Dariusz Plewczynski

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 35

Top Topics

Dendritic Spines

Top Venues

J. Comput. Biol.

Nucleic Acids Res.

Publications

Mateusz Chilinski, Anup Kumar Halder, Dariusz Plewczynski
Prediction of chromatin looping using deep hybrid learning (DHL). Quant. Biol. 11 (2) (2023)
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)
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)
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) (2023)
Michal Wlasnowolski, Pawel Z. Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski
cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling. Bioinform. 39 (10) (2023)
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) (2023)
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 (2022)
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) (2022)
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) (2022)
Mateusz Chilinski, Dariusz Plewczynski
ConsensuSV - from the whole-genome sequencing data to the complete variant list. Bioinform. 38 (24) (2022)
Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa J. 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)
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) (2022)
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) (2022)
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) (2021)
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) (2020)
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) (2020)
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) (2020)
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)
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) (2019)
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)
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) (2019)
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)
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) (2019)
Anup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu
3gClust: Human Protein Cluster Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (6) (2019)
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)
Somnath Rakshit, Indrajit Saha, Subha Shankar Chakraborty, Dariusz Plewczynski
Deep Learning for Integrated Analysis of Breast Cancer Subtype Specific Multi-omics Data. TENCON (2018)
Ziad Al Bkhetan, Dariusz Plewczynski
Multi-levels 3D Chromatin Interactions Prediction Using Epigenomic Profiles. ISMIS (2017)
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 (2016)
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)
Julian Zubek, Dariusz Plewczynski
Complexity curve: a graphical measure of data complexity and classifier performance. PeerJ Comput. Sci. 2 (2016)
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) (2016)
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) (2016)
Julian Zubek, Dariusz Plewczynski
Complexity curve: a graphical measure of data complexity and classifier performance. PeerJ Prepr. 4 (2016)
Jan Kostrzewa, Giovanni Mazzocco, Dariusz Plewczynski
Divide and Conquer Ensemble Method for Time Series Forecasting. Trans. Comput. Collect. Intell. 24 (2016)
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)
Piyali Chatterjee, Subhadip Basu, Julian Zubek, Mahantapas Kundu, Mita Nasipuri, Dariusz Plewczynski
PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier. PReMI (2015)
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)
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 (2015)
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) (2015)
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)
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)
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) (2014)
Lukasz Bieniasz-Krzywiec, Maciej Cytowski, Leszek Rychlewski, Dariusz Plewczynski
3D-Hit: fast structural comparison of proteins on multicore architectures. Optim. Lett. 8 (5) (2014)
Brijesh Kumar Sriwastava, Subhadip Basu, Ujjwal Maulik, Dariusz Plewczynski
A Consensus Approach for Identification of Protein-Protein Interaction Sites in Homo Sapiens. PReMI (2013)
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)
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)
Indrajit Saha, Ujjwal Maulik, Michal Lukasik, Dariusz Plewczynski
Multiobjective Differential Evolution: A Comparative Study on Benchmark Problems. ICMMI (2013)
Michal Denkiewicz, Joanna Raczaszek-Leonardi, Piotr Migdal, Dariusz Plewczynski
Information-Sharing in Three Interacting Minds Solving a Simple Perceptual Task. CogSci (2013)
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)
Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay
Improved differential evolution for microarray analysis. Int. J. Data Min. Bioinform. 6 (1) (2012)
Debasree Maity, Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
Soft Computing Approach for VLSI Mincut Partitioning: The State of the Arts. SocProS (2012)
Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation. IEEE Geosci. Remote. Sens. Lett. 9 (1) (2012)
Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
Application of High Quality Amino Acid Indices to AMS 3.0: A Update Note. BIC-TA (1) (2012)
Tomas Klingström, Dariusz Plewczynski
Protein-protein interaction and pathway databases, a graphical review. Briefings Bioinform. 12 (6) (2011)
Dariusz Plewczynski
Landau Theory of Meta-learning. SIIS (2011)
Dariusz Plewczynski
Brainstorming - Agent based Meta-learning Approach. ICAART (2) (2011)
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) (2011)
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) (2011)
Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
Unsupervised and Supervised Learning Approaches Together for Microarray Analysis. Fundam. Informaticae 106 (1) (2011)
Piotr Migdal, Michal Denkiewicz, Joanna Raczaszek-Leonardi, Dariusz Plewczynski
Information-sharing and aggregation models for interacting minds CoRR (2011)
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) (2011)
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) (2011)
Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
PMAFC: A New Probabilistic Memetic Algorithm Based Fuzzy Clustering. ISMIS (2011)
Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
Multiobjective Differential Crisp Clustering for Evaluation of Clusters Dynamically. ICMMI (2011)
Indrajit Saha, Ujjwal Maulik, Dariusz Plewczynski
A new multi-objective technique for differential fuzzy clustering. Appl. Soft Comput. 11 (2) (2011)
Indrajit Saha, Dariusz Plewczynski, Ujjwal Maulik, Sanghamitra Bandyopadhyay
Consensus Multiobjective Differential Crisp Clustering for Categorical Data Analysis. RSCTC (2010)
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)
Subhadip Basu, Dariusz Plewczynski
AMS 3.0: prediction of post-translational modifications. BMC Bioinform. 11 (2010)
Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
Cancer Classification using SVM-boosted Multiobjective Differential Fuzzy Clustering. STAIRS (2010)
Dariusz Plewczynski
Landau Theory of Adaptive Integration in Computational Intelligence CoRR (2010)
Indrajit Saha, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski
Real-coded differential crisp clustering for MRI brain image segmentation. IEEE Congress on Evolutionary Computation (2010)
Dariusz Plewczynski
TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections. BIOTECHNO (2008)
Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski
3D-Fun: predicting enzyme function from structure. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
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 (2006)
Dariusz Plewczynski, Stéphane A. H. Spieser, Uwe Koch
Assessing Different Classification Methods for Virtual Screening. J. Chem. Inf. Model. 46 (3) (2006)
Dariusz Plewczynski, Adrian Tkacz, Lucjan Stanislaw Wyrwicz, Leszek Rychlewski
AutoMotif server: prediction of single residue post-translational modifications in proteins. Bioinform. 21 (10) (2005)
Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik
Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. 5 (2004)