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List of works by Lukasz Kurgan

A comment on "Prediction of protein structural classes by a new measure of information discrepancy".

scientific article published on 26 July 2006

A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues.

scientific article published on May 2015

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

scientific article published on 13 August 2013

A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds

scientific article

A divide and conquer method for learning large Fuzzy Cognitive Maps

A new synaptic plasticity rule for networks of spiking neurons

scientific article published in January 2006

A tree-projection-based algorithm for multi-label recurrent-item associative-classification rule generation

APOD: accurate sequence-based predictor of disordered flexible linkers

scientific article published on 01 December 2020

ATPsite: sequence-based prediction of ATP-binding residues

scientific article published on 14 October 2011

Accuracy of protein-level disorder predictions

scientific article published on 15 October 2019

Accurate prediction of ATP-binding residues using sequence and sequence-derived structural descriptors

Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus

article published in 2013

Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility

scientific article published in July 2010

Accurate sequence-based prediction of catalytic residues

scientific article published on 18 August 2008

Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility

scientific article published in November 2010

Analyzing the effects of protecting osmolytes on solute–water interactions by solvatochromic comparison method: II. Globular proteins

scholarly article in RSC Advances, vol. 5 no. 73, 2015

Autophagy-related intrinsically disordered proteins in intra-nuclear compartments

scientific article published on 5 July 2016

BEST: improved prediction of B-cell epitopes from antigen sequences

scientific article (publication date: 2012)

CRYSTALP2: sequence-based protein crystallization propensity prediction

scientific article

Classification of Cell Membrane Proteins

Classifier ensembles for protein structural class prediction with varying homology

scientific article published on 31 July 2006

Codon selection reduces GC content bias in nucleic acids encoding for intrinsically disordered proteins

scientific article published on 07 June 2019

Comparative Analysis of the Impact of Discretization on the Classification with Naïve Bayes and Semi-Naïve Bayes Classifiers

Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins

scientific article published on 04 December 2020

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

scientific article

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

scientific article published on 19 September 2020

Comprehensive comparative assessment of in-silico predictors of disordered regions

scientific article published in February 2012

Comprehensive overview and assessment of computational prediction of microRNA targets in animals

scientific article

Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains

scientific article published on 15 December 2017

Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions

scientific article published on 6 June 2017

Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.

scientific article published on 9 January 2013

Computational Prediction of Intrinsic Disorder in Protein Sequences with the disCoP Meta-predictor

scientific article published on 01 January 2020

Computational Prediction of Intrinsic Disorder in Proteins

scientific article published on 3 April 2017

Computational Prediction of Protein Secondary Structure from Sequence

scientific article published in November 2016

Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences

scientific article published on 01 January 2019

Computational prediction of B cell epitopes from antigen sequences

scientific article

Computational prediction of functions of intrinsically disordered regions

scientific article published on 20 May 2019

Computational prediction of secondary and supersecondary structures

scientific article

Consensus-Based Prediction of RNA and DNA Binding Residues from Protein Sequences

Correction to disordered proteinaceous machines

scientific article published on 26 March 2015

Covering complete proteomes with X-ray structures: a current snapshot

scientific article

Critical assessment of high-throughput standalone methods for secondary structure prediction

scientific article published on 20 January 2011

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity

scientific article published on 27 February 2017

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.

scientific article published on 22 June 2017

DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server

scientific article published on 21 December 2019

DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences

scientific article published on June 2016

DISOselect: Disorder predictor selection at the protein level

scientific article published on 07 November 2019

Data-driven Nonlinear Hebbian Learning method for Fuzzy Cognitive Maps

DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions

scientific article published on 27 May 2019

DescribePROT: database of amino acid-level protein structure and function predictions

scientific article published on 29 October 2020

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility

Disordered Function Conjunction: On the in-silico function annotation of intrinsically disordered regions

scientific article published on 01 January 2020

Disordered RNA-Binding Region Prediction with DisoRDPbind

scientific article published on 01 January 2020

Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea

scientific article

Disordered proteinaceous machines

scientific article

D²P²: database of disordered protein predictions

scientific article

Ensemble of classifiers to improve accuracy of the CLIP4 machine-learning algorithm

scholarly article published 8 March 2002

Evolutionary Development of Fuzzy Cognitive Maps

article

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

scientific article published on 18 June 2014

Expert-Based and Computational Methods for Developing Fuzzy Cognitive Maps

Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions

scientific article published in November 2012

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

scientific article published on 19 December 2017

Genes encoding intrinsic disorder in Eukaryota have high GC content

scientific article published on 15 December 2016

Genetic learning of fuzzy cognitive maps

Genome-scale prediction of proteins with long intrinsically disordered regions

scientific article

Genome-wide analysis of thapsigargin-induced microRNAs and their targets in NIH3T3 cells

scientific article

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

article by Daniel J Klionsky et al published January 2021 in Autophagy

High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder

scientific article

High-throughput prediction of disordered moonlighting regions in protein sequences

scholarly article by Fanchi Meng published in September 2018

Higher-order Fuzzy Cognitive Maps

Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences

scientific article published in September 2005

Highly scalable and robust rule learner: performance evaluation and comparison

scientific article published in February 2006

How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe

scientific article

HuMiTar: a sequence-based method for prediction of human microRNA targets

scientific article published on 22 December 2008

Human structural proteome-wide characterization of Cyclosporine A targets

scientific article published on 28 August 2014

IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell

scientific article published on 30 September 2020

Identification of tubulin drug binding sites and prediction of relative differences in binding affinities to tubulin isotypes using digital signal processing

scientific article published on 10 September 2008

Impact of imputation of missing values on classification error for discrete data

Impact of the Predicted Protein Structural Content on Prediction of Structural Classes for the Twilight Zone Proteins

Improved Prediction of Relative Solvent Accessibility Using Two-stage Support Vector Regression

article published in 2007

Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information

scientific article

Improved machine learning method for analysis of gas phase chemistry of peptides

scientific article

Improved prediction of residue flexibility by embedding optimized amino acid grouping into RSA-based linear models.

scientific article published on 9 August 2014

Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

scientific article

Improved sequence-based prediction of strand residues

scientific article published in February 2011

In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces

scientific article published on 19 August 2015

In-silico prediction of disorder content using hybrid sequence representation

scientific article

Interplay between the oxidoreductase PDIA6 and microRNA-322 controls the response to disrupted endoplasmic reticulum calcium homeostasis.

scientific article published on 10 June 2014

Intrinsic disorder in the BK channel and its interactome

scientific article

Investigation of atomic level patterns in protein--small ligand interactions

scientific article

Knowledge discovery approach to automated cardiac SPECT diagnosis.

scientific article

Learning fuzzy cognitive maps with required precision using genetic algorithm approach

Learning of fuzzy cognitive maps using density estimate

scientific article published on 14 February 2012

MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles

scientific article published on January 2013

Machine learning in the life sciences

scientific article published on March 2007

Machine learning models in protein bioinformatics.

scientific article published in September 2011

Meta prediction of protein crystallization propensity.

scientific article

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

scientific article

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences

scientific article

Molecular recognition features (MoRFs) in three domains of life

scientific article published on 09 December 2015

Monocytes from patients with osteoarthritis display increased osteoclastogenesis and bone resorption: the In Vitro Osteoclast Differentiation in Arthritis study.

scientific article

More than just tails: intrinsic disorder in histone proteins

scientific article published on 27 April 2012

Multi-label Associative Classification of Medical Documents from MEDLINE

Multilabel associative classification categorization of MEDLINE articles into MeSH keywords

scientific article published in March 2007

NOT THAT RIGID MIDGETS AND NOT SO FLEXIBLE GIANTS: ON THE ABUNDANCE AND ROLES OF INTRINSIC DISORDER IN SHORT AND LONG PROTEINS

Novel scales based on hydrophobicity indices for secondary protein structure.

scientific article

ON THE COMPLEMENTARITY OF THE CONSENSUS-BASED DISORDER PREDICTION

article published in 2011

On the intrinsic disorder status of the major players in programmed cell death pathways

scientific article published on 17 September 2013

On the relation between residue flexibility and local solvent accessibility in proteins

scientific article published in August 2009

On the relation between the predicted secondary structure and the protein size

scientific article

Optimization of the Sliding Window Size for Protein Structure Prediction

PDID: database of molecular-level putative protein-drug interactions in the structural human proteome

scientific article

PFRES: protein fold classification by using evolutionary information and predicted secondary structure.

scientific article

PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection

scientific article published on 01 December 2020

PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types

scientific article

PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types

scientific article published on 07 June 2020

Parallel Learning of Large Fuzzy Cognitive Maps

Predicting Functions of Disordered Proteins with MoRFpred

scientific article published on 01 January 2019

Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors

scientific article published on 29 November 2011

Prediction and characterization of cyclic proteins from sequences in three domains of life

scientific article published on 10 May 2013

Prediction of DNA-binding residues in local segments of protein sequences with Fuzzy Cognitive Maps

scientific article published on 28 December 2018

Prediction of Disordered RNA, DNA, and Protein Binding Regions Using DisoRDPbind

scientific article published in January 2017

Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER

scientific article published on 01 January 2020

Prediction of Protein Structural Class Using PSI-BLAST Profile Based Collocation of Amino Acid Pairs

Prediction of Secondary Protein Structure Content from Primary Sequence Alone – A Feature Selection Based Approach

Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments.

scientific article

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

scientific article

Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs

scientific article

Prediction of intrinsic disorder in proteins using MFDp2.

scientific article

Prediction of protein crystallization using collocation of amino acid pairs

scientific article published on 15 February 2007

Prediction of protein folding rates from primary sequences using hybrid sequence representation

scientific article published in April 2009

Prediction of protein secondary structure content for the twilight zone sequences.

scientific article

Prediction of protein structural class for the twilight zone sequences

scientific article published on 5 April 2007

Prediction of protein structural class using novel evolutionary collocation-based sequence representation

scientific article published in July 2008

Prediction of the Number of Helices for the Twilight Zone Proteins

Prediction of three dimensional structure of calmodulin

scientific article published on January 2006

Protein intrinsic disorder as a flexible armor and a weapon of HIV-1.

scientific article published on 28 October 2011

QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores

scientific article published on 27 April 2021

Quality Assessment for the Putative Intrinsic Disorder in Proteins

scientific article published on 01 May 2019

Quantitative analysis of the conservation of the tertiary structure of protein segments

scientific article published in July 2006

RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale

scientific article

Recognition of partially occluded and rotated images with a network of spiking neurons

scientific article

Resilience of death: intrinsic disorder in proteins involved in the programmed cell death

scientific article

Review and comparative assessment of sequence-based predictors of protein-binding residues

scientific article published on March 2017

Review and comparative assessment of similarity-based methods for prediction of drug–protein interactions in the druggable human proteome

article

SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

scientific article published on May 2008

SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences

scientific article published on 01 July 2019

SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

scientific article published on 2 November 2011

Secondary structure-based assignment of the protein structural classes

scientific article

Sequence based prediction of relative solvent accessibility using two-stage support vector regression with confidence values

article

Sequence based residue depth prediction using evolutionary information and predicted secondary structure

scientific article

Sequence representation and prediction of protein secondary structure for structural motifs in twilight zone proteins.

scientific article

Sequence-Based Methods for Real Value Predictions of Protein Structure

Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis

article

Sequence-Only Based Prediction of β -Turn Location and Type Using Collocation of Amino Acid Pairs

article

Sequence-based Gaussian network model for protein dynamics

scientific article published on 12 December 2013

Sequence-based prediction of protein crystallization, purification and production propensity ⬇️

scientific article

Stochastic machines as a colocalization mechanism for scaffold protein function

scientific article

Structural and functional analysis of "non-smelly" proteins

scientific article published on 05 September 2019

Structural disorder in viral proteins

scientific article published on 13 May 2014

Structural features important for differences in protein partitioning in aqueous dextran-polyethylene glycol two-phase systems of different ionic compositions.

scientific article

Structural protein descriptors in 1-dimension and their sequence-based predictions

scientific article

Survey of Similarity-based Prediction of Drug-protein Interactions

scientific article published on 08 August 2019

Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures

scientific article published on 20 September 2017

Systematic investigation of sequence and structural motifs that recognize ATP.

scientific article

Taxonomic Landscape of the Dark Proteomes: Whole-Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity

scientific article published on 08 October 2018

The WWW Based Data Mining Toolbox Architecture

scholarly article published 2003

The increased in vitro osteoclastogenesis in patients with rheumatoid arthritis is due to increased percentage of precursors and decreased apoptosis - the In Vitro Osteoclast Differentiation in Arthritis (IODA) study.

scientific article published on 17 October 2010

The intrinsic disorder status of the human hepatitis C virus proteome

scientific article published on 22 April 2014

Unstructural biology of the Dengue virus proteins.

scientific article

Untapped Potential of Disordered Proteins in Current Druggable Human Proteome.

scientific article

What are the structural features that drive partitioning of proteins in aqueous two-phase systems?

scientific article

fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization.

scientific article published on 3 January 2018

flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

scientific article published on 21 July 2021

iFC2: an integrated web-server for the improved prediction of protein fold type, structural class, and secondary structure content

iFC²: an integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content

scientific article

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

scientific article published on 01 June 2021

mi-DS: Multiple-Instance Learning Algorithm

scientific article published on 18 June 2012

xGENIA: A comprehensive OWL ontology based on the GENIA corpus

scientific article published on 20 March 2007

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