Integrated web service for improving alignment quality based on segments comparison. - Dariusz Plewczynski; Leszek Rychlewski; Yuzhen Ye; Lukasz Jaroszewski; Adam Godzik (BMC Bioinform., 2004)

AutoMotif server: prediction of single residue post-translational modifications in proteins. - Dariusz Plewczynski; Adrian Tkacz; Lucjan Stanislaw Wyrwicz; Leszek Rychlewski (Bioinform., 2005)

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. - Marcin von Grotthuss; Dariusz Plewczynski; Krzysztof Ginalski; Leszek Rychlewski; Eugene I. Shakhnovich (BMC Bioinform., 2006)

Assessing Different Classification Methods for Virtual Screening. - Dariusz Plewczynski; Stéphane A. H. Spieser; Uwe Koch (J. Chem. Inf. Model., 2006)

TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections. - Dariusz Plewczynski (BIOTECHNO, 2008)

3D-Fun: predicting enzyme function from structure. - Marcin von Grotthuss; Dariusz Plewczynski; Gert Vriend; Leszek Rychlewski (Nucleic Acids Res., 2008)

Real-coded differential crisp clustering for MRI brain image segmentation. - Indrajit Saha; Ujjwal Maulik; Sanghamitra Bandyopadhyay; Dariusz Plewczynski (IEEE Congress on Evolutionary Computation, 2010)

Improvement of Differential Crisp Clustering using ANN Classifier for Unsupervised Pixel Classification of Satellite Image. - Indrajit Saha; Dariusz Plewczynski; Ujjwal Maulik; Sanghamitra Bandyopadhyay (ICEIS (2), 2010)

Consensus Multiobjective Differential Crisp Clustering for Categorical Data Analysis. - Indrajit Saha; Dariusz Plewczynski; Ujjwal Maulik; Sanghamitra Bandyopadhyay (RSCTC, 2010)

Cancer Classification using SVM-boosted Multiobjective Differential Fuzzy Clustering. - Indrajit Saha; Ujjwal Maulik; Sanghamitra Bandyopadhyay; Dariusz Plewczynski (STAIRS, 2010)

AMS 3.0: prediction of post-translational modifications. - Subhadip Basu; Dariusz Plewczynski (BMC Bioinform., 2010)

Landau Theory of Adaptive Integration in Computational Intelligence - Dariusz Plewczynski (CoRR, 2010)

Cognitive architectures in multi-agent systems. - Dariusz Plewczynski (Biology, Computation and Linguistics, 2011)

Brainstorming - Agent based Meta-learning Approach. - Dariusz Plewczynski (ICAART (2), 2011)

Multiobjective Differential Crisp Clustering for Evaluation of Clusters Dynamically. - Indrajit Saha; Ujjwal Maulik; Dariusz Plewczynski (ICMMI, 2011)

Landau Theory of Meta-learning. - Dariusz Plewczynski (SIIS, 2011)

PMAFC: A New Probabilistic Memetic Algorithm Based Fuzzy Clustering. - Indrajit Saha; Ujjwal Maulik; Dariusz Plewczynski (ISMIS, 2011)

A new multi-objective technique for differential fuzzy clustering. - Indrajit Saha; Ujjwal Maulik; Dariusz Plewczynski (Appl. Soft Comput., 2011)

Protein-protein interaction and pathway databases, a graphical review. - Tomas Klingström; Dariusz Plewczynski (Briefings Bioinform., 2011)

Information-sharing and aggregation models for interacting minds - Piotr Migdal; Michal Denkiewicz; Joanna Raczaszek-Leonardi; Dariusz Plewczynski (CoRR, 2011)

Improvement of new automatic differential fuzzy clustering using SVM classifier for microarray analysis. - Indrajit Saha; Ujjwal Maulik; Sanghamitra Bandyopadhyay; Dariusz Plewczynski (Expert Syst. Appl., 2011)

Unsupervised and Supervised Learning Approaches Together for Microarray Analysis. - Indrajit Saha; Ujjwal Maulik; Sanghamitra Bandyopadhyay; Dariusz Plewczynski (Fundam. Informaticae, 2011)

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. - Dariusz Plewczynski; Michal Lazniewski; Rafal Augustyniak; Krzysztof Ginalski (J. Comput. Chem., 2011)

VoteDock: Consensus docking method for prediction of protein-ligand interactions. - Dariusz Plewczynski; Michal Lazniewski; Marcin von Grotthuss; Leszek Rychlewski; Krzysztof Ginalski (J. Comput. Chem., 2011)

Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine. - Marcin Nowosielski; Marcin Hoffmann; Lucjan Stanislaw Wyrwicz; Piotr Stepniak; Dariusz Plewczynski; Michal Lazniewski; Krzysztof Ginalski; Leszek Rychlewski (J. Chem. Inf. Model., 2011)

Application of High Quality Amino Acid Indices to AMS 3.0: A Update Note. - Indrajit Saha; Ujjwal Maulik; Dariusz Plewczynski (BIC-TA (1), 2012)

Soft Computing Approach for VLSI Mincut Partitioning: The State of the Arts. - Debasree Maity; Indrajit Saha; Ujjwal Maulik; Dariusz Plewczynski (SocProS, 2012)

Improved differential evolution for microarray analysis. - Indrajit Saha; Dariusz Plewczynski; Ujjwal Maulik; Sanghamitra Bandyopadhyay (Int. J. Data Min. Bioinform., 2012)

SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation. - Indrajit Saha; Ujjwal Maulik; Sanghamitra Bandyopadhyay; Dariusz Plewczynski (IEEE Geosci. Remote. Sens. Lett., 2012)

Information-Sharing in Three Interacting Minds Solving a Simple Perceptual Task. - Michal Denkiewicz; Joanna Raczaszek-Leonardi; Piotr Migdal; Dariusz Plewczynski (CogSci, 2013)

Generic Framework for Simulation of Cognitive Systems: A Case Study of Color Category Boundaries. - Dariusz Plewczynski; Michal Lukasik; Konrad Kurdej; Julian Zubek; Franciszek Rakowski; Joanna Raczaszek-Leonardi (ICMMI, 2013)

Evaluation of Machine Learning Algorithms on Protein-Protein Interactions. - Indrajit Saha; Tomas Klingström; Simon Forsberg; Johan Wikander; Julian Zubek; Marcin Kierczak; Dariusz Plewczynski (ICMMI, 2013)

Erratum: Evaluation of Machine Learning Algorithms on Protein-Protein Interactions. - Indrajit Saha; Tomas Klingström; Simon Forsberg; Johan Wikander; Julian Zubek; Marcin Kierczak; Dariusz Plewczynski (ICMMI, 2013)

Multiobjective Differential Evolution: A Comparative Study on Benchmark Problems. - Indrajit Saha; Ujjwal Maulik; Michal Lukasik; Dariusz Plewczynski (ICMMI, 2013)

A Consensus Approach for Identification of Protein-Protein Interaction Sites in Homo Sapiens. - Brijesh Kumar Sriwastava; Subhadip Basu; Ujjwal Maulik; Dariusz Plewczynski (PReMI, 2013)

A Meta-learning Approach for Protein Function Prediction. - Dariusz Plewczynski; Subhadip Basu (Advanced Computational Approaches to Biomedical Engineering, 2014)

Application of RotaSVM for HLA Class II Protein-Peptide Interaction Prediction. - Shib Sankar Bhowmick; Indrajit Saha; Giovanni Mazzocco; Ujjwal Maulik; Luís Rato; Debotosh Bhattacharjee; Dariusz Plewczynski (BIOINFORMATICS, 2014)

HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking. - Dariusz Plewczynski; Anna Philips; Marcin von Grotthuss; Leszek Rychlewski; Krzysztof Ginalski (J. Comput. Biol., 2014)

3D-Hit: fast structural comparison of proteins on multicore architectures. - Lukasz Bieniasz-Krzywiec; Maciej Cytowski; Leszek Rychlewski; Dariusz Plewczynski (Optim. Lett., 2014)

PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier. - Piyali Chatterjee; Subhadip Basu; Julian Zubek; Mahantapas Kundu; Mita Nasipuri; Dariusz Plewczynski (PReMI, 2015)

MaER: A New Ensemble Based Multiclass Classifier for Binding Activity Prediction of HLA Class II Proteins. - Giovanni Mazzocco; Shib Sankar Bhowmick; Indrajit Saha; Ujjwal Maulik; Debotosh Bhattacharjee; Dariusz Plewczynski (PReMI, 2015)

Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer. - Indrajit Saha; Shib Sankar Bhowmick; Filippo Geraci; Marco Pellegrini 001; Debotosh Bhattacharjee; Ujjwal Maulik; Dariusz Plewczynski (SEMCCO, 2015)

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. - Denis Kazakiewicz; Jonathan R. Karr; Karol M. Langner; Dariusz Plewczynski (Comput. Biol. Chem., 2015)

Binding Activity Prediction of Cyclin-Dependent Inhibitors. - Indrajit Saha; Benedykt Rak; Shib Sankar Bhowmick; Ujjwal Maulik; Debotosh Bhattacharjee; Uwe Koch; Michal Lazniewski; Dariusz Plewczynski (J. Chem. Inf. Model., 2015)

3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. - Giovanni Mazzocco; Michal Lazniewski; Piotr Migdal; Teresa Szczepinska; Jan P. Radomski; Dariusz Plewczynski (Database J. Biol. Databases Curation, 2016)

2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity. - Subhadip Basu; Dariusz Plewczynski; Satadal Saha; Matylda Roszkowska; Marta Magnowska; Ewa Baczynska; Jakub Wlodarczyk (Bioinform., 2016)

Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis. - Grzegorz Bokota; Marta Magnowska; Tomasz Kusmierczyk; Michal Lukasik; Matylda Roszkowska; Dariusz Plewczynski (Frontiers Comput. Neurosci., 2016)

3D-GNOME: an integrated web service for structural modeling of the 3D genome. - Przemyslaw Szalaj; Paul J. Michalski; Przemyslaw Wróblewski; Zhonghui Tang; Michal Kadlof; Giovanni Mazzocco; Yijun Ruan; Dariusz Plewczynski (Nucleic Acids Res., 2016)

Complexity curve: a graphical measure of data complexity and classifier performance. - Julian Zubek; Dariusz Plewczynski (PeerJ Prepr., 2016)

Divide and Conquer Ensemble Method for Time Series Forecasting. - Jan Kostrzewa; Giovanni Mazzocco; Dariusz Plewczynski (Trans. Comput. Collect. Intell., 2016)

Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. - 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; et al. (BMC Bioinform., 2016)

Multi-levels 3D Chromatin Interactions Prediction Using Epigenomic Profiles. - Ziad Al Bkhetan; Dariusz Plewczynski (ISMIS, 2017)

Deep Learning for Integrated Analysis of Breast Cancer Subtype Specific Multi-omics Data. - Somnath Rakshit; Indrajit Saha; Subha Shankar Chakraborty; Dariusz Plewczynski (TENCON, 2018)

A new evolutionary rough fuzzy integrated machine learning technique for microRNA selection using next-generation sequencing data of breast cancer. - Jnanendra Prasad Sarkar; Indrajit Saha; Somnath Rakshit; Monalisa Pal; Michal Wlasnowolski; Anasua Sarkar; Ujjwal Maulik; Dariusz Plewczynski (GECCO (Companion), 2019)

Deep Learning for Detection and Localization of Thoracic Diseases Using Chest X-Ray Imagery. - Somnath Rakshit; Indrajit Saha; Michal Wlasnowolski; Ujjwal Maulik; Dariusz Plewczynski (ICAISC (2), 2019)

Survival Analysis with the Integration of RNA-Seq and Clinical Data to Identify Breast Cancer Subtype Specific Genes. - Indrajit Saha; Somnath Rakshit; Michal Denkiewicz; Jnanendra Prasad Sarkar; Debasree Maity; Ujjwal Maulik; Dariusz Plewczynski (PReMI (2), 2019)

Identification of Epigenetic Biomarkers with the use of Gene Expression and DNA Methylation for Breast Cancer Subtypes. - Indrajit Saha; Somnath Rakshit; Michal Wlasnowolski; Dariusz Plewczynski (TENCON, 2019)

A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data. - Denis Kazakiewicz; Jürgen Claesen; Katarzyna Górczak; Dariusz Plewczynski; Tomasz Burzykowski (J. Comput. Biol., 2019)

Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation. - Paulina Urban; Vahid Rezaei; Grzegorz Bokota; Michal Denkiewicz; Subhadip Basu; Dariusz Plewczynski (J. Comput. Biol., 2019)

An empirical Bayes approach for learning directed acyclic graph using MCMC algorithm. - Vahid Rezaei Tabar; Hamid Zareifard; Selva Salimi; Dariusz Plewczynski (Stat. Anal. Data Min., 2019)

3gClust: Human Protein Cluster Analysis. - Anup Kumar Halder; Piyali Chatterjee; Mita Nasipuri; Dariusz Plewczynski; Subhadip Basu (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Chromatin: A Semi-Structured Polymer. - Wayne K. Dawson; Michal Lazniewski; Dariusz Plewczynski (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Disentangling the complexity of low complexity proteins. - 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; et al. (Briefings Bioinform., 2020)

The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process. - Paulina Urban; Vahid Rezaei Tabar; Michal Denkiewicz; Grzegorz Bokota; Nirmal Das; Subhadip Basu; Dariusz Plewczynski (J. Comput. Biol., 2020)

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. - Michal Wlasnowolski; Michal Sadowski; Tymon Czarnota; Karolina Jodkowska; Przemyslaw Szalaj; Zhonghui Tang; Yijun Ruan; Dariusz Plewczynski (Nucleic Acids Res., 2020)

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. - Grzegorz Bokota; Jacek Sroka; Subhadip Basu; Nirmal Das; Pawel Trzaskoma; Yana Yushkevich; Agnieszka Grabowska; Adriana Magalska; Dariusz Plewczynski (BMC Bioinform., 2021)

Genome-Wide Analysis to Identify Palindromes, Mirror and Inverted Repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1. - Nimisha Ghosh; Indrajit Saha; Dariusz Plewczynski (IEEE Access, 2022)

MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification. - Simon Zhongyuan Tian; Guoliang Li 002; Duo Ning; Kai Jing; Yewen Xu; Yang Yang; Melissa Jane Fullwood; Pengfei Yin; Guangyu Huang; Dariusz Plewczynski; Jixian Zhai; Ziwei Dai; et al. (Briefings Bioinform., 2022)

3DGenBench: a web-server to benchmark computational models for 3D Genomics. - Polina Belokopytova; Emil Viesná; Mateusz Chilinski; Yifeng Qi; Hossein Salari; Marco Di Stefano; Andrea Esposito 001; Mattia Conte; Andrea Maria Chiariello; Vladimir B. Teif; Dariusz Plewczynski; Bin Zhang; et al. (Nucleic Acids Res., 2022)

3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. - Nirmal Das; Ewa Baczynska; Monika Bijata; Blazej Ruszczycki; Andre Zeug; Dariusz Plewczynski; Punam Kumar Saha; Evgeni Ponimaskin; Jakub Wlodarczyk; Subhadip Basu (Neuroinformatics, 2022)

Correction to: 3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. - Nirmal Das; Ewa Baczynska; Monika Bijata; Blazej Ruszczycki; Andre Zeug; Dariusz Plewczynski; Punam Kumar Saha; Evgeni Ponimaskin; Jakub Wlodarczyk; Subhadip Basu (Neuroinformatics, 2022)

JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment. - Anup Kumar Halder; Soumyendu Sekhar Bandyopadhyay; Piyali Chatterjee; Mita Nasipuri; Dariusz Plewczynski; Subhadip Basu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

ConsensuSV - from the whole-genome sequencing data to the complete variant list. - Mateusz Chilinski; Dariusz Plewczynski (Bioinform., 2022)

ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model. - Anup Kumar Halder; Abhishek Agarwal; Sevastianos Korsak; Karolina Jodkowska; Dariusz Plewczynski (PReMI, 2023)

Prediction of chromatin looping using deep hybrid learning (DHL). - Mateusz Chilinski; Anup Kumar Halder; Dariusz Plewczynski (Quant. Biol., 2023)

3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome. - Michal Wlasnowolski; Michal Kadlof; Kaustav Sengupta; Dariusz Plewczynski (Nucleic Acids Res., 2023)

BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. - Alexander Myronov; Giovanni Mazzocco; Paulina Król; Dariusz Plewczynski (Bioinform., 2023)

Inferring CTCF-binding patterns and anchored loops across human tissues and cell types. - Hang Xu; Xianfu Yi; Xutong Fan; Chengyue Wu; Wei Wang; Xinlei Chu; Shijie Zhang; Xiaobao Dong; Zhao Wang; Jianhua Wang; Yao Zhou; Ke Zhao; et al. (Patterns, 2023)

cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling. - Michal Wlasnowolski; Pawel Z. Grabowski; Damian Roszczyk; Krzysztof Kaczmarski; Dariusz Plewczynski (Bioinform., 2023)

RapidDock: Unlocking Proteome-scale Molecular Docking. - Rafal Powalski; Bazyli Klockiewicz; Maciej Jaskowski; Bartosz Topolski; Pawel Dabrowski-Tumanski; Maciej Wisniewski; Lukasz Kucinski; Piotr Milos; Dariusz Plewczynski (CoRR, 2024)