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Items: 1 to 20 of 175

1.

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities.

Juhász J, Bihary D, Jády A, Pongor S, Ligeti B.

Biol Direct. 2017 Sep 15;12(1):22. doi: 10.1186/s13062-017-0192-3.

2.

CX, DPX, and PCW: Web Servers for the Visualization of Interior and Protruding Regions of Protein Structures in 3D and 1D.

Ligeti B, Vera R, Juhász J, Pongor S.

Methods Mol Biol. 2017;1484:301-309. doi: 10.1007/978-1-4939-6406-2_20.

PMID:
27787834
3.

Propagation on Molecular Interaction Networks: Prediction of Effective Drug Combinations and Biomarkers in Cancer Treatment.

Ligeti B, Menyhart O, Petric I, Gyorffy B, Pongor S.

Curr Pharm Des. 2017;23(1):5-28. doi: 10.2174/1381612822666161021162727. Review.

PMID:
27774896
4.

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA.

Nagy G, Czipa E, Steiner L, Nagy T, Pongor S, Nagy L, Barta E.

BMC Genomics. 2016 Aug 15;17(1):637. doi: 10.1186/s12864-016-2940-7.

5.

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.

Kuzniar A, Dhir S, Nijveen H, Pongor S, Leunissen JA.

Bioinformatics. 2015 Oct 1;31(19):3240. doi: 10.1093/bioinformatics/btv479. Epub 2015 Sep 1. No abstract available.

6.

A Network-Based Target Overlap Score for Characterizing Drug Combinations: High Correlation with Cancer Clinical Trial Results.

Ligeti B, Pénzváltó Z, Vera R, Győrffy B, Pongor S.

PLoS One. 2015 Jun 5;10(6):e0129267. doi: 10.1371/journal.pone.0129267. eCollection 2015.

7.

Census of solo LuxR genes in prokaryotic genomes.

Hudaiberdiev S, Choudhary KS, Vera Alvarez R, Gelencsér Z, Ligeti B, Lamba D, Pongor S.

Front Cell Infect Microbiol. 2015 Mar 12;5:20. doi: 10.3389/fcimb.2015.00020. eCollection 2015.

8.

Nuclear architecture dictates HIV-1 integration site selection.

Marini B, Kertesz-Farkas A, Ali H, Lucic B, Lisek K, Manganaro L, Pongor S, Luzzati R, Recchia A, Mavilio F, Giacca M, Lusic M.

Nature. 2015 May 14;521(7551):227-31. doi: 10.1038/nature14226. Epub 2015 Mar 2.

PMID:
25731161
9.

Modeling bacterial quorum sensing in open and closed environments: potential discrepancies between agar plate and culture flask experiments.

Bihary D, Tóth M, Kerényi Á, Venturi V, Pongor S.

J Mol Model. 2014 Jul;20(7):2248. doi: 10.1007/s00894-014-2248-y. Epub 2014 Jun 19.

PMID:
24944091
10.

ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes.

Dogsa I, Choudhary KS, Marsetic Z, Hudaiberdiev S, Vera R, Pongor S, Mandic-Mulec I.

PLoS One. 2014 May 2;9(5):e96122. doi: 10.1371/journal.pone.0096122. eCollection 2014.

11.

Emergence of collective territorial defense in bacterial communities: horizontal gene transfer can stabilize microbiomes.

Juhász J, Kertész-Farkas A, Szabó D, Pongor S.

PLoS One. 2014 Apr 22;9(4):e95511. doi: 10.1371/journal.pone.0095511. eCollection 2014.

12.

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA.

Popovic M, Wienk H, Coglievina M, Boelens R, Pongor S, Pintar A.

Proteins. 2014 Apr;82(4):537-45. doi: 10.1002/prot.24507. Epub 2014 Jan 25.

PMID:
24403087
13.

PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra.

Kertész-Farkas A, Reiz B, Vera R, Myers MP, Pongor S.

Bioinformatics. 2014 Jan 15;30(2):234-41. doi: 10.1093/bioinformatics/btt642. Epub 2013 Nov 8.

PMID:
24215026
14.

Biomedical hypothesis generation by text mining and gene prioritization.

Petric I, Ligeti B, Gyorffy B, Pongor S.

Protein Pept Lett. 2014;21(8):847-57.

PMID:
23855662
15.

Precursor mass dependent filtering of mass spectra for proteomics analysis.

Reiz B, Myers MP, Pongor S, Kertesz-Farkas A.

Protein Pept Lett. 2014;21(8):858-63.

PMID:
23855660
16.

JBioWH: an open-source Java framework for bioinformatics data integration.

Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S.

Database (Oxford). 2013 Jul 11;2013:bat051. doi: 10.1093/database/bat051. Print 2013.

17.

The organization of the quorum sensing luxI/R family genes in Burkholderia.

Choudhary KS, Hudaiberdiev S, Gelencsér Z, Gonçalves Coutinho B, Venturi V, Pongor S.

Int J Mol Sci. 2013 Jul 2;14(7):13727-47. doi: 10.3390/ijms140713727.

18.

Obituary: In memory of Jack Leunissen.

Luo J, Nijveen H, Attwood T, Judge D, Pongor S, Landsman D, Bishop M.

Brief Bioinform. 2013 May;14(3):261-2. doi: 10.1093/bib/bbt036. No abstract available.

PMID:
23696635
19.

Stability of multispecies bacterial communities: signaling networks may stabilize microbiomes.

Kerényi Á, Bihary D, Venturi V, Pongor S.

PLoS One. 2013;8(3):e57947. doi: 10.1371/journal.pone.0057947. Epub 2013 Mar 4. Erratum in: PLoS One. 2014;9(10):e111290.

20.

Chemical rule-based filtering of MS/MS spectra.

Reiz B, Kertész-Farkas A, Pongor S, Myers MP.

Bioinformatics. 2013 Apr 1;29(7):925-32. doi: 10.1093/bioinformatics/btt061. Epub 2013 Feb 15.

PMID:
23418188

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