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(*) 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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