Discovering motifs that induce sequencing errors. - Manuel Allhoff; Alexander Schönhuth; Marcel Martin; Ivan G. Costa; Sven Rahmann; Tobias Marschall (BMC Bioinform., 2013)

Detecting differential peaks in ChIP-seq signals with ODIN. - Manuel Allhoff; Kristin Seré; Heike Chauvistré; Qiong Lin; Martin Zenke; Ivan G. Costa (Bioinform., 2015)

Solving the differential peak calling problem in ChIP-seq data. - Manuel Allhoff (2016)

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. - Zhijian Li; Chao-Chung Kuo; Fabio Ticconi; Mina Shaigan; Julia Gehrmann; Eduardo G. Gusmão; Manuel Allhoff; Martin Manolov; Martin Zenke; Ivan G. Costa (BMC Bioinform., 2023)