Teaching Materials


  • Calculus for Mathematics
    Bachalor Course (10 ECTS)
  • Mathematical Perspectives
    Bachalor Course (5 ECTS)
  • Complex Analysis
    Bachalor Course (5 ECTS)
  • Programming for Evolutionary Biology
    Network: an introduction
  • Weekly Graph Algorithm Seminar
    Lecture notes: algorithm intro, matroid, shortest path, spanning tree, flows...,
    Graphs, Networks and Algorithms.
  • These materials can be sent by request!

    Softwares


  • Basin hopping graph framework: Download
  • We introduced the basin hopping graph (BHG) to capture more information regarding adjacency between LMs. Nodes in the BHG are local minima (LMs), and two LMs are neighbored only if the direct transition between their corresponding basins are 'energetically favorable'. The corresponding saddle height is annotated on the edge. In this abstraction, possible folding pathways are represented as sequences of adjacent basins represented by their LMs. The BHG is particularly suitable to describe the ruggedness of RNA folding landscapes and to explain the interconversion between multiple 'active' LMs as observed by Solomatin et al. (2010). Details see homepage of BHG.

    If you think it is helpful to your research, please do not forget to cite us when you achieve your success!
    Marcel Kucharik, Ivo L. Hofacker, Peter F. Stadler and Jing Qin
    Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
    Bioinformatics (2014) 30 (14): 2009-2017.
    Marcel Kucharik, Ivo L. Hofacker, Peter F. Stadler and Jing Qin
    Psedudoknots in RNA folding landscapes
    Bioinformatics (2015) doi: 10.1093/bioinformatics/btv572.

  • RNA-RNA interaction prediction: RNAripalign download
  • The input RNAripalign consists of two (given) multiple sequence alignments (MSA). ripalign outputs (i) the partition function, (ii) base pairing probabilities, (iii) hybrid probabilities and (iv) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm rip, ripalign requires negligible additional memory resource but offers much better sensitivity and specificity, once alignments of suitable quality are given. ripalign additionally allows to incorporate structure constraints as input parameters. Details see README in the package.

    If you think it is helpful to your research, please do not forget to cite us when you achieve your success!
    Andrew X. Li, Manja Marz, Jing Qin and Christian M. Reidys
    RNA-RNA interaction prediction based on multiple sequence alignments
    Bioinformatics (2011) 27 (4): 456-463.

  • Graph distance distribution in secondary structure ensemble: RNAgraphdist download
  • Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure.
    The RNAgraphdist calculates the equilibrium distribution of graph-distances between arbitrary pair of nucleotides in an RNA molecule. The program reads RNA structures generated from RNAsubopt, calculates their equilibrium distribution and outputs the graph-distances in a tab delimited list or in the terminal Details see README in the package.

    If you think it is helpful to your research, please do not forget to cite us when you achieve your success!
    Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler and Rolf Backofen
    Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
    Algorithms for Molecular Biology 2014, 9:19.