Kalign - an accurate and fast multiple sequence alignment algorithm. - Timo Lassmann; Erik L. L. Sonnhammer (BMC Bioinform., 2005)

Pfam: clans, web tools and services. - Robert D. Finn; Jaina Mistry; Benjamin Schuster-Böckler; Sam Griffiths-Jones; Volker Hollich; Timo Lassmann; Simon Moxon; Mhairi Marshall; Ajay Khanna; Richard Durbin; Sean R. Eddy; Erik L. L. Sonnhammer; et al. (Nucleic Acids Res., 2006)

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. - Timo Lassmann; Erik L. L. Sonnhammer (Nucleic Acids Res., 2006)

Automatic extraction of reliable regions from multiple sequence alignments. - Timo Lassmann; Erik L. L. Sonnhammer (BMC Bioinform., 2007)

TagDust - a program to eliminate artifacts from next generation sequencing data. - Timo Lassmann; Yoshihide Hayashizaki; Carsten O. Daub (Bioinform., 2009)

SAMStat: monitoring biases in next generation sequencing data. - Timo Lassmann; Yoshihide Hayashizaki; Carsten O. Daub (Bioinform., 2011)

MOIRAI: A Compact Workflow System for CAGE Analysis. - Timo Lassmann; Akira Hasegawa; Carsten O. Daub; Piero Carninci; Yoshihide Hayashizaki (BMC Bioinform., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

TagDust2: a generic method to extract reads from sequencing data. - Timo Lassmann (BMC Bioinform., 2015)

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response. - Stuart Aitken; Shigeyuki Magi; Ahmad M. N. Alhendi; Masayoshi Itoh; Hideya Kawaji; Timo Lassmann; Carsten O. Daub; Erik Arner; Piero Carninci; Alistair R. R. Forrest; Yoshihide Hayashizaki; Levon M. Khachigian; et al. (PLoS Comput. Biol., 2015)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. - Hans Ienasescu; Kang Li; Robin Andersson; Morana Vitezic; Sarah Rennie; Yun Chen; Kristoffer Vitting-Seerup; Emil Lagoni; Mette Boyd; Jette Bornholdt; Michiel J. L. de Hoon; Hideya Kawaji; et al. (Database J. Biol. Databases Curation, 2016)

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. - David J. Arenillas; Alistair R. R. Forrest; Hideya Kawaji; Timo Lassmann; Wyeth W. Wasserman; Anthony Mathelier (Bioinform., 2016)

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. - J. Kenneth Baillie; Andrew Bretherick; Christopher S. Haley; Sara Clohisey; Alan Gray; Lucile P. A. Neyton; Jeffrey Barrett; Eli A. Stahl; Albert Tenesa; Robin Andersson; J. Ben Brown; Geoffrey J. Faulkner; et al. (PLoS Comput. Biol., 2018)

Kalign 3: multiple sequence alignment of large datasets. - Timo Lassmann (Bioinform., 2020)

SAMStat 2: quality control for next generation sequencing data. - Timo Lassmann (Bioinform., 2023)