D. Plewczyński

发表

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Dariusz M Plewczynski, E. Liu, Chia-Lin Wei, 2015, Cell.

The interactome: predicting the protein-protein interactions in cells.

Krzysztof Ginalski, Dariusz Plewczyński, K. Ginalski, 2009, Cellular & molecular biology letters.

PPIcons: identification of protein-protein interaction sites in selected organisms

Ujjwal Maulik, Subhadip Basu, Dariusz Plewczynski, 2013, Journal of Molecular Modeling.

ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning

Julian Zubek, Dariusz Plewczynski, Lucjan S Wyrwicz, 2018, PeerJ.

A support vector machine approach to the identification of phosphorylation sites.

Dariusz M Plewczynski, A. Godzik, L. Rychlewski, 2005, Cellular & molecular biology letters.

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

Dariusz M Plewczynski, D. Plewczyński, Ziad Al Bkhetan, 2018, Scientific Reports.

Data Complexity and Classifier

Julian Zubek, D. Plewczyński, 2016 .

Molecular modeling of phosphorylation sites in proteins using a database of local structure segments

Dariusz Plewczynski, Leszek Rychlewski, Andrzej Kloczkowski, 2005, Journal of molecular modeling.

Ab Initio server prototype for prediction of phosphorylation sites in proteins

Dariusz Plewczynski, Leszek Rychlewski, L. Rychlewski, 2003 .

Quantitative 3-D morphometric analysis of individual dendritic spines

Subhadip Basu, Dariusz Plewczynski, Ewa Baczynska, 2018, Scientific Reports.

Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells

Dariusz M Plewczynski, Y. Ruan, Ping Wang, 2019, bioRxiv.

Clinical and molecular characteristics of newly reported mitochondrial disease entity caused by biallelic PARS2 mutations

Dariusz M Plewczynski, R. Płoski, D. Plewczyński, 2018, Journal of Human Genetics.

Towards Improving Self-adaptive Differential Evolution for Numerical Optimization: A Progress Note

U. Maulik, D. Plewczyński, Indrajit Saha, 2012 .

FIREcaller: Detecting frequently interacting regions from Hi-C data

B. Ren, Yun Li, Ming Hu, 2020, Computational and structural biotechnology journal.

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Mulin Jun Li, Dariusz M Plewczynski, D. Plewczyński, 2020, Computational and structural biotechnology journal.

One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease.

Dariusz Plewczynski, Michal Lazniewski, Dariusz M Plewczynski, 2019, Seminars in cell & developmental biology.

Meta-basic estimates the size of druggable human genome

L. Rychlewski, D. Plewczyński, 2009, Journal of molecular modeling.

Species Used for Drug Testing Reveal Different Inhibition Susceptibility for 17beta-Hydroxysteroid Dehydrogenase Type 1

Dariusz M Plewczynski, L. Rychlewski, J. Adamski, 2010, PloS one.

Consensus classification of human leukocyte antigen class II proteins

Dariusz Plewczynski, Indrajit Saha, Giovanni Mazzocco, 2012, Immunogenetics.

Learning directed acyclic graphs by determination of candidate causes for discrete variables

Vahid Rezaei Tabar, D. Plewczyński, Hamid Zareifard, 2019, Journal of Statistical Computation and Simulation.

Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation

Jnanendra Prasad Sarkar, D. Plewczyński, Indrajit Saha, 2019, Front. Genet..

Aggregated Network Centrality Shows Non-Random Structure of Genomic and Proteomic Networks.

Anup Kumar Halder, Dariusz M Plewczynski, Subhadip Basu, 2019, Methods.

Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

A. F. Mollah, Y. Ruan, D. Plewczyński, 2022, bioRxiv.

MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification

Dariusz M Plewczynski, M. Fullwood, Meizhen Zheng, 2022, bioRxiv.

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome

Dariusz M Plewczynski, Y. Ruan, Zhonghui Tang, 2020, Nucleic Acids Res..

Multi-levels 3 D Chromatin Interactions Prediction Using Epigenomic Pro fi les

Ziad Al Bkhetan, D. Plewczyński, 2018 .

Corrigendum: Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation

Jnanendra Prasad Sarkar, D. Plewczyński, Indrajit Saha, 2020, Frontiers in Genetics.

Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods

Dariusz M Plewczynski, A. Malhotra, Przemyslaw Szalaj, 2016 .

The structural variability of the influenza A hemagglutinin receptor-binding site

Dariusz M Plewczynski, W. Dawson, D. Plewczyński, 2017, Briefings in functional genomics.

Inferring CTCF insulators and anchored loops across human tissues and cell types

P. Sham, Weiqi Wang, D. Plewczyński, 2022, bioRxiv.

Mixture of Forward-Directed and Backward-Directed Autoregressive Hidden Markov Models for Time series Modeling

Vahid Rezaei Tabar, D. Plewczyński, F. Eskandari, 2019, Journal of the Iranian Statistical Society.

Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images

Subhadip Basu, A. Magalska, G. Wilczynski, 2019, Front. Neuroanat..

Online Predictor Using Machine Learning to Predict Novel Coronavirus and Other Pathogenic Viruses

Jnanendra Prasad Sarkar, D. Plewczyński, Nimisha Ghosh, 2022, ACS omega.

Single-hit inactivation drove tumor suppressor genes out of the X chromosome during evolution.

Danny C. W. Chan, Dariusz M Plewczynski, S. Wong, 2022, Cancer research.

Modelling of potentially promising SARS protease inhibitors

M. Hoffmann, K. Ginalski, D. Plewczyński, 2007, Journal of Physics.

Fun : predicting enzyme function from structure

Dariusz M Plewczynski, G. Vriend, L. Rychlewski, 2017 .

nar / gkn 308 3 D-Fun : predicting enzyme function from structure

G. Vriend, L. Rychlewski, D. Plewczyński, 2008 .

Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population Scale

Y. Ruan, Zhonghui Tang, Przemyslaw Szalaj, 2018, bioRxiv.

Reorientational angle distribution and diffusion coefficient for nodal and cylindrical surfaces

Dariusz M Plewczynski, D. Plewczyński, R. Hołyst, 2000 .

Oncogenes expand during evolution to withstand somatic amplification

A. Cheng, L. Zhang, D. Plewczyński, 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases

A. Kolinski, K. Ginalski, L. Rychlewski, 2008, Cell cycle.

ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning

Dariusz M Plewczynski, Julian Zubek, D. Plewczyński, 2018, PeerJ.

Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

Dariusz M Plewczynski, Y. Ruan, Ping Wang, 2022, Scientific Reports.

3DGenBench: a web-server to benchmark computational models for 3D Genomics

Dariusz M Plewczynski, V. B. Teif, D. Plewczyński, 2022, Nucleic Acids Res..

Intrinsic linking of chromatin fiber in human cells

Dariusz M Plewczynski, Y. Ruan, D. Plewczyński, 2022, bioRxiv.

Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN

Anup Kumar Halder, Subhadip Basu, M. Nasipuri, 2022, Cells.

Modeling of Cognitive Agents

D. Plewczyński, 2016 .

PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms

Anup Kumar Halder, Dariusz M Plewczynski, Subhadip Basu, 2022, Frontiers in Genetics.

ML-DTD: Machine Learning-Based Drug Target Discovery for the Potential Treatment of COVID-19

Anup Kumar Halder, Dariusz M Plewczynski, Subhadip Basu, 2022, Vaccines.

The 3D enhancer network of the developing T cell genome is shaped by SATB1

Dariusz M Plewczynski, D. Plewczyński, Christoforos Nikolaou, 2022, Nature Communications.

Genome-wide Analysis to Identify Palindromes, Mirror and Inverted Repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1

D. Plewczyński, Nimisha Ghosh, I. Saha, 2022, IEEE Access.

Unveiling the Biomarkers of Cancer and COVID-19 and Their Regulations in Different Organs by Integrating RNA-Seq Expression and Protein–Protein Interactions

Dariusz M Plewczynski, D. Plewczyński, Nimisha Ghosh, 2022, ACS omega.

Identification of Human miRNA Biomarkers Targeting the SARS-CoV-2 Genome

Dariusz M Plewczynski, D. Plewczyński, Nimisha Ghosh, 2022, ACS omega.

Current challenges in understanding the role of enhancers in disease.

Judith B. Zaugg, Dariusz M Plewczynski, G. Natoli, 2022, Nature structural & molecular biology.

Three-dimensional organization and dynamics of the genome

Dariusz Plewczynski, Przemyslaw Szalaj, Dariusz M Plewczynski, 2018, Cell Biology and Toxicology.

Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism

D. Plewczyński, Indrajit Saha, Nimisha Ghosh, 2021, Virus Research.

3gClust: Human Protein Cluster Analysis

Piyali Chatterjee, Subhadip Basu, Mita Nasipuri, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

In Silico Prediction of SARS Protease Inhibitors by Virtual High Throughput Screening

Dariusz Plewczynski, Marcin Hoffmann, Krzysztof Ginalski, 2007, Chemical biology & drug design.

NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology

Michal J. Pietal, Dariusz M Plewczynski, D. Plewczyński, 2022, PeerJ.

Multiobjective Differential Evolution: A Comparative Study on Benchmark Problems

Ujjwal Maulik, Dariusz Plewczynski, Indrajit Saha, 2013, ICMMI.

Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine

Leszek Rychlewski, Marcin Hoffmann, Krzysztof Ginalski, 2011, J. Chem. Inf. Model..

Role of the host genetic variability in the influenza A virus susceptibility.

Dariusz M Plewczynski, D. Plewczyński, J. Radomski, 2014, Acta biochimica Polonica.

2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity

Subhadip Basu, Dariusz Plewczynski, Ewa Baczynska, 2016, Bioinform..

Landau Theory of Meta-learning

Dariusz Plewczynski, Dariusz M Plewczynski, D. Plewczyński, 2011, SIIS.

Landau Theory of Adaptive Integration in Computational Intelligence pdf

Dariusz Plewczynski, Dariusz M Plewczynski, D. Plewczyński, 2010, ArXiv.

From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect.

D. Plewczyński, Kaustav Sengupta, Mateusz Chiliński, 2021, Seminars in cell & developmental biology.

Intermingling of chromosome territories

D. Plewczyński, Teresa Szczepińska, A. Rusek, 2019, Genes, chromosomes & cancer.

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

Dariusz Plewczynski, Yijun Ruan, Xingwang Li, 2016, Genome research.

Promoter‐pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

Dariusz M Plewczynski, D. Plewczyński, R. Yatusevich, 2023, The EMBO journal.

Using Dali for structural comparison of proteins.

Liisa Holm, Dariusz Plewczynski, Sakari Kääriäinen, 2006, Current protocols in bioinformatics.

A new evolutionary rough fuzzy integrated machine learning technique for microRNA selection using next-generation sequencing data of breast cancer

Ujjwal Maulik, Somnath Rakshit, Dariusz Plewczynski, 2019, GECCO.

Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer

Ujjwal Maulik, Dariusz Plewczynski, Debotosh Bhattacharjee, 2015, SEMCCO.

Improved differential evolution for microarray analysis

Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski, 2012, Int. J. Data Min. Bioinform..

Improvement of new automatic differential fuzzy clustering using SVM classifier for microarray analysis

Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski, 2011, Expert Syst. Appl..

Fuzzy clustering of physicochemical and biochemical properties of amino Acids

Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski, 2011, Amino Acids.

A new multi-objective technique for differential fuzzy clustering

Ujjwal Maulik, Indrajit Saha, Dariusz Plewczynski, 2011, Appl. Soft Comput..

Unsupervised and Supervised Learning Approaches Together for Microarray Analysis

Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski, 2011, Fundam. Informaticae.

Mean-field theory of meta-learning

Dariusz Plewczynski, D. Plewczyński, 2009, 0907.4643.

3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines

Subhadip Basu, P. Saha, J. Włodarczyk, 2021, Neuroinformatics.

The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process

Dariusz Plewczynski, Paulina Urban, Grzegorz Bokota, 2020, J. Comput. Biol..

3dSpAn: an interactive software for 3D segmentation and analysis of dendritic spines

Ewa Baczynska, Nirmal Das, Jakub Wlodarczyk, 2019, bioRxiv.

Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation

Subhadip Basu, Dariusz Plewczynski, Vahid Rezaei, 2019, J. Comput. Biol..

Quantitative 3-D morphometric analysis of individual dendritic spines

Subhadip Basu, P. Saha, J. Włodarczyk, 2018, Scientific Reports.

Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis

Dariusz Plewczynski, Matylda Roszkowska, Marta Magnowska, 2016, bioRxiv.

Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia

E. Liu, Chia-Lin Wei, Y. Ruan, 2020, Genome Biology.

Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia

Dariusz M Plewczynski, E. Liu, Chia-Lin Wei, 2020, Genome Biology.

TBC1D24 emerges as an important contributor to progressive postlingual dominant hearing loss

Dariusz M Plewczynski, D. Plewczyński, M. Lazniewski, 2021, Scientific Reports.

Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization

Y. Ruan, Pawel Trzaskoma, A. Magalska, 2020, Nature Communications.

FIREcaller: Detecting frequently interacting regions from Hi-C data

Di Wu, Yuchen Yang, Yun Li, 2019, bioRxiv.

Potent but transient immunosuppression of T-cells is a general feature of CD71+ erythroid cells

Dariusz M Plewczynski, D. Nowis, J. Gołąb, 2021, Communications Biology.

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale

Y. Ruan, Zhonghui Tang, Przemyslaw Szalaj, 2019, Genome Biology.

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale

Dariusz Plewczynski, Yijun Ruan, Zhonghui Tang, 2018, Genome Biology.

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

Dariusz M Plewczynski, D. Plewczyński, Ziad Al Bkhetan, 2018, Scientific Reports.

3D-GNOME: an integrated web service for structural modeling of the 3D genome

Dariusz Plewczynski, Giovanni Mazzocco, Yijun Ruan, 2016, Nucleic Acids Res..

Highlights from the 11th ISCB Student Council Symposium 2015

Giovanni Felici, Farzana Rahman, M. Michael Gromiha, 2016, BMC Bioinformatics.

Identification of miRNA Biomarkers for Diverse Cancer Types Using Statistical Learning Methods at the Whole-Genome Scale

Indrajit Saha, Grzegorz Bokota, Adrian Lancucki, 2020, Frontiers in Genetics.

Protein-protein interaction and pathway databases, a graphical review

Dariusz Plewczynski, Tomas Klingström, Dariusz M Plewczynski, 2011, Briefings Bioinform..

COVID-DeepPredictor: Recurrent Neural Network to Predict SARS-CoV-2 and Other Pathogenic Viruses

Dariusz M Plewczynski, D. Plewczyński, Indrajit Saha, 2021, Frontiers in Genetics.

FunPred 3.0: improved protein function prediction using protein interaction network

Piyali Chatterjee, Subhadip Basu, Mita Nasipuri, 2019, PeerJ.

RNA structure interactions and ribonucleoprotein processes of the influenza A virus

Dariusz M Plewczynski, W. Dawson, D. Plewczyński, 2017, Briefings in functional genomics.

Disentangling the complexity of low complexity proteins

Silvio C. E. Tosatto, Dariusz Plewczynski, Aleksandra Gruca, 2019, Briefings Bioinform..

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

Mulin Jun Li, Dariusz M Plewczynski, P. Sham, 2023, bioRxiv.

Novel neuro-audiological findings and further evidence for TWNK involvement in Perrault syndrome

Dariusz M Plewczynski, R. Płoski, D. Plewczyński, 2017, Journal of Translational Medicine.

Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows

A. F. Mollah, Dariusz M Plewczynski, D. Plewczyński, 2021, International journal of molecular sciences.

Prediction of signal peptides in protein sequences by neural networks.

Dariusz Plewczynski, Leszek Rychlewski, Lukasz Slabinski, 2008, Acta biochimica Polonica.

The RPSP: Web server for prediction of signal peptides

Dariusz Plewczynski, Leszek Rychlewski, Liisa Holm, 2007 .

Support-vector-machine classification of linear functional motifs in proteins

Dariusz Plewczynski, Andrzej Kloczkowski, Adam Godzik, 2006, Journal of molecular modeling.

AMS 3.0: prediction of post-translational modifications

Subhadip Basu, Dariusz Plewczynski, Subhadip Basu, 2010, BMC Bioinformatics.

Activation-induced chromatin reorganization in neurons depends on HDAC1 activity.

C. Bramham, Pawel Trzaskoma, A. Magalska, 2022, Cell reports.

The Changes of the Nuclear Landscape Upon Stimulation of Neuronal Cells are Dependent on the Histone Deacetylase HSAC1

C. Bramham, Pawel Trzaskoma, A. Magalska, 2021 .

MaER: A New Ensemble Based Multiclass Classifier for Binding Activity Prediction of HLA Class II Proteins

Ujjwal Maulik, Dariusz Plewczynski, Debotosh Bhattacharjee, 2015, PReMI.

Application of RotaSVM for HLA Class II Protein-Peptide Interaction Prediction

Ujjwal Maulik, Dariusz Plewczynski, Debotosh Bhattacharjee, 2014, BIOINFORMATICS.

Erratum to: Consensus classification of human leukocyte antigen class II proteins

D. Plewczyński, Indrajit Saha, G. Mazzocco, 2013 .

Brainstorming - Agent based Meta-learning Approach

Dariusz Plewczynski, D. Plewczyński, 2011, ICAART.

Complexity curve: a graphical measure of data complexity and classifier performance

Julian Zubek, Dariusz Plewczynski, Dariusz M Plewczynski, 2016, PeerJ Prepr..

Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)

Dariusz M Plewczynski, Y. Ruan, Pawel Trzaskoma, 2020, bioRxiv.

Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations

W. Dawson, D. Plewczyński, M. Lazniewski, 2022, Methods.

Application of Machine Learning Method in Genomics and Proteomics

Dariusz Plewczynski, Wei Chen, Hao Lin, 2015, TheScientificWorldJournal.

Assessing Different Classification Methods for Virtual Screening

Dariusz Plewczynski, Uwe Koch, Dariusz M Plewczynski, 2006, J. Chem. Inf. Model..

3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale

Dariusz Plewczynski, Giovanni Mazzocco, Jan P. Radomski, 2016, Database J. Biol. Databases Curation.

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

Dariusz M Plewczynski, Subhadip Basu, Pawel Trzaskoma, 2021, BMC Bioinformatics.

PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies

Jacek Sroka, Agnieszka Grabowska, Grzegorz Bokota, 2020, bioRxiv.

Deep Learning for Integrated Analysis of Breast Cancer Subtype Specific Multi-omics Data

Somnath Rakshit, Dariusz Plewczynski, Indrajit Saha, 2018, TENCON 2018 - 2018 IEEE Region 10 Conference.

Comparison of proteins based on segments structural similarity.

Dariusz Plewczynski, Jakub Pas, Leszek Rychlewski, 2004, Acta biochimica Polonica.

Landau theory of social clustering

Dariusz Plewczynski, D. Plewczyński, 1998 .

Performance of machine learning methods for ligand-based virtual screening.

Dariusz Plewczynski, Uwe Koch, Stéphane A H Spieser, 2009, Combinatorial chemistry & high throughput screening.

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

Dariusz Plewczynski, Jonathan R. Karr, Karol M. Langner, 2015, Comput. Biol. Chem..

Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods.

A Srivastava, G Mazzocco, A Kel, 2016, Molecular bioSystems.

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Dariusz Plewczynski, Michal Lazniewski, Krzysztof Ginalski, 2011, J. Comput. Chem..

Ensemble learning prediction of protein-protein interactions using proteins functional annotations.

Ujjwal Maulik, Julian Zubek, Dariusz Plewczynski, 2014, Molecular bioSystems.

Upregulation of MLK4 promotes migratory and invasive potential of breast cancer cells

D. Nowis, J. Gołąb, D. Plewczyński, 2018, Oncogene.

A Consensus Approach for Identification of Protein-Protein Interaction Sites in Homo Sapiens

Ujjwal Maulik, Subhadip Basu, Dariusz Plewczynski, 2013, PReMI.

Prediction of E.coli Protein-Protein Interaction Sites Using Inter-Residue Distances and High-Quality-Index Features

Ujjwal Maulik, Subhadip Basu, Dariusz Plewczynski, 2012, ICIS 2012.

AMS 4.0: consensus prediction of post-translational modifications in protein sequences

Subhadip Basu, D. Plewczyński, Indrajit Saha, 2012, Amino Acids.

Fuzzy clustering of physicochemical and biochemical properties of amino Acids

S. Bandyopadhyay, U. Maulik, D. Plewczyński, 2011, Amino Acids.

PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines

Piyali Chatterjee, Subhadip Basu, Mahantapas Kundu, 2011, Journal of molecular modeling.

PPI_SVM: Prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables

Piyali Chatterjee, Subhadip Basu, Mahantapas Kundu, 2011, Cellular & Molecular Biology Letters.

Brainstorming: weighted voting prediction of inhibitors for protein targets

Dariusz Plewczynski, Dariusz M Plewczynski, D. Plewczyński, 2010, Journal of molecular modeling.

PRDX-1 Supports the Survival and Antitumor Activity of Primary and CAR-Modified NK Cells under Oxidative Stress

Dariusz M Plewczynski, D. Plewczyński, M. Lazniewski, 2021, Cancer Immunology Research.

Inhibition of protein disulfide isomerase induces differentiation of acute myeloid leukemia cells

Dariusz M Plewczynski, D. Nowis, J. Gołąb, 2018, Haematologica.

Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae

Subhadip Basu, Julian Zubek, Dariusz Plewczynski, 2015, PeerJ.

Computational inference of H3K4me3 and H3K27ac domain length

Julian Zubek, Duygu Ucar, Dariusz M Plewczynski, 2016, PeerJ.

AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update

Dariusz Plewczynski, Leszek Rychlewski, Adrian Tkacz, 2008, Journal of molecular modeling.

AutoMotif server: prediction of single residue post-translational modifications in proteins

Dariusz Plewczynski, Leszek Rychlewski, Adrian Tkacz, 2005, Bioinform..

Integrated web service for improving alignment quality based on segments comparison

Dariusz Plewczynski, Leszek Rychlewski, Adam Godzik, 2004, BMC Bioinformatics.

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

Dariusz M Plewczynski, Y. Ruan, D. Plewczyński, 2023, bioRxiv.

Divide and Conquer Ensemble Method for Time Series Forecasting

Dariusz Plewczynski, Giovanni Mazzocco, Jan Kostrzewa, 2016, Trans. Comput. Collect. Intell..

Social adaptation in multi-agent model of linguistic categorization is affected by network information flow

Julian Zubek, Dariusz Plewczynski, Joanna Rączaszek-Leonardi, 2017, PloS one.

Approach to equilibrium of particles diffusing on curved surfaces

Dariusz M Plewczynski, D. Plewczyński, R. Hołyst, 2001 .

A Gibbs sampler for learning DAG: a unification for discrete and Gaussian domains

Dariusz M Plewczynski, D. Plewczyński, Vahid Rezaei Tabar, 2021, Journal of Statistical Computation and Simulation.

The 3D enhancer network of the developing T cell genome is controlled by SATB1

Dariusz M Plewczynski, D. Plewczyński, Christoforos Nikolaou, 2021, bioRxiv.

The 3 D enhancer network of the developing T cell genome is controlled by 1 SATB 1 2 3

Dariusz M Plewczynski, D. Plewczyński, Christoforos Nikolaou, 2021 .

Evaluation of Machine Learning Algorithms on Protein-Protein Interactions

Julian Zubek, Dariusz Plewczynski, Indrajit Saha, 2013, ICMMI.

kNNsim: k-Nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules

Dariusz Plewczynski, D. Plewczyński, 2009, Journal of molecular modeling.

TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections

Dariusz Plewczynski, D. Plewczyński, 2008, 2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies.

VoteDock: Consensus docking method for prediction of protein–ligand interactions

Dariusz Plewczynski, Marcin von Grotthuss, Leszek Rychlewski, 2011, J. Comput. Chem..

Three-dimensional organization and dynamics of the genome

Przemyslaw Szalaj, D. Plewczyński, 2018, Cell Biology and Toxicology.

Predicting Post-Translational Modifications from Local Sequence Fragments Using Machine Learning Algorithms: Overview and Best Practices.

Dariusz Plewczynski, Marcin Kierczak, Marcin Tatjewski, 2017, Methods in molecular biology.

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

M. Grynberg, A. Gruca, D. Plewczyński, 2016, Molecular reproduction and development.

Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization

Dariusz M Plewczynski, Y. Ruan, Pawel Trzaskoma, 2020, Nature Communications.

3D-Hit: fast structural comparison of proteins on multicore architectures

Dariusz Plewczynski, Leszek Rychlewski, Maciej Cytowski, 2014, Optim. Lett..

3D-Hit: fast structural comparison of proteins on multicore architectures

L. Rychlewski, D. Plewczyński, M. Cytowski, 2013, Optimization Letters.

Computational modelling of three-dimensional genome structure.

Dariusz Plewczynski, D. Plewczyński, 2020, Methods.

Free energy-based model of CTCF-mediated chromatin looping in the human genome.

Dariusz Plewczynski, Michal Lazniewski, Wayne Dawson, 2020, Methods.

Spring Model - chromatin modeling tool based on OpenMM.

Dariusz Plewczynski, Julia Rozycka, Michal Kadlof, 2019, Methods.

Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

Dariusz Plewczynski, Ziad Al Bkhetan, Michal Kadlof, 2019, Methods.

Spring Model – chromatin modeling tool based on OpenMM

Dariusz Plewczynski, Michal Kadlof, Julia Rozycka, 2019, bioRxiv.

The World Color Survey: Data Analysis and Simulations

Dariusz Plewczynski, Franciszek Rakowski, Michal Lukasik, 2019, Complexity Applications in Language and Communication Sciences.

Diffusion on curved, periodic surfaces.

K. Burdzy, A. Aksimentiev, D. Plewczyński, 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

Chromatin: A Semi-Structured Polymer

Dariusz Plewczynski, Michal Lazniewski, Wayne Dawson, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Multi-levels 3D Chromatin Interactions Prediction Using Epigenomic Profiles

Dariusz Plewczynski, Ziad Al Bkhetan, D. Plewczyński, 2017, ISMIS.

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

Y. Ruan, D. Plewczyński, Jakub Lipiński, 2023, Scientific reports.

Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome

Dariusz Plewczynski, Wayne Dawson, W. Dawson, 2017, bioRxiv.

SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation

Ujjwal Maulik, Sanghamitra Bandyopadhyay, Dariusz Plewczynski, 2012, IEEE Geoscience and Remote Sensing Letters.

Inferring CTCF-binding patterns and anchored loops across human tissues and cell types

Mulin Jun Li, Dariusz M Plewczynski, P. Sham, 2023, Patterns.

ConsensuSV—from the whole-genome sequencing data to the complete variant list

D. Plewczyński, Mateusz Chiliński, 2022, Bioinform..

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale

Dariusz Plewczynski, Yijun Ruan, Zhonghui Tang, 2019, Genome Biology.

Highlights from the 11th ISCB Student Council Symposium 2015

Zdenka Kuncic, Westa Domanova, Dan F. DeBlasio, 2016, BMC Bioinformatics.

3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture

Dariusz Plewczynski, Yijun Ruan, Xingwang Li, 2016 .

Highlights from the eleventh ISCB Student Council Symposium 2015

Dan F. DeBlasio, Sean J. Humphrey, P. Bertolazzi, 2016 .

Identification of Epigenetic Biomarkers with the use of Gene Expression and DNA Methylation for Breast Cancer Subtypes

Somnath Rakshit, Dariusz Plewczynski, Indrajit Saha, 2019, TENCON 2019 - 2019 IEEE Region 10 Conference (TENCON).

Simulation Model on Network Public Opinion Communication Model of Major Public Health Emergency and Management System Design

Dariusz M Plewczynski, D. Plewczyński, Mei Zhi, 2022, Scientific Programming.

Deep Learning for Detection and Localization of Thoracic Diseases Using Chest X-Ray Imagery

Ujjwal Maulik, Somnath Rakshit, Dariusz Plewczynski, 2019, ICAISC.

Soft Computing Approach for VLSI Mincut Partitioning: The State of the Arts

Ujjwal Maulik, Dariusz Plewczynski, Indrajit Saha, 2012, SocProS.

Novel COL12A1 variant as a cause of mild familial extracellular matrix‐related myopathy

A. Jezela-Stanek, R. Płoski, D. Plewczyński, 2019, Clinical genetics.

A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data

D. Plewczyński, T. Burzykowski, J. Claesen, 2019, J. Comput. Biol..

Information-sharing and aggregation models for interacting minds pdf

Dariusz Plewczynski, Michal Denkiewicz, Joanna Raczaszek-Leonardi, 2011, ArXiv.

AutoMotif server: prediction of single residue post-translational modifications in proteins

L. Rychlewski, D. Plewczyński, L. Wyrwicz, 2005, Bioinform..

SeqPIP-2020: Sequence based Protein Interaction Prediction Contest

Piyali Chatterjee, Ayatullah Faruk Mollah, Anup Kumar Halder, 2020, bioRxiv.

2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity

Subhadip Basu, J. Włodarczyk, D. Plewczyński, 2016, Bioinform..

Information-Sharing in Three Interacting Minds Solving a Simple Perceptual Task

Dariusz Plewczynski, Michal Denkiewicz, Joanna Raczaszek-Leonardi, 2013, CogSci.