Dariusz Plewczynski

83 papers B 2C 4Journal 51Unranked 23

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	INFERMed: A PK/PD-Aware Retrieval-Augmented System for Explainable Drug-Drug Interaction Analysis. BDA (Astronomy, Science, and Engineering) Pranjul Mishra, Maria Ganzha, Dariusz Plewczynski, Marcin Paprzycki
2025	J	`jnl`	The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon. PLoS Comput. Biol. Jedrzej Kubica, Sevastianos Korsak, Krzysztof H. Banecki, Dvir Schirman, Anurupa Devi Yadavalli, Ariana Brenner Clerkin, David Kouril, Michal Kadlof, Ben Busby, Dariusz Plewczynski
2024	J	`jnl`	RapidDock: Unlocking Proteome-scale Molecular Docking. CoRR Rafal Powalski, Bazyli Klockiewicz, Maciej Jaskowski, Bartosz Topolski, Pawel Dabrowski-Tumanski, Maciej Wisniewski, Lukasz Kucinski, Piotr Milos, Dariusz Plewczynski
2023	J	`jnl`	3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome. Nucleic Acids Res. Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski
2023	J	`jnl`	BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. Bioinform. Alexander Myronov, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski
2023	J	`jnl`	Inferring CTCF-binding patterns and anchored loops across human tissues and cell types. Patterns 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
2023	J	`jnl`	Prediction of chromatin looping using deep hybrid learning (DHL). Quant. Biol. Mateusz Chilinski, Anup Kumar Halder, Dariusz Plewczynski
2023	—	`conf`	ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model. PReMI Anup Kumar Halder, Abhishek Agarwal, Sevastianos Korsak, Karolina Jodkowska, Dariusz Plewczynski
2023	J	`jnl`	cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling. Bioinform. Michal Wlasnowolski, Pawel Z. Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski
2022	J	`jnl`	3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Res. 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
2022	J	`jnl`	3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. Neuroinformatics Nirmal Das, Ewa Baczynska, Monika Bijata, Blazej Ruszczycki, Andre Zeug, Dariusz Plewczynski, Punam Kumar Saha, Evgeni Ponimaskin, Jakub Wlodarczyk, Subhadip Basu
2022	J	`jnl`	ConsensuSV - from the whole-genome sequencing data to the complete variant list. Bioinform. Mateusz Chilinski, Dariusz Plewczynski
2022	J	`jnl`	Correction to: 3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. Neuroinformatics Nirmal Das, Ewa Baczynska, Monika Bijata, Blazej Ruszczycki, Andre Zeug, Dariusz Plewczynski, Punam Kumar Saha, Evgeni Ponimaskin, Jakub Wlodarczyk, Subhadip Basu
2022	J	`jnl`	Genome-Wide Analysis to Identify Palindromes, Mirror and Inverted Repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1. IEEE Access Nimisha Ghosh, Indrajit Saha, Dariusz Plewczynski
2022	J	`jnl`	JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment. IEEE ACM Trans. Comput. Biol. Bioinform. Anup Kumar Halder, Soumyendu Sekhar Bandyopadhyay, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu
2022	J	`jnl`	MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification. Briefings Bioinform. 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
2021	J	`jnl`	PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. BMC Bioinform. Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski
2020	J	`jnl`	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. Michal Wlasnowolski, Michal Sadowski, Tymon Czarnota, Karolina Jodkowska, Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski
2020	J	`jnl`	Disentangling the complexity of low complexity proteins. Briefings Bioinform. 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
2020	J	`jnl`	The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process. J. Comput. Biol. Paulina Urban, Vahid Rezaei Tabar, Michal Denkiewicz, Grzegorz Bokota, Nirmal Das, Subhadip Basu, Dariusz Plewczynski
2019	J	`jnl`	3gClust: Human Protein Cluster Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. Anup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu
2019	J	`jnl`	A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data. J. Comput. Biol. Denis Kazakiewicz, Jürgen Claesen, Katarzyna Górczak, Dariusz Plewczynski, Tomasz Burzykowski
2019	—	`conf`	A new evolutionary rough fuzzy integrated machine learning technique for microRNA selection using next-generation sequencing data of breast cancer. GECCO (Companion) Jnanendra Prasad Sarkar, Indrajit Saha, Somnath Rakshit, Monalisa Pal, Michal Wlasnowolski, Anasua Sarkar, Ujjwal Maulik, Dariusz Plewczynski
2019	J	`jnl`	An empirical Bayes approach for learning directed acyclic graph using MCMC algorithm. Stat. Anal. Data Min. Vahid Rezaei Tabar, Hamid Zareifard, Selva Salimi, Dariusz Plewczynski
2019	—	`ch.`	Chromatin: A Semi-Structured Polymer. Encyclopedia of Bioinformatics and Computational Biology (2) Wayne K. Dawson, Michal Lazniewski, Dariusz Plewczynski
2019	—	`conf`	Deep Learning for Detection and Localization of Thoracic Diseases Using Chest X-Ray Imagery. ICAISC (2) Somnath Rakshit, Indrajit Saha, Michal Wlasnowolski, Ujjwal Maulik, Dariusz Plewczynski
2019	J	`jnl`	Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation. J. Comput. Biol. Paulina Urban, Vahid Rezaei, Grzegorz Bokota, Michal Denkiewicz, Subhadip Basu, Dariusz Plewczynski
2019	C	`conf`	Identification of Epigenetic Biomarkers with the use of Gene Expression and DNA Methylation for Breast Cancer Subtypes. TENCON Indrajit Saha, Somnath Rakshit, Michal Wlasnowolski, Dariusz Plewczynski
2019	—	`conf`	Survival Analysis with the Integration of RNA-Seq and Clinical Data to Identify Breast Cancer Subtype Specific Genes. PReMI (2) Indrajit Saha, Somnath Rakshit, Michal Denkiewicz, Jnanendra Prasad Sarkar, Debasree Maity, Ujjwal Maulik, Dariusz Plewczynski
2018	C	`conf`	Deep Learning for Integrated Analysis of Breast Cancer Subtype Specific Multi-omics Data. TENCON Somnath Rakshit, Indrajit Saha, Subha Shankar Chakraborty, Dariusz Plewczynski
2017	C	`conf`	Multi-levels 3D Chromatin Interactions Prediction Using Epigenomic Profiles. ISMIS Ziad Al Bkhetan, Dariusz Plewczynski
2016	J	`jnl`	2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity. Bioinform. Subhadip Basu, Dariusz Plewczynski, Satadal Saha, Matylda Roszkowska, Marta Magnowska, Ewa Baczynska, Jakub Wlodarczyk
2016	J	`jnl`	3D-GNOME: an integrated web service for structural modeling of the 3D genome. Nucleic Acids Res. Przemyslaw Szalaj, Paul J. Michalski, Przemyslaw Wróblewski, Zhonghui Tang, Michal Kadlof, Giovanni Mazzocco, Yijun Ruan, Dariusz Plewczynski
2016	J	`jnl`	3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. Database J. Biol. Databases Curation Giovanni Mazzocco, Michal Lazniewski, Piotr Migdal, Teresa Szczepinska, Jan P. Radomski, Dariusz Plewczynski
2016	J	`jnl`	Complexity curve: a graphical measure of data complexity and classifier performance. PeerJ Comput. Sci. Julian Zubek, Dariusz Plewczynski
2016	J	`jnl`	Complexity curve: a graphical measure of data complexity and classifier performance. PeerJ Prepr. Julian Zubek, Dariusz Plewczynski
2016	J	`jnl`	Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis. Frontiers Comput. Neurosci. Grzegorz Bokota, Marta Magnowska, Tomasz Kusmierczyk, Michal Lukasik, Matylda Roszkowska, Dariusz Plewczynski
2016	J	`jnl`	Divide and Conquer Ensemble Method for Time Series Forecasting. Trans. Comput. Collect. Intell. Jan Kostrzewa, Giovanni Mazzocco, Dariusz Plewczynski
2016	J	`jnl`	Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. BMC Bioinform. 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, Raju Nagarajan, 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
2015	J	`jnl`	A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. Comput. Biol. Chem. Denis Kazakiewicz, Jonathan R. Karr, Karol M. Langner, Dariusz Plewczynski
2015	—	`conf`	Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer. SEMCCO Indrajit Saha, Shib Sankar Bhowmick, Filippo Geraci, Marco Pellegrini, Debotosh Bhattacharjee, Ujjwal Maulik, Dariusz Plewczynski
2015	J	`jnl`	Binding Activity Prediction of Cyclin-Dependent Inhibitors. J. Chem. Inf. Model. Indrajit Saha, Benedykt Rak, Shib Sankar Bhowmick, Ujjwal Maulik, Debotosh Bhattacharjee, Uwe Koch, Michal Lazniewski, Dariusz Plewczynski
2015	—	`conf`	MaER: A New Ensemble Based Multiclass Classifier for Binding Activity Prediction of HLA Class II Proteins. PReMI Giovanni Mazzocco, Shib Sankar Bhowmick, Indrajit Saha, Ujjwal Maulik, Debotosh Bhattacharjee, Dariusz Plewczynski
2015	—	`conf`	PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier. PReMI Piyali Chatterjee, Subhadip Basu, Julian Zubek, Mahantapas Kundu, Mita Nasipuri, Dariusz Plewczynski
2014	J	`jnl`	3D-Hit: fast structural comparison of proteins on multicore architectures. Optim. Lett. Lukasz Bieniasz-Krzywiec, Maciej Cytowski, Leszek Rychlewski, Dariusz Plewczynski
2014	—	`ch.`	A Meta-learning Approach for Protein Function Prediction. Advanced Computational Approaches to Biomedical Engineering Dariusz Plewczynski, Subhadip Basu
2014	—	`conf`	Application of RotaSVM for HLA Class II Protein-Peptide Interaction Prediction. BIOINFORMATICS Shib Sankar Bhowmick, Indrajit Saha, Giovanni Mazzocco, Ujjwal Maulik, Luís Rato, Debotosh Bhattacharjee, Dariusz Plewczynski
2014	J	`jnl`	HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking. J. Comput. Biol. Dariusz Plewczynski, Anna Philips, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski
2013	—	`conf`	A Consensus Approach for Identification of Protein-Protein Interaction Sites in Homo Sapiens. PReMI Brijesh Kumar Sriwastava, Subhadip Basu, Ujjwal Maulik, Dariusz Plewczynski
2013	—	`conf`	Erratum: Evaluation of Machine Learning Algorithms on Protein-Protein Interactions. ICMMI Indrajit Saha, Tomas Klingström, Simon Forsberg, Johan Wikander, Julian Zubek, Marcin Kierczak, Dariusz Plewczynski
2013	—	`conf`	Evaluation of Machine Learning Algorithms on Protein-Protein Interactions. ICMMI Indrajit Saha, Tomas Klingström, Simon Forsberg, Johan Wikander, Julian Zubek, Marcin Kierczak, Dariusz Plewczynski
2013	—	`conf`	Generic Framework for Simulation of Cognitive Systems: A Case Study of Color Category Boundaries. ICMMI Dariusz Plewczynski, Michal Lukasik, Konrad Kurdej, Julian Zubek, Franciszek Rakowski, Joanna Raczaszek-Leonardi
2013	B	`conf`	Information-Sharing in Three Interacting Minds Solving a Simple Perceptual Task. CogSci Michal Denkiewicz, Joanna Raczaszek-Leonardi, Piotr Migdal, Dariusz Plewczynski
2013	—	`conf`	Multiobjective Differential Evolution: A Comparative Study on Benchmark Problems. ICMMI Indrajit Saha, Ujjwal Maulik, Michal Lukasik, Dariusz Plewczynski
2012	—	`conf`	Application of High Quality Amino Acid Indices to AMS 3.0: A Update Note. BIC-TA (1) Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
2012	J	`jnl`	Improved differential evolution for microarray analysis. Int. J. Data Min. Bioinform. Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay
2012	J	`jnl`	SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation. IEEE Geosci. Remote. Sens. Lett. Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
2012	—	`conf`	Soft Computing Approach for VLSI Mincut Partitioning: The State of the Arts. SocProS Debasree Maity, Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
2011	J	`jnl`	A new multi-objective technique for differential fuzzy clustering. Appl. Soft Comput. Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
2011	—	`conf`	Brainstorming - Agent based Meta-learning Approach. ICAART (2) Dariusz Plewczynski
2011	J	`jnl`	Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J. Comput. Chem. Dariusz Plewczynski, Michal Lazniewski, Rafal Augustyniak, Krzysztof Ginalski
2011	—	`ch.`	Cognitive architectures in multi-agent systems. Biology, Computation and Linguistics Dariusz Plewczynski
2011	J	`jnl`	Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine. J. Chem. Inf. Model. Marcin Nowosielski, Marcin Hoffmann, Lucjan Stanislaw Wyrwicz, Piotr Stepniak, Dariusz Plewczynski, Michal Lazniewski, Krzysztof Ginalski, Leszek Rychlewski
2011	J	`jnl`	Improvement of new automatic differential fuzzy clustering using SVM classifier for microarray analysis. Expert Syst. Appl. Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
2011	J	`jnl`	Information-sharing and aggregation models for interacting minds CoRR Piotr Migdal, Michal Denkiewicz, Joanna Raczaszek-Leonardi, Dariusz Plewczynski
2011	—	`conf`	Landau Theory of Meta-learning. SIIS Dariusz Plewczynski
2011	—	`conf`	Multiobjective Differential Crisp Clustering for Evaluation of Clusters Dynamically. ICMMI Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
2011	C	`conf`	PMAFC: A New Probabilistic Memetic Algorithm Based Fuzzy Clustering. ISMIS Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
2011	J	`jnl`	Protein-protein interaction and pathway databases, a graphical review. Briefings Bioinform. Tomas Klingström, Dariusz Plewczynski
2011	J	`jnl`	Unsupervised and Supervised Learning Approaches Together for Microarray Analysis. Fundam. Informaticae Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
2011	J	`jnl`	VoteDock: Consensus docking method for prediction of protein-ligand interactions. J. Comput. Chem. Dariusz Plewczynski, Michal Lazniewski, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski
2010	J	`jnl`	AMS 3.0: prediction of post-translational modifications. BMC Bioinform. Subhadip Basu, Dariusz Plewczynski
2010	—	`conf`	Cancer Classification using SVM-boosted Multiobjective Differential Fuzzy Clustering. STAIRS Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
2010	—	`conf`	Consensus Multiobjective Differential Crisp Clustering for Categorical Data Analysis. RSCTC Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay
2010	—	`conf`	Improvement of Differential Crisp Clustering using ANN Classifier for Unsupervised Pixel Classification of Satellite Image. ICEIS (2) Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay
2010	J	`jnl`	Landau Theory of Adaptive Integration in Computational Intelligence CoRR Dariusz Plewczynski
2010	B	`conf`	Real-coded differential crisp clustering for MRI brain image segmentation. IEEE Congress on Evolutionary Computation Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
2008	J	`jnl`	3D-Fun: predicting enzyme function from structure. Nucleic Acids Res. Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski
2008	—	`conf`	TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections. BIOTECHNO Dariusz Plewczynski
2006	J	`jnl`	Assessing Different Classification Methods for Virtual Screening. J. Chem. Inf. Model. Dariusz Plewczynski, Stéphane A. H. Spieser, Uwe Koch
2006	J	`jnl`	PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinform. Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I. Shakhnovich
2005	J	`jnl`	AutoMotif server: prediction of single residue post-translational modifications in proteins. Bioinform. Dariusz Plewczynski, Adrian Tkacz, Lucjan Stanislaw Wyrwicz, Leszek Rychlewski
2004	J	`jnl`	Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik