Statistical multi-Omics UNDerstanding of Patient Samples

Livrables

Software supporting the molecular tumour characterization pipeline and predicting perturbed pathways

Opensource software supporting the molecular tumour characterization pipeline and predicting perturbed pathways

Software package for automated benchmarking
Open-source software with updated Renjin and code library of benchmarks and technical report describing most significant performance bottlenecks

Opensource 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

Open-source software CAUSEXPR, to prioritize likely causal mutations from genotype and gene expression

Open-source software CAUSEXPR to prioritize likely causal mutations from genotype and gene expression

Open-source software that implements tumour diversity time series analysis
Technical report and software for predictive modelling of drug response and detection of outlier samples

Technical report and accompanying open-source software for predictive modelling of drug response and detection of outlier samples in lymphomas and leukaemias.

Open-source software CAUSAMET and BIOMARK

Open-source software CAUSAMET, to prioritize likely causal mutations from genotype, gene expression, metabolite and phenotypes; and BIOMARK, to detect biomarkers for disease progression from longitudinal blood sample transcriptome and metabolome profiling.

Open-source software to implement causal stability ranking for high-dimensional genotype data

Opensource software that implements causal stability ranking for highdimensional genotype data

Open-source software for the standardized application of existing methods in liquid biopsy data analysis

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.

Open-source software implementing InteractiveReports and catalogue of standard templates.

Open-source software implementing InteractiveReports for displaying and scripting reproducible workflows; and a software catalogue of standard templates for informed decision-making.

Open-source software to estimate structured sparse models from multi-omics data

Release of open-source software to estimate structured sparse models from multi-omics data.

Open-source software implementing end-to-end analysis and integrating the results from T1.1-1.5

Open-source software implementing end-to-end analysis and integrating the results from T1.1-1.5, with documentation suitable for end-users.

Technical report on disease classification based on multilevel data integration
Technical report on approaches to outlier detection in patient ’omics data
Technical report on biomarkers analysed with transcriptome and metabolome data and technical report on novel pathomechanisms

Technical report on biomarkers analysed in >=100 samples with transcriptome and metabolome data; and technical report on novel pathomechanism(s) leading to impaired energy metabolism discovered by multi-omic patient data analysis

Technical report on existing and novel methods

Technical report on existing methods and novel methods developed in WP2

Technical report with best practice guidelines and software package

Technical report with definitions and best practice guidelines; and software package for simulation of experimental design and choice of validation sites in cancer genomics.

Technical report with evaluation of performance improvement or regression from D9.2

Technical report with evaluation of performance improvement or regression from D9.1

White paper description software design principles and open-source software implementation of SOUNDHub and SOUNDData.

White paper describing software design principles and implementations; and open-source software implementation of SOUNDHub (annotation) amd SOUNDData (experiment data) services and clients, with specific development of controlled and federated data access.

Technical report describing the design of re-capture platform for deep sequencing and validation

Technical report describing the design of re-capture platform for deep sequencing and validation on independent patient cohort.

Technical report on new disease entities that were identified using novel statistical methods
Technical report describing the data structure and methods for operating on screening data, as described in T1.1

Technical report describing the data structure and methods for operating on screening data as described in T11

SOUNDData and SOUNDHub public data resources

Three or more SOUNDData public data resources as identified and developed in collaboration with WP leads; four or more SOUNDHub/AnnotationHub public data resources.

Website of InteractiveReports for select outcomes of WP2, 5-7.

Make available InteractiveReports for select outcomes of WP2, 5-7 on website.

Publications

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

Auteurs: Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle
Publié dans: Molecular Systems Biology, Numéro 14/6, 2018, Page(s) e8124, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20178124

Drug-perturbation-based stratification of blood cancer

Auteurs: Sascha Dietrich, Małgorzata Oleś, Junyan Lu, Leopold Sellner, Simon Anders, Britta Velten, Bian Wu, Jennifer Hüllein, Michelle da Silva Liberio, Tatjana Walther, Lena Wagner, Sophie Rabe, Sonja Ghidelli-Disse, Marcus Bantscheff, Andrzej K. Oleś, Mikołaj Słabicki, Andreas Mock, Christopher C. Oakes, Shihui Wang, Sina Oppermann, Marina Lukas, Vladislav Kim, Martin Sill, Axel Benner, Anna Jauch
Publié dans: Journal of Clinical Investigation, Numéro 128/1, 2018, Page(s) 427-445, ISSN 0021-9738
Éditeur: American Society for Clinical Investigation
DOI: 10.1172/JCI93801

Genetic diagnosis of Mendelian disorders via RNA sequencing

Auteurs: Laura S. Kremer, Daniel M. Bader, Christian Mertes, Robert Kopajtich, Garwin Pichler, Arcangela Iuso, Tobias B. Haack, Elisabeth Graf, Thomas Schwarzmayr, Caterina Terrile, Eliška Koňaříková, Birgit Repp, Gabi Kastenmüller, Jerzy Adamski, Peter Lichtner, Christoph Leonhardt, Benoit Funalot, Alice Donati, Valeria Tiranti, Anne Lombes, Claude Jardel, Dieter Gläser, Robert W. Taylor, Daniele G
Publié dans: Nature Communications, Numéro 8, 2017, Page(s) 15824, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms15824

GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes

Auteurs: Georg Stricker, Mathilde Galinier, Julien Gagneur
Publié dans: BMC Bioinformatics, Numéro 19/1, 2018, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-018-2238-7

OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer

Auteurs: Vicente A. Yépez, Laura S. Kremer, Arcangela Iuso, Mirjana Gusic, Robert Kopajtich, Eliška Koňaříková, Agnieszka Nadel, Leonhard Wachutka, Holger Prokisch, Julien Gagneur
Publié dans: PLOS ONE, Numéro 13/7, 2018, Page(s) e0199938, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0199938

Ensemble outlier detection and gene selection in triple-negative breast cancer data

Auteurs: Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
Publié dans: BMC Bioinformatics, Numéro 19/1, 2018, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-018-2149-7

Identification of influential observations in high-dimensional cancer survival data through the rank product test

Auteurs: Eunice Carrasquinha, André Veríssimo, Marta B. Lopes, Susana Vinga
Publié dans: BioData Mining, Numéro 11/1, 2018, ISSN 1756-0381
Éditeur: BioMed Central
DOI: 10.1186/s13040-018-0162-z

Robust identification of target genes and outliers in triple-negative breast cancer data

Auteurs: Pieter Segaert, Marta B Lopes, Sandra Casimiro, Susana Vinga, Peter J Rousseeuw
Publié dans: Statistical Methods in Medical Research, 2018, Page(s) 096228021879472, ISSN 0962-2802
Éditeur: SAGE Publications
DOI: 10.1177/0962280218794722

Advancing genomic approaches to the molecular diagnosis of mitochondrial disease

Auteurs: Sarah Louise Stenton, Holger Prokisch
Publié dans: Essays In Biochemistry, Numéro 62/3, 2018, Page(s) 399-408, ISSN 0071-1365
Éditeur: Portland Press, Ltd.
DOI: 10.1042/EBC20170110

Mutations in PPCS , Encoding Phosphopantothenoylcysteine Synthetase, Cause Autosomal-Recessive Dilated Cardiomyopathy

Auteurs: Arcangela Iuso, Marit Wiersma, Hans-Joachim Schüller, Ben Pode-Shakked, Dina Marek-Yagel, Mathias Grigat, Thomas Schwarzmayr, Riccardo Berutti, Bader Alhaddad, Bart Kanon, Nicola A. Grzeschik, Jürgen G. Okun, Zeev Perles, Yishay Salem, Ortal Barel, Amir Vardi, Marina Rubinshtein, Tal Tirosh, Gal Dubnov-Raz, Ana C. Messias, Caterina Terrile, Iris Barshack, Alex Volkov, Camilla Avivi, Eran Eyal, E
Publié dans: The American Journal of Human Genetics, Numéro 102/6, 2018, Page(s) 1018-1030, ISSN 0002-9297
Éditeur: University of Chicago Press
DOI: 10.1016/j.ajhg.2018.03.022

Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts

Auteurs: Miroslav P Milev, Claudio Graziano, Daniela Karall, Willemijn F E Kuper, Noraldin Al-Deri, Duccio Maria Cordelli, Tobias B Haack, Katharina Danhauser, Arcangela Iuso, Flavia Palombo, Tommaso Pippucci, Holger Prokisch, Djenann Saint-Dic, Marco Seri, Daniela Stanga, Giovanna Cenacchi, Koen L I van Gassen, Johannes Zschocke, Christine Fauth, Johannes A Mayr, Michael Sacher, Peter M van Hasselt
Publié dans: Journal of Medical Genetics, 2018, Page(s) jmedgenet-2018-105441, ISSN 0022-2593
Éditeur: British Medical Association
DOI: 10.1136/jmedgenet-2018-105441

Clinical, biochemical and genetic spectrum of 70 patients with ACAD9 deficiency: is riboflavin supplementation effective?

Auteurs: Birgit M. Repp, Elisa Mastantuono, Charlotte L. Alston, Manuel Schiff, Tobias B. Haack, Agnes Rötig, Anna Ardissone, Anne Lombès, Claudia B. Catarino, Daria Diodato, Gudrun Schottmann, Joanna Poulton, Alberto Burlina, An Jonckheere, Arnold Munnich, Boris Rolinski, Daniele Ghezzi, Dariusz Rokicki, Diana Wellesley, Diego Martinelli, Ding Wenhong, Eleonora Lamantea, Elsebet Ostergaard, Ewa Pronicka
Publié dans: Orphanet Journal of Rare Diseases, Numéro 13/1, 2018, ISSN 1750-1172
Éditeur: BioMed Central
DOI: 10.1186/s13023-018-0784-8

Biallelic C1QBP Mutations Cause Severe Neonatal-, Childhood-, or Later-Onset Cardiomyopathy Associated with Combined Respiratory-Chain Deficiencies

Auteurs: René G. Feichtinger, Monika Oláhová, Yoshihito Kishita, Caterina Garone, Laura S. Kremer, Mikako Yagi, Takeshi Uchiumi, Alexis A. Jourdain, Kyle Thompson, Aaron R. D’Souza, Robert Kopajtich, Charlotte L. Alston, Johannes Koch, Wolfgang Sperl, Elisa Mastantuono, Tim M. Strom, Saskia B. Wortmann, Thomas Meitinger, Germaine Pierre, Patrick F. Chinnery, Zofia M. Chrzanowska-Lightowlers, Robert N.
Publié dans: The American Journal of Human Genetics, Numéro 101/4, 2017, Page(s) 525-538, ISSN 0002-9297
Éditeur: University of Chicago Press
DOI: 10.1016/j.ajhg.2017.08.015

“Transcriptomics”: molecular diagnosis of inborn errors of metabolism via RNA-sequencing

Auteurs: Laura S. Kremer, Saskia B. Wortmann, Holger Prokisch
Publié dans: Journal of Inherited Metabolic Disease, Numéro 41/3, 2018, Page(s) 525-532, ISSN 0141-8955
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10545-017-0133-4

Bi-allelic Mutations in Phe-tRNA Synthetase Associated with a Multi-system Pulmonary Disease Support Non-translational Function

Auteurs: Zhiwen Xu, Wing-Sze Lo, David B. Beck, Luise A. Schuch, Monika Oláhová, Robert Kopajtich, Yeeting E. Chong, Charlotte L. Alston, Elias Seidl, Liting Zhai, Ching-Fun Lau, Donna Timchak, Charles A. LeDuc, Alain C. Borczuk, Andrew F. Teich, Jane Juusola, Christina Sofeso, Christoph Müller, Germaine Pierre, Tom Hilliard, Peter D. Turnpenny, Matias Wagner, Matthias Kappler, Frank Brasch, John Paul B
Publié dans: The American Journal of Human Genetics, Numéro 103/1, 2018, Page(s) 100-114, ISSN 0002-9297
Éditeur: University of Chicago Press
DOI: 10.1016/j.ajhg.2018.06.006

Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits

Auteurs: Ruth I. C. Glasgow, Kyle Thompson, Inês A. Barbosa, Langping He, Charlotte L. Alston, Charu Deshpande, Michael A. Simpson, Andrew A. M. Morris, Axel Neu, Ulrike Löbel, Julie Hall, Holger Prokisch, Tobias B. Haack, Maja Hempel, Robert McFarland, Robert W. Taylor
Publié dans: neurogenetics, Numéro 18/4, 2017, Page(s) 227-235, ISSN 1364-6745
Éditeur: Springer Verlag
DOI: 10.1007/s10048-017-0526-4

Network-based integration of multi-omics data for prioritizing cancer genes

Auteurs: Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Luca Häfliger, Jonas Behr, Hesam Montazeri, Michael N Hall, Niko Beerenwinkel
Publié dans: Bioinformatics, Numéro 34/14, 2018, Page(s) 2441-2448, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty148

DegreeCox – a network-based regularization method for survival analysis

Auteurs: André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga
Publié dans: BMC Bioinformatics, Numéro 17/S16, 2016, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-016-1310-4

Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy

Auteurs: Samira Ait-El-Mkadem, Manal Dayem-Quere, Mirjana Gusic, Annabelle Chaussenot, Sylvie Bannwarth, Bérengère François, Emmanuelle C. Genin, Konstantina Fragaki, Catharina L.M. Volker-Touw, Christelle Vasnier, Valérie Serre, Koen L.I. van Gassen, Françoise Lespinasse, Susan Richter, Graeme Eisenhofer, Cécile Rouzier, Fanny Mochel, Anne De Saint-Martin, Marie-Thérèse Abi Warde, Monique G.M. de
Publié dans: The American Journal of Human Genetics, Numéro 100/1, 2017, Page(s) 151-159, ISSN 0002-9297
Éditeur: University of Chicago Press
DOI: 10.1016/j.ajhg.2016.11.014

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

Auteurs: Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
Publié dans: BMC Bioinformatics, Numéro 18/1, 2017, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-016-1417-7

Biallelic IARS Mutations Cause Growth Retardation with Prenatal Onset, Intellectual Disability, Muscular Hypotonia, and Infantile Hepatopathy

Auteurs: Robert Kopajtich, Kei Murayama, Andreas R. Janecke, Tobias B. Haack, Maximilian Breuer, A.S. Knisely, Inga Harting, Toya Ohashi, Yasushi Okazaki, Daisaku Watanabe, Yoshimi Tokuzawa, Urania Kotzaeridou, Stefan Kölker, Sven Sauer, Matthias Carl, Simon Straub, Andreas Entenmann, Elke Gizewski, René G. Feichtinger, Johannes A. Mayr, Karoline Lackner, Tim M. Strom, Thomas Meitinger, Thomas Müll
Publié dans: The American Journal of Human Genetics, Numéro 99/2, 2016, Page(s) 414-422, ISSN 0002-9297
Éditeur: University of Chicago Press
DOI: 10.1016/j.ajhg.2016.05.027

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis

Auteurs: Georg Stricker, Alexander Engelhardt, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur
Publié dans: Bioinformatics, 2017, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx150

Unsupervised learning of pharmacokinetic responses

Auteurs: Elson Tomás, Susana Vinga, Alexandra M. Carvalho
Publié dans: Computational Statistics, 2017, ISSN 0943-4062
Éditeur: Physica-Verlag Gmbh und Co.
DOI: 10.1007/s00180-016-0707-x

Deficient methylation and formylation of mt-tRNAMet wobble cytosine in a patient carrying mutations in NSUN3

Auteurs: Lindsey Van Haute, Sabine Dietmann, Laura Kremer, Shobbir Hussain, Sarah F. Pearce, Christopher A. Powell, Joanna Rorbach, Rebecca Lantaff, Sandra Blanco, Sascha Sauer, Urania Kotzaeridou, Georg F. Hoffmann, Yasin Memari, Anja Kolb-Kokocinski, Richard Durbin, Johannes A. Mayr, Michaela Frye, Holger Prokisch, Michal Minczuk
Publié dans: Nature Communications, Numéro 7, 2016, Page(s) 12039, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms12039

Genomic variant annotation workflow for clinical applications

Auteurs: Thomas Thurnherr, Franziska Singer, Daniel J. Stekhoven, Niko Beerenwinkel
Publié dans: F1000Research, Numéro 5, 2016, Page(s) 1963, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.9357.2

OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data

Auteurs: Felix Brechtmann, Agne Matuseviciute, Christian Mertes, Vicente A Yepez, Ziga Avsec, Maximilian Herzog, Daniel Magnus Bader, Holger Prokisch, Julien Gagneur
Publié dans: bioRxiv, 2018
Éditeur: bioRxiv
DOI: 10.1101/322149

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

Auteurs: Dongxue Wang, Basak Eraslan, Thomas Wieland, Bjorn M Hallstrom, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Li-hua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Fredrik Ponten, Mathias Uhlen, Julien Gagneur, Hannes Hahne, Bernhard Kuster
Publié dans: bioRxiv, 2018
Éditeur: bioRxiv
DOI: 10.1101/357137

Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues

Auteurs: Basak Eraslan, Dongxue Wang, Mirjana Gusic, Holger Prokisch, Bjorn M Hallstrom, Mathias Uhlen, Anna Asplund, Fredrik Ponten, Thomas Wieland, Thomas Hopf, Hannes Hahne, Bernhard Kuster, Julien Gagneur
Publié dans: bioRxiv, 2018
Éditeur: bioRxiv
DOI: 10.1101/353763

Sparse network-based regularization for the analysis of patientomics high-dimensional survival data

Auteurs: André Veríssimo, Eunice Carrasquinha, Marta B. Lopes, Arlindo L. Oliveira, Marie-France Sagot, Susana Vinga
Publié dans: 2018
Éditeur: bioRxiv

Consensus outlier detection in survival analysis using the rank product test

Auteurs: Eunice Carrasquinha, André Veríssimo, Susana Vinga
Publié dans: 2018
Éditeur: bioRxiv
DOI: 10.1101/421917

Genetic diagnosis of Mendelian disorders via RNA sequencing

Auteurs: Laura S Kremer, View ORCID ProfileDaniel M Bader, Christian Mertes, Robert Kopajtich, Garwin Pichler, Arcangela Iuso, Tobias B Haack, Elisabeth Graf, Thomas Schwarzmayr, Caterina Terrile, Eliska Konafikova, Birgit Repp, Gabi Kastenmüller, Jerzy Adamski, Peter Lichtner, Christoph Leonhardt, Benoit Funalot, Alice Donati, Valeria Tiranti, Anne Lombes, Claude Jardel, Dieter Gläser, Robert W Taylor,
Publié dans: 2016
Éditeur: bioRxiv
DOI: 10.1101/066738

Using R language based bioinformatic workflows as PaaS

Auteurs: Solaimani P., Kallen M., Bertram A.
Publié dans: F1000Research, 2016
Éditeur: F1000Research
DOI: 10.7490/f1000research.1113288.1

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