. PMID 31198622 DOI: 10.7717/Peerj.6830  0.381
2019 Bkhetan ZA, Kadlof M, Kraft A, Plewczynski D. Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells. Methods. 166: 83-90. PMID 30853548 DOI: 10.1016/J.Ymeth.2019.03.002  0.368
2019 Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, et al. Disentangling the complexity of low complexity proteins. Briefings in Bioinformatics. PMID 30698641 DOI: 10.1093/Bib/Bbz007  0.348
2018 Malkowska M, Zubek J, Plewczynski D, Wyrwicz LS. ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. Peerj. 6. PMID 30519505 DOI: 10.7717/Peerj.5742  0.348
2018 Lazniewski M, Dawson WK, Rusek AM, Plewczynski D. One protein to rule them all: the role of CCCTC-binding factor in shaping Human genome in health and disease. Seminars in Cell & Developmental Biology. PMID 30096365 DOI: 10.1016/J.Semcdb.2018.08.003  0.331
2018 Halder AK, Chatterjee P, Nasipuri M, Plewczynski D, Basu S. 3gClust: Human Protein Cluster Analysis. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29993556 DOI: 10.1109/Tcbb.2018.2840996  0.324
2018 Bkhetan ZA, Plewczynski D. Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. Scientific Reports. 8: 5217-5217. PMID 29581440 DOI: 10.1038/S41598-018-23276-8  0.335
2017 Tatjewski M, Kierczak M, Plewczynski D. Predicting Post-Translational Modifications from Local Sequence Fragments Using Machine Learning Algorithms: Overview and Best Practices. Methods of Molecular Biology. 1484: 275-300. PMID 27787833 DOI: 10.1007/978-1-4939-6406-2_19  0.355
2016 Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D. An integrated 3-dimensional genome modeling engine for data-driven simulation of spatial genome organization. Genome Research. PMID 27789526 DOI: 10.1101/Gr.205062.116  0.334
2016 Mazzocco G, Lazniewski M, Migdał P, Szczepińska T, Radomski JP, Plewczynski D. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale Database. 2016. PMID 27694207 DOI: 10.1093/Database/Baw130  0.327
2016 Szalaj P, Michalski PJ, Wróblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczynski D. 3D-GNOME: an integrated web service for structural modeling of the 3D genome. Nucleic Acids Research. PMID 27185892 DOI: 10.1093/Nar/Gkw437  0.313
2016 Chatterjee P, Basu S, Zubek J, Kundu M, Nasipuri M, Plewczynski D. PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach. Journal of Molecular Modeling. 22: 72. PMID 26969678 DOI: 10.1007/S00894-016-2933-0  0.407
2016 Tatjewski M, Gruca A, Plewczynski D, Grynberg M. The proline-rich region of glyceraldehyde-3-phosphate dehydrogenase from human sperm may bind SH3 domains, as revealed by a bioinformatic study of low-complexity protein segments. Molecular Reproduction and Development. 83: 144-148. PMID 26660717 DOI: 10.1002/Mrd.22606  0.327
2016 Srivastava A, Mazzocco G, Kel A, Wyrwicz LS, Plewczynski D. Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods Molecular Biosystems. 12: 778-785. DOI: 10.1039/C5Mb00672D  0.408
2015 Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, ... ... Plewczynski D, et al. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell. 163: 1611-27. PMID 26686651 DOI: 10.1016/J.Cell.2015.11.024  0.327
2015 Kazakiewicz D, Karr JR, Langner KM, Plewczynski D. A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. Computational Biology and Chemistry. PMID 26271684 DOI: 10.1016/J.Compbiolchem.2015.07.007  0.319
2015 Zubek J, Tatjewski M, Boniecki A, Mnich M, Basu S, Plewczynski D. Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae. Peerj. 3: e1041. PMID 26157620 DOI: 10.7717/Peerj.1041  0.41
2015 Saha I, Rak B, Bhowmick SS, Maulik U, Bhattacharjee D, Koch U, Lazniewski M, Plewczynski D. Binding Activity Prediction of Cyclin-Dependent Inhibitors. Journal of Chemical Information and Modeling. PMID 26079845 DOI: 10.1021/Ci500633C  0.328
2015 Lin H, Chen W, Anandakrishnan R, Plewczynski D. Application of machine learning method in genomics and proteomics. Thescientificworldjournal. 2015: 914780. PMID 25961076 DOI: 10.1155/2015/914780  0.413
2014 Saha I, Zubek J, Klingström T, Forsberg S, Wikander J, Kierczak M, Maulik U, Plewczynski D. Ensemble learning prediction of protein-protein interactions using proteins functional annotations. Molecular Biosystems. 10: 820-30. PMID 24469380 DOI: 10.1039/C3Mb70486F  0.403
2014 Plewczynski D, Philips A, Von Grotthuss M, Rychlewski L, Ginalski K. HarmonyDOCK: the structural analysis of poses in protein-ligand docking. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 247-56. PMID 21091053 DOI: 10.1089/Cmb.2009.0111  0.354
2014 Bieniasz-Krzywiec Ł, Cytowski M, Rychlewski LJ, Plewczyński D. 3D-Hit: fast structural comparison of proteins on multicore architectures Optimization Letters. 8: 1783-1794. DOI: 10.1007/S11590-013-0697-3  0.371
2013 Sriwastava BK, Basu S, Maulik U, Plewczynski D. PPIcons: identification of protein-protein interaction sites in selected organisms. Journal of Molecular Modeling. 19: 4059-70. PMID 23729008 DOI: 10.1007/S00894-013-1886-9  0.374
2012 Plewczynski D, Basu S, Saha I. AMS 4.0: consensus prediction of post-translational modifications in protein sequences. Amino Acids. 43: 573-82. PMID 22555647 DOI: 10.1007/S00726-012-1290-2  0.383
2011 Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D. PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines. Journal of Molecular Modeling. 17: 2191-201. PMID 21594694 DOI: 10.1007/S00894-011-1102-8  0.385
2011 Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D. PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables. Cellular & Molecular Biology Letters. 16: 264-78. PMID 21442443 DOI: 10.2478/S11658-011-0008-X  0.39
2011 Plewczynski D, Klingström T. GIDMP: good protein-protein interaction data metamining practice. Cellular & Molecular Biology Letters. 16: 258-63. PMID 21394448 DOI: 10.2478/S11658-011-0004-1  0.316
2011 Plewczynski D. Brainstorming: weighted voting prediction of inhibitors for protein targets. Journal of Molecular Modeling. 17: 2133-41. PMID 20857153 DOI: 10.1007/S00894-010-0854-X  0.365
2011 Klingström T, Plewczynski D. Protein-protein interaction and pathway databases, a graphical review. Briefings in Bioinformatics. 12: 702-13. PMID 20851835 DOI: 10.1093/Bib/Bbq064  0.33
2011 Plewczynski D, ?a?niewski M, von Grotthuss M, Rychlewski L, Ginalski K. VoteDock: consensus docking method for prediction of protein-ligand interactions. Journal of Computational Chemistry. 32: 568-81. PMID 20812324 DOI: 10.1002/Jcc.21642  0.378
2011 Plewczynski D, ?a?niewski M, Augustyniak R, Ginalski K. Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. Journal of Computational Chemistry. 32: 742-55. PMID 20812323 DOI: 10.1002/Jcc.21643  0.336
2010 Basu S, Plewczynski D. AMS 3.0: prediction of post-translational modifications. Bmc Bioinformatics. 11: 210. PMID 20423529 DOI: 10.1186/1471-2105-11-210  0.355
2009 Plewczynski D, von Grotthuss M, Rychlewski L, Ginalski K. Virtual high throughput screening using combined random forest and flexible docking. Combinatorial Chemistry & High Throughput Screening. 12: 484-9. PMID 19519327 DOI: 10.2174/138620709788489000  0.341
2009 Plewczynski D, Spieser SA, Koch U. Performance of machine learning methods for ligand-based virtual screening. Combinatorial Chemistry & High Throughput Screening. 12: 358-68. PMID 19442065 DOI: 10.2174/138620709788167962  0.306
2009 Plewczynski D. kNNsim: k-nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules. Journal of Molecular Modeling. 15: 591-6. PMID 18663491 DOI: 10.1007/S00894-008-0349-1  0.338
2009 Plewczynski D, Rychlewski L. Meta-basic estimates the size of druggable human genome. Journal of Molecular Modeling. 15: 695-9. PMID 18663489 DOI: 10.1007/S00894-008-0353-5  0.375
2008 von Grotthuss M, Plewczynski D, Vriend G, Rychlewski L. 3D-Fun: predicting enzyme function from structure. Nucleic Acids Research. 36: W303-7. PMID 18515349 DOI: 10.1093/Nar/Gkn308  0.361
2008 Plewczynski D, Slabinski L, Ginalski K, Rychlewski L. Prediction of signal peptides in protein sequences by neural networks. Acta Biochimica Polonica. 55: 261-7. PMID 18506221 DOI: 10.18388/Abp.2008_3073  0.322
2008 Plewczynski D, Tkacz A, Wyrwicz LS, Rychlewski L, Ginalski K. AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update. Journal of Molecular Modeling. 14: 69-76. PMID 17994256 DOI: 10.1007/S00894-007-0250-3  0.378
2007 Plewczynski D, Hoffmann M, von Grotthuss M, Ginalski K, Rychewski L. In silico prediction of SARS protease inhibitors by virtual high throughput screening. Chemical Biology & Drug Design. 69: 269-79. PMID 17461975 DOI: 10.1111/J.1747-0285.2007.00475.X  0.33
2007 Plewczynski D, von Grotthuss M, Spieser SA, Rychlewski L, Wyrwicz LS, Ginalski K, Koch U. Target specific compound identification using a support vector machine. Combinatorial Chemistry & High Throughput Screening. 10: 189-96. PMID 17346118 DOI: 10.2174/138620707780126705  0.323
2007 Wyrwicz LS, Koczyk G, Rychlewski L, Plewczynski D. ProteinSplit : splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics Journal of Physics: Condensed Matter. 19: 285222. DOI: 10.1088/0953-8984/19/28/285222  0.395
2007 Plewczynski D, Hoffmann M, Von Grotthuss M, Knizewski L, Rychewski L, Eitner K, Ginalski K. Modelling of potentially promising SARS protease inhibitors Journal of Physics Condensed Matter. 19. DOI: 10.1088/0953-8984/19/28/285207  0.345
2007 Plewczynski D, Tkacz A. AutoMotif Server: a computational protocol for identification of post-translational modifications in protein sequences Nature Protocols. 2. DOI: 10.1038/Nprot.2007.183  0.315
2006 Holm L, Kääriäinen S, Wilton C, Plewczynski D. Using Dali for structural comparison of proteins. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 5.5. PMID 18428766 DOI: 10.1002/0471250953.Bi0505S14  0.359
2006 Plewczynski D, Spieser SA, Koch U. Assessing different classification methods for virtual screening. Journal of Chemical Information and Modeling. 46: 1098-106. PMID 16711730 DOI: 10.1021/Ci050519K  0.344
2006 von Grotthuss M, Plewczynski D, Ginalski K, Rychlewski L, Shakhnovich EI. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. Bmc Bioinformatics. 7: 53. PMID 16460560 DOI: 10.1186/1471-2105-7-53  0.379
2006 Plewczynski D, Tkacz A, Wyrwicz LS, Godzik A, Kloczkowski A, Rychlewski L. Support-vector-machine classification of linear functional motifs in proteins. Journal of Molecular Modeling. 12: 453-61. PMID 16341901 DOI: 10.1007/S00894-005-0070-2  0.387
2005 Plewczynski D, Jaroszewski L, Godzik A, Kloczkowski A, Rychlewski L. Molecular modeling of phosphorylation sites in proteins using a database of local structure segments. Journal of Molecular Modeling. 11: 431-8. PMID 16094535 DOI: 10.1007/S00894-005-0235-Z  0.373
2005 Plewczynski D, Tkacz A, Wyrwicz LS, Rychlewski L. AutoMotif server: prediction of single residue post-translational modifications in proteins. Bioinformatics (Oxford, England). 21: 2525-7. PMID 15728119 DOI: 10.1093/Bioinformatics/Bti333  0.377
2004 Plewczynski D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A. Integrated web service for improving alignment quality based on segments comparison. Bmc Bioinformatics. 5: 98. PMID 15271224 DOI: 10.1186/1471-2105-5-98  0.396
2004 Plewczynski D, Pas J, Von Grotthuss M, Rychlewski L. Comparison of proteins based on segments structural similarity. Acta Biochimica Polonica. 51: 161-72. PMID 15094837 DOI: 10.18388/Abp.2004_3608  0.384
2003 Plewczynski D, Rychlewski L. Ab Initio server prototype for prediction of phosphorylation sites in proteins Computational Methods in Science and Technology. 9: 93-100. DOI: 10.12921/Cmst.2003.09.01.93-100  0.301
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