Personal Information

  • Name: Dr. sc. Armin Töpfer
  • Date of birth: 24 May 1986
  • Nationality: Citizen of Germany
  • Address: Gelsenkirchen, Germany
  • Langues: German and English
  • Github: armintoepfer
  • Email: armin.toepfer@gmail.com

Professional Profile

I'm a researcher with a Doctor of Sciences ETH Zürich in computational biology, specialized in statistical modelling and analysis of next/third-generation sequencing technologies. I combine academic curiosity and industry standards to develop bleeding-edge, yet robust and carefully tested, software for every day use. Expert in the field of viral quasispecies reconstruction, who offers experience with laboratory work. Also highly experienced in scientific computing and real-time processing of large data sets with High-Performance Computing Clusters.

Research Interest

Algorithm Design --- High-Performance Computing --- Statistical Modelling --- Translational Genomics --- Viral Genomics --- Population Structure Reconstruction --- Next-Generation/Single-Molecule Sequence Analysis --- Code Optimization --- Data Visualization

Education

October 2011 - August 2014

Swiss Federal Institute of Technology Zürich (ETH)

Dr. sc. ETH Zürich
Thesis topic: Studies in viral quasispecies reconstruction

October 2009 - July 2011

University of Bielefeld

M.Sc. in Bioinformatics and Genome Research
Thesis topic: Prediction of Group I Introns under structure variation

October 2006 - March 2009

University of Bielefeld

B.Sc. in Bioinformatics and Genome Research
Thesis topic: Ideas for and implementation of an automated statistical data analysis

Work Experience

August 2018 - now

Senior Staff Engineer, Bioinformatics

Pacific Biosciences, Menlo Park, CA, USA; 100% Remote, Germany

Technical leader, help individual members of the team to become amazing. Shape product roadmap from a technical perspective. Identify and fix performance bottlenecks in existing products. Enable customers to use command-line tools, by maintaining bioconda packages.
Additionally responsible for following new products:

October 2015 - July 2018

Staff Engineer, Bioinformatics

Pacific Biosciences, Menlo Park, CA, USA; 100% Remote, Germany

Development of bleeding edge statistical algorithms in C++14.
Core projects:

September 2014 - October 2015

Senior Engineer, Bioinformatics

Pacific Biosciences, Menlo Park, CA, USA; 100% Remote, Germany

Hardware-near C++11 development on x86_64 and MIC architectures on the Sequel instrument to enhance the base-call accuracy and hotspot parallelization and vectorization to enable real-time base calling. Design and implementation of custom binary formats to store high-throughput real-time data. Post process raw base-call data to provide customer-friendly BAM files, including SMRTbell adapters removal, demultiplexing, and spike-in control filtering.

July 2011 - August 2014

Graduate research assistant

Computational Biology Group, ETH Zürich, Basel

Development of statistical methods and machine learning approaches for viral quasispecies assembly from next-generation and single-molecule sequencing data. Application to intra-host samples of HBV, HCV, CSFV, and HIV-1 infected individuals.

October 2009 - May 2011

Research assistant

Bielefeld University Bioinformatics Service, University of Bielefeld, Germany

Continuation as Java developer at the BiBiServ2 project. Migrating architecture from JavaServer Faces (JSF) 1.2 to JSF 2. Introduction of PrimeFaces as the main component suite.

September 2009 - May 2011

Programmer

High performance computing laboratory, Bergen Center for Computational Science, UNIFOB AS, Bergen, Norway

Development of a parsing library for Web Services Description Language and XML Schema files, resolving complete XML Schema structures. Project is funded by the EMBRACE Network of Excellence coordinated by EBI. Further development of a Business Process Execution Language (BPEL) editor to construct complex workflows using the NetBeans Platform.

November 2009

Professional Trainer

International Institute (Training, Assessment, Certification), Cognitive Core UG, Germany

Binary auditing trainer for developers at Symantec India. Full practical online workshop on analysis and exploitation of stack based buffer overflows and reverse code engineering of copy protections.

April 2009 - August 2009

Bioinformatics internship

Computational Biology Unit, BCCS, UNIFOB AS, Bergen, Norway

Implementation of a fully functional web-based BPEL editor to construct and execute simple linear workflows. Working as a team member on the eSysbio project, funded by the Research Council of Norway through its e-science program eVita.

October 2008 - May 2009

Research assistant

Bielefeld University Bioinformatics Service, University of Bielefeld, Germany

Development of automatically generated web surfaces with JSF for the new BiBiServ2 project.

August 2008 - September 2008

Freelance JSF developer

Teamkollegen.de, Bielefeld, Germany

Responsible for the web development of an AJAX based JSF frontend, i.e., a messaging system and user friendly search interface. A project supported by the Heinz Nixdorf Foundation and the Foundation of the German Economy (sdw).

Talks

4th ICCABS (IEEE) - Viral quasispecies assembly from paired-end reads - Miami, USA, 2014
RECOMB 2014 - Viral quasispecies assembly via maximal clique enumeration - Pittsburgh, USA, 2014
SMIDDY - Global haplotype prediction of HIV-1 - Zürich, Switzerland, 2013
3rd ICCABS (IEEE) - Probing of viral diversity by global haplotype prediction - New Orleans, USA, 2013
2nd CHAIN NGS Meeting - Computational and Statistical Challenges of Ultradeep Sequencing of Viral Quasispecies - Rome, Italy, 2013
Virus goes Bioinformatics - Estimating viral genetic diversity from next-generation sequencing data - Jena, Germany, 2012
RECOMB 2012 - Probabilistic inference of viral quasispecies subject to recombination - Barcelona, Spain, 2012
RUBIES - Amsterdam, Netherlands, 2011
Nil-University - Cairo, Egypt, 2010
EMBRACE - Amsterdam, Netherlands, 2009

Posters

CROI 2015 - A Comprehensive Analysis of PrimerIDs to Study Heterogenous HIV-1 Populations - Seattle, USA, 2015
CROI 2014 - Full-length HIV-1 Haplotype Reconstruction from Heterogeneous Virus Populations - Boston, USA, 2014
Statistical Genomics and Data Integration for Personalized Medicine Ascona - Probing of viral diversity by global haplotype prediction - Switzerland, 2013
SIB Days 2103 - Visualization of viral populations - Biel Switzerland, 2013
ECCB 2012 - QuasiRecomb: prediction of recombinant viral quasispecies - Basel, Switzerland, 2012
SIB Days 2012 - Probabilistic inference of viral quasispecies subject to recombination - Biel, Switzerland, 2012

Publications

2016

Single-molecule sequencing reveals complex genomic variation of hepatitis B virus during 15 years of chronic infection following liver transplantation.

Brigid Betz-Stablein, Armin Töpfer, M Littlejohn, L Yuen, D Colledge, V Sozzi, P Angus, A Thompson, P Revill, Niko Beerenwinkel, N Warner, Fabio Luciani
10.1186/s12864-016-2575-8
BMC genomics.

2016

A method for near full-length amplification and sequencing for six hepatitis C virus genotypes.

Rowena A Bull, Auda A Eltahla, Chaturaka Rodrigo, Sylvie M Koekkoek, Melanie Walker, Mehdi R Pirozyan, Brigid Betz-Stablein, Armin Töpfer, Melissa Laird, Steve Oh, Cheryl Heiner, Lisa Maher, Janke Schinkel, Andrew R Lloyd, Fabio Luciani
10.1128/JVI.00243-16
Journal of Virology.

2015

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations.

David Seifert, Francesca Di Giallonardo, Armin Töpfer, Jochen Singer, Stefan Schmutz, Huldrych F. Günthard, Niko Beerenwinkel, Karin J. Metzner
10.1016/j.jmb.2015.12.012
Journal of Molecular Biology.

2014

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.

Francesca Di Giallonardo*, Armin Töpfer*, Melanie Rey, Sandhya Prabhakaran, Yannick Duport, Christine Leemann, Stefan Schmutz, Nottania K. Campbell, Beda Joos, Maria Rita Lecca, Andrea Patrignani, Martin Däumer, Christian Beisel, Peter Rusert, Alexandra Trkola, Huldrych F. Günthard, Volker Roth, Niko Beerenwinkel, and Karin J. Metzner.
10.1093/nar/gku537
Nucleic Acids Research.

2014

Viral Quasispecies Assembly via Maximal Clique Enumeration.

Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, and Niko Beerenwinkel.
10.1371/journal.pcbi.1003515

PLOS Computational Biology.

Abstract appears in R. Sharan, RECOMB 2014 - Research in Computational Molecular Biology, volume 8394 of Lecture Notes in Bioinformatics, pages 309–310. Springer, 2014.
10.1007/978-3-319-05269-4_25

2013

Challenges in RNA Virus Bioinformatics.

Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo Hofacker, Dieter Hoffmann, Thomas Rattei, Peter Stadler, and Armin Töpfer .
10.1093/bioinformatics/btu105
Bioinformatics.

2013

Sequencing approach to analyze the role of quasispecies for classical swine fever.

Armin Töpfer, Dirk Höper, Sandra Blome, Martin Beer, Niko Beerenwinkel, Nicolas Ruggli, and Immanuel Leifer.
10.1016/j.virol.2012.11.020
Virology.

2013

Probabilistic inference of viral quasispecies subject to recombination.

Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin, and Niko Beerenwinkel.
10.1089/cmb.2012.0232

Journal of Computational Biology.

Extended abstract appeared in B. Chor, editor, RECOMB 2012 – Research in Computational Molecular Biology, volume 7262 of Lecture Notes in Bioinformatics, pages 342–354. Springer, 2012.
10.1007/978-3-642-29627-7_36

2010

BioXSD: the common data-exchange format for everyday bioinformatics web services.

Kalas M., Puntervoll P., Joseph A., Bartaseviciute E., Töpfer A. , Venkataraman P., Pettifer S., Bryne J.C., Ison J., Blanchet C., Rapacki K., and Jonassen I.
10.1093/bioinformatics/btq391
Bioinformatics.

Software

pbmm2 - A minimap2 frontend for PacBio native data formats.
pbsv - Fast, accurate, population-scale structural variant analysis from single-molecule data.
IsoSeq3 - Scalable de novo isoform discovery from single-molecule data.
Juliet - Reference guided phasing of low-frequency de-novo discovered variants in heterogeneous samples.
Lima - Demultiplex pooled barcoded single-molecule data.
HaploClique - Viral quasispecies assembly from paired-end data.
QuasiRecomb - Reconstruction of recombinant viral quasispecies structures.
InDelFixer - Iterative and very sensitive NGS sequence alignment software.
ConsensusFixer - Consensus sequence caller with ambiguous bases and in-frame insertions.

Awards

  • Young investigator scholarship, CROI, 2014
  • Best poster award, SIB Days, 2013
  • Conference fellowship, RECOMB, 2012
  • Studentship for foreign internships, ERASMUS, 2009

Master students adviced

  • Monica-Andreea Drăgan, Research assistant, 2014
    Minimal path cover with paired-end constraints.
  • Kee Pang Soh, Lab-rotation, 2014
    Error correction of Pacific Biosciences data.
  • Veronika Boskova, Lab-rotation, 2013
    Visualization of HIV quasispecies data.
  • David Seifert, Master thesis, 2012
    Computational studies in HIV diversity.

Technical skills

C++14, SIMD incl. KNC, Java, JSF, Python, R, Haskell, SQL, Assembly
XML, XML Schema, Web services, BPEL, HTML, JavaScript, CSS
VSCode, Netbeans, Photoshop, Illustrator, Latex, IDA Pro, UNIX CLI
Git, CI, TDD, Scrum

Interests

  • Web design, photography, and painting
  • Learning bleeding edge technologies
  • Cinema and TV series