Martin Mokrejš, Ph.D. started bioinformatics.cz in 2003. His main business interest is cleanup of Roche 454-based sequencing data including those based on extended protocols from Clontech and Evrogen. He starred into raw read sequences of thousands of datasets for so long that he discovered lots of artifacts here and there. His aim was always to systematically purify the raw data so that assemblies contain less errors. He transformed his ideas into a piece of software, verified what the software can find, eliminated false positives and eventually the software pipeline started to save his eyes while inspecting other datasets. Finally to note, he communciated some issues and improvements of sfffile/sffinfo with Roche developers and with Ketil Malde who improved flower and introduced the so much missing fclip utility.
His other interests are mRNA splice variant analysis (Sanger-based data), RNA secondary structure analysis, prediction and searches. He is fond of Gentoo Linux, contributed several package definitions to its sci-biology herd and in general, uses python and biopython for daily work. In previous century, while being a student of molecular biology he also administered several UNIX servers housed at the Department of computer sciences running SGI IRIX, DEC OSF1, SUN Solaris and later on Linux.
Publications:
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
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
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. (in press), doi:10.1093/nar/gkp981