Beat Wolf - PhD Student
This page contains information about my PhD thesis and the different projects I’m involved in. You can also find different publications made by me or related to my work.

Thesis

Reducing the complexity of OMICS data analysis

DNA sequence analysis is a complex and time consuming process. While the amount of data produced that needs to be analysed rapidly increases, neither the available computational resources nor human resources grow fast enough to keep up with the analysis. The goal of this thesis is to approach both of those bottlenecks in DNA and RNA analysis in the context of diagnostics.
The basis of this thesis is the GensearchNGS project which was developed as a prototype during the author's Master project. Large parts of the the prototype where rewritten and extended depending on the needs of the diagnostics laboratories, always with the goal to lower the technical and computational complexity. This is achieved through an intuitive user interface, hiding as much of the complexity from the user as possible, to increase the amount of people able to perform the analysis.
The other approach is to create more efficient algorithms, lowering the time to do the analysis, as well as lowering the infrastructure requirements. Parts of this effort have been released in the GNATY project, which is a collection of free tools to perform common bio-informatics tasks in a more efficient manner.
When better algorithms and optimized code reach their limits on what is possible to speed up the data analysis, we turn to distributed computing. This is achieved among other techniques with the POP-Java programming language, which has been vastly improved and extended over the course of this thesis.
The thesis is a collaboration between the institute iCoSys at the HES-SO and the Departement of bioinformatics at the University of Würzburg.

Projects

Industrial projects

Here is a list of projects i worked on. Some are directly, some indirectly and some not at all related to the thesis.

Abstract:
Trusted friend computing expands our in house parallel object programming (POP) framework for distributed computing to allow individuals to easily share their computing resources, both for computation and data sharing.

Role: Project leader

Gammaknife

Abstract:
The Gammaknife project is a direct successor of the BigMat project.

Role: Supervisor

PSA Valeo

Abstract:
Modern automobiles integrate more and more advanced technologies to assist the driver. During this project in collaboration with the EPFL, a complex algorithm has been ported to an embedded system to be used in an automobile.

Role: Advisor

Abstract:
GensearchNGS is a NGS framework that contains all the features needed to analyse NGS data. From raw data statistics, filterting and alignment to patient management alignment visualization and variant report generation, everything is present. All features where developed during my master thesis and during my time working directly for Phenosystems SA. The development of GensearchNGS continues during my PHD thesis and useful parts of my thesis will be intergrated into the framework when it makes sense. GensearchNGS-Viewer is a subproject of GensearchNGS, only containing the visualization part of GensearchNGS.

Role: Project leader, lead developer

GNATY

Abstract:
GNATY is a library of Bioinformatics related tools. Some of the have been developed inside of GensearchNGS and are now released as stand alone utilities. A publication is being prepared right now, with more details to follow once it is published.

Role: Project leader, lead developer

Abstract:
POP-Java is a Java implementation of the POP programming model. POP-Java allows programmers to easily distribute object orientated Java applications over the network, without having to handle the low level distribution work themselves. The code is open source and can be found on Github.

Role: Project leader, lead developer

BigMat

Abstract:
BigMat is a project which has as its goal to implement an algorithm used in cancer treatment in a fast and efficient way.
The project included the work with huge matrices, efficient usage of multi-core systems and GPGPU calculations using cuda.

Role: Scientific collaborator

Abstract:
SAGeDa stands for "Streaming and Analysing Genome Data". It is an exploratory project inside the HEFR Gridgroup to determine the viability of a stream based approach for DNA sequence alignments. The target data is generated by next generation sequencing technology. To evaluate the approach, POP-C++ and DSPE will be used. POP-C++ beeing C++ language extension that allows the distribution of C++ objects over the network. DSPE is a stream processing framework.

Role: Scientific collaborator

International research projects

cHiPSet
Description: Cost action
Contribution: Parallel algorithm research
Nesus
Description: Cost action
Contribution: Distributed computing research
NMD-CHip
Description: FP7 research project
Contribution: Next-generation sequencing genome browser

(Co)Supervised student projects

Gammaknive - 2017
Description: Using CPU and GPU acceleration to speed up algorithms in the domain of medicine
Project type: Master project
Student: Marco Lourenço
Keywords: GPU, Algorithms, parallelization
Genome-Wide Association Studies (GWAS) from Low Coverage Data - 2017
Description: Optimization and parallization of an existing GWAS algorithm to adapt to large datasets
Project type: Master semester project
Student: Christophe Blanquet
Keywords: GWAS, Algorithms, parallelization
Trusted friend computing - 2017
Description: Design and implementation of TFC inside of POP-Java
Project type: Master semester project
Student: Mazzoleni Davide
Keywords: POP-Java, distributed computing
Visualisation circulaires de données complexes - 2016
Description: Circos WYSIWYG editor
Project type: Bachelor semester project
Student: Laetitia Nell
Keywords: Circos, Visualization
Distributed object programming for high performance DNA analysis II - 2016
Description: Bringing POP-Java to supercomputers using YARN
Project type: Bachelor project
Student: Davide Mazzoleni
Keywords: POP-Java, YARN
Distributed object programming for high performance DNA analysis. POP-DNA I - 2016
Description: Distributed meta-alignment using POP-Java on a supercomputer
Project type: Bachelor project
Student: Christophe Blanquet
Keywords: POP-Java, NGS, Meta-alignment
Java GPU - 2016
Description: Exploration and evaluation of current GPGPU capabilities of Java
Project type: Bachelor semester project
Student: Noémien Kocher
Keywords: GPU
Eclipse Plug-in for POP-C++ - 2016
Description: Development of a POP-C++ and POP-Java eclipse plugin
Project type: Bachelor semester project
Student: Mouad El Merchichi
Keywords: POP-C++, POP-Java, Eclipse
FriendComputing-II - 2015
Description: Move the FriendComputing project from a prototype to a useable release.
Project type: Bachelor semester project
Student: Valentin Gazzola
Keywords: POP-Java, Collaborative computing
VisuDNA - 2014
Description: Visualization of gene interactions, annotated with variant information of specific patients.
Project type: Bachelor semester project
Student: Maria Sisto
Keywords: Interactome, Data visualization, Graph analysis
CloudDNA 2 - 2014
Description: Follow up project on the 2013 project CloudADN.
The goal is to finalize the POP-Java cloud prototype and to use it for a sequence alignment application.
Project type: Bachelor thesis
Student: Xavier Barrelet
Keywords: POP-Java, Cloudcomputing
Sharing computing power through a network of friends - 2014
Description: Extend POP-Java to allow its users to create a a group of friends sharing computing resources
Project type: Bachelor thesis
Student: Monney Loïc
Keywords: POP-Java, Collaborative computing
HadoopDNA 1, distributing the GensearchNGS alignment algorithm using Hadoop - 2014
Description: Executing the GensearchNGS alignment algorithm on a hadoop cluster.
Project type: Bachelor semester project
Student: Demierre Luc
Keywords: Sequence alignment, Cloudcomputing, hadoop
HadoopDNA 2, distributing existing Alignment algorithms using Hadoop - 2014
Description: Executing generic DNA alignment algorithms (bwa, bowtie2 etc.) on a hadoop cluster.
Project type: Bachelor semester project
Student: Roulin David
Keywords: Sequence alignment, Cloudcomputing, hadoop
CloudADN, Bringing POP-Java to the cloud - 2013
Description: Porting POP-Java to the cloud, allowing the transparent cloud integration.
Project type: Bachelor thesis
Student: Andrea Marcacci
Keywords: POP-Java, Cloudcomputing
GPUADN, DNA sequence alignment using GPUs - 2013
Description: Exploring the possibilities of using GPUs to speed up DNA alignments
Project type: Bachelor thesis
Student: Tiago Miguel De Deus
Keywords: Sequence alignment, GPU
MLPA III - 2013
Description: Java replacement of the raw data threatement needed in the first steps of the MLPA analysis.
Project type: Bachelor semester project
Student: Monney Loïc
Keywords: MLPA
MLPA II - 2013
Description: Improvements to the Java library created in the MLPA I project.
Project type: Bachelor thesis
Student: Benoît Volet
Keywords: MLPA
Integration of MLPA into GensearchNGS - 2011
Description: Integration of the MLPA I results into GensearchNGS
Project type: Bachelor thesis
Student: Nicolas Codourey
Keywords: MLPA
MLPA I - 2011
Description: Java library replacement for the excel sheets used for MLPA analysis.
Project type: Bachelor semester project
Student: Nicolas Codourey
Keywords: MLPA

Other projects

Several patches where contributed to HTSJDK, a subproject of picard. Those patches consisted of bugfixes and major performance improvements for certain usecases.

Publications

Publications I'm the main author of:

GNATY: Optimized NGS variant calling and coverage analysis
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: IWBBIO 2016
Multilevel parallelism in sequence alignment using a streaming approach
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Workshop: Nesus 2015 workshop
FriendComputing: Organic application centric distributed computing
Authors: Beat Wolf, Monney Loïc, Pierre Kuonen
Conference: Nesus 2015 workshop
Comment reproduire les résultats de l'article: "POP-Java: Parallélisme et distribution orienté objet"
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: Realis 2014: Reproductibilité expérimentale pour l'informatique en parallélisme, architecture et système
Comment: My feedback lead to most of the content of the REALIS 2014 presentation

Publications I coauthored:

Non-coding RNAs in lung cancer: Contribution of bioinformatics analysis to the development of non-invasive diagnostic tools
Authors: Meik Kunz, Beat Wolf, Harald Schulze, David Atlan, Thorsten Walles, Heike Walles, Thomas Dandekar
Journal: Human Genetics and Genomics
The unmethylated allele of oppositely imprinted (i.e. MEST and MEG3) genes is highly susceptible to epimutations during
early development and may contribute an additional layer of complexity to phenotypic variation

Authors: Haertle Lara, Maierhofer A., Böck Julia, Lehnen H., Böttcher Y., Blüher M., Schorsch M., Potabattula R., Kuhtz J., Beat Wolf, Appenzeller S., El Hajj N., Haaf T.
Workshop: GfH Jahrestagung, 2016
Comment: Oral presentation, not a full publication.
A WoT approach to eHealth: case study of a hospital laboratory alert escalation system
Authors: Andreas Ruppen, Jacques Pasquier, Jean-Frédéric Wagen, Beat Wolf, Raphael Guye
Workshop: WoT 2012 - Third International Workshop on the Web of Things

Publications that used my work:

ALS and MMN mimics in patients with BSCL2 mutations: the expanding clinical spectrum of SPG17 hereditary spastic paraplegia
Authors: Thomas Musacchi, Ann-Kathrin Zaum, Nurcan Ü├žeyler, Claudia Sommer, Nora Pfeifroth, Karlheinz Reiners, Erdmute Kunstmann, Jens Volkmann, Simone Rost, Stephan Klebe
Journal: Journal of Neurology
Date: October 2016
The human RHOX gene cluster: target genes and functional analysis of gene variants in infertile men
Authors: Jennifer Borgmann, Frank T├╝ttelmann, Bernd Dworniczak, Albrecht Röpke, Hye-Won Song, Sabine Kliesch, Miles F. Wilkinson, Sandra Laurentino and Jörg Gromoll
Journal: Human Molecular Genetics
Date: September 2016
Identification of variants in MBNL1 in patients with a myotonic dystrophy-like phenotype
Authors: Mirjam Larsen, Wolfram Kress, Benedikt Schoser, Ute Hehr, Clemens R Müller and Simone Rost
Journal: European Journal of Human Genetics, Nature
Date: May 2016
A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment
Authors: Michaela A.H. Hofrichter, Indrajit Nanda, Jens Gräf, Jörg Schröder, Wafaa Shehata-Dieler, Barbara Vona, Thomas Haaf
Journal: Molecular Syndromology
Date: August 2015
Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1
Authors: Mirjam Larsen, Simone Rost, Nady El Hajj, Andreas Ferbert, Marcus Deschauer,
Maggie C Walter, Benedikt Schoser, Pawel Tacik, Wolfram Kress and Clemens R Müller
Journal: European Journal of Human Genetics, Nature
Date: June 2015
Nail-Patella Syndrome: clinical and molecular data in 55 families raising the hypothesis of a genetic heterogeneity
Authors: Jamal Ghoumid, Florence Petit, Muriel Holder-Espinasse, Anne-Sophie Jourdain
José Guerra, Anne Dieux-Coeslier, Martin Figeac, Nicole Porchet, Sylvie Manouvrier-Hanu and Fabienne Escande
Journal: European Journal of Human Genetics, Nature
Date: April 2015
Novel recessive myotilin mutation causes severe myofibrillar myopathy
Authors: Joachim Schessl, Elisa Bach, Simone Rost, Sarah Feldkirchner, Christiana Kubny, Stefan Müller,
Franz-Georg Hanisch, Wolfram Kress, Benedikt Schoser
Journal: Neurogenetics
Date: August 2014
Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6
Authors: Simone Rost, Elisa Bach, Cordula Neuner, Indrajit Nanda, Sandra Dysek, Reginald E Bittner,
Alexander Keller, Oliver Bartsch, Robert Mlynski, Thomas Haaf, Clemens R Müller and Erdmute Kunstmann
Journal: European Journal of Human Genetics, Nature
Date: May 2013

Publications that mentioned my work:

Posters

Posters I'm the main author of:

Safe variant annotation sharing across laboratories
Authors: Beat Wolf, Pierre Kuonen, David Atlan, Jonathan Stoppani, Davide Mazzoleni, Thomas Dandekar
Conference: Variant Detection 2017
Trusted Friend Computing: data mining federated OMICS knowledge source
Authors: Beat Wolf, Pierre Kuonen, David Atlan, Marco Lourenço, Jonathan Stoppani, Thomas Dandekar
Conference: ESHG 2017
Meta-alignment: Combining multiple sequence aligners to improve alignment quality
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: ESHG 2016
GensearchNGS : Integrating OMICs analysis and visualization
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: VIZBI 2016
Building blocks
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: VIZBI 2016
GNATY: A tools library for faster variant calling and coverage analysis
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: GCB 2015
Speeding up NGS analysis through local and remote computing resources
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar, David Atlan
Conference: European Human Genetics Conference 2015
Everybody's uniqueness
Authors: Beat Wolf, Pierre Kuonen, Thomas Dandekar
Conference: Visualizing Biological Data, VIZBI 2014
Store, align and explore your genome outside the Cloud, at home, on your PC
Authors: Beat Wolf, Pierre Kuonen, David Atlan, Thomas Dandekar, Johan T. den Dunnen
Conference: European Human Genetics Conference 2013

Posters I coauthored:

Genotype-Phenotype correlation-The many facets of heterogeneous hearing loss in the context of molecular
Authors: Michaela Hofrichter, Barbara Vona, R. Maroofian , Linda Schnapp, Julia Doll, Tabea Röder, I. Nanda, Barry Chioza, Beat Wolf, Wafaa Shehata-Dieler, Erdmute Kunstmann,
Jörg-Gunther Schröder, Tobias Müller, Ulrich Zechner, Oliver Bartsch, Marcus Dittrich, Andrew Crosby, Thomas Haaf
Conference: GfH Jahrestagung, 2017
Identification of a molecular signature for prognostic classification and individualized cancer therapy in adrenocortical carcinoma
Authors: Juliane Lippert, S. Appenzeller, S. Steinhauer, Simone Rost, Beat Wolf, Anrea Gehrig, C.R. Müller, M. Fassnacht, C.L. Ronchi
Conference: GfH Jahrestagung, 2017
Deep bisulfite sequencing for quantification of constitutive epimutations in tumor suppressor genes
Authors: Böck Julia, Haertle Lara, Appenzeller S, Beat Wolf, Schneider T., Sutter C, Haaf T.
Conference: GfH Jahrestagung, 2016
Novel dominant case of de-novo mutation in Ullrich congenital muscular dystrophy
Authors: Ann-Kathrin Zaum, Wolfram Kreß, Beat Wolf, Simone Rost
Conference: GfH Jahrestagung, 2016
Recessive truncating mutations in the TTN gene of two patients with muscular dystrophies
Authors: Pluta Nathalie, Kress Wolfram, Clemens R. Müller, Beat Wolf, Rost Simone
Conference: GfH Jahrestagung, 2016
Distal hereditary motor neuropathy due to BSCL2 mutation in a two generation family
Authors: Ann-Kathrin Zaum, Simone Rost, Beat Wolf, Clemens R. Müller, Thomas Musacchio, Erdmute Kunstmann, Stephan Klebe
Conference: GfH Jahrestagung, 2015
Deep intronic variants in the factor VIII gene
Authors: J Elisa Bach, Beat Wolf, Johannes Oldenburg, Clemens R Müller, Simone Rost
Conference: GfH Jahrestagung, 2015
NGS panel for diagnostics of myofibrillar myopathies
Authors: J Elisa Bach, Simone Rost, Anna-Lena Semmler, Kristl G Claeys, Beat Wolf, Wolfram Kress, Clemens R Müller
Conference: GfH Jahrestagung, 2014
Connecting diagnostic labs: Cafe Variome and DNA sequencing software
Authors: David Atlan, Tim Beck, J.Brookes, Raymond Dalgleish, Owen Lancaster, Beat Wolf
Conference: Joint meeting of EURenOmics, NeurOmics and RDConnect in Heidelberg, 2014

Posters that used or cited my work:

2015

Novel compound heterozygous mutations in PLEC1 causing epidermolysis bullosa simplex with muscular dystrophy
Authors: Simone Rost, Ann-Kathrin Zaum, Andrea Gehrig, Birgit Halliger-Keller, Wolfram Kress, Clemens R. Müller, Mathias Buttmann, Erdmute Kunstmann
Conference: GfH Jahrestagung, 2015

2014

SMCHD1 mutations cause FSHD type 2 and act as modifiers of disease severity
Authors: Mirjam Larsen, Wolfram Kress, Simone Rost, Nady El Hajj, Clemens R Müller
Conference: 19th International Congress of The World Muscle Society, Berlin, 2014
DMD deletions comprising partial exonic sequences not detected by MLPA analyses
Authors: Simone Rost, Schrooten K., Emmert G., Meng G., Clemens R Müller
Conference: GfH Jahrestagung, 2014

2013

Nail-Patella Syndrome: evidence for genetic heterogeneity
Authors: F. Petit, F. Escande, A. Jourdain, C. Baumann, F. Fellmann, D. Lacombe, S. Marlin, S. Odent, N. Porchet, M. Holder-Espinasse, S. Manouvrier-Hanu
Conference: European Human Genetics Conference 2013
NGS goes diagnostics: Multiplex analysis of genes for limb-girdle muscular dystrophies
Authors: Bach J.E., Rost S., Gehrig A., Kress W., Müller C.R.
Conference: GfH Jahrestagung, 2013
Novel form of X-linked nonsyndromic hearing loss caused by a mutation in a type IV collagen gene
Authors: Rost, Bach, Neuner, Nanda, Dysek, Bittner, Keller, Bartsch O., Mlynski, Haaf, Müller, Kunstmann
Conference: GfH Jahrestagung, 2013

2012

IonTorrent: 2nd generation sequencing in a diagnostic laboratory
Authors: B. Dworniczak, S. Fleige-Menzen, N. Bogdanova-Markov, P. Pennekamp
Conference: European Human Genetics Conference 2012

Other activities

14th International Symposium on Variants in the Genome: detection, sequencing and interpretation - 2017
Description: Presentation about "Safe variant annotation sharing across laboratories"
Event type: Conference
Contribution: 20 minute presentation
University of Fribourg - 2017
Description: Seminar about how my PhD thesis.
Course type: Seminar
Contribution: 1 hour seminar
University of Stirling - 2017
Description: Seminar about how computer-science can make the life of geneticists easier.
Course type: Seminar
Contribution: 1 hour seminar
3Gb-test - 2016, Lisbon
Description: A 4-day course on NGS in Lisbon was organized in the period of 24-27 October 2016.
The focus of the course was on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practicals.
86 Participants followed the interesting lectures and 46 also did the afternoon practicals.
Course type: Workshop
Contribution: Invited speaker + 2 x 1.5 hour practical
Modeling Change - Changing the world - 2015, Würzburg
Description: During a one week international workshop i was an invited speaker. The theme of the workshop was modeling of complex systems and prediction changes.
My talk focused on the different ways on how to analyse NGS data and how they differ.
Those differences have a direct impact on the type of predictions that can be made when using genotype to phenotype prediction models.
Course type: Workshop
Contribution: 30min lecture
3Gb-test - 2015, Prag
Description: A 4-day course on NGS in Athens was organized in the period of 20-23 April 2015.
The focus of the course was on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practicals.
148 Participants followed the interesting lectures and 32 also did the afternoon practicals. The course even prompted one participant to write a course report
Course type: Workshop
Contribution: Invited speaker + 2 x 1 hour practical
3Gb-test - 2014, Athen
Description: A 4-day course on NGS in Athens was organized in the period of 8-11 September 2014.
The focus of the course was on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practicals.
42 Participants followed the interesting lectures and 32 also did the afternoon practicals.
Course type: Workshop
Contribution: Invited speaker + 1 hour practical
FCST-2017 - 2017, Exeter, UK
Type: Conference
Contribution: Paper reviews
BMC Bioinformatics - 2016
Type: Journal
Contribution: Paper reviews
TAPEMS-2016 - 2016, Granada, Spain
Type: Conference
Contribution: Paper reviews
ICA3PP-2016 - 2016, Granada, Spain
Type: Conference
Contribution: Paper reviews
RIVF-2016 - 2015, Hanoi, Vietnam
Type: Conference
Contribution: Paper reviews
RIVF-2015 - 2015, Cantho, Vietnam
Type: Conference
Contribution: Paper reviews

Diploma works

Analysis and visualization of DNA sequences using cloud computing - 2011
Project type: Master thesis
Domain: Computer science
Grid-based model for Marine Accidents - 2008
Project type: Engineer/Bachelor thesis
Domain: Computer science

Contact information

Beat Wolf,
ORCID: 0000-0002-9307-7212
Google scholar: Beat Wolf
Research Gate: Beat Wolf