CECAD: Bioinformatics Facility

Bioinformatics Facility

The facility supports CECAD research groups in their data analysis needs at all stages of a project, starting from experimental design all the way to obtaining publication-ready figures. Importantly, we are closely interacting with the researchers to help them answering their specific scientific questions with the data they have generated.

Our repertoire of computational methods encompasses the latest bioinformatics tools and best-practices, including the community-driven nf-core pipeline suite for standardized data analysis. Additionally, we streamline complex, custom analyses using advanced techniques, including make-like pipelining tools with meta-programming features, to enhance workflow efficiency and expand our support capabilities. To ensure reproducibility of results, we employ modern tools such as containerization and package management software, underscoring our commitment to reliable and verifiable science.

Services

Our team covers a wide spectrum of expertise, offering high-quality consulting throughout the project lifecycle in both computational and biological aspects.

We analyze a broad range of omics data, including transcriptomics, proteomics, and metabolomics, in addition to integrating multiple omics layers. Specializing in a diverse array of NGS data applications, we provide comprehensive support for cutting-edge research, with a particular focus on modern single-cell technologies. Beyond analysis, our services include educational programs, such as R-courses, empowering researchers to independently analyze their data.

The lab operates an in-house software package which trains models of molecular regulatory networks by taking advantage of the large and ever increasing RNA-Seq/ChIP-Seq databases behind the QuickNGS framework. Integration of these networks with additional a-priori knowledge from public databases has established a very powerful tool for downstream analysis of RNA-Seq data from the labs within CECAD.

Future plans

Looking forward, we aim to further elevate the standardization and efficiency of our bioinformatics workflows and to drive the development of integrative, multi-omics analysis techniques.
Our efforts to harness the latest methodologies for diverse data analysis purposes, our commitment to innovation and high-quality support, and our suite of services are set to empower scientists to transform their data into deep biological understanding. This positions the CECAD Bioinformatics Facility as an indispensable unit in advancing research on aging-associated diseases and beyond.

Publications Highlights

Steculorum SM, Ruud J, Karakasilioti I, Backes H, Engström Ruud L, Timper K, Hess ME, Tsaousidou E, Mauer J, Vogt MC, Paeger L, Bremser S, Klein AC, Morgan DA, Frommolt P, Brinkkötter PT, Hammerschmidt P, Benzing T, Rahmouni K, Wunderlich FT, Kloppenburg P, Brüning JC (2016):AgRP Neurons Control Systemic Insulin Sensitivity via Myostatin Expression in Brown Adipose Tissue. Cell; 165(1): 125-38 [...]
Oliverio M, Schmidt E, Mauer J, Baitzel C, Hansmeier N, Khani S, Konieczka S, Pradas-Juni M, Brodesser S, Van TM, Bartsch D, Brönneke HS, Heine M, Hilpert H, Tarcitano E, Garinis GA, Frommolt P, Heeren J, Mori MA, Brüning JC, Kornfeld JW (2016): Dicer1-miR-328-Bace1 signalling controls brown adipose tissue differentiation and function. Nat Cell Biol; 18(3): 328-36 [...]
Respuela P, Nikolic M, Tan M, Frommolt P, Zhao Y, Wysocka J, Rada-Iglesias A (2016): Foxd3 promotes exit from naive pluripotency through enhancer decommissioning and inhibits germline specification.Cell Stem Cell; 18(1): 118-33 [...]
Abdallah AT, Fischer M, Nürnberg P, Nothnagel M, Frommolt P (2015): CoNCoS: Copy number estimation in cancer with controlled support. J Bioinf Comp Biol; 13(5): 1550027 [...]
Wagle P, Nikolic M, Frommolt P (2015): QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation. BMC Genomics; 16: 487[...]
Frommolt P, Schumacher B (2015): Wormpath: Searching for molecular interaction networks in Caenorhabditis elegans. Source Code Biol Med; 10: 5[...]
Müller MM, Castells-Roca L, Babu V, Ermolaeva MA, Müller RU, Frommolt P, Williams AB, Greiss S, Schneider JI, Benzing T, Schermer B, Schumacher B (2014): DAF-16/FoxO and EGL-27/GATA promote developmental growth in response to persistent somatic DNA damage. Nat Cell Biol; 16(12): 1168-79[...]
Rosewich H, Thiele H, Ohlenbusch A, Maschke U, Altmüller J, Frommolt P, Zirn B, Ebinger F, Siemes H, Nürnberg P, Brockmann K, Gärtner J (2012):Heterozygous de-novo mutations in ATP1A3 in patients with alternative hemiplegia of childhood: a whole-exome sequencing gene-identification study. Lancet Neurol, 11(9): 764-73 [...]
Meimaridou E, Kowalczyk J, Guasti L, Hughes CR, Wagner F, Frommolt P, Nürnberg P, Mann NP, Banerjee R, Saka HN, Chapple JP, King PJ, Clark AJL, Metherell LA (2012): Mutations in NNT encoding nicotinamide nucleotide transhydrogenase cause familial glucocorticoid deficiency. Nat Genet, 44(7): 740-2 [...]
Frommolt P, Abdallah AT, Altmüller J, Motameny S, Thiele H, Becker C, Stemshorn K, Fischer M, Freilinger T, Nürnberg P (2012): Assessing the enrichment performance in targeted resequencing experiments. Hum Mutat; 33(4):635-41 [...]