Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. - Jens Reeder; Robert Giegerich (BMC Bioinform., 2004)

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. - Jens Reeder; Robert Giegerich (Bioinform., 2005)

RNAshapes: an integrated RNA analysis package based on abstract shapes. - Peter Steffen; Björn Voß; Marc Rehmsmeier; Jens Reeder; Robert Giegerich (Bioinform., 2006)

Locomotif: from graphical motif description to RNA motif search. - Janina Reeder; Jens Reeder; Robert Giegerich (ISMB/ECCB (Supplement of Bioinformatics), 2007)

pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. - Jens Reeder; Peter Steffen; Robert Giegerich (Nucleic Acids Res., 2007)

Shape based indexing for faster search of RNA family databases. - Stefan Janssen; Jens Reeder; Robert Giegerich (BMC Bioinform., 2008)

GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality. - Thomas D. Wu; Jens Reeder; Michael Lawrence; Gabe Becker; Matthew J. Brauer (Statistical Genomics, 2016)

Identifying and mitigating batch effects in whole genome sequencing data. - Jennifer A. Tom; Jens Reeder; William F. Forrest; Robert R. Graham; Julie Hunkapiller; Timothy W. Behrens; Tushar R. Bhangale (BMC Bioinform., 2017)