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ORCIDDariusz Plewczynski
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2020 – today
- 2023
[j46]Alexander Myronov
, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski:
BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. Bioinform. 39(8) (2023)- [j45]Michal Wlasnowolski, Pawel Z. Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski:
cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling. Bioinform. 39(10) (2023) - [j44]Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski:
3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome. Nucleic Acids Res. 51(W1): 5-10 (2023) - [j43]Hang Xu, Xianfu Yi, Xutong Fan, Chengyue Wu, Wei Wang, Xinlei Chu, Shijie Zhang, Xiaobao Dong, Zhao Wang, Jianhua Wang, Yao Zhou, Ke Zhao, Hongcheng Yao, Nan Zheng, Junwen Wang, Yupeng Chen, Dariusz Plewczynski, Pak Chung Sham, Kexin Chen, Dandan Huang, Mulin Jun Li:
Inferring CTCF-binding patterns and anchored loops across human tissues and cell types. Patterns 4(8): 100798 (2023) - [j42]Mateusz Chilinski, Anup Kumar Halder, Dariusz Plewczynski:
Prediction of chromatin looping using deep hybrid learning (DHL). Quant. Biol. 11(2): 155-162 (2023) - [c28]Anup Kumar Halder, Abhishek Agarwal, Sevastianos Korsak, Karolina Jodkowska, Dariusz Plewczynski:
ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model. PReMI 2023: 871-878 - 2022
- [j41]Nimisha Ghosh, Indrajit Saha, Dariusz Plewczynski:
Genome-Wide Analysis to Identify Palindromes, Mirror and Inverted Repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1. IEEE Access 10: 23708-23715 (2022) - [j40]Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa Jane Fullwood, Pengfei Yin, Guangyu Huang, Dariusz Plewczynski, Jixian Zhai, Ziwei Dai, Wei Chen, Meizhen Zheng:
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification. Briefings Bioinform. 23(6) (2022) - [j39]Mateusz Chilinski, Dariusz Plewczynski:
ConsensuSV - from the whole-genome sequencing data to the complete variant list. Bioinform. 38(24): 5440-5442 (2022) - [j38]Polina Belokopytova, Emil Viesná, Mateusz Chilinski, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea Maria Chiariello, Vladimir B. Teif, Dariusz Plewczynski, Bin Zhang, Daniel Jost, Veniamin Fishman:
3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Res. 50(W1): 4-12 (2022) - [j37]Nirmal Das, Ewa Baczynska, Monika Bijata, Blazej Ruszczycki, Andre Zeug, Dariusz Plewczynski, Punam Kumar Saha, Evgeni Ponimaskin, Jakub Wlodarczyk, Subhadip Basu:
3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. Neuroinformatics 20(3): 679-698 (2022) - [j36]Nirmal Das, Ewa Baczynska, Monika Bijata, Blazej Ruszczycki, Andre Zeug, Dariusz Plewczynski, Punam Kumar Saha, Evgeni Ponimaskin, Jakub Wlodarczyk, Subhadip Basu:
Correction to: 3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. Neuroinformatics 20(3): 699 (2022) - [j35]Anup Kumar Halder, Soumyendu Sekhar Bandyopadhyay, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu:
JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 531-542 (2022) - 2021
- [j34]Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski:
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. BMC Bioinform. 22(1): 72 (2021) - 2020
- [j33]Pablo Mier, Lisanna Paladin, Stella Tamana, Sophia Petrosian, Borbála Hajdu-Soltész, Annika Urbanek, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg, Pau Bernadó, Zoltán Gáspári, Christos A. Ouzounis, Vasilis J. Promponas, Andrey V. Kajava, John M. Hancock, Silvio C. E. Tosatto, Zsuzsanna Dosztányi, Miguel A. Andrade-Navarro:
Disentangling the complexity of low complexity proteins. Briefings Bioinform. 21(2): 458-472 (2020) - [j32]Paulina Urban, Vahid Rezaei Tabar, Michal Denkiewicz, Grzegorz Bokota, Nirmal Das, Subhadip Basu, Dariusz Plewczynski:
The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process. J. Comput. Biol. 27(9): 1471-1485 (2020) - [j31]Michal Wlasnowolski, Michal Sadowski, Tymon Czarnota, Karolina Jodkowska, Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski:
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 Res. 48(Webserver-Issue): W170-W176 (2020)
2010 – 2019
- 2019
- [j30]Paulina Urban, Vahid Rezaei, Grzegorz Bokota, Michal Denkiewicz, Subhadip Basu, Dariusz Plewczynski:
Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation. J. Comput. Biol. 26(4): 322-335 (2019) - [j29]Denis Kazakiewicz, Jürgen Claesen, Katarzyna Górczak, Dariusz Plewczynski, Tomasz Burzykowski:
A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data. J. Comput. Biol. 26(12): 1339-1348 (2019) - [j28]Vahid Rezaei Tabar, Hamid Zareifard, Selva Salimi, Dariusz Plewczynski:
An empirical Bayes approach for learning directed acyclic graph using MCMC algorithm. Stat. Anal. Data Min. 12(5): 394-403 (2019) - [j27]Anup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu:
3gClust: Human Protein Cluster Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 16(6): 1773-1784 (2019) - [c27]Jnanendra Prasad Sarkar, Indrajit Saha, Somnath Rakshit, Monalisa Pal, Michal Wlasnowolski, Anasua Sarkar, Ujjwal Maulik, Dariusz Plewczynski:
A new evolutionary rough fuzzy integrated machine learning technique for microRNA selection using next-generation sequencing data of breast cancer. GECCO (Companion) 2019: 1846-1854 - [c26]Somnath Rakshit, Indrajit Saha, Michal Wlasnowolski, Ujjwal Maulik, Dariusz Plewczynski:
Deep Learning for Detection and Localization of Thoracic Diseases Using Chest X-Ray Imagery. ICAISC (2) 2019: 271-282 - [c25]Indrajit Saha, Somnath Rakshit, Michal Denkiewicz, Jnanendra Prasad Sarkar, Debasree Maity, Ujjwal Maulik, Dariusz Plewczynski:
Survival Analysis with the Integration of RNA-Seq and Clinical Data to Identify Breast Cancer Subtype Specific Genes. PReMI (2) 2019: 139-146 - [c24]Indrajit Saha, Somnath Rakshit, Michal Wlasnowolski, Dariusz Plewczynski:
Identification of Epigenetic Biomarkers with the use of Gene Expression and DNA Methylation for Breast Cancer Subtypes. TENCON 2019: 417-422 - [r1]Wayne K. Dawson, Michal Lazniewski, Dariusz Plewczynski:
Chromatin: A Semi-Structured Polymer. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 288-307 - 2018
- [c23]Somnath Rakshit, Indrajit Saha, Subha Shankar Chakraborty, Dariusz Plewczynski:
Deep Learning for Integrated Analysis of Breast Cancer Subtype Specific Multi-omics Data. TENCON 2018: 1917-1922 - 2017
- [c22]Ziad Al Bkhetan, Dariusz Plewczynski:
Multi-levels 3D Chromatin Interactions Prediction Using Epigenomic Profiles. ISMIS 2017: 19-28 - 2016
- [j26]Giovanni Mazzocco, Michal Lazniewski, Piotr Migdal, Teresa Szczepinska, Jan P. Radomski, Dariusz Plewczynski:
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. Database J. Biol. Databases Curation 2016 (2016) - [j25]Subhadip Basu, Dariusz Plewczynski, Satadal Saha, Matylda Roszkowska, Marta Magnowska, Ewa Baczynska, Jakub Wlodarczyk:
2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity. Bioinform. 32(16): 2490-2498 (2016) - [j24]Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob B. Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan F. DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman, Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau, Nagarajan Raju, Sonia P. Chothani, C. Ramakrishnan, Masakazu Sekijima, M. Michael Gromiha, Paddy J. Slator, Nigel J. Burroughs, Przemyslaw Szalaj, Zhonghui Tang, Paul J. Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski, Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens, Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic:
Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. BMC Bioinform. 17(S-3) (2016) - [j23]Grzegorz Bokota, Marta Magnowska, Tomasz Kusmierczyk, Michal Lukasik, Matylda Roszkowska, Dariusz Plewczynski:
Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis. Frontiers Comput. Neurosci. 10: 140 (2016) - [j22]Przemyslaw Szalaj, Paul J. Michalski, Przemyslaw Wróblewski, Zhonghui Tang, Michal Kadlof, Giovanni Mazzocco, Yijun Ruan, Dariusz Plewczynski:
3D-GNOME: an integrated web service for structural modeling of the 3D genome. Nucleic Acids Res. 44(Webserver-Issue): W288-W293 (2016) - [j21]Julian Zubek, Dariusz Plewczynski:
Complexity curve: a graphical measure of data complexity and classifier performance. PeerJ Comput. Sci. 2: e76 (2016) - [j20]Jan Kostrzewa, Giovanni Mazzocco, Dariusz Plewczynski:
Divide and Conquer Ensemble Method for Time Series Forecasting. Trans. Comput. Collect. Intell. 24: 134-152 (2016) - [i3]Julian Zubek, Dariusz Plewczynski:
Complexity curve: a graphical measure of data complexity and classifier performance. PeerJ Prepr. 4: e2095 (2016) - 2015
- [j19]Denis Kazakiewicz, Jonathan R. Karr, Karol M. Langner, Dariusz Plewczynski:
A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. Comput. Biol. Chem. 59: 91-97 (2015) - [j18]Indrajit Saha, Benedykt Rak, Shib Sankar Bhowmick, Ujjwal Maulik, Debotosh Bhattacharjee, Uwe Koch, Michal Lazniewski, Dariusz Plewczynski:
Binding Activity Prediction of Cyclin-Dependent Inhibitors. J. Chem. Inf. Model. 55(7): 1469-1482 (2015) - [c21]Piyali Chatterjee, Subhadip Basu, Julian Zubek, Mahantapas Kundu, Mita Nasipuri, Dariusz Plewczynski:
PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier. PReMI 2015: 441-450 - [c20]Giovanni Mazzocco, Shib Sankar Bhowmick, Indrajit Saha, Ujjwal Maulik, Debotosh Bhattacharjee, Dariusz Plewczynski:
MaER: A New Ensemble Based Multiclass Classifier for Binding Activity Prediction of HLA Class II Proteins. PReMI 2015: 462-471 - [c19]Indrajit Saha, Shib Sankar Bhowmick, Filippo Geraci, Marco Pellegrini, Debotosh Bhattacharjee, Ujjwal Maulik, Dariusz Plewczynski:
Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer. SEMCCO 2015: 116-127 - 2014
- [j17]Dariusz Plewczynski, Anna Philips, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski:
HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking. J. Comput. Biol. 21(3): 247-256 (2014) - [j16]Lukasz Bieniasz-Krzywiec, Maciej Cytowski, Leszek Rychlewski, Dariusz Plewczynski:
3D-Hit: fast structural comparison of proteins on multicore architectures. Optim. Lett. 8(5): 1783-1794 (2014) - [c18]Shib Sankar Bhowmick, Indrajit Saha, Giovanni Mazzocco, Ujjwal Maulik, Luís Rato, Debotosh Bhattacharjee, Dariusz Plewczynski:
Application of RotaSVM for HLA Class II Protein-Peptide Interaction Prediction. BIOINFORMATICS 2014: 178-185 - [p2]Dariusz Plewczynski, Subhadip Basu:
A Meta-learning Approach for Protein Function Prediction. Advanced Computational Approaches to Biomedical Engineering 2014: 113-128 - 2013
- [c17]Michal Denkiewicz, Joanna Raczaszek-Leonardi, Piotr Migdal, Dariusz Plewczynski:
Information-Sharing in Three Interacting Minds Solving a Simple Perceptual Task. CogSci 2013 - [c16]Indrajit Saha, Tomas Klingström, Simon Forsberg, Johan Wikander, Julian Zubek, Marcin Kierczak, Dariusz Plewczynski:
Evaluation of Machine Learning Algorithms on Protein-Protein Interactions. ICMMI 2013: 211-218 - [c15]Dariusz Plewczynski, Michal Lukasik, Konrad Kurdej, Julian Zubek, Franciszek Rakowski, Joanna Raczaszek-Leonardi:
Generic Framework for Simulation of Cognitive Systems: A Case Study of Color Category Boundaries. ICMMI 2013: 385-393 - [c14]Indrajit Saha, Tomas Klingström, Simon Forsberg, Johan Wikander, Julian Zubek, Marcin Kierczak, Dariusz Plewczynski:
Erratum: Evaluation of Machine Learning Algorithms on Protein-Protein Interactions. ICMMI 2013 - [c13]Indrajit Saha, Ujjwal Maulik, Michal Lukasik, Dariusz Plewczynski:
Multiobjective Differential Evolution: A Comparative Study on Benchmark Problems. ICMMI 2013: 529-536 - [c12]Brijesh Kumar Sriwastava, Subhadip Basu, Ujjwal Maulik, Dariusz Plewczynski:
A Consensus Approach for Identification of Protein-Protein Interaction Sites in Homo Sapiens. PReMI 2013: 674-679 - 2012
- [j15]Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay:
Improved differential evolution for microarray analysis. Int. J. Data Min. Bioinform. 6(1): 86-103 (2012) - [j14]Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski:
SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation. IEEE Geosci. Remote. Sens. Lett. 9(1): 52-55 (2012) - [c11]Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski:
Application of High Quality Amino Acid Indices to AMS 3.0: A Update Note. BIC-TA (1) 2012: 217-225 - [c10]Debasree Maity, Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski:
Soft Computing Approach for VLSI Mincut Partitioning: The State of the Arts. SocProS 2012: 895-903 - 2011
- [j13]Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski:
A new multi-objective technique for differential fuzzy clustering. Appl. Soft Comput. 11(2): 2765-2776 (2011) - [j12]Tomas Klingström, Dariusz Plewczynski:
Protein-protein interaction and pathway databases, a graphical review. Briefings Bioinform. 12(6): 702-713 (2011) - [j11]Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski:
Improvement of new automatic differential fuzzy clustering using SVM classifier for microarray analysis. Expert Syst. Appl. 38(12): 15122-15133 (2011) - [j10]Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski:
Unsupervised and Supervised Learning Approaches Together for Microarray Analysis. Fundam. Informaticae 106(1): 45-73 (2011) - [j9]Dariusz Plewczynski, Michal Lazniewski, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski:
VoteDock: Consensus docking method for prediction of protein-ligand interactions. J. Comput. Chem. 32(4): 568-581 (2011) - [j8]Dariusz Plewczynski, Michal Lazniewski, Rafal Augustyniak, Krzysztof Ginalski:
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J. Comput. Chem. 32(4): 742-755 (2011) - [j7]Marcin Nowosielski, Marcin Hoffmann, Lucjan Stanislaw Wyrwicz, Piotr Stepniak, Dariusz Plewczynski, Michal Lazniewski, Krzysztof Ginalski, Leszek Rychlewski:
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine. J. Chem. Inf. Model. 51(2): 455-462 (2011) - [c9]Dariusz Plewczynski:
Brainstorming - Agent based Meta-learning Approach. ICAART (2) 2011: 487-490 - [c8]Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski:
Multiobjective Differential Crisp Clustering for Evaluation of Clusters Dynamically. ICMMI 2011: 307-313 - [c7]Dariusz Plewczynski:
Landau Theory of Meta-learning. SIIS 2011: 142-153 - [c6]Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski:
PMAFC: A New Probabilistic Memetic Algorithm Based Fuzzy Clustering. ISMIS 2011: 602-611 - [p1]Dariusz Plewczynski:
Cognitive architectures in multi-agent systems. Biology, Computation and Linguistics 2011: 237-245 - [i2]Piotr Migdal, Michal Denkiewicz, Joanna Raczaszek-Leonardi, Dariusz Plewczynski:
Information-sharing and aggregation models for interacting minds. CoRR abs/1109.2044 (2011) - 2010
- [j6]Subhadip Basu, Dariusz Plewczynski:
AMS 3.0: prediction of post-translational modifications. BMC Bioinform. 11: 210 (2010) - [c5]Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski:
Real-coded differential crisp clustering for MRI brain image segmentation. IEEE Congress on Evolutionary Computation 2010: 1-8 - [c4]Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay:
Improvement of Differential Crisp Clustering using ANN Classifier for Unsupervised Pixel Classification of Satellite Image. ICEIS (2) 2010: 21-29 - [c3]Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay:
Consensus Multiobjective Differential Crisp Clustering for Categorical Data Analysis. RSCTC 2010: 30-39 - [c2]Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski:
Cancer Classification using SVM-boosted Multiobjective Differential Fuzzy Clustering. STAIRS 2010: 290-302 - [i1]Dariusz Plewczynski:
Landau Theory of Adaptive Integration in Computational Intelligence. CoRR abs/1006.1828 (2010)
2000 – 2009
- 2008
- [j5]Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski:
3D-Fun: predicting enzyme function from structure. Nucleic Acids Res. 36(Web-Server-Issue): 303-307 (2008) - [c1]Dariusz Plewczynski:
TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections. BIOTECHNO 2008: 59-63 - 2006
- [j4]Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I. Shakhnovich:
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinform. 7: 53 (2006) - [j3]Dariusz Plewczynski, Stéphane A. H. Spieser, Uwe Koch:
Assessing Different Classification Methods for Virtual Screening. J. Chem. Inf. Model. 46(3): 1098-1106 (2006) - 2005
- [j2]Dariusz Plewczynski, Adrian Tkacz, Lucjan Stanislaw Wyrwicz, Leszek Rychlewski:
AutoMotif server: prediction of single residue post-translational modifications in proteins. Bioinform. 21(10): 2525-2527 (2005) - 2004
- [j1]Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik:
Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. 5: 98 (2004)
Coauthor Index
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