Publications
• Lucic, B.*, Chen, H.-C.*, Kuzman, M.*, Zorita, E*., Wegner, J., Minnerker, V., Weng, W., Fronza, R., Laufs, S., Schmidt, M., Stadhouders, R., V., Roukos, Vlahovicek, K.#, Filion, J. G.#, Lusic, M.# Spatially clustered loci with multiple enhancers are frequent targets of HIV-1. Nat Commun. 10.1038/s41467-019-12046-3 (2019)
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•Elek A, Kuzman M, Vlahovicek K . coRdon: Codon Usage Analysis and Prediction of Gene Expressivity. 10.18129/B9.bioc.coRdon (2018)
•Polak, P., Kim, J., Braunstein, L.Z., Karlic, R., Haradhavala, N.J., Tiao, G., Rosebrock, D., Livitz, D., Kübler, K., Mouw, K.W., et al.
A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. – at. Nat. Genet. 49 (2017), 1476–1486.
• Maruvka, Y.E., Mouw, K.W., Karlic, R., Parasuraman, P., Kamburov, A., Polak, P., Haradhvala, N.J., Hess, J.M., Rheinbay, E., Brody, Y., et al.
Analysis of somatic microsatellite indels identifies driver events in human tumors. – Nat. Biotechnol. (2017)
• Karlic, R., Ganesh, S., Franke, V., Svobodova, E., Urbanova, J., Suzuki, Y., Aoki, F., Vlahovicek, K., and Svoboda, P.
Long non-coding RNA exchange during the oocyte-to-embryo transition in mice. – DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes. (2017)
• Franke, V., Ganesh, S., Karlic, R., Malik, R., Pasulka, J., Horvat, F., Kuzman, M., Fulka, H., Cernohorska, M., Urbanova, J., et al.
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.– Genome Res. gr.216150.116. (2017)
• Fabijanić, M., and Vlahoviček, K.
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles.– In Data Mining Techniques for the Life Sciences, O. Carugo, and F. Eisenhaber, eds. (Springer New York) (2016), pp. 509–531
• Akalin, A., Franke, V., Vlahoviček, K., Mason, C.E., and Schübeler, D.
Genomation: a toolkit to summarize, annotate and visualize genomic intervals.– Bioinforma. Oxf. Engl. 31 (2015), 1127–1129.
• Abe, K.-I., Yamamoto, R., Franke, V., Cao, M., Suzuki, Y., Suzuki, M.G., Vlahovicek, K., Svoboda, P., Schultz, R.M., and Aoki, F.
The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3’ processing. – EMBO J. 34 (2015), 1523–1537.
• Polak, Paz; Karlić, Rosa; Koren, Amnon; Thurman, Robert; Sandstrom, Richard; Lawrence, Michael S.; Reynolds, Alex; Rynes, Eric; Vlahoviček, Kristian; Stamatoyannopoulos, John A.; Sunyaev, Shamil R.
Cell-of-origin chromatin organization shapes the mutational landscape of cancer. – Nature. 518 (2015) , 7539; 360-364
• Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, Viren Amin, John W Whitaker, Matthew D Schultz, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Andreas R Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas A Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip L De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven J M Jones, Wei Li, Marco A Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Q Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis, and Roadmap Epigenomics Consortium.
Integrative Analysis of 111 Reference Human Epigenomes. – Nature. 518 (2015) , 7539; 317-330
• Koren, Amnon; Handsaker, Robert E.; Kamitaki, Nolan; Karlić, Rosa; Ghosh, Sulagna; Polak, Paz; Eggan, Kevin; McCarroll, Steven A.
Genetic variation in human DNA replication timing. – Cell. 159 (2014) , 5; 1015-1026
• Flemr, Matyas; Malik, Radek; Franke, Vedran; Nejepinska, Jana; Sedlacek, Radislav; Vlahoviček, Kristian; Svoboda, Petr.
A retrotransposon-driven Dicer isoform directs endogenous siRNA production in mouse oocytes. – Cell. 155 (2013) , 4; 807-816
• Karlić, Rosa; Chung, Ho-Ryun; Lasserre, Julia; Vlahoviček, Kristian; Vingron, Martin.
Histone modification levels are predictive for gene expression. – Proceedings of the National Academy of Sciences of the United States of America. 107 (2010) , 7; 2926-2931
• Roller, Maša; Lucić, Vedran; Nagy, István; Perica, Tina; Vlahoviček, Kristian.
Environmental shaping of codon usage and functional adaptation across microbial communities. – Nucleic acids research. 41 (2013) , 19; 8842-8852
• Šegota, Igor; Bartoniček, Nenad; Vlahoviček, Kristian.
MADNet: MicroArray Database Network web server. – Nucleic Acids Research. 36 (2008) , Suppl. S; W332-W335
• Supek, Fran; Škunca, Nives; Repar, Jelena; Vlahoviček, Kristian; Šmuc, Tomislav.
Translational Selection Is Ubiquitous in Prokaryotes. – Plos genetics. 6 (2010) ; e1001004-1-e1001004-13
• Šikić, Mile; Tomić, Sanja; Vlahoviček, Kristian.
Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests. – Plos computational biology. 5 (2009) , 1; e1000278-1-e1000278-9
• Harcet, Matija; Roller, Maša; Ćetković, Helena; Perina, Dragutin; Wiens, Matthias; Müller, Werner E.G.; Vlahoviček, Kristian.
Demosponge EST sequencing reveals a complex genetic toolkit of the simplest metazoans. – Molecular biology and evolution. 27 (2010) , 12; 2747-2756
• Zampieri, Stefania; Montalvo, Annalisa; Blanco, Mariana; Zanin, Irene; Amartino, Hernan; Vlahoviček, Kristian; Szlago, Marina; Schenone, Andrea; Pittis, Gabriela; Bembi, Bruno; Dardis, Andrea.
Molecular analysis of HEXA gene in Argentinean patients affected with Tay–Sachs disease: Possible common origin of the prevalent c.459 + 5A>G mutation. – Gene. 499 (2012) , 2; 262-265
• Perina, Dragutin; Korolija, Marina; Roller, Maša; Harcet, Matija; Jeličić, Branka; Mikoč, Andreja; Ćetković, Helena.
Over-represented localized sequence motifs in ribosomal protein gene promoters of basal metazoans. – Genomics. 98 (2011) , 1; 56-63
• Pinto, Sofia; Vlahoviček, Kristian; Buratti, Emanuele.
PRO-MINE: A Bioinformatics Repository and Analytical Tool for TARDBP Mutations. – Human mutation. 32 (2011) , 1; E1948-E1958
• Pučić, Maja; Pinto, Sofia; Novokmet, Mislav; Knežević, Ana; Gornik, Olga; Polašek, Ozren; Vlahoviček, Kristian; Wang, Wei; Rudd, Pauline M,; Wright, Alan F.; Campbell, Harry; Rudan, Igor; Lauc, Gordan.
Common aberrations from the normal human plasma N-glycan profile. – Glycobiology. 20 (2010) , 8; 970-975
• Supek, Fran; Vlahoviček, Kristian.
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. – BMC bioinformatics. 6 (2005) , 1; 182-