EMPRR: a high-dimensional EM-based peicewise regression algorithm. - Manimozhiyan Arumugam; Stephen D. Scott 001 (ICMLA, 2004)

The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs. - Evan Keibler; Manimozhiyan Arumugam; Michael R. Brent (Bioinform., 2007)

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. - David V. Lu; Randall H. Brown; Manimozhiyan Arumugam; Michael R. Brent (Bioinform., 2009)

SmashCommunity: a metagenomic annotation and analysis tool. - Manimozhiyan Arumugam; Eoghan D. Harrington; Konrad U. Foerstner; Jeroen Raes; Peer Bork (Bioinform., 2010)

SmashCell: a software framework for the analysis of single-cell amplified genome sequences. - Eoghan D. Harrington; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork; David A. Relman (Bioinform., 2010)

Addendum: Enterotypes of the human gut microbiome. - Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R. Mende; Gabriel R. Fernandes; Julien Tap; Thomas Brüls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; et al. (Nat., 2014)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - Kristoffer Forslund; Falk Hildebrand; Trine Nielsen; Gwen Falony; Emmanuelle Le Chatelier; Shinichi Sunagawa; Edi Prifti; Sara Vieira-Silva; Valborg Gudmundsdottir; Helle Krogh Pedersen; Manimozhiyan Arumugam; Karsten Kristiansen; et al. (Nat., 2015)

MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration. - Carmen Saenz; Eleonora Nigro; Vithiagaran Gunalan; Manimozhiyan Arumugam (Frontiers Bioinform., 2022)