Results

Publications

  1. Ait-El-Mkadem S, Dayem-Quere M, Gusic M, Chaussenot A, François B, Genin EC, Fragaki K (2017), Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy. Am J Hum Genet. PDF
  2. Floyd BJ, Wilkerson EM, Veling MT, …, Prokisch H, Kim JJ P, Coon JJ and Pagliarini DJ (2016), Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Mol Cell. PDF
  3. Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H and Beerenwinkel N (2017). Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics, 3;18(1):8. PDF
  4. Kopajtich R, Murayama K, Janecke AR, …, Georg F. Hoffmann GF, Prokisch H and Staufner C (2016), Biallelic IARS Mutations Cause Growth Retardation with Prenatal Onset, Intellectual Disability, Muscular Hypotonia, and Infantile Hepatopathy. Am J Hum Genet. PDF
  5. Kremer S, Bader DM, Mertes C, Kopajtich R, …, Meitinger T, Gagneur J and Prokisch H (2017), Genetic diagnosis of Mendelian disorders via RNA sequencing. PDF
  6. Stricker G, Engelhardt A, Schulz D, Schmid M, Tresch A and Julien Gagneur J (2017), GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis. Bioinformatics (in press). bioRxiv.
  7. Thurnherr T, Singer F, Stekhoven DJ and Beerenwinkel N (2016). Genomic variant annotation workflow for clinical applications [version 2; referees: 2 approved]. F1000Research, 5:1963. PDF
  8. Tomás, E, Vinga, S, and Carvalho, A M (2017). Unsupervised learning of pharmacokinetic responses. Computational Statistics, 1-20. PDF
  9. Van Haute L, Dietmann S, Kremer L, …, Frye M, Prokisch H & Minczuk M (2016). Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. Nat Commun. PDF
  10. Veríssimo, A, Oliveira, AL, Sagot, M-F, & Vinga, S (2016). DegreeCox – a network-based regularization method for survival analysis. BMC Bioinformatics, 17(S16), 449. PDF
  11. Witzel M, Petersheim D, Fan Y, Bahrami E, Racek T, Rohlfs M, Puchałka J, Mertes C, Gagneur J, …, Schmidt H, Schäffer AA and Klein C (2017). Chromatin-remodeling factors SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Nat. Genet. Link

 

Deliverables

  1. Technical report describing the data structure and methods for operating on screening data. PDF
  2. Open-source software for the standardized application of existing methods in liquid biopsy data analysis, supported by online catalogue of existing methods and data resources. PDF
  3. Open-source software CAUSEXPR, to prioritize likely causal mutations from genotype and gene expression. PDF
  4. Technical report on approaches to outlier detection in patient ’omics data. PDF
  5. Open-source software that implements causal stability ranking for high-dimensional genotype data. PDF
  6. Open-source software supporting the molecular tumour characterization pipeline and predicting perturbed pathways. PDF
  7. Technical report on new disease entities that were identified using novel statistical methods. PDF
  8. Open-source software implementing an updated version of Renjin that supports the major Bioconductor packages; a code library of benchmarks; and a technical report describing the most significant performance bottlenecks. PDF
  9. Technical report with definitions and best practice guidelines; and software package for simulation of experimental design and choice of validation sites in cancer genomics. PDF
  10. Database of solved cases. PDF