Major research issues/sites:
The Helmholtz-University Young Investigators Group “Bioinformatics and Transcriptomics” studies disease relevant differentiation processes of immune cells. The group aims at elucidating the link between non-protein coding RNAs and epigenetic modifications in response to Th cell differentiation. It strives to gain a systems biology perspective of this differentiation process. The group investigates how environmental toxicants affect the epigenome of immune cells and whether long non-coding RNAs are involved in this process. It combines bioinformatic and experimental competencies, relying mainly on transcriptomic, epi- and genomic high-throughput methods and on bioinformatic approaches to analyze and integrate these data.
Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M, Hackermüller J, Hoffmann S, Sartoris F, Pörtner HO, Timofeyev M, Luckenbach T, Stadler PF. A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. J. Exp. Zool. B. 322(3):177-89. 2014. | DOI: 10.1002/jez.b.22560
Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermüller J, Stadler PF. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biology 15:R34. 2014.
Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Comput Biol 5: e1000502. 2009.
Short technical description:
The platform comprises
- Illumina Hiseq 2000 ultra-highthroughput sequencer
- Instrumentation for library preparation for short and long RNAseq, genome sequencing, targeted re-sequencing, ChIPseq and Clipseq
- UFZ high performance computing cluster eve with currently more than 2400 cores and greater 400 terabytes of storage
- Software pipelines for the efficient processing of data e.g. for
- De novo transcript assembly
- Differential expression of transcripts
- Identification of alternative transcript structures
- Genome assembly
Options and conditions for visiting scientists:
Available for joint projects if (co)-funding for consumables is available.
Unit Cost of use and principles of costing:
Costs apply for library preparation and sequencing consumables and need to be estimated for specific projects.
centre running the infrastructure:
UFZ - Helmholtz Centre for Environmental Research
type of facility:
Laboratory / high-end instrument
- UFZ - Helmholtz Centre for Environmental Research
- Phone: +49 341 235-0