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List of works by Dariusz Plewczynski

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

scientific article published on April 2016

3D-Fun: predicting enzyme function from structure

scientific article published on 30 May 2008

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

scientific article published on 22 May 2020

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

scientific article published on 16 May 2016

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

3D-Hit: fast structural comparison of proteins.

scientific article published in January 2002

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

scientific article published on 02 October 2016

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

scientific article

3gClust: Human Protein Cluster Analysis

scientific article published on 30 May 2018

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

scientific article published in 2013

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

scientific article published on 17 July 2019

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

scientific article

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

scientific article

A new multi-objective technique for differential fuzzy clustering

scientific article published in March 2011

A support vector machine approach to the identification of phosphorylation sites

scientific article published in January 2005

AMS 3.0: prediction of post-translational modifications.

scientific article

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

scientific article published on May 4, 2012

Abstract 5347: SK053, a small molecule inhibitor of enzymes involved in allosteric disulfide bonds formation, shows potent anti-leukemic effects and induces differentiation of human AML cells

Aggregated network centrality shows non-random structure of genomic and proteomic networks

scientific article published on 15 November 2019

An empirical Bayes approach for learning directed acyclic graph using MCMC algorithm

scientific article

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

scientific article

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

scientific article

Application of High Quality Amino Acid Indices to AMS 3.0: A Update Note

scientific article published on 4 December 2012

Application of machine learning method in genomics and proteomics

scientific article published on 19 April 2015

Assessing different classification methods for virtual screening

scientific article published in May 2006

Author Correction: Quantitative 3-D morphometric analysis of individual dendritic spines

scientific article published in Scientific Reports

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

scientific article published on 8 November 2007

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

scientific article

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

article by Dariusz Plewczynski et al published 15 May 2005 in Bioinformatics

Binding Activity Prediction of Cyclin-Dependent Inhibitors.

scientific article

Brainstorming: weighted voting prediction of inhibitors for protein targets ⬇️

scientific article published on September 21, 2010

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

scientific article

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

scientific article published in September 2010

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

scientific article published on 11 May 2020

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

scientific article

Comparison of proteins based on segments structural similarity.

scientific article published on January 2004

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

scientific article

Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis

scientific article published on 23 December 2016

Computational approach to dendritic spine taxonomy and shape transition analysis

scientific article

Computational inference of H3K4me3 and H3K27ac domain length

scientific article

Computational inference of H3K4me3 and H3K27ac domain length

scientific article published on 14 March 2016

Computational modelling of three-dimensional genome structure

scientific article published on 29 September 2020

Consensus Multiobjective Differential Crisp Clustering for Categorical Data Analysis

scientific article published in 2010

Consensus classification of human leukocyte antigen class II proteins

scientific article published on 16 November 2012

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

scientific article published on 03 September 2019

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

scientific article published on 01 January 2019

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

scientific article

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

scientific article published on 27 February 2019

Detailed mechanism of squalene epoxidase inhibition by terbinafine

scientific article published on 13 January 2011

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

scientific article published on 7 January 2016

Disentangling the complexity of low complexity proteins

scientific article published on 30 January 2019

Divide and Conquer Ensemble Method for Time Series Forecasting

scientific article

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

scientific article published on 12 February 2022

Emerging and threatening infectious diseases

scientific article published on 01 November 2018

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

scientific article published on 27 January 2014

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

scientific article published in February 2013

Evaluation of Machine Learning Algorithms on Protein-Protein Interactions

scientific article

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

scientific article published on 28 February 2020

FIREcaller: Detecting frequently interacting regions from Hi-C data

scientific article published on 29 December 2020

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

scientific article

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

scientific article published on 06 July 2020

FunPred 3.0: improved protein function prediction using protein interaction network

scientific article published on 22 May 2019

Fuzzy clustering of physicochemical and biochemical properties of amino acids

scientific article published on 13 October 2011

GIDMP: good protein-protein interaction data metamining practice.

scientific article

Generalized Baum-Welch and Viterbi Algorithms Based on the Direct Dependency among Observations

scientific article

Generic Framework for Simulation of Cognitive Systems: A Case Study of Color Category Boundaries

scientific article

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

scientific article

HarmonyDOCK: the structural analysis of poses in protein-ligand docking

scientific article published on 20 November 2010

Highlights from the 11th ISCB Student Council Symposium 2015 : Dublin, Ireland. 10 July 2015

scientific article

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

scientific article published on 31 October 2019

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

scientific article

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

scientific article published on 13 November 2020

Improved differential evolution for microarray analysis

scientific article published in January 2012

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

scientific article published in November 2011

In silico prediction of SARS protease inhibitors by virtual high throughput screening

scientific article published in April 2007

Influence of colored noise on chaotic systems

scientific article published on 24 September 2002

Information-sharing and aggregation models for interacting minds

scientific article

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

scientific article published on 12 July 2018

Integrated web service for improving alignment quality based on segments comparison

scientific article

Intermingling of chromosome territories

scientific article published on 03 March 2019

JUPPI: A multi-level feature based method for PPI prediction and a refined strategy for performance assessment

scientific article published on 26 June 2020

Landau Theory of Meta-learning

scientific article

Landau theory of social clustering

scientific article

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

scientific article

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

scientific article

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

scientific article published on 07 March 2019

Mean-field theory of meta-learning

scientific article

Meta-basic estimates the size of druggable human genome

scientific article published on 29 July 2008

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

scientific article

Modelling of potentially promising SARS protease inhibitors

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

scientific article published on 11 August 2005

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

scientific article published on 2 July 2015

Multi-levels 3D Chromatin Interactions Prediction Using Epigenomic Profiles

scientific article

Multiobjective Differential Crisp Clustering for Evaluation of Clusters Dynamically

scientific article published in 2011

Multiobjective Differential Evolution: A Comparative Study on Benchmark Problems

scientific article

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

scientific article published on 29 March 2022

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

scientific article published on 28 March 2019

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

scientific article

Oncogenes expand during evolution to withstand somatic amplification

scientific article published on 01 November 2018

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

scientific article published on 11 October 2018

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

scientific article

PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.

scientific article

PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier

scientific article

PMAFC: A New Probabilistic Memetic Algorithm Based Fuzzy Clustering

scientific article published in 2011

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

scientific article published on 20 March 2011

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Performance of machine learning methods for ligand-based virtual screening

scientific article published on May 2009

Potent but transient immunosuppression of T-cells is a general feature of CD71<sup>+</sup> erythroid cells

scientific article published on 10 December 2021

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

scientific article

Prediction of signal peptides in protein sequences by neural networks.

scientific article published on 26 May 2008

Protein-protein interaction and pathway databases, a graphical review ⬇️

scientific article published on September 17, 2010

ProteinSplit: splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics

scientific article

Quantitative 3-D morphometric analysis of individual dendritic spines.

scientific article published on 23 February 2018

RNA structure interactions and ribonucleoprotein processes of the influenza A virus

scientific article published on 10 October 2017

Real-coded differential crisp clustering for MRI brain image segmentation

scientific article published in July 2010

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

scientific article published on 04 September 2014

SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation

scientific article published in January 2012

SeqPIP-2020: Sequence based Protein Interaction Prediction Contest

scientific article

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

scientific article

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

scientific article published on 29 November 2018

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

scientific article published on 15 August 2017

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

scientific article published in 2014

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

scientific article

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

scientific article published on 30 July 2019

Species used for drug testing reveal different inhibition susceptibility for 17beta-hydroxysteroid dehydrogenase type 1

scientific article

Spring Model - Chromatin Modeling Tool Based on OpenMM

scientific article published on 30 November 2019

Spring Model – chromatin modeling tool based on OpenMM

scientific article

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

scientific article

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

scientific article published in 2022

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

scientific article

Survival Analysis with the Integration of RNA-Seq and Clinical Data to Identify Breast Cancer Subtype Specific Genes

scientific article

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

scientific article

TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections

scientific article

Target specific compound identification using a support vector machine.

scientific article

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

scientific article

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

scientific article published on 12 March 2020

The RPSP: Web server for prediction of signal peptides

scientific article

The interactome: Predicting the protein-protein interactions in cells

scientific article published on 6 October 2008

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

scientific article published on 11 December 2015

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

scientific article published on 13 December 2017

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

scientific article published on 20 August 2019

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

scientific article published on 26 March 2018

Three-dimensional organization and dynamics of the genome.

scientific article published on 22 March 2018

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

scientific article published on 01 May 2020

Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases

scientific article

Unsupervised and Supervised Learning Approaches Together for Microarray Analysis

scientific article

Unveiling the Molecular Mechanism of Trastuzumab Resistance in SKBR3 and BT474 Cell Lines for HER2 Positive Breast Cancer

scientific article published in 2024

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

scientific article

Using Dali for structural comparison of proteins

scientific article published in July 2006

Virtual high throughput screening using combined random forest and flexible docking

scientific article

VoteDock: consensus docking method for prediction of protein-ligand interactions

scientific article

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

scientific article

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