Publications

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. 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-