PUB - Publikationen an der Universität Bielefeld

Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Droge M, Gartemann KH, Junemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Puhler A, Schluter A, Goesmann A., PLoS ONE 6(1), 2011
PMID: 21297863

Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach.
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J., Gut 55(2), 2005
PMID: 16188921

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jorgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvociute M, Hansen LH, Sorensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Goker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC., Nat. Methods 14(11), 2017
PMID: 28967888

Coming of age: ten years of next-generation sequencing technologies.
Goodwin S, McPherson JD, McCombie WR., Nat. Rev. Genet. 17(6), 2016
PMID: 27184599

Classification of metagenomic sequences: methods and challenges.
Mande SS, Mohammed MH, Ghosh TS., Brief. Bioinformatics 13(6), 2012
PMID: 22962338

S, Nucleic Acids Res 39(), 2010

IMG/M: the integrated metagenome data management and comparative analysis system.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22086953

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA., BMC Bioinformatics 9(), 2008
PMID: 18803844

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24165880

AUTHOR UNKNOWN, 0

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.
Merchant N, Lyons E, Goff S, Vaughn M, Ware D, Micklos D, Antin P., PLoS Biol. 14(1), 2016
PMID: 26752627

Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites.
Jimenez DJ, Dini-Andreote F, Ottoni JR, de Oliveira VM, van Elsas JD, Andreote FD., Microb Biotechnol 8(3), 2014
PMID: 25171437

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.
Goecks J, Nekrutenko A, Taylor J; Galaxy Team, Afgan E, Ananda G, Baker D, Blankenberg D, Chakrabarty R, Coraor N, Goecks J, Von Kuster G, Lazarus R, Li K, Nekrutenko A, Taylor J, Vincent K., Genome Biol. 11(8), 2010
PMID: 20738864

Conveyor: a workflow engine for bioinformatic analyses.
Linke B, Giegerich R, Goesmann A., Bioinformatics 27(7), 2011
PMID: 21278189

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array.
Suzuki S, Kakuta M, Ishida T, Akiyama Y., PLoS ONE 9(8), 2014
PMID: 25099887

Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH., Nat. Methods 12(1), 2014
PMID: 25402007

AUTHOR UNKNOWN, 0

S, 2003

Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL., Genome Biol. 15(3), 2014
PMID: 24580807

Fast and sensitive taxonomic classification for metagenomics with Kaiju.
Menzel P, Ng KL, Krogh A., Nat Commun 7(), 2016
PMID: 27071849

Centrifuge: rapid and sensitive classification of metagenomic sequences.
Kim D, Song L, Breitwieser FP, Salzberg SL., Genome Res. 26(12), 2016
PMID: 27852649

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.
Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N., Nat. Methods 12(10), 2015
PMID: 26418763

AUTHOR UNKNOWN, 0

The Pfam protein families database.
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681378

TIGRFAMs and Genome Properties in 2013.
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23197656

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22096231

KD, Nucleic Acids Res 35(suppl_1), 2006

IMG/M: integrated genome and metagenome comparative data analysis system.
Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T, Ivanova NN, Kyrpides NC., Nucleic Acids Res. 45(D1), 2016
PMID: 27738135