PUB - Publikationen an der Universität Bielefeld

AMBER: Assessment of Metagenome BinnERs.
Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC., Gigascience 7(6), 2018
PMID: 29893851

[Nextflow, an efficient tool to improve computation numerical stability in genomic analysis].
Tommaso PD, Floden EW, Magis C, Palumbo E, Notredame C., Biol Aujourdhui 211(3), 2017
PMID: 29412134

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.
O'Connor BD, Yuen D, Chung V, Duncan AG, Liu XK, Patricia J, Paten B, Stein L, Ferretti V., F1000Res 6(), 2017
PMID: 28344774

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.
Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capotă M, Chakravarty MM, Churchill NW, Cohen AL, Craddock RC, Devenyi GA, Eklund A, Esteban O, Flandin G, Ghosh SS, Guntupalli JS, Jenkinson M, Keshavan A, Kiar G, Liem F, Raamana PR, Raffelt D, Steele CJ, Quirion PO, Smith RE, Strother SC, Varoquaux G, Wang Y, Yarkoni T, Poldrack RA., PLoS Comput Biol 13(3), 2017
PMID: 28278228

General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J., F1000Res 6(), 2017
PMID: 28443186

Nextflow enables reproducible computational workflows.
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C., Nat Biotechnol 35(4), 2017
PMID: 28398311

Singularity: Scientific containers for mobility of compute.
Kurtzer GM, Sochat V, Bauer MW., PLoS One 12(5), 2017
PMID: 28494014

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis.
Costa RL, Gadelha L, Ribeiro-Alves M, Porto F., PeerJ 5(), 2017
PMID: 28695067

BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y., Bioinformatics 33(16), 2017
PMID: 28379341

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.
Kim B, Ali T, Lijeron C, Afgan E, Krampis K., Gigascience 6(8), 2017
PMID: 28854616

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.
Piro VC, Matschkowski M, Renard BY., Microbiome 5(1), 2017
PMID: 28807044

Systematic integration of biomedical knowledge prioritizes drugs for repurposing.
Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE., Elife 6(), 2017
PMID: 28936969

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen 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, Göker 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

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters.
Cheng G, Lu Q, Ma L, Zhang G, Xu L, Zhou Z., PeerJ 5(), 2017
PMID: 29204317

Tools and techniques for computational reproducibility.
Piccolo SR, Frampton MB., Gigascience 5(1), 2016
PMID: 27401684

Big Data and Uveitis.
Lee CS, Lee AY, Holland GN, Van Gelder RN, Tufail A., Ophthalmology 123(11), 2016
PMID: 27772646

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.
Narayanasamy S, Jarosz Y, Muller EE, Heintz-Buschart A, Herold M, Kaysen A, Laczny CC, Pinel N, May P, Wilmes P., Genome Biol 17(1), 2016
PMID: 27986083

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.
Moreews F, Sallou O, Ménager H, Le Bras Y, Monjeaud C, Blanchet C, Collin O., F1000Res 4(), 2015
PMID: 26913191