Full professor of Bioinformatics at École Polytechnique since March, 2020. Formerly, Researcher (Universitätsassistent) with Ivo Hofacker at the TBI, University Vienna. Until 2016, Researcher with Peter Stadler at the Bioinformatics group, Computer Science, University of Leipzig. 2005-2012, "Akademischer Rat" (comparable to "assistant professor") at Rolf Backofen's Bioinformatics group at the University of Freiburg. 2011, Instructor at the Mathematical Department of MIT. 2010-2011, post-doc with Bonnie Berger at the Computation and Artificial Intelligence Lab (CSAIL) at the Massachusetts Institute of Technology (MIT), Cambridge, MA. Research Scholarship by DFG (German Research Foundation). PhD Fellowship of GKLI (PhD programme 'Graduiertenkolleg Logic in Computer Science') of the LMU until move to University of Jena. Computer Science PhD (Dr.rer.nat.) in Jena.

Internships @ X

• RNA structure clustering and sampling of multiple alignments
• Pseudoknot alignment with Infrared
• Local optimization of multi-target designs
• Bac internship: modeling large RNAs (2022)
• Bac internship: generic local search in Infrared (2023)

Current and previous teaching @ X

• Coordination of the bioinformatics specialization program "PA Bioinformatique"
• Coordination INF511: long project
• INF589: down-stream analysis of high throughput sequencing data
• BIO/INF588: bioinformatics programming lab class
• TD CSE201: C++ intro + projects
• TD CSE102: Python introduction
• PSC structure probing (in 2022)
• Combinatorial Optimization (Paris Saclay)
• TD INF442 (in 2020): C++ data analysis
• TD INF371 (in 2020): Java intro

Previous teaching

Before Polytechnique, I have been teaching bioinformatics and general computer science classes at the Universities of Vienna, Leipzig, Freiburg, and the MIT Math Department.

• Algorithms and Program development for the Biological Chemistry (Summers 17, 18, and 19)
• Structure and Dynamics of Biopolymers (Winters 17/18 and 18/19)
• Algorithmic Bioinformatics (Summers 17, 18, and 19) with Heiko Schmidt and Arndt v. Haeseler
• Algorithms and Data Structures I+II (15/16): organisation of recitation classes, assignments
• Theoretical Biology (Summer 16) (w/ P. Stadler)
• Graphs and biological networks (Winter 14/15) (Graph Theory; w/ P. Stadler)
• Advanced Methods in Bioinformatics (Winter 14/15 and 12/13) (with Peter Stadler)
• Recent Methods in RNA Structure Prediction (Winter 14/15)
• Algorithms and Datastructures I (Winter 13/14) and
  Algorithms and Datastructures II (Summer 14) (with Peter Stadler)
• Class 18.417: Foundations of Structural Bioinformatics (Summer 2011)
  (as instructor of the MIT Math Department)
• RNA Bioinformatics (Winters 09/10 and 08/09)
• Protein folding and energy landscapes (Summers 09 and 08)
• Introduction to Bioinformatics (Summer 07) and Bioinformatics II (Winter 07/08)
• Constraint Programming (Winter 06/07)
• Structure Prediction in Simple Protein Models (Summer 06)

publication list

bibtex references

Google Scholar

DBLP

• Dagstuhl 2022: RNA Design in Infrared

• Benasque 2022: The Infrared framework, RNA-RNA interaction kinetics

• sRNA 2019 Freiburg Keynote Talk: A brief overview of RNA Bionformatics

• RECOMB 2018. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures

• Benasque RNA meeting 2018. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures (update of RECOMB slides)

• Vienna RNAMeeting 2018 "Regulatory Circutes in RNA Biology". Detection and rational design of RNA switches

• WEPA 2018, Pisa. Nucleic Acids design targeting integer-valued features: FPT counting and uniform sampling (update/extension of Benasque slides)

• WABI 2015. Sparse RNA folding revisited: space-efficient minimum free energy prediction (update to Benasque'15)

• Benasque RNA 2015. Sparse RNA folding revisited: space-efficient minimum free energy prediction

• Benasque RNA 2015. SPARSE: Quadratic Time SA&F of RNAs without Sequence-Based Heuristics (update to RECOMB'13)

• WABI 2014. A Common Framework for Linear and Cyclic Multiple Sequence Alignment

• RECOMB 2013. SPARSE: Quadratic Time SA&F of RNAs without Sequence-Based Heuristics

• RECOMB 2012. Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs (REAPR)

• Benasque RNA 2009. Match Probabilities from Sankoff-style Alignment in LocARNA (LocARNA-P)

• LocARNA - fast and space-efficient simultaneous folding and alignment of RNAs

  The LocARNA package contains several tools for structure-based comparison of multiple RNAs (of potentially unknown structure), which integrate practically relevant features like structure and sequence anchor constraints. A previous version of LocARNA is also accessible online as web server.

  Find the latest release on Github. LocARNA 2.0 can be installed via conda (channel bioconda)---find more info on release 2.0 in this book chapter.

• Infrared - A generic C++/Python hybrid library for efficient (fixed-parameter tractable) Boltzmann sampling. Infrared provides the infrastructure for RNARedprint 2.0, which implements sampling for multi-target RNA design. The first version of RNARedprint was written for our RECOMB18 publication [Preprint]. Find more information in our book chapter on RNA design with Infrared, my publications and Infrared's Gitlab repository .

• BiAlign - bi-alignment of RNAs and proteins. See research papers Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure and Bi-alignments with affine gaps costs.

• Knotty - Efficient prediciton of complex pseudoknots. Knotty predicts minimum free energy pseudoknot structures of RNAs. It predicts the structures efficiently, implementing a sparsified CCJ algorithm. While this algorithm can predict versatile pseudoknot structures, including kissing hairpins, and guarantees the optimality of solutions, it requires relatively small time and space. (I contributed to code of Hosna Jabbari and Ian Wark.)

• SPARSE - very efficient simultaneous folding and alignment of RNAs with strong ensemble-based sparsification (with Milad Miladi). SPARSE is part of the LocARNA package.

• ExpARNA-P - exact simultaneous folding and pattern matching in RNAs (implemented by Christina Schmiedl as part of the LocARNA package)

• REAPR - Realignment for Prediction of Structural Non-coding RNA. A pipeline for whole genome realignment and de-novo prediction of non-coding RNA candidates (implemented by Michael Yu)

• SparseMFEFold - Very space-efficient RNA structure prediction (implemented for the research paper Sparse RNA folding revisited: space-efficient minimum free energy prediction)

• MEA - prediction of maximum expected accuracy structures of RNAs with penalties for long base pairs. Comparison of structures by F-measure and MCC.

• LocARNAscan - scanning variant of the LocARNA-algorithm (implemented by Michael Siebauer)

• LocARNA-P - fast and space-efficient computation of reliabilities for simultaneous folding and alignment of RNAs (with Tejal Joshi)

  The tool is accessible online from the LocARNA web server. Please select alignment mode "LocARNA-P (probabilistic)". It is part of the LocARNA package.

• CARNA - Constraint-based alignment of RNA Ensembles. CARNA supports many non-standard alignment cases like pseudoknots and multiple stable structures. The tool is available on Github. Moreover, there is a CARNA web server.

• CTE-Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination

• LSSA - Local Sequence Structure Alignment. Supports structure-local alignment of RNAs with known input structure. C++ implementation for my paper Local Sequence-Structure Motifs in RNA

• PSP - Protein structure prediction in HP-type models (using Constraint Programming). The original software, written for Mozart/Oz in the course of my Master's Thesis, is superseeded by the C++/Gecode implementation CPSP Tools of Martin Mann.