Publications by authors named "Dariusz Plewczynski"

93Publications

FIREcaller: Detecting frequently interacting regions from Hi-C data.

Comput Struct Biotechnol J 2021 29;19:355-362. Epub 2020 Dec 29.

Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.

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December 2020

Computational modelling of three-dimensional genome structure.

Methods 2020 10 29;181-182:1-4. Epub 2020 Sep 29.

Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland.

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October 2020

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

Methods 2020 10 6;181-182:35-51. Epub 2020 Jul 6.

Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-089, Poland; Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland. Electronic address:

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October 2020

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

Comput Struct Biotechnol J 2020 28;18:558-570. Epub 2020 Feb 28.

2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China.

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February 2020

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

Front Genet 2019;10:1382. Epub 2020 Feb 10.

Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland.

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February 2020

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

Front Genet 2019 31;10:1047. Epub 2019 Oct 31.

Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland.

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October 2019

Spring Model - Chromatin Modeling Tool Based on OpenMM.

Methods 2020 10 30;181-182:62-69. Epub 2019 Nov 30.

Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland. Electronic address:

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October 2020

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

Methods 2020 10 15;181-182:5-14. Epub 2019 Nov 15.

Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland; Computer Science Department, University of California, 2063 Kemper Hall, One Shields Avenue, Davis, CA 95616-8562, United States. Electronic address:

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October 2020

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

J Comput Biol 2019 12 17;26(12):1339-1348. Epub 2019 Jul 17.

Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.

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December 2019

FunPred 3.0: improved protein function prediction using protein interaction network.

PeerJ 2019 22;7:e6830. Epub 2019 May 22.

Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland.

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May 2019