Our Publications

List of our papers

2020

  1. Urban P, Rezaei Tabar V, Denkiewicz M, Bokota G, Das N, Basu S, Plewczyński D, (2020)
    The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process.
    (J. Comput. Biol.) [Pub Med ID: 32175768]
  2. Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczyński D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis C, Promponas V, Kajava A, Hancock J, Tosatto S, Dosztanyi Z, Andrade-Navarro M, (2020)
    Disentangling the complexity of low complexity proteins.
    (Brief. Bioinformatics) [Pub Med ID: 24939692]
  3. Xu H, Zhang S, Yi X, Plewczyński D, Li M, (2020)
    Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.
    (Comput Struct Biotechnol J) [Pub Med ID: 29419817]
  4. Wang P, Tang Z, Lee B, Zhu J, Cai L, Szałaj P, Tian S, Zheng M, Plewczyński D, Ruan X, Liu E, Wei C, Ruan Y, (2020)
    Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia.
    (Genome Biol.) [Pub Med ID: 22265404]
  5. Trzaskoma P, Ruszczycki B, Lee B, Pels K, Krawczyk K, Bokota G, Szczepankiewicz A, Aaron J, Walczak A, Śliwińska M, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczynski G, (2020)
    Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.
    (Nat Commun) [Pub Med ID: 25768903]
  6. Własnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szałaj P, Tang Z, Ruan Y, Plewczyński D, (2020)
    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.) [Pub Med ID: 32442297]

2019

  1. Denkiewicz M, Saha I, Rakshit S, Sarkar J, Plewczyński D, (2019)
    Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation.
    (Front Genet) [Pub Med ID: 30207593]
  2. Kadlof M, Różycka J, Plewczyński D, (2019)
    Spring Model - Chromatin Modeling Tool Based on OpenMM.
    (Methods) [Pub Med ID: 31790732]
  3. Halder A, Denkiewicz M, Sengupta K, Basu S, Plewczyński D, (2019)
    Aggregated network centrality shows non-random structure of genomic and proteomic networks.
    (Methods) [Pub Med ID: 31740366]
  4. Jezela-Stanek A, Walczak A, Łaźniewski M, Kosińska J, Stawiński P, Murcia Pienkowski V, Biernacka A, Rydzanicz M, Kostrzewa G, Krajewski P, Plewczyński D, Płoski R, (2019)
    Novel COL12A1 variant as a cause of mild familial extracellular matrix-related myopathy.
    (Clin. Genet.) [Pub Med ID: 30920656]
  5. Kazakiewicz D, Claesen J, Górczak K, Plewczyński D, Burzykowski T, (2019)
    A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data.
    (J. Comput. Biol.) [Pub Med ID: 31314581]
  6. Ruszczycki B, Pels K, Walczak A, Zamłyńska K, Such M, Szczepankiewicz A, Hall M, Magalska A, Magnowska M, Wolny A, Bokota G, Basu S, Pal A, Plewczyński D, Wilczynski G, (2019)
    Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images.
    (Front Neuroanat) [Pub Med ID: 27412086]
  7. Sadowski M, Kraft A, Szałaj P, Własnowolski M, Tang Z, Ruan Y, Plewczyński D, (2019)
    Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.
    (Genome Biol.) [Pub Med ID: 28406212]
  8. Saha S, Chatterjee P, Basu S, Nasipuri M, Plewczyński D, (2019)
    FunPred 3.0: improved protein function prediction using protein interaction network.
    (PeerJ) [Pub Med ID: 8609628]
  9. Szczepińska T, Rusek A, Plewczyński D, (2019)
    Intermingling of chromosome territories.
    (Genes Chromosomes Cancer) [Pub Med ID: 30828902]
  10. Halder A, Chatterjee P, Nasipuri M, Plewczyński D, Basu S, (2019)
    3gClust: Human Protein Cluster Analysis.
    (IEEE/ACM Trans Comput Biol Bioinform) [Pub Med ID: 29993556]
  11. Rakshit S, Saha I, Własnowolski M, Maulik U, Plewczyński D, (2019)
    Deep Learning for Detection and Localization of Thoracic Diseases Using Chest X-Ray Imagery.
    (ICAISC 2019) [Pub Med ID: -]
  12. Maszczyk P, Babkiewicz E, Ciszewski K, Dabrowski K, Dynak P, Krajewski K, Urban P, Żebrowski M, Wilczynski W, (2019)
    Combined effects of elevated epilimnetic temperature and metalimnetic hypoxia on the predation rate of planktivorous fish.
    (J. Plankton Res.) [Pub Med ID: 15821280]
  13. Urban P, Rezaei V, Bokota G, Denkiewicz M, Basu S, Plewczyński D, (2019)
    Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation.
    (J. Comput. Biol.) [Pub Med ID: 28158194]

2018

  1. Basu S, Saha P, Roszkowska M, Magnowska M, Baczynska E, Das N, Plewczyński D, Wlodarczyk J, (2018)
    Quantitative 3-D morphometric analysis of individual dendritic spines.
    (Sci Rep) [Pub Med ID: 29476060]
  2. Ciara E, Rokicki D, Łaźniewski M, Mierzewska H, Jurkiewicz E, Bekiesińska-Figatowska M, Piekutowska-Abramczuk D, Iwanicka-Pronicka K, Szymańska E, Stawiński P, Kosińska J, Pollak A, Pronicki M, Plewczyński D, Płoski R, Pronicka E, (2018)
    Clinical and molecular characteristics of newly reported mitochondrial disease entity caused by biallelic PARS2 mutations.
    (J. Hum. Genet.) [Pub Med ID: 29410512]
  3. Szałaj P, Plewczyński D, (2018)
    Three-dimensional organization and dynamics of the genome.
    (Cell Biol. Toxicol.) [Pub Med ID: 29568981]
  4. Al Bkhetan Z, Plewczyński D, (2018)
    Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction.
    (Sci Rep) [Pub Med ID: 29581440]
  5. Marusiak A, Prelowska M, Mehlich D, Łaźniewski M, Kaminska K, Gorczynski A, Korwat A, Sokolowska O, Kedzierska H, Gołąb J, Biernat W, Plewczyński D, Brognard J, Nowis D, (2018)
    Upregulation of MLK4 promotes migratory and invasive potential of breast cancer cells.
    (Oncogene) [Pub Med ID: 30552384]
  6. Chlebowska-Tuz J, Sokolowska O, Gaj P, Łaźniewski M, Firczuk M, Borowiec K, Sas-Nowosielska H, Bajor M, Malinowska A, Muchowicz A, Ramji K, Stawiński P, Sobczak M, Pilch Z, Rodziewicz-Lurzynska A, Zajac M, Giannopoulos K, Juszczynski P, Basak G, Plewczyński D, Płoski R, Gołąb J, Nowis D, (2018)
    Inhibition of protein disulfide isomerase induces differentiation of acute myeloid leukemia cells.
    (Haematologica) [Pub Med ID: 24464223]
  7. Łaźniewski M, Dawson W, Rusek A, Plewczyński D, (2018)
    One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease.
    (Semin. Cell Dev. Biol.) [Pub Med ID: 30096365]
  8. Basu S, Plewczyński D, (2018)
    Emerging and threatening infectious diseases.
    (Brief Funct Genomics) [Pub Med ID: 30476067]
  9. Malkowska M, Zubek J, Plewczyński D, Wyrwicz L, (2018)
    ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning.
    (PeerJ) [Pub Med ID: 12704603]
  10. Rezaei Tabar V, Plewczyński D, (2018)
    Mixture of Forward-Directed and Backward-Directed Autoregressive Hidden Markov Models for Time Series Modeling
    (JIRSS) [Pub Med ID: -]

2017

  1. Łaźniewski M, Dawson W, Szczepińska T, Plewczyński D, (2017)
    The structural variability of the influenza A hemagglutinin receptor-binding site.
    (Brief Funct Genomics) [Pub Med ID: 29253080]
  2. Dawson W, Łaźniewski M, Plewczyński D, (2017)
    RNA structure interactions and ribonucleoprotein processes of the influenza A virus.
    (Brief Funct Genomics) [Pub Med ID: 29040388]
  3. Zubek J, Denkiewicz M, Barański J, Wróblewski P, Rączaszek-Leonardi J, Plewczyński D, (2017)
    Social adaptation in multi-agent model of linguistic categorization is affected by network information flow.
    (PLoS ONE) [Pub Med ID: 28809957]
  4. Ołdak M, Oziębło D, Pollak A, Stępniak I, Łaźniewski M, Lechowicz U, Kochanek K, Furmanek M, Tacikowska G, Plewczyński D, Wolak T, Płoski R, Skarżyński H, (2017)
    Novel neuro-audiological findings and further evidence for TWNK involvement in Perrault syndrome.
    (J Transl Med) [Pub Med ID: 28178980]
  5. Tatjewski M, Kierczak M, Plewczyński D, (2017)
    Predicting Post-Translational Modifications from Local Sequence Fragments Using Machine Learning Algorithms: Overview and Best Practices.
    (Methods Mol. Biol.) [Pub Med ID: 27787833]

2016

  1. Bokota G, Magnowska M, Kuśmierczyk T, Łukasik M, Roszkowska M, Plewczyński D, (2016)
    Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis.
    (Front Comput Neurosci) [Pub Med ID: 28066226]
  2. Szałaj P, Tang Z, Michalski P, Piętal M, Luo O, Sadowski M, Li X, Radew K, Ruan Y, Plewczyński D, (2016)
    An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.
    (Genome Res.) [Pub Med ID: 27789526]
  3. Mazzocco G, Łaźniewski M, Migdał P, Szczepińska T, Radomski J, Plewczyński D, (2016)
    3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale.
    (Database (Oxford)) [Pub Med ID: 27694207]
  4. Szałaj P, Michalski P, Wróblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczyński D, (2016)
    3D-GNOME: an integrated web service for structural modeling of the 3D genome.
    (Nucleic Acids Res.) [Pub Med ID: 27185892]
  5. Basu S, Plewczyński D, Saha S, Roszkowska M, Magnowska M, Baczynska E, Wlodarczyk J, (2016)
    2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity.
    (Bioinformatics) [Pub Med ID: 27153678]
  6. Zubek J, Stitzel M, Ucar D, Plewczyński D, (2016)
    Computational inference of H3K4me3 and H3K27ac domain length.
    (PeerJ) [Pub Med ID: 26989607]
  7. Chatterjee P, Basu S, Zubek J, Kundu M, Nasipuri M, Plewczyński D, (2016)
    PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.
    (J Mol Model) [Pub Med ID: 26969678]
  8. Tatjewski M, Gruca A, Plewczyński D, Grynberg M, (2016)
    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.
    (Mol. Reprod. Dev.) [Pub Med ID: 26660717]

2015

  1. Tang Z, Luo O, Li X, Zheng M, Zhu J, Szałaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian S, Penrad-Mobayed M, Sachs L, Ruan X, Wei C, Liu E, Wilczynski G, Plewczyński D, Li G, Ruan Y, (2015)
    CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
    (Cell) [Pub Med ID: 26686651]
  2. Kazakiewicz D, Karr J, Langner K, Plewczyński D, (2015)
    A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium.
    (Comput Biol Chem) [Pub Med ID: 26271684]
  3. Zubek J, Tatjewski M, Boniecki A, Mnich M, Basu S, Plewczyński D, (2015)
    Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae.
    (PeerJ) [Pub Med ID: 26157620]
  4. Saha I, Rak B, Bhowmick S, Maulik U, Bhattacharjee D, Koch U, Łaźniewski M, Plewczyński D, (2015)
    Binding Activity Prediction of Cyclin-Dependent Inhibitors.
    (J Chem Inf Model) [Pub Med ID: 26079845]
  5. Lin H, Chen W, Anandakrishnan R, Plewczyński D, (2015)
    Application of machine learning method in genomics and proteomics.
    (ScientificWorldJournal) [Pub Med ID: 25961076]

2014

  1. Arcanjo A, Mazzocco G, De Oliveira S, Plewczyński D, Radomski J, (2014)
    Role of the host genetic variability in the influenza A virus susceptibility.
    (Acta Biochim. Pol.) [Pub Med ID: 25184407]
  2. Saha I, Zubek J, Klingström T, Forsberg S, Wikander J, Kierczak M, Maulik U, Plewczyński D, (2014)
    Ensemble learning prediction of protein-protein interactions using proteins functional annotations.
    (Mol Biosyst) [Pub Med ID: 24469380]
  3. Plewczyński D, Philips A, Von Grotthuss M, Rychlewski L, Ginalski K, (2014)
    HarmonyDOCK: the structural analysis of poses in protein-ligand docking.
    (J. Comput. Biol.) [Pub Med ID: 21091053]

2013

  1. Sriwastava B, Basu S, Maulik U, Plewczyński D, (2013)
    PPIcons: identification of protein-protein interaction sites in selected organisms.
    (J Mol Model) [Pub Med ID: 23729008]
  2. Saha I, Mazzocco G, Plewczyński D, (2013)
    Consensus classification of human leukocyte antigen class II proteins.
    (Immunogenetics) [Pub Med ID: 23229472]

2012

  1. Plewczyński D, Basu S, Saha I, (2012)
    AMS 4.0: consensus prediction of post-translational modifications in protein sequences.
    (Amino Acids) [Pub Med ID: 22555647]
  2. Saha I, Plewczyński D, Maulik U, Bandyopadhyay S, (2012)
    Improved differential evolution for microarray analysis.
    (Int J Data Min Bioinform) [Pub Med ID: 22479820]
  3. Saha I, Maulik U, Bandyopadhyay S, Plewczyński D, (2012)
    Fuzzy clustering of physicochemical and biochemical properties of amino acids.
    (Amino Acids) [Pub Med ID: 21993537]

2011

  1. Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczyński D, (2011)
    PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines.
    (J Mol Model) [Pub Med ID: 21594694]
  2. Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczyński D, (2011)
    PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables.
    (Cell. Mol. Biol. Lett.) [Pub Med ID: 21442443]
  3. Plewczyński D, Klingström T, (2011)
    GIDMP: good protein-protein interaction data metamining practice.
    (Cell. Mol. Biol. Lett.) [Pub Med ID: 21394448]
  4. Nowosielski M, Hoffmann M, Wyrwicz L, Stepniak P, Plewczyński D, Łaźniewski M, Ginalski K, Rychlewski L, (2011)
    Detailed mechanism of squalene epoxidase inhibition by terbinafine.
    (J Chem Inf Model) [Pub Med ID: 21229992]
  5. Plewczyński D, (2011)
    Brainstorming: weighted voting prediction of inhibitors for protein targets.
    (J Mol Model) [Pub Med ID: 20857153]
  6. Klingström T, Plewczyński D, (2011)
    Protein-protein interaction and pathway databases, a graphical review.
    (Brief. Bioinformatics) [Pub Med ID: 20851835]
  7. Plewczyński D, Łaźniewski M, Von Grotthuss M, Rychlewski L, Ginalski K, (2011)
    VoteDock: consensus docking method for prediction of protein-ligand interactions.
    (J Comput Chem) [Pub Med ID: 20812324]
  8. Plewczyński D, Łaźniewski M, Augustyniak R, Ginalski K, (2011)
    Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.
    (J Comput Chem) [Pub Med ID: 20812323]

2010

  1. Möller G, Husen B, Kowalik D, Hirvelä L, Plewczyński D, Rychlewski L, Messinger J, Thole H, Adamski J, (2010)
    Species used for drug testing reveal different inhibition susceptibility for 17beta-hydroxysteroid dehydrogenase type 1.
    (PLoS ONE) [Pub Med ID: 20544026]
  2. Basu S, Plewczyński D, (2010)
    AMS 3.0: prediction of post-translational modifications.
    (BMC Bioinformatics) [Pub Med ID: 20423529]

2009

  1. Plewczyński D, Von Grotthuss M, Rychlewski L, Ginalski K, (2009)
    Virtual high throughput screening using combined random forest and flexible docking.
    (Comb. Chem. High Throughput Screen.) [Pub Med ID: 19519327]
  2. Plewczyński D, Spieser S, Koch U, (2009)
    Performance of machine learning methods for ligand-based virtual screening.
    (Comb. Chem. High Throughput Screen.) [Pub Med ID: 19442065]
  3. Plewczyński D, Ginalski K, (2009)
    The interactome: predicting the protein-protein interactions in cells.
    (Cell. Mol. Biol. Lett.) [Pub Med ID: 18839074]
  4. Plewczyński D, (2009)
    kNNsim: k-nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules.
    (J Mol Model) [Pub Med ID: 18663491]
  5. Plewczyński D, Rychlewski L, (2009)
    Meta-basic estimates the size of druggable human genome.
    (J Mol Model) [Pub Med ID: 18663489]

2008

  1. Von Grotthuss M, Plewczyński D, Vriend G, Rychlewski L, (2008)
    3D-Fun: predicting enzyme function from structure.
    (Nucleic Acids Res.) [Pub Med ID: 18515349]
  2. Plewczyński D, Slabinski L, Ginalski K, Rychlewski L, (2008)
    Prediction of signal peptides in protein sequences by neural networks.
    (Acta Biochim. Pol.) [Pub Med ID: 18506221]
  3. Knizewski L, Steczkiewicz K, Kuchta K, Wyrwicz L, Plewczyński D, Kolinski A, Rychlewski L, Ginalski K, (2008)
    Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases.
    (Cell Cycle) [Pub Med ID: 18235229]
  4. Plewczyński D, Tkacz A, Wyrwicz L, Rychlewski L, Ginalski K, (2008)
    AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update.
    (J Mol Model) [Pub Med ID: 17994256]

2007

  1. Plewczyński D, Hoffmann M, Von Grotthuss M, Ginalski K, Rychewski L, (2007)
    In silico prediction of SARS protease inhibitors by virtual high throughput screening.
    (Chem Biol Drug Des) [Pub Med ID: 17461975]
  2. Plewczyński D, Von Grotthuss M, Spieser S, Rychlewski L, Wyrwicz L, Ginalski K, Koch U, (2007)
    Target specific compound identification using a support vector machine.
    (Comb. Chem. High Throughput Screen.) [Pub Med ID: 17346118]

2006

  1. Holm L, Kääriäinen S, Wilton C, Plewczyński D, (2006)
    Using Dali for structural comparison of proteins.
    (Curr Protoc Bioinformatics) [Pub Med ID: 18428766]
  2. Plewczyński D, Spieser S, Koch U, (2006)
    Assessing different classification methods for virtual screening.
    (J Chem Inf Model) [Pub Med ID: 16711730]
  3. Von Grotthuss M, Plewczyński D, Ginalski K, Rychlewski L, Shakhnovich E, (2006)
    PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
    (BMC Bioinformatics) [Pub Med ID: 16460560]
  4. Plewczyński D, Tkacz A, Wyrwicz L, Godzik A, Kloczkowski A, Rychlewski L, (2006)
    Support-vector-machine classification of linear functional motifs in proteins.
    (J Mol Model) [Pub Med ID: 16341901]

2005

  1. Plewczyński D, Jaroszewski L, Godzik A, Kloczkowski A, Rychlewski L, (2005)
    Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.
    (J Mol Model) [Pub Med ID: 16094535]
  2. Plewczyński D, Tkacz A, Godzik A, Rychlewski L, (2005)
    A support vector machine approach to the identification of phosphorylation sites.
    (Cell. Mol. Biol. Lett.) [Pub Med ID: 15809681]
  3. Plewczyński D, Tkacz A, Wyrwicz L, Rychlewski L, (2005)
    AutoMotif server: prediction of single residue post-translational modifications in proteins.
    (Bioinformatics) [Pub Med ID: 15728119]

2004

  1. Plewczyński D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A, (2004)
    Integrated web service for improving alignment quality based on segments comparison.
    (BMC Bioinformatics) [Pub Med ID: 15271224]
  2. Plewczyński D, Paś J, Von Grotthuss M, Rychlewski L, (2004)
    Comparison of proteins based on segments structural similarity.
    (Acta Biochim. Pol.) [Pub Med ID: 15094837]

2002

  1. Plewczyński D, Paś J, Von Grotthuss M, Rychlewski L, (2002)
    3D-Hit: fast structural comparison of proteins.
    (Appl. Bioinformatics) [Pub Med ID: 15130838]
  2. Redaelli S, Plewczyński D, Macek W, (2002)
    Influence of colored noise on chaotic systems.
    (Phys Rev E Stat Nonlin Soft Matter Phys) [Pub Med ID: 12366173]