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