(*) Papers that all authors contributed equally (by alphabetical order)


  • Marcel Kucharik, Ivo L. Hofacker, Peter F. Stadler and Jing Qin
    Psedudoknots in RNA folding landscapes,
    Bioinformatics (2015) doi: 10.1093/bioinformatics/btv572

  • 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 9:19

  • 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

  • * Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin and Peter F. Stadler
    Distribution of graph-distance in Boltzmann ensembles of RNA secondary structures,
    Algorithms in Bioinformatics (13th International Workshop, WABI 2013), Lecture Notes in Computer Science, 8126: 112-125.

  • * Qin J. and Reidys C.M.
    On topological RNA interaction structures,
    Journal of Computational Biology, 20 (7): 495-513.

  • * Klemm K., Qin J. and Stadler P.F.
    Geometry and coarse-grained representations of landscapes,
    Invited chapter, to appear in the Springer book series Emergence, Complexity and Computation.

  • Lorenz R., Bernhart S., Qin J., Hoener zu Siederdissen C., Tanzer A., Amman F., Hofacker I.L. and Stadler P.F.,
    2D meets 4G: G-quadruplexes in RNA secondary structure prediction,
    IEEE Trans. Comp. Biol. Bioinf.

  • Lorenz R., Bernhart S., Externbrink F., Qin J., Hoener zu Siederdissen C., Amman F., Hofacker I.L. and Stadler P.F.
    RNA folding algorithms with G quadruplexes,
    Advances in Bioinformatics and Computational Biology, Lecture Notes in Computer Science, {7409}: 49-60.

  • *Li A.X., Qin, J., Marz, M. and Reidys, C.M.
    RNA-RNA interaction prediction based on multiple sequence alignments,
    Bioinformatics, {27} (4): 456-463.

  • *Huang F.W.D, Qin J., Reidys C.M. and Stadler P.F.
    Target prediction and a statistical sampling algorithm for RNA-RNA interaction,
    Bioinformatics, {26} (2): 175-181.

  • *Huang F.W.D, Qin J., Reidys C.M. and Stadler P.F.
    Partition function and base pairing probabilities for RNA-RNA interaction prediction,
    Bioinformatics, {25}(20): 2646-2654.

  • *Chen W.Y.C., Qin J., Reidys C.M. and Zeilberger D.
    Efficient Counting and Asymptotics of $k$-noncrossing tangled-diagrams,
    Electr. J. Combin., {16}, R37.

  • *Chen W.Y.C., Qin J. and Reidys C.M.
    Crossings and Nestings of tangled-diagrams,
    Electr. J. Combin., {15}, R86.

  • *Jin E.Y., Qin J. and Reidys C.M.
    Neutral networks of sequence to shape maps,
    J. Theoret. Biol., {250}, 484-497.

  • *Jin E.Y., Qin J. and Reidys C.M.
    Combinatorics of RNA structures with pseudoknots,
    Bull. Math. Biol. , {70}: 45-67.

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