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Herbert MayerLet me just briefly introduce myself to you. My name is Herbert Mayer. I was born in Vienna in 1969, a few months before Neil Armstrong said "...one small step for a man, one giant leap for mankind." Very soon, I became fascinated by the two central questions of life, namely "Where do we come from ?" and " Where do we go to ?". I realized that there are (at least) two different approaches to this question, which is to either study the "big space", meaning astrophysics, or the "small space", molecular biology. I finally decided to do the latter one.

During my PhD thesis at the University of Vienna (Univie), Institute of Biochemistry - now part of Max F. Perutz Laboratories (MFPL) -, where I investigated a previously unknown family of proteins in several different species, I found myself spending more and more time in front of the computer searching for bioinformatics tools and databases as compared to working at the lab bench. It became clear to me that this work is definitely a full-time job, which can be done by the lab scientist only in a very unsatisfying manner. It is often not only the search for a needle in a haystack but to pick the best from dozens of needles. I believe that it is extremely important to establish an "interface" between the bench scientist and the world of bioinformatics. It is exactly this function which is my central bioinformatics philosophy. And it is exactly this function which I have been fulfilling from 2001 to 2005 at the competence center Bio-Molecular Therapeutics (BMT) and the Department of Vascular Biology and Thrombosis Research (Vascbio) of the Medical University of Vienna (MUV). In January 2006, I joined the section Biomedical Computer Simulation and Bioinformatics (BCB) at the Core Unit for Medical Statistics and Informatics (MSI) of the MUV. Also in 2006, I started working as a lector at two different technical colleges in Vienna, the FH Campus Wien (Bioengineering) and the FH Technikum Wien (Biomedical Engineering).

Even people who focus their work on just a small group of genes are often totally puzzled by the wealth of information which can be extracted from databases. You only have to know where to look, what to use and how to use it. This thought was the main reason to create a web portal which collects personal descriptions, evaluations, and comparisons of bioinformatics tools and databases. In addition, it is essential to also spread this knowledge in seminars and training courses. Finally, I would like to state that these data have been produced in a very fruitful and tight cooperation with the scientists in the lab who come up with specific biological questions which suggest bioinformatics solutions.

Contact: mailto                  
                    
"It would be a full-time job just to update a Web page of bioinformatics tools. I can only come to grips with a small piece of the field."
Lincoln Stein, Cold Spring Harbor Laboratory, New York
               
           
What others say
                                 
“I love your website and I think you've done a great job. Unlike most similar websites which just give a list of links to useful resources, you have made an effort to take it one step further by evaluating these tools.“
Allen Chong, Institute for Infocomm Research (I2R), Singapore
                  
“A big compliment for putting so much useful information on Bioinformatics World and thanks for evaluating Toucan!”
Stein Aerts, bioinformatics group at the department of electrical engineering (ESAT) at the Katholieke Universiteit Leuven , Belgium
                 
“I am writing a diploma work on motif discovery. The site which helped me most was Bioinformatics World!”
Maximilian Haeussler, IRISA, "Institut de recherche en informatique et systèmes aléatoires", Rennes, France
             
”Great web page, incredibly useful.”
Rich Neve, UCSF Comprehensive Cancer Center, San Francisco
                    
“If someone asks me for descriptions of bioinformatics resources, I am recommending your web site.”
Ulrike Gausmann, Dept. of Genome Analysis, Institute of Molecular Biotechnology, Jena, Germany
            
“Your Bioinformatics World web site is just great! It is the only web site that I know that combines a majority of useful bioinformatics sites with very detailed descriptions. Thanks a lot for creating it!”
Ivan Ovcharenko, Ph.D. , Bioinformatics Scientist , Lawrence Livermore National Laboratory, California, USA
              
“I just wanted to say that your collection is impressive and very useful, especially with your comments! Thanks for providing a very good site !!”
Morten Mattingsdal, Bioinformatics Platform Norway

"I have recently come across your website which I would like to compliment you on. It is a great resource and I will certainly make use of it and encourage others to do the same."
Anelda Boardman, UWC NBN Node Manager, SANBI, UWC, South Africa

“Nice web site!  I'm impressed by the wide scope of tools described!”
Aaron Darling, University of Wisconsin
   
"Bioinformatics World is one of those sites that collects links to bioinfo-software. But it's far from listing just links. There's comments everywhere, a lot of practical experience for many programs and an extensive FAQ on how to combine some of them to solve typical problems. The tutorials from the FAQ are often better than the manuals that come with many of the bioinformatics tools, with some kind of preference for transcriptional regulation/promotor analysis, though."
taken from the Bioinformatics.org discussion forum, posted by "maximilian" on Oct. 27, 2004

"From the Medical University of Vienna, Austria, Herbert Mayer has created this fantastic collection of bioinformatics tools. We will have no problem to find the lists of bioinformatics programs and databases on the web, however, BIOINFORMATICS WORLD is more than a simple linkpage. Programs and tools are categorized, described, evaluated, and compared, allowing the user to choose the site which fits best his/her needs. There is also introduction to the usage of some of the softwares, such as this detailed description for toucan."
Bing Zhang, taken from the "Bing Zhang Blog", posted on Feb. 22, 2005

"Your web-site is extremely helpful for the community. I have not seen another resource that would describe genomic tools in such details providing hints on the easiest way to use them and describing capabilities of each of the tools."
Ivan Ovcharenko, Ph.D., Bioinformatics Scientist , Lawrence Livermore National Laboratory, California, USA
  
"I am leading a task force in the ISCB education committee to identify and catalogue available resources and tutorials in computational biology/bioinformatics. I think you already have a very good lead on this."
Lakshmanan Iyer, Ph. D., Manager of Collaboration and Training, Computational Biology Group, Bauer Center for Genomics Research, Harvard University

"Pages like yours are extremely important for the visibility of non-commercial systems from the academic domain. Thanks again!"
Robert Hoffmann, PhD, Memorial Sloan-Kettering Cancer Center, MSKCC, Computational Biology Center, cBIO, Chris Sander's Lab, New York

"Thanks for the service of providing your site - it is very useful. I used your site recently to find a website with some key information."
Mark Bieda, PhD, Farnham Lab Postdoctoral Fellow, UC (University of California)-Davis

                
Personal Publications

1.    Mayer, H., Salzer, U., Breuss, J., Ziegler, S., Marchler-Bauer, A., and Prohaska, R., 1998a, Isolation, molecular characterization, and tissue-specific expression of a novel putative G protein-coupled receptor, Biochim. Biophys. Acta 1395: 301-308. (Abstract)

2.    Mayer, H., Breuss, J., Ziegler, S., and Prohaska, R., 1998b, Molecular characterization and tissue-specific expression of a murine putative G protein-coupled receptor, Biochim. Biophys. Acta 1399: 51-56. (Abstract)

3.    Bauer, H., Mayer, H., Marchler-Bauer, A., Salzer, U., and Prohaska, R., 2000, Characterization of p40/GPR69A as a peripheral membrane protein related to the lantibiotic synthetase component C, Biochem. Biophys. Res. Commun. 275: 69-74. (Abstract; Full-Text PDF)

4.    Mayer, H., Bauer, H., Breuss, J., Ziegler, S., and Prohaska, R., 2001, Characterization of rat LANCL1, a novel member of the lanthionine synthetase C-like protein family, highly expressed in testis and brain, Gene 269(1-2): 73-80. (Abstract; Full-Text PDF)

5.    Mayer, H., Bauer, H., and Prohaska, R., 2001, Organization and chromosomal localization of the human and mouse genes coding for LanC-like protein 1 (LANCL1), Cytogenet. Cell Genet. 93(1-2): 100-104. (Abstract; Full-Text PDF)

6.    Mayer, H., Pongratz, M., and Prohaska, R., 2001, Molecular cloning, characterization, and tissue-specific expression of human LANCL2, a novel member of the LanC-like protein family, DNA Sequence 12(3): 161-166. (Abstract) 

7.    Mayer, H., Bilban, M., Kurtev, V., Gruber, F., Wagner, O., Binder, B.R., and De Martin, R., 2004, Deciphering Regulatory Patterns of Inflammatory Gene Expression From Interleukin-1-Stimulated Human Endothelial Cells, Arterioscler. Thromb. Vasc. Biol. 24(7): 1192-1198. Epub 2004 May 06. (Abstract, Full-Text PDF, Data Supplement at ATVB)

8.    Hofer-Warbinek, R., Schmid, J.A., Mayer, H., Winsauer, G., Orel, L., Mueller, B., Wiesner, Ch., Binder, B.R., and De Martin, R., 2004, A highly conserved pro-apoptotic gene, IKIP, located next to the Apaf-1 gene locus, is regulated by p53, Cell Death Differ. 11(12): 1317-25. (Abstract; Full-Text PDF)

9.    Hochrainer, K., Mayer, H., Baranyi, U., Binder, B.R., Lipp, J., and Kroismayr, R., 2005, The human HERC family of ubiquitin ligases: novel members, genomic organization, expression profiling, and evolutionary aspects, Genomics 85(2):153-64. (Abstract; Full-Text PDF)

10.  Aerts, S., Van Loo, P., Thijs, G., Mayer, H., De Martin, R., and De Moor, B., 2005, TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis, Nucleic Acids Res. Jul 1;33 (Web Server issue):W393-6. (Abstract; Full-Text PDF; Online Tutorial)
                     
              
Personal Database Submissions

A) LANCL1 sequences:
                             
1.    (ad Ref. 1) Homo sapiens mRNA for lanthionine synthetase C-like protein 1 (LANCL1 gene), 21-Feb-1997, GB: Y11395, GI:2894085.
2.    (ad Ref. 2) Mus musculus mRNA for lanthionine synthetase C-like protein 1 (LANCL1 gene), 28-Feb-1997, GB: Y11550, GI:3492807.
3.    (ad Ref. 2) Mus musculus mRNA for lanthionine synthetase C-like protein 1 (LANCL1 gene), 11-Feb-1998, GB: Y16518, GI:3492792.
4.    (---------) Danio rerio mRNA for LanC-like protein 1 (lancl1 gene), 30-May-2000, GB: AJ278244, GI:14275549.
5.    (ad Ref. 5) Homo sapiens partial LANCL1 gene for LanC-like protein 1, exons 1-2 and joined CDS, 26-May-2000, GB: AJ289236, GI:12232623.
6.    (ad Ref. 5) Homo sapiens partial LANCL1 gene for LanC-like protein 1, exon 3, 26-May-2000, GB: AJ289237, GI:12227255.
7.    (ad Ref. 5) Homo sapiens partial LANCL1 gene for LanC-like protein 1, exon 4, 26-May-2000, GB: AJ289238, GI:12227256.
8.    (ad Ref. 5) Homo sapiens partial LANCL1 gene for LanC-like protein 1, exons 5-10, 26-May-2000, GB: AJ289239, GI:12227257.
9.    (ad Ref. 5) Mus musculus partial Lancl1 gene for LanC-like protein 1, exons 1-2 and joined CDS, 30-May-2000, GB: AJ289603, GI:14277706.
10.  (ad Ref. 5) Mus musculus partial Lancl1 gene for LanC-like protein 1, exon 3, 30-May-2000, GB: AJ289604, GI:14275832.
11.  (ad Ref. 5) Mus musculus partial Lancl1 gene for LanC-like protein 1, exon 4, 30-May-2000, GB: AJ289605, GI:14275833.
12.  (ad Ref. 5) Mus musculus partial Lancl1 gene for LanC-like protein 1, exons 5-6, 30-May-2000, GB: AJ289606, GI:14275834.
13.  (ad Ref. 5) Mus musculus partial Lancl1 gene for LanC-like protein 1, exon 7, 30-May-2000, GB: AJ289607, GI:14275835.
14.  (ad Ref. 5) Mus musculus partial Lancl1 gene for LanC-like protein 1, exons 8-10, 30-May-2000, GB: AJ289608, GI:14275836.
15.  (ad Ref. 2) Mus musculus mRNA for LanC-like protein 1 (Lancl1 gene), 6-Sep-2000, GB: AJ294535, GI:15528442.
16.  (ad Ref. 4) Rattus norvegicus partial mRNA for lanthionine synthetase C-like protein 1 (Lancl1 gene), 9-Nov-2000, GB: AJ295233, GI:11140165.
 
 B) LANCL2 sequences:

1.    (ad Ref. 6) Homo sapiens mRNA for LanC-like protein 2 (lancl2 gene), 30-May-2000, GB: AJ278245, GI:12227251.

C) Microarray Datasets of HUVEC treated with Interleukin-1 (time course):

1.    (ad Ref. 7) IL-1 stimulation of HUVEC, 20-Jul-2004, NCBI-GEO GSE973 (GEO series record).
2.    (ad Ref. 7) IL-1 stimulation of HUVEC, 20-Jul-2004, NCBI-GEO GSM15389 (GEO sample record, 0 hr control).   
3.    (ad Ref. 7) IL-1 stimulation of HUVEC, 20-Jul-2004, NCBI-GEO GSM15390 (GEO sample record, 0,5 hr IL1).   
4.    (ad Ref. 7) IL-1 stimulation of HUVEC, 20-Jul-2004, NCBI-GEO GSM15391 (GEO sample record, 1 hr IL1).
5.    (ad Ref. 7) IL-1 stimulation of HUVEC, 20-Jul-2004, NCBI-GEO GSM15392 (GEO sample record, 2,5 hr IL1).
6.    (ad Ref. 7) IL-1 stimulation of HUVEC, 20-Jul-2004, NCBI-GEO GSM15393 (GEO sample record, 6 hr IL1).
7.     Note: This series of data is also available as GEO Dataset record GDS649 (created by NCBI staff) providing many options for interactive data analysis and download.

D) IKIP sequences:
                             
1.    (ad Ref. 8) Homo sapiens mRNA for IKIP1 (IKIP gene), 30-Jan-2003, GB: AJ539425, GI:41529133.
2.    (ad Ref. 8) Homo sapiens mRNA for IKIP2 (IKIP gene), 30-Jan-2003, GB: AJ539426, GI:41529135.
3.    (ad Ref. 8) Homo sapiens mRNA for IKIP3 (IKIP gene), 30-Jan-2003, GB: AJ539427, GI:41529137.
4.    (ad Ref. 8) Rattus norvegicus mRNA for IKIP1 (Ikip gene), 30-Jan-2003, GB: BN000112, GI:59276009.
5.    (ad Ref. 8) Rattus norvegicus mRNA for IKIP2 (Ikip gene), 30-Jan-2003, GB: BN000113, GI:59276011.  
                 
   Bioinformatics World was developed by Herbert Mayer, Medical University of Vienna, Austria (2001-2006)