Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. - Martti T. Tammi; Erik Arner; Tom Britton; Björn Andersson (Bioinform., 2002)

TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences. - Martti T. Tammi; Erik Arner; Björn Andersson (Comput. Methods Programs Biomed., 2003)

ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aid. - Martti T. Tammi; Erik Arner; Ellen Kindlund; Björn Andersson (Bioinform., 2004)

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions. - Erik Arner; Martti T. Tammi; Anh-Nhi Tran; Ellen Kindlund; Björn Andersson (BMC Bioinform., 2006)

GRAT - genome-scale rapid alignment tool. - Ellen Kindlund; Martti T. Tammi; Erik Arner; Daniel Nilsson; Björn Andersson (Comput. Methods Programs Biomed., 2007)

NGSView: an extensible open source editor for next-generation sequencing data. - Erik Arner; Yoshihide Hayashizaki; Carsten O. Daub (Bioinform., 2010)

Optimization of turn-back primers in isothermal amplification. - Yasumasa Kimura; Michiel J. L. de Hoon; Shintaro Aoki; Yuri Ishizu; Carsten O. Daub; Alexander Lezhava; Erik Arner; Yoshihide Hayashizaki; Yuki Kawai; Yasushi Kogo (BIBM Workshops, 2011)

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)

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)

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. - Trisevgeni Rapakoulia; Xin Gao 001; Yi Huang; Michiel J. L. de Hoon; Mariko Okada-Hatakeyama; Harukazu Suzuki; Erik Arner (Bioinform., 2017)

DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment. - Ramzan Umarov; Yu Li 006; Erik Arner (PLoS Comput. Biol., 2021)

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. - Ramzan Umarov; Yu Li 006; Takahiro Arakawa; Satoshi Takizawa; Xin Gao 001; Erik Arner (PLoS Comput. Biol., 2021)