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    Academic Journals

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

  Authors:Anna Czmil, Michal Wronski, Sylwester Czmil, Marta Sochacka-Pietal, Michal Cmil, Jan Gawor, et al.From:PeerJ (Vol. 10) Peer-Reviewed

  Mar. 29, 20224,472 words Article 1440LBackground Next Generation Sequencing (NGS) techniques dominate today's landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of the leading...

• GIDMP: Good protein-protein interaction data metamining practice

  Authors:Dariusz Plewczynski and Tomas KlingstromFrom:Cellular & Molecular Biology Letters (Vol. 16, Issue 2) Peer-Reviewed

  June 2011 Report

   Citation Only

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

  Authors:Julian Zubek, Marcin Tatjewski, Adam Boniecki, Maciej Mnich, Subhadip Basu, and Dariusz PlewczynskiFrom:PeerJ (Vol. 3) Peer-Reviewed

  July 2, 20157,810 words Article 1310LAccurate identification of protein-protein interactions (PPI) is the key step in understanding proteins' biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated...

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

  Authors:Zhonghui Tang, Oscar Junhong Luo, Xingwang Li, Meizhen Zheng, Jacqueline Jufen Zhu, Przemyslaw Szalaj, et al.From:Cell (Vol. 163, Issue 7) Peer-Reviewed

  Dec. 17, 2015512 words Article

   Abstract Only

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

  Authors:Sovan Saha, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri, and Dariusz PlewczynskiFrom:PeerJ (Vol. 7) Peer-Reviewed

  May 22, 20198,270 words Article 1490LProteins are the most versatile macromolecules in living systems and perform crucial biological functions. In the advent of the post-genomic era, the next generation sequencing is done routinely at the population scale...

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

  Authors:Przemys?aw Sza?aj, Zhonghui Tang, Paul Michalski, Michal J. Pietal, Oscar J. Luo, Micha? Sadowski, et al.From:Genome Research (Vol. 26, Issue 12) Peer-Reviewed

  Dec. 2016 Article

   Citation Only

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

  Authors:Gabriele Moller, Bettina Husen, Dorota Kowalik, Leena Hirvela, Dariusz Plewczynski, Leszek Rychlewski, et al.From:PLoS ONE (Vol. 5, Issue 6) Peer-Reviewed

  June 8, 20106,154 words Article 1510LSteroid-related cancers can be treated by inhibitors of steroid metabolism. In searching for new inhibitors of human 17beta-hydroxysteroid dehydrogenase type 1 (17[beta]-HSD 1) for the treatment of breast cancer or...

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

  Authors:Maja Malkowska, Julian Zubek, Dariusz Plewczynski, and Lucjan S. WyrwiczFrom:PeerJ (Vol. 6) Peer-Reviewed

  Nov. 29, 20186,971 words Report 1370LMotivation The identification of functional sequence variations in regulatory DNA regions is one of the major challenges of modern genetics. Here, we report results of a combined multifactor analysis of properties...

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

  Authors:Julian Zubek, Michal Denkiewicz, Juliusz Baranski, Przemyslaw Wroblewski, Joanna Raczaszek-Leonardi, and Dariusz PlewczynskiFrom:PLoS ONE (Vol. 12, Issue 8) Peer-Reviewed

  Aug. 15, 20178,480 words Report 1380LThis paper explores how information flow properties of a network affect the formation of categories shared between individuals, who are communicating through that network. Our work is based on the established...

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

  Authors:Piyali Chatterjee, Subhadip Basu, Mahantapas Kundu, Mita Nasipuri, and Dariusz PlewczynskiFrom:Cellular & Molecular Biology Letters (Vol. 16, Issue 2) Peer-Reviewed

  June 2011 Report

   Citation Only

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

  Authors:Julian Zubek and Dariusz M. PlewczynskiFrom:PeerJ Computer Science (Vol. 2) Peer-Reviewed

  Aug. 8, 201611,244 words Report 1340LWe describe a method for assessing data set complexity based on the estimation of the underlining probability distribution and Hellinger distance. In contrast to some popular complexity measures, it is not focused on...

• Computational inference of H3K4me3 and H3K27ac domain length

  Authors:Julian Zubek, Michael L. Stitzel, Duygu Ucar, and Dariusz M. PlewczynskiFrom:PeerJ (Vol. 4) Peer-Reviewed

  Mar. 14, 20164,476 words Article 1520LBackground. Recent epigenomic studies have shown that the length of a DNA region covered by an epigenetic mark is not just a byproduct of the assaying technologies and has functional implications for that locus. For...