Tobias Jakobi

Project

Development of a data evaluation pipeline for the functional annotation of eukaryotic cDNA sequence data of a Chinese Hamster Ovary cell line.

Info

Area: polyomics
Project Start: 1.04.2010
Supervisor(s): Dr. Alexander Goesmann, Prof. Dr. Alfred Pühler, Prof. Dr. Jens Stoye
University: Bielefeld

More

Tobias Jakobi was a fellow of the CLIB-GC and defended his doctoral thesis in October 2014. Tobias Jacobi has an M. Sc. in Bioinformatics and Genome Research from Bielefeld University.

Dr. Jakobi joined the Research Group on Computational RNA Biology and Ageing at the Max-Planck Institute for the Biology of Ageing in Cologne as a postdoctoral fellow and then moved to the University Hospital in Heidelberg.

Project overview

First genomes assembled from short reads only are dominated by members of the prokaryotic domain. Recently it has become feasible to assemble even eukaryotic genomes with short reads only. Genomic CHO Illumina reads together with 454 cDNA reads are building the data foundation for this project. This novel approach uses assembled cDNA sequences as seeds for so called “micro assemblies”. Up- & downstream regions of cDNA seeds are assembled in order to gather knowledge of regulatory elements in those areas.

Development of a data evaluation pipeline for the functional annotation of eukaryotic cDNA sequence data of a Chinese Hamster Ovary cell line

Publications

2012

Hackl M, Jadhav V, Jakobi T, Rupp O, Brinkrolf K, Goesmann A, Pühler A, Noll T, Borth N, Grillari J (2012) Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Journal of biotechnology 158(3): 151 - 155.

Cox AJ, Bauer MJ, Jakobi T, Rosone G (2012) Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics (Oxford, England) .

Cox AJ, Jakobi T, Rosone G, Schulz-Trieglaff OB (2012) Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes. In: Algorithms in Bioinformatics. Raphael B, Tang J (Eds); Lecture Notes in Computer Science, 7534: 214 - 224.

2011

Becker J, Hackel M, Jakobi T, Rupp O, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, Noll T, Pühler A, Tauch A, Brinkrolf K (2011) Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology 156(3): 227 - 235.

Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011) Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27(10): 1351 - 1358.

Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner zu Siederdissen C, Bort JAH, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Pühler A, Borth N, Grillari J (2011) Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. J Biotechnol 153(1-2): 62 - 75.

2009

Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A (2009) TRUNCATULIX - a data warehouse for the legume community. BMC PLANT BIOLOGY 9:19.

Documents


Tobias’ project
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Tobias´ CV
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Tobias´ latest poster April 2011
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