Researcher at the TBI (Theoretical Chemistry)
University of Vienna
1090 Wien, Austria
|Phone||Office: +43 1 4277 52749|
Algorithms for bio-data. Bioinformatics of RNA and protein structure. Methods for the computational prediction of RNA structure, RNA interactions, and folding dynamics; comparative analysis of RNAs; and applications to big data (e.g. transcriptome-wide de-novo prediction of non-coding RNAs or RNA switches).
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.
Algorithms and Program development for the Biological Chemistry (Summers 17 & 18)
Structure and Dynamics of Biopolymers (Winters 17/18 and 18/19)
Algorithmic Bioinformatics (Summers 17/18 and 18/19) 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)
Class 18.417: Foundations of Structural Bioinformatics (Summer 2011)
(as instructor of the MIT Math Department)
This publication list in PDF adds first and corresponding author annotations and is broken down into publication categories; also contains my theses.
To cite my work, this bibtex file may be handy.
Please find a collection of slides from my recent conference talks.
Benasque RNA meeting 2018. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures (update of RECOMB slides)
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: Quadratic Time SA&F of RNAs without Sequence-Based Heuristics (update to RECOMB'13)
LocARNA - fast and space-efficient simultaneous folding and alignment of RNAs.
LocARNA is part of the LocARNA package. The 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. LocARNA is also accessible online as web server.
Find the latest release on LocARNA's Github Home
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].
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. (Contributing 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)
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. Demo implementation 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)".
CARNA - Constraint-based alignment of RNA Ensembles. CARNA supports many non-standard alignment cases like pseudoknots and multiple stable structures. The tool is available for download (as source code) and accessible online via the CARNA web server.
CTE-Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination.
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.