Computational biology and bioinformatics articles within The ISME Journal

Featured

• Original Article | 06 February 2015

  Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents

  • Daniel C Reed
  • , John A Breier
  •  & Gregory J Dick

• Original Article
  17 October 2014 | Open Access

  Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

  • A Murat Eren
  • , Hilary G Morrison
  •  & Mitchell L Sogin

• Commentary
  29 August 2014 | Open Access

  Which is more important for classifying microbial communities: who’s there or what they can do?

  • Zhenjiang Xu
  • , Daniel Malmer
  •  & Rob Knight

• Original Article | 11 July 2014

  Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

  • Mikhail Tikhonov
  • , Robert W Leach
  •  & Ned S Wingreen

• Original Article | 15 August 2013

  Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

  • Ilias Lagkouvardos
  • , Thomas Weinmaier
  •  & Matthias Horn

• Commentary
  25 October 2012 | Open Access

  Collaborative cloud-enabled tools allow rapid, reproducible biological insights

  • Benjamin Ragan-Kelley
  • , William Anton Walters
  •  & J Gregory Caporaso

• Short Communication
  12 January 2012 | Open Access

  Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

  • David A W Soergel
  • , Neelendu Dey
  •  & Steven E Brenner

• Original Article | 23 June 2011

  Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

  • Christian G Klatt
  • , Jason M Wood
  •  & David M Ward

• Original Article | 12 May 2011

  Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

  • Alyson E Santoro
  •  & Karen L Casciotti

• Original Article | 03 March 2011

  Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

  • Tancredi Caruso
  • , Yuki Chan
  •  & Stephen B Pointing

• Original Article | 24 February 2011

  Reproducibility and quantitation of amplicon sequencing-based detection

  • Jizhong Zhou
  • , Liyou Wu
  •  & Yunfeng Yang

• Original Article | 17 February 2011

  Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria

  • Daniel Sher
  • , Jessie W Thompson
  •  & Sallie W Chisholm

• Original Article | 16 December 2010

  Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

  • Marc Weber
  • , Hanno Teeling
  •  & Frank Oliver Glöckner

• Original Article | 09 December 2010

  Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

  • Yanmei Shi
  • , Gene W Tyson
  •  & Edward F DeLong

• Original Article | 02 December 2010

  Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon

  • Daniel Aguirre de Cárcer
  • , Páraic Ó Cuív
  •  & Mark Morrison

• Original Article | 02 December 2010

  Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons

  • Corinne F Maurice
  • , David Mouillot
  •  & Thierry Bouvier

• Original Article | 02 December 2010

  An integrative study of a meromictic lake ecosystem in Antarctica

  • Federico M Lauro
  • , Matthew Z DeMaere
  •  & Ricardo Cavicchioli

• Commentary | 25 November 2010

  The Future of microbial metagenomics (or is ignorance bliss?)

  • Jack A Gilbert
  • , Folker Meyer
  •  & Mark J Bailey

• Original Article | 04 November 2010

  Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis

  • Catherine Burke
  • , Torsten Thomas
  •  & Staffan Kjelleberg

• Original Article | 21 October 2010

  BIPES, a cost-effective high-throughput method for assessing microbial diversity

  • Hong-Wei Zhou
  • , Dong-Fang Li
  •  & Fei Zou

• Commentary | 07 October 2010

  Supervised classification of microbiota mitigates mislabeling errors

  • Dan Knights
  • , Justin Kuczynski
  •  & Scott T Kelley

• Original Article | 07 October 2010

  Structure of the human gastric bacterial community in relation to Helicobacter pylori status

  • Ana Maldonado-Contreras
  • , Kate C Goldfarb
  •  & Maria G Dominguez-Bello

• Commentary | 09 September 2010

  UniFrac: an effective distance metric for microbial community comparison

  • Catherine Lozupone
  • , Manuel E Lladser
  •  & Rob Knight

• Original Article | 25 February 2010

  PANGEA: pipeline for analysis of next generation amplicons

  • Adriana Giongo
  • , David B Crabb
  •  & Eric W Triplett