First of all I'd like to say, I'm currently rewriting these pages (time to time) into English. However, there are and always will be parts written in Czech language. Because lots of Czech understand English as well, it might change one day.
Education:
2005 - PhD. degree in Molecular biology at the Faculty of Science, Charles University, Prague, Czech Republic
2000 - MSc. degree in Biology at the Faculty of Science, Charles University, Prague, Czech Republic
1994 - Grammar School at Stepanska street.
Additional education/courses:
April - September 1999 - 6 month study stay in Novartis Pharma AG, Basel, Switzerland
February 2000 - Computational genomics course, Marc van Ranst, Catholic University in Leuven, Belgium
June 2001 - Dec 2003 - scientific stay at MIPS GSF, Munich, Germany
In 1994 I finished studies at the grammar school in Štěpánská street in Prague and in 2000 graduated in Molecular biology at The Faculty of Science, Charles University. The topic of my diploma thesis was "Characterization of the dsRNA virus of yeast-like organism Dipodascus magnusii". The aim was to isolate, purify and clone the dsRNA virus, to obtain sequence of it's genome and prepare mutants cured away from the virus. Along with that we described putative viral proteins associated with viral dsRNA nucleic acid molecules. The work on this topic is still being continued in a lab of RNDr. Martin Pospíšek, PhD..
Since 1996 I administered some of our campus Unix servers at the Faculty of Science in Prague till 1999. I have quite good Unix user/admin experience and also knowledge about network administration (routing, ATM, DNS, kerberos, AFS), mostly with Tru64Unix (formerly Digital Unix/OSF1), but also Irix, Solaris, Linux. I've written some document related to SENDMAIL installation and configuration, have some filter recipes for procmail to forward your emails to a pager (capable to split messages into chunks of 160 chars, convert charsets, kill attachments etc.).
In 2000 I was elected as a representative of university students in the Academic Senate of the Charles University and also a member of the Board of Academic Senate. This took me a lot of time, but gave me an idea how can one solve problems, how to communicate with people, how to explain/present something or how to convince them in some favour. ;-)
In my scientific carrier, I am interested in partitioning proteins into clusters and use such clusters to isolate protein domains and use such for protein families description. I prefer the approach to define first a list of known functions, sort it somehow and later on assign unknown proteins to this catalogue. A lot of time I've spent with PEDANT, which is a database system allowing us to receive and store information about proteins in a fully automatic fashion. For example, one can ask which proteins of a certain organism do NOT have homologs to known proteins, which proteins have 7 transmembrane regions etc.
I'm interested in secondary structure prediction of nucleic acids.
At the moment I'm working on analysis of IRES (Internal Ribosome Entry Site) elements. For the purpose I created with help of others IRESite database.
In 1998 I organised with couple of friends course/camp for secondary school students in biology. The course was practically oriented and gave them some more clue about the nature (half of the time were lectures or field excursions). They've been cultivating microbes, studying plants, animals, cellular structure, how immune system works, what ecology is and how evolution slowly changes living organisms in an unpredictable way, what genetics, molecular biology and cloning is about and that there's nothing wrong with it. We tried to give them also time to enjoy friendship, so every day half of the program was filled up with games. You can be sure they never got into bed until 11pm, sometimes even later. That kept them quiet. ;) It seems it started good tradition, so this camp happens yearly now. The style or type of games is similar to what happens at courses organised by Prazdninova skola Lipnice and Ceska cesta - members of Outward bound International. Briefly, outdoor and indoor training, using games to simulate real world and to show you and others, how do you behave, what might you improve, where are your strong/weak points, how funny might be sitting in mud and that it's enough to sleep only few hours per day. Some people definitely reach their physical and/or mental limits, but it's not necessary. I participated in "Impuls 2002" and we had a lot of fun!
During my free time I like walking/climbing in mountains, I do a bit rock climbing but I really enjoy kayaking. I also used to do beekeeping and as our family owns a little farm, I ride a horse few times a year. One of my most exciting tours was to Caucassus [RU] - text in Czech only, climbing the mountain Elbrus (5621 m) and a number of tours in Alps (Switzerland). In autumn 2002 we planned to go to Guinea-Conakry and Mali. Our idea was to explore upper parts of the river Niger by an inflatable boat, but our group broke as it was too risky. Regarding the facts, there are many unknown diseases, lot's of diseases against which there's no vaccination available at all, rain forest complicating physical access to those remote areas, hippos and crocodiles in the river, insects like bees, flies and ants, worms and amoebas in all those the brownish and muddy rivers ... possibly we saved our lives.
Publication activity:
Gabriel J., Mokrejš M., Bílý J., Rychlovský P. (1994) Accumulation of Heavy Metals by Some Wood-Rotting Fungi, Folia Microbiol. 39: 115-118
Pospíšek M., Zikánová B., Mokrejš M. (2001) Purification and characterization of the Dipodascus (Endomyces) magnusii toxin, Yeast 18: S334-S334 Suppl. 1
Mewes H. W., Frishman D., Guldener U., Mannhaupt G., Mayer K., Mokrejš M., Morgenstern B., Munsterkotter M., Rudd S., and Weil B. (2002) MIPS: a database for genomes and protein sequences, Nucleic Acids Res. 30: 31-34
Frishman D., Mokrejš M., Kosykh D., Karstenmuller G., Kolesov G., Zubrzycki I., Gruber C., Geier B., Kaps A., Volz A., Wagner C., Fellenberg M., Heumann K., Mewes H.-W. (2003) The Pedant genome database, Nucleic Acids Res. 31: 207-211
Crass T., Antes I, Basekow R., Bork P., Buning C., Christensen M., Claußen H., Ebeling C., Ernst P., Gailus-Durner V., Glatting K.-H., Gohla R., Gößling F., Grote K., Heidtke K., Herrmann A., O'Keeffe S., Kießlich O., Kolibal S., Korbel J. O., Lengauer T., Liebich I., van der Linden M., Luz H., Meissner K., von Mering C., Mevissen H.-T., Mewes H.-W., Michael H., Mokrejs M., Müller T., Pospisil H., Rarey M., Reich J. G., Schneider R., Schomburg D., Schulze-Kremer S., Schwarzer K., Sommer I., Springstubbe S., Suhai S., Thoppae G., Vingron M., Warfsmann J., Werner T., Wetzler D., Wingender E., Zimmer R. (2004) The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics. 20: 268-270
Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejš M., Tetko I., Güldener U., Mannhaupt G., Münsterkötter M., Mewes H.-W. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acid Res. 32: 5539-5545
Mokrejš M., Vopálenský V., Kolenatý O., Mašek T., Feketová Z., Sekyrová P., Škaloudová B., Kříž V., Pospíšek M. (2006) IRESite: The database of experimentally verified IRES structures (www.iresite.org). Nucleic Acids Res. 34: D125-D130; doi:10.1093/nar/gkj081; Supplementary material
Mokrejš M., Vopálenský V., Mašek T., Pospíšek M. (2007) Title: A Bioinformatical Approach to the Analysis of Viral and Cellular Internal Ribosome Entry Sites In: Columbus F editors. New Messenger RNA Research Communications. Hauppauge, NY: Nova Science Publishers; pp. 133-166
Mokrejš M., Vopálenský V., Mašek T., Pospíšek M. (2007) Title: A Bioinformatical Approach to the Analysis of Viral and Cellular Internal Ribosome Entry Sites In: Columbus F editors. New Messenger RNA Research Communications. Hauppauge, NY: Nova Science Publishers; pp. 133-166 (abstract)
Vopálenský V., Mašek T., Horváth O., Vicenová B., Mokrejš M., Pospíšek M. (2008) Firefly luciferase gene contains a cryptic promoter. RNA 14:1720-1729, doi:10.1261/rna.831808
Martinez D. et al. (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. PNAS 106:1954-1959, doi: 10.1073/pnas.0809575106 (main article, appendix, supplements)
Mokrejš M., Mašek T., Hlubuček P., Delbos P., Pospíšek M. (2010) IRESite—a tool for the examination of viral and cellular internal ribosome entry sites. Nucleic Acids Res. 38:D131-D136; doi:10.1093/nar/gkp981
Dvorakova S., Sykorova V., Vaclavikova E., Sykorova P., Vlcek P., Kodetova D., Lastuvka P., Betka J., Mokrejs M., Vcelak J., Bendlova B. (2015) A 3-bp Deletion VK600-1E in the BRAF Gene Detected in a Young Woman with Papillary Thyroid Carcinoma. Endocr. Pathol. 26:309-314; DOI:10.1007/s12022-015-9387-2
Zemkova M., Zahradnik D., Mokrejs M., Flegr J. (2017) Parasitism as the Main Factor Shaping Peptide Vocabularies in Current Organisms. Parasitology 144: 975-983, DOI:10.1017/S0031182017000191
Chyra Z, Sevcikova T, Vojta P, Puterova J, Brozova L, Growkova K, Filipova J, Zatopkova M, Grosicki S, Barchnicka A, Jedrzejczak WW, Waszczuk-Gajda A, Jungova A, Mikulasova A, Hajduch M, Mokrejs M, Pour L, Stork M, Harvanova L, Mistrik M, Mikala G, Robak P, Czyz A, Debski J, Usnarska-Zubkiewicz L, Jurczyszyn A, Stejskal L, Morgan G, Kryukov F, Budinska E, Simicek M, Jelinek T, Hrdinka M, Hajek R. (2020) Heterogenous mutation spectrum and deregulated cellular pathways in aberrant plasma cells underline molecular pathology of light-chain amyloidosis. Haematologica. 106(2): DOI:10.3324/haematol.2019.239756. PMID: 32381580
Červená K., Pardini B., Urbanová M., Voděnková S., Pazourková E., Veškrnová V., Levý M., Buchler T., Mokrejš M., Naccarati A., Vodička P., Vymetálková V. (2021) Mutational landscape of plasma cell-free DNA identifies molecular features associated with therapeutic response in patients with colon cancer. A pilot study. Mutagenesis. DOI:10.1093/mutage/geab024
Janko K., Bartoš O., Kočí J., Roslein J., Drdová,-Janková E., Kotusz J., Eisner, J., Mokrejš M., Štefková-Kašparová E. (2021) Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol. Biol. Evol.; DOI:10.1093/molbev/msab249
Fallon T.R., Čalounová T., Mokrejš M., Jing-Ke Weng, Pluskal T. (2023) transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation. BMC Bioinformatics 24:133; DOI:10.1186/s12859-023-05254-8
Study and research stays:
Apr - Sept 1999 - Novartis Pharma AG, Basel, Switzerland
Jun 2001 - Dec 2003 - MIPS - GSF, Munich, Germany
My GPG public key is as of Feb 13 2003 available here. My PGP keys 97 and 99 have been revoked. Here are my public ssh1 and ssh2 keys.