BioInformatics

Bioinformatics is crucial to handle the exponential increasing data (terabytes) in our Molecular Genetics department generated by techniques such as Next Generation Sequencing of DNA and RNA, DNA microarrays, proteomics analysis and time laps microscopy. Furthermore, mining and integrating the publically available literature and databases if of outmost importance to translate big-data to biological knowledge.

The goal of our small bioinformatics group is on integrating the data mining and statistics in user friendly pipelines and webservers. To do so, we focus is on reduction of data to human interpretable tables, graphics and gene networks. This means that choices of methods, statistics and algorithms are mainly made by the bioinformaticians.

To facilitate the above, our group has two Linux servers, one for simple daily work and one Linux ‘work-horse’ that can handle 32 threads in its 256G memory.

For more information or internship contact dr. Anne de Jong (anne.de.jong [@] rug.nl

Interface for our bioinformatics server: http://genome2d.molgenrug.nl

References

1. van Heel AJ, de Jong A, Montalban-Lopez M, Kok J, Kuipers OP: BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 2013, 41(Web Server issue):W448-53.

2. de Jong A, Pietersma H, Cordes M, Kuipers OP, Kok J: PePPER: a webserver for prediction of prokaryote promoter elements and regulons BMC Genomics 2012, 13:299-2164-13-299.

3. de Jong A, Auke J. van Heel, Auke J., Kuipers K: Genome Exploitation and Bioinformatic Tools. In Prokaryotic Antimicrobial Peptides: From Genes to Applications. 1st Edition. edition (March 8, 2011) edition. Edited by Drider D, Rebuffat S. Springer; 2011:.

4. Blom EJ, Roerdink JB, Kuipers OP, van Hijum SA: MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. Bioinformatics 2009, 25(4):550-551.

5. Brouwer RW, van Hijum SA, Kuipers OP: MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinformatics 2009, 25(1):139-140.

6. Blom EJ, van Hijum SA, Hofstede KJ, Silvis R, Roerdink JB, Kuipers OP: DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. BMC Bioinformatics 2008, 9:535.

7. Blom EJ, Breitling R, Hofstede KJ, Roerdink JB, van Hijum SA, Kuipers OP: Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics 2008, 9:495-2164-9-495.

8. Westenberg MA, van Hijum SA, Lulko AT, Kuipers OP, Roerdink JB: Interactive visualization of gene regulatory networks with associated gene expression time series data. In Visualization in Medicine and Life Sciences. Edited by Anonymous Springer; 2008:293-311.

9. Blom EJ, Bosman DW, van Hijum SA, Breitling R, Tijsma L, Silvis R, Roerdink JB, Kuipers OP: FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinformatics 2007, 23(9):1161-1163.

10. Jong A, Hijum SAFT, Bijlsma JJE, Kok J, Kuipers OP: BAGEL: a web-based bacteriocin genome mining tool. 2006, .

11. van Hijum SA, de Jong A, Baerends RJ, Karsens HA, Kramer NE, Larsen R, den Hengst CD, Albers CJ, Kok J, Kuipers OP: A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics 2005, 6:77.

12. van Hijum SA, Zomer AL, Kuipers OP, Kok J: Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 2005, 33(Web Server issue):W560-6.

13. Baerends R, Smits W, De Jong A, Hamoen L, Kok J, Kuipers O: Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biol 2004, 5(5):R37.

14. van Hijum SA, de Jong A, Buist G, Kok J, Kuipers OP: UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons Bioinformatics 2003, 19(12):1580-1582.

15. Van Hijum SAFT, de la Nava JG, Trelles O, Kok J, Kuipers OP: MicroPreP: a cDNA microarray data pre-processing framework. Appl.Bioinformatics 2003, 2:241-244.