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Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

Lucic B, Chen HC, Kuzman M, Zorita E, Wegner J, Minneker V, Wang W, Fronza R, Laufs S, Schmidt M, Stadhouders R, Roukos V, Vlahovicek K, Filion GJ, Lusic M.

Nat Commun. 2019 Sep 6;10(1):4059. doi: 10.1038/s41467-019-12046-3.


Dynamics of exhaled breath temperature after smoking a cigarette and its association with lung function changes predictive of COPD risk in smokers: a cross-sectional study.

Šipoš IH, Labor S, Jurić I, Plavec D, Vlahoviček K, Bogović S, Vukelić JP, Labor M.

Arh Hig Rada Toksikol. 2019 Jun 1;70(2):123-129. doi: 10.2478/aiht-2019-70-3211.


Coupling AAV-mediated promoterless gene targeting to SaCas9 nuclease to efficiently correct liver metabolic diseases.

De Caneva A, Porro F, Bortolussi G, Sola R, Lisjak M, Barzel A, Giacca M, Kay MA, Vlahoviček K, Zentilin L, Muro AF.

JCI Insight. 2019 Jun 18;5. pii: 128863. doi: 10.1172/jci.insight.128863.


Role of Cnot6l in maternal mRNA turnover.

Horvat F, Fulka H, Jankele R, Malik R, Jun M, Solcova K, Sedlacek R, Vlahovicek K, Schultz RM, Svoboda P.

Life Sci Alliance. 2018 Jul 16;1(4):e201800084. doi: 10.26508/lsa.201800084. eCollection 2018 Aug.


Heat-induced longevity in budding yeast requires respiratory metabolism and glutathione recycling.

Musa M, Perić M, Bou Dib P, Sobočanec S, Šarić A, Lovrić A, Rudan M, Nikolić A, Milosević I, Vlahoviček K, Raimundo N, Kriško A.

Aging (Albany NY). 2018 Sep 17;10(9):2407-2427. doi: 10.18632/aging.101560.


TORC1-mediated sensing of chaperone activity alters glucose metabolism and extends lifespan.

Perić M, Lovrić A, Šarić A, Musa M, Bou Dib P, Rudan M, Nikolić A, Sobočanec S, Mikecin AM, Dennerlein S, Milošević I, Vlahoviček K, Raimundo N, Kriško A.

Aging Cell. 2017 Oct;16(5):994-1005. doi: 10.1111/acel.12623. Epub 2017 Jun 14.


Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.

Franke V, Ganesh S, Karlic R, Malik R, Pasulka J, Horvat F, Kuzman M, Fulka H, Cernohorska M, Urbanova J, Svobodova E, Ma J, Suzuki Y, Aoki F, Schultz RM, Vlahovicek K, Svoboda P.

Genome Res. 2017 Aug;27(8):1384-1394. doi: 10.1101/gr.216150.116. Epub 2017 May 18.


Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.

Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P.

DNA Res. 2017 Apr 1;24(2):219-220. doi: 10.1093/dnares/dsx008. No abstract available.


Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.

Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P.

DNA Res. 2017 Apr 1;24(2):129-141. doi: 10.1093/dnares/dsw058. Erratum in: DNA Res. 2017 Apr 1;24(2):219-220.


Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles.

Fabijanić M, Vlahoviček K.

Methods Mol Biol. 2016;1415:509-31. doi: 10.1007/978-1-4939-3572-7_26.


The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing.

Abe K, Yamamoto R, Franke V, Cao M, Suzuki Y, Suzuki MG, Vlahovicek K, Svoboda P, Schultz RM, Aoki F.

EMBO J. 2015 Jun 3;34(11):1523-37. doi: 10.15252/embj.201490648. Epub 2015 Apr 20.


Cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence M, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, Sunyaev SR.

Nature. 2015 Feb 19;518(7539):360-364. doi: 10.1038/nature14221.


Genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.

Bioinformatics. 2015 Apr 1;31(7):1127-9. doi: 10.1093/bioinformatics/btu775. Epub 2014 Nov 21.


Exonic splicing signals impose constraints upon the evolution of enzymatic activity.

Falanga A, Stojanović O, Kiffer-Moreira T, Pinto S, Millán JL, Vlahoviček K, Baralle M.

Nucleic Acids Res. 2014 May;42(9):5790-8. doi: 10.1093/nar/gku240. Epub 2014 Apr 1.


Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells.

Yukawa M, Akiyama T, Franke V, Mise N, Isagawa T, Suzuki Y, Suzuki MG, Vlahovicek K, Abe K, Aburatani H, Aoki F.

PLoS One. 2014 Mar 21;9(3):e92689. doi: 10.1371/journal.pone.0092689. eCollection 2014.


A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes.

Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K, Svoboda P.

Cell. 2013 Nov 7;155(4):807-16. doi: 10.1016/j.cell.2013.10.001.


Environmental shaping of codon usage and functional adaptation across microbial communities.

Roller M, Lucić V, Nagy I, Perica T, Vlahovicek K.

Nucleic Acids Res. 2013 Oct;41(19):8842-52. doi: 10.1093/nar/gkt673. Epub 2013 Aug 5.


Molecular analysis of HEXA gene in Argentinean patients affected with Tay-Sachs disease: possible common origin of the prevalent c.459+5A>G mutation.

Zampieri S, Montalvo A, Blanco M, Zanin I, Amartino H, Vlahovicek K, Szlago M, Schenone A, Pittis G, Bembi B, Dardis A.

Gene. 2012 May 15;499(2):262-5. doi: 10.1016/j.gene.2012.03.022. Epub 2012 Mar 13.


Prediction of interacting protein residues using sequence and structure data.

Franke V, Sikić M, Vlahoviček K.

Methods Mol Biol. 2012;819:233-51. doi: 10.1007/978-1-61779-465-0_16.


PRO-MINE: A bioinformatics repository and analytical tool for TARDBP mutations.

Pinto S, Vlahoviček K, Buratti E.

Hum Mutat. 2011 Jan;32(1):E1948-58. doi: 10.1002/humu.21393.


Demosponge EST sequencing reveals a complex genetic toolkit of the simplest metazoans.

Harcet M, Roller M, Cetković H, Perina D, Wiens M, Müller WE, Vlahovicek K.

Mol Biol Evol. 2010 Dec;27(12):2747-56. doi: 10.1093/molbev/msq174. Epub 2010 Jul 9.


Translational selection is ubiquitous in prokaryotes.

Supek F, Skunca N, Repar J, Vlahovicek K, Smuc T.

PLoS Genet. 2010 Jun 24;6(6):e1001004. doi: 10.1371/journal.pgen.1001004.


Common aberrations from the normal human plasma N-glycan profile.

Pucic M, Pinto S, Novokmet M, Knezevic A, Gornik O, Polasek O, Vlahovicek K, Wang W, Rudd PM, Wright AF, Campbell H, Rudan I, Lauc G.

Glycobiology. 2010 Aug;20(8):970-5. doi: 10.1093/glycob/cwq052. Epub 2010 Apr 8.


Histone modification levels are predictive for gene expression.

Karlić R, Chung HR, Lasserre J, Vlahovicek K, Vingron M.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2926-31. doi: 10.1073/pnas.0909344107. Epub 2010 Feb 1.


Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.

Sikić M, Tomić S, Vlahovicek K.

PLoS Comput Biol. 2009 Jan;5(1):e1000278. doi: 10.1371/journal.pcbi.1000278. Epub 2009 Jan 30.


Molecular and functional analysis of the HEXB gene in Italian patients affected with Sandhoff disease: identification of six novel alleles.

Zampieri S, Filocamo M, Buratti E, Stroppiano M, Vlahovicek K, Rosso N, Bignulin E, Regis S, Carnevale F, Bembi B, Dardis A.

Neurogenetics. 2009 Feb;10(1):49-58. doi: 10.1007/s10048-008-0145-1. Epub 2008 Aug 29.


MADNet: microarray database network web server.

Segota I, Bartonicek N, Vlahovicek K.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W332-5. doi: 10.1093/nar/gkn289. Epub 2008 May 14.


PSAIA - protein structure and interaction analyzer.

Mihel J, Sikić M, Tomić S, Jeren B, Vlahovicek K.

BMC Struct Biol. 2008 Apr 9;8:21. doi: 10.1186/1472-6807-8-21.


Molecular analysis of the HEXA gene in Italian patients with infantile and late onset Tay-Sachs disease: detection of fourteen novel alleles.

Montalvo AL, Filocamo M, Vlahovicek K, Dardis A, Lualdi S, Corsolini F, Bembi B, Pittis MG.

Hum Mutat. 2005 Sep;26(3):282.


Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity.

Supek F, Vlahovicek K.

BMC Bioinformatics. 2005 Jul 19;6:182. Erratum in: BMC Bioinformatics. 2010;11:463.


CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures.

Vlahovicek K, Pintar A, Parthasarathi L, Carugo O, Pongor S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W252-4.


Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.

Gáspári Z, Vlahovicek K, Pongor S.

Bioinformatics. 2005 Aug 1;21(15):3322-3. Epub 2005 May 24.


The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines.

Vlahovicek K, Kaján L, Agoston V, Pongor S.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D223-5.


Identification and functional characterization of five novel mutant alleles in 58 Italian patients with Gaucher disease type 1.

Miocić S, Filocamo M, Dominissini S, Montalvo AL, Vlahovicek K, Deganuto M, Mazzotti R, Cariati R, Bembi B, Pittis MG.

Hum Mutat. 2005 Jan;25(1):100.


INCA: synonymous codon usage analysis and clustering by means of self-organizing map.

Supek F, Vlahovicek K.

Bioinformatics. 2004 Sep 22;20(14):2329-30. Epub 2004 Apr 1.


Highly reactive cysteine residues are part of the substrate binding site of mammalian dipeptidyl peptidases III.

Abramić M, Simaga S, Osmak M, Cicin-Sain L, Vukelić B, Vlahovicek K, Dolovcak L.

Int J Biochem Cell Biol. 2004 Mar;36(3):434-46.


Design of peptide mimetics of HIV-1 gp120 for prevention and therapy of HIV disease.

Veljkovic N, Branch DR, Metlas R, Prljic J, Vlahovicek K, Pongor S, Veljkovic V.

J Pept Res. 2003 Oct;62(4):158-66.


DNA analysis servers:,, and IS.

Vlahovicek K, Kaján L, Pongor S.

Nucleic Acids Res. 2003 Jul 1;31(13):3686-7.


The DNA secondary structure of the Bacillus subtilis genome.

Tosato V, Gjuracic K, Vlahovicek K, Pongor S, Danchin A, Bruschi CV.

FEMS Microbiol Lett. 2003 Jan 21;218(1):23-30.


The SBASE domain sequence library, release 10: domain architecture prediction.

Vlahovicek K, Kaján L, Murvai J, Hegedus Z, Pongor S.

Nucleic Acids Res. 2003 Jan 1;31(1):403-5.


The SBASE protein domain library, release 9.0: an online resource for protein domain identification.

Vlahovicek K, Murvai J, Barta E, Pongor S.

Nucleic Acids Res. 2002 Jan 1;30(1):273-5.


Prediction of protein functional domains from sequences using artificial neural networks.

Murvai J, Vlahovicek K, Szepesvári C, Pongor S.

Genome Res. 2001 Aug;11(8):1410-7.

43. building three dimensional DNA models from sequence data.

Vlahovicek K, Pongor S.

Bioinformatics. 2000 Nov;16(11):1044-5.


A simple probabilistic scoring method for protein domain identification.

Murvai J, Vlahovicek K, Pongor S.

Bioinformatics. 2000 Dec;16(12):1155-6.


Sequence-dependent modelling of local DNA bending phenomena: curvature prediction and vibrational analysis.

Vlahovicek K, Munteanu MG, Pongor S.

Genetica. 1999;106(1-2):63-73. Review.


The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments.

Murvai J, Vlahovicek K, Barta E, Pongor S.

Nucleic Acids Res. 2001 Jan 1;29(1):58-60.


The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments.

Murvai J, Vlahovicek K, Barta E, Cataletto B, Pongor S.

Nucleic Acids Res. 2000 Jan 1;28(1):260-2.


The domain-server: direct prediction of protein domain-homologies from BLAST search.

Murvai J, Vlahovicek K, Barta E, Parthasarathy S, Hegyi H, Pfeiffer F, Pongor S.

Bioinformatics. 1999 Apr;15(4):343-4.


The SBASE protein domain library, release 6.0: a collection of annotated protein sequence segments.

Murvai J, Vlahovicek K, Barta E, Szepesvári C, Acatrinei C, Pongor S.

Nucleic Acids Res. 1999 Jan 1;27(1):257-9.


Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena.

Munteanu MG, Vlahovicek K, Parthasarathy S, Simon I, Pongor S.

Trends Biochem Sci. 1998 Sep;23(9):341-7. Review.


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