People

Team

Enrico Seiler Senior Developer & PhD Student

Biography:

Enrico Seiler works on algorithms and data structures for massive collections of DNA sequences, with a main focus on developing the Interleaved Bloom Filter (IBF). He obtained both BSc and MSc degree in Bioinformatics from the Freie Universität Berlin.

Developed Application(s):

• Raptor

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Evelin Aasna Research Assistant & PhD Student

Biography:

Evelin is working as a student assistant for the FONDA project and studying at the Freie Universität Berlin to obtain her M.Sc. in Bioinformatics.

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Knut Reinert Head of the group

Biography:

Head of the group. My research is influenced by the training I received as an algorithmicist at the Max-Planck-Institute for Computer Science in Saarbrücken, Germany and by my subsequent research as a senior scientist at Celera Genomics in Rockville, MD, USA. I aim to enable translational research in computationally based life sciences by removing existing (communication) gaps between theoretical algorithmicists, statisticians, programmers, and users in the biomedical field.I obtained my Diploma in Computer Science from Saarbrücken University and my PhD from the Max-Planck-Institute for Computer Science in Saarbrücken.

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René Rahn Senior Developer & PhD Student

Biography:

René Rahn works on data parallel data structures in SeqAn. He holds an MSc and BSc degree from the Freie Universität Berlin and works for the CIBI project as one of the senior maintainers of SeqAn.

Developed Application(s):

• JST

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Svenja Mehringer Senior Developer & PhD Student

Biography:

Svenja Mehringer holds an M.Sc. degree in Bioinformatics from Freie Universität Berlin and is now working as a PhD student. Besides maintaining and expanding the SeqAn library, she works on optimizing the space consumption of Hierarchical Binning Directories.

Developed Application(s):

• Chopper

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Contributor

Birte Kehr

Biography:

Prof. Dr. Birte Kehr works at the RCI Regensburg Center for Interventional Immunology leading the Research Group Algorithmic Bioinformatics.

Developed Application(s):

• Popins

• Stellar

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Gianvito Urgese

Biography:

Gianvito Urgese is Assistant Professor at the Interuniversity Department of Regional and Urban Studies and Planning of Politecnico di Torino. He received his M.Sc. degree (summa cum laude) in Electrical Engineering at Politecnico di Torino. He designed, during his M.Sc. thesis, an optimized HW accelerator for sequence alignment, implemented in VHDL on a systolic array architecture. He was, in 2011, research trainee at Teseo S.p.A. involved in the design of a system for structural health monitoring in composite materials. In 2008, he collaborated with the INRIM institute for a project concerning the redefinition of Boltzmann constant.

His research interests focus on:

• Research and design of optimized task-specific bioinformatics algorithms.
• Development of tools for the study of non coding biological sequences (miRNA, siRNA, and lncRNA).
• Design of heterogeneous SW/HW architectures to accelerate bioinformatics algorithms, including parallel implementation on FPGA and GPU.
• Design of placement and routing algorithms for the mapping of Spiking Neural Networks in the SpiNNaker neuromorphic platform.

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Kathrin Trappe

Biography:

Kathrin Trappe acquired her PhD in Bernhard Renard’s lab at the Robert Koch Institute.

Developed Application(s):

• Gustaf

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User

Alumni

Chengxu Pan

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Christopher Pockrandt

Biography:

Christopher Pockrandt holds B.Sc. and M.Sc. degrees in Computer Science from Freie Universität Berlin. He spent part of his studies at the National University of Singapore and the National Taiwan University. As an IMPRS student of the Max Planck Institute for Molecular Genetics, he acquired his Ph.D. in bioinformatics focussing on string indices (especially the FM-Index) with applications in lncRNA search. He is currently working as a postdoctoral fellow at the Johns Hopkins University.

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David Weese

Developed Application(s):

• DFI

• RazerS 3

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Enrico Siragusa

Biography:

Enrico finished his PhD in 2015 with work in SeqAn and now works at IBM Research in New York City.

Developed Application(s):

• String Similarity Search/Join

• Yara

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Hannes Hauswedell

Biography:

Hannes Hauswedell obtained B.Sc. and M.Sc. degrees in Bioinformatics from Freie Universität Berlin, but he also spent some time studying in Uppsala, Sweden and in Shanghai, China. He obtained his Ph.D. between the Max Planck Institute for Molecular Genetics and Freie Universität Berlin where he also used to teach. Outside of work he enjoys mountains and the sea.

Developed Application(s):

• LAMBDA

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Jörg Winkler

Biography:

As a PhD candidate at Freie Universität Berlin and member of the graduate school IMPRS-BAC at the Max Planck Institute for Molecular Genetics I work on algorithms for the analysis of long non-coding RNA. I hold a Master of Science degree in Bioinformatics from University of Hamburg.

I have developed the two applications LaRA for rapid structural RNA alignment and MaRs for RNA motif search. Furthermore, I contribute to the C++ SeqAn library with focus on multiple sequence alignment and structure analysis, and I participate in the design and implementation of SeqAn’s application template.

Generally, I am interested in nature and sustainability. When I am not at work, you can find me climbing, hiking or kayaking.

Developed Application(s):

• LaRA 2

• MaRs

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Jongkyu Kim

Developed Application(s):

• Vaquita

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Kerstin Neubert

Biography:

Kerstin Neubert developed applications for the characterization of microbial species in environmental samples based on metagenomic and peptide profiling. She holds a B.Sc. and M.Sc. degree in Bioinformatics from the Freie Universität Berlin and currently works at the German Federal Institute for Risk Assessment.

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Lydia Buntrock

Biography:

I am working on algorithms to find and classify structural variations of DNA. Funded by the BMBF, I am persuing my PhD at Freie Universität Berlin. I hold two Bachelor of Science degrees in Mathematics and Informatics and a Master of Science degree in Bioinformatics from Freie Universität Berlin.

I am developing a new application for the detection of structural variations. Furthermore, I contribute to the C++ SeqAn library and I participate in the design and implementation of SeqAn’s application template.

Generally, I am curious about mathematics and its connection to nature.

Developed Application(s):

• iGenVar

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Manuel Holtgrewe

Developed Application(s):

• ANISE and BASIL

• Mason

• Rabema

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Marcel Ehrhardt

Biography:

Marcel is C++ senior developer, software architect, and PhD student of SeqAn since 2015. His main interests are high performance computing, algorithms, (succinct) data structures, C++, software development, and building infrastructures. He is currently employed in a project funded by de.NBI/CIBI and holds a master’s degree from the Freie Universität Berlin in computer science with focus on theoretical computer science.

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Mitra Darvish

Biography:

Mitra Darvish is a PhD student at the Max Planck Institute of Molecular Genetics and works on finding cancer motifs in large NGS data sets using probabilistic data structures and compression strategies. She obtained her Bachelor of Science and her Master of Science in Bioinformatics from the Freie Universität Berlin, but she also spent parts of her studies at the University of Helsinki and at the University of Oxford. Outside of work, she enjoys reading and tries to find the best ice cream parlour in Berlin.

Developed Application(s):

• Needle

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Simon Sasse

Biography:

Simon works as a student assistant at SeqAn. He achieved his B.Sc. in bioinformatics at the Freie Universität Berlin and continues his studies in the M.Sc. of Computer Science.

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Sven Bönigk

Biography:

Sven obtained his M.Sc. in Bioinformatics from Freie Universität Berlin. Currently, he is pursuing his PhD with a focus on approximate string matching and its applications for read mapping.

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Temesgen Dadi

Biography:

Temesgen H. Dadi works in Comparative metagenomics of microbial communities using machine learning methods. He graduated from Arba Minch University, Ethiopia in Computer Science and IT (B.Sc.) and received his Masters degree from University of Trento, Italy in Bioinformatics. Currently he works in the InfectControl 2020 project with partners from the VetMed department.

Developed Application(s):

• SLIMM

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Tobias Rausch

Developed Application(s):

• SeqAn::T-Coffee

• SeqCons2

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Wiep van der Toorn

Biography:

Wiep van der Toorn worked as a student assistant at SeqAn. She holds a B.Sc. degree in Life Science and Technology from the Technical University Delft and University Leiden, and an M.Sc. Bioinformatics from the Freie Universität Berlin. Currently, she is working as a researcher in Generative Chemistry at Novartis.

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