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. Argelaguet, R, Velten, B, Arnol, D, Dietrich, S, Zenz, T, Marioni, JC, Buettner, F, Huber, W and Stegle, O (2018). Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol. Syst. Biol., 14, e8124. PDF
  3. Brechtmann F, Matuseviciute A, Mertes C, Yepez VA, Avsec Z, Herzog M, Bader DM, Prokisch H, Gagneur J (2018). OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data. bioRxiv; https://doi.org/10.1101/322149.
  4. Carrasquinha E, Vinga S, Veríssimo A (2018), Consensus outlier detection in survival analysis using the rank product test. bioRxiv 421917; (doi: https://doi.org/10.1101/421917).
  5. Carrasquinha E, Veríssimo A, Lopes MB, and Vinga S (2018). Identification of influential observations in high-dimensional cancer survival data through the rank product test. BioData Mining201811:1. PDF
  6. Cheng PF (2018). Medical bioinformatics in melanoma. Curr Opin Oncol. 30; 113-117. PDF
  7. Dietrich, S, Oleś, M, Lu, J, …, Hüllein, J, da Silva Liberio, M, Huber, W, and Zenz, T (2018). Drug-perturbation-based stratification of blood cancer. J. Clin. Invest., 128. PDF
  8. Dimitrakopoulos, C, Hindupur, S, Haefliger, L, …, Montazeri, H, Hall, M, & Beerenwinkel, N (2018). Network-based integration of multi-omics data for prioritizing cancer genes. Bioinformatics, bty148. PDF
  9. Eraslan B, Wang D, Gusic M, … Hahne H, Kuster B, Gagneur J (2018). Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues. bioRxiv; doi: https://doi.org/10.1101/353763.
  10. Feichtinger RG, Oláhová M, Kishita Y, …, Kopajtich R, …, Okazaki Y, Minczuk M, Prokisch H (2017). Biallelic C1QBP Mutations Cause Severe Neonatal-, Childhood-, or Later-Onset Cardiomyopathy Associated with Combined Respiratory-Chain Deficiencies. Am J Hum Genet. 101(4):525-538. PDF
  11. 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
  12. Glasgow RIC, Thompson K, Barbosa IA, …, Prokisch H, Haack TB, Hempel M, McFarland R, Taylor RW (2017). Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits. Neurogenetics. 18(4):227-235. PDF
  13. 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
  14. Hogan SA, Levesque MP, and Cheng PF (2018). Melanoma Immunotherapy: Next-Generation Biomarkers. Front Oncol. 8; 178. PDF
  15. Iuso A, Wiersma M, Schüller HJ, …, Prokisch H, Haack TB, Brundel BJJM, Haas D, Sibon OCM, Anikster Y (2018). Mutations in PPCS, Encoding Phosphopantothenoylcysteine Synthetase, Cause Autosomal-Recessive Dilated Cardiomyopathy. Am J Hum Genet. 102(6):1018-1030. doi:10.1016/j.ajhg.2018.03.022. PDF
  16. Jahn K, Kuipers J and Beerenwinkel N (2016). Tree inference for single-cell data. Genome Biology, 17. (doi: 10.1186/s13059-016-0936-x). PDF
  17. 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
  18. 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
  19. Kremer LS, Wortmann SB, Prokisch H (2018). “Transcriptomics”: molecular diagnosis of inborn errors of metabolism via RNA-sequencing. J Inherit Metab Dis. doi: 10.1007/s10545-017-0133-4. [Epub ahead of print]. PDF
  20. Kuipers, J, Jahn, K, Raphael, BJ, & Beerenwinkel, N (2017). Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors. Genome research, 27(11), 1885-1894. PDF
  21. Leung, M, Davis, A, Gao, R, Casasent, A, et al. (2017). Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Research, 27(8).
  22. Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S (2018). Ensemble outlier detection and gene selection in triple-negative breast cancer data. JBMC Bioinformatics, 19:168. doi: 10.1186/s12859-018-2149-7. LINK
  23. Loureiro H, Carrasquinha E, Alho I, Ferreira A, Costa L, Carvalho AM, and Vinga S (2018), Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of Type I Collagen (NTX) dynamics through Joint Models. BMC Medical Informatics and Decision Making. Under Review.
  24. Mangana J, Cheng PF, Kaufmann C, …, von Moos R, Michielin O, Braun RP, et al. (2017). Multicenter, real-life experience with checkpoint inhibitors and targeted therapy agents in advanced melanoma patients in Switzerland. Melanoma Res. PDF
  25. Milev MP, Graziano C, Karall D, …, Prokisch H, …, Mayr JA, Sacher M, van Hasselt PM (2018). Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts. J Med Genet. pii: jmedgenet-2018-105441. doi: 10.1136/jmedgenet-2018-105441. PDF
  26. Reyes A and Huber W (2017). Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Res; 46(2):582-592. PDF
  27. Segaert P, Lopes MB, Casimiro S, Vinga S, and Rousseeuw P (2018). Robust identification of target genes and outliers in triple-negative breast cancer data. Statistical Methods in Medical Research, First Published August 27, 2018. doi:10.1177/0962280218794722. PDF
  28. Singer J, Ruscheweyh HJ, Hofmann AL, …, Wüst T, Rinn B, Beerenwinkel N (2018). NGS-pipe: next-generation sequencing pipelines for precision oncology, Bioinformatics. Jan 1;34(1):107-108. doi: 10.1093/bioinformatics/btx540. PDF
  29. Singer, J, Kuipers, J, Jahn, K, & Beerenwinkel, N (2018). Bioarxiv, https://doi.org/10.1101/290908.
  30. 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.
  31. Stricker G, Galinier M, and Gagneur J (2018). GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes. BMC; doi: https://doi.org/10.1186/s12859-018-2238-7. PMID 29945559. PDF
  32. Stenton SL, Prokisch H (2018). Advancing genomic approaches to the molecular diagnosis of mitochondrial disease. Essays Biochem. pii:EBC20170110. doi: 10.1042/EBC20170110. PDF
  33. 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
  34. Tomás, E, Vinga, S, and Carvalho, A M (2017). Unsupervised learning of pharmacokinetic responses. Computational Statistics, 1-20. PDF
  35. 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
  36. 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
  37. Veríssimo A, Carrasquinha E, Lopes MB, Oliveira AL, Sagot M-F, & Vinga S (2018). Sparse network-based regularization for the analysis of patientomics high-dimensional survival data. bioRxiv 403402; (doi: https://doi.org/10.1101/403402).
  38. Wagner AH, Coffman AC, Ainscough BJ, …, Mardis ER, Griffith M, Griffith OL (2016). DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Research, 44(D1):D1036-44 (doi: 10.1093/nar/gkv1165).
  39. Wang D, Eraslan B, Wieland T, …, Gagneur J, Hahne H, Kuster B (2018). A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. bioRxiv; doi: https://doi.org/10.1101/357137.
  40. 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
  41. Yepez VA, Kremer LS, Iuso A, …, Wachutka L, Prokisch H, Gagneur J (2018). OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. doi: https://doi.org/10.1371/journal.pone.0199938. PMID 29995917. PDF
  42. Xu Z, Lo WS, Beck DB, …, Prokisch H, Griese M, Chung WK, Schimmel P (2018). Bi-allelic Mutations in Phe-tRNA Synthetase Associated with a Multi-system Pulmonary Disease Support Non-translational Function. Am J Hum Genet. ;103(1):100-114. doi: 10.1016/j.ajhg.2018.06.006. PDF