PUB - Publikationen an der Universität Bielefeld

A catalog of reference genomes from the human microbiome.
Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D., Science 328(5981), 2010
PMID: 20489017

Diversity and genomes of uncultured microbial symbionts in the termite gut.
Hongoh Y., Biosci. Biotechnol. Biochem. 74(6), 2010
PMID: 20530908

Expanding genomics of mycorrhizal symbiosis.
Kuo A, Kohler A, Martin FM, Grigoriev IV., Front Microbiol 5(), 2014
PMID: 25408690

AUTHOR UNKNOWN, 1991

Rosenberg E, Zilber-Rosenberg I., 2013

Diversity and distribution of coral-associated bacteria
Rohwer F, Seguritan V, Azam F., 2002

Reef corals: mutualistic symbioses adapted to nutrient-poor environments
Muscatine L, Porter JW., 1977

Metagenomic analysis of the microbial community associated with the coral Porites astreoides.
Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F., Environ. Microbiol. 9(11), 2007
PMID: 17922755

The “other” coral symbiont: Ostreobium diversity and distribution
del Campo J, Pombert J-F, Šlapeta J., 2017

Fungi in corals: symbiosis or disease? Interaction between polyps and fungi causes pearl-like skeleton biomineralization
Le Campion-Alsumard T, Golubic S, Priess K., 1995

Coral-the world's most diverse symbiotic ecosystem.
Blackall LL, Wilson B, van Oppen MJ., Mol. Ecol. 24(21), 2015
PMID: 26414414

Molecular characterization of vulnibactin biosynthesis in Vibrio vulnificus indicates the existence of an alternative siderophore.
Tan W, Verma V, Jeong K, Kim SY, Jung CH, Lee SE, Rhee JH., Front Microbiol 5(), 2014
PMID: 24478763

Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise.
Wood-Charlson EM, Weynberg KD, Suttle CA, Roux S, van Oppen MJ., Environ. Microbiol. 17(10), 2015
PMID: 25708646

Marine invertebrate larvae associated with Symbiodinium: a mutualism from the start?
Mies M, Sumida PYG, Rädecker N., 2017

Using the Acropora digitifera genome to understand coral responses to environmental change.
Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N., Nature 476(7360), 2011
PMID: 21785439

Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.
Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, Takeuchi T, Hisata K, Tanaka M, Fujiwara M, Hamada M, Seidi A, Fujie M, Usami T, Goto H, Yamasaki S, Arakaki N, Suzuki Y, Sugano S, Toyoda A, Kuroki Y, Fujiyama A, Medina M, Coffroth MA, Bhattacharya D, Satoh N., Curr. Biol. 23(15), 2013
PMID: 23850284

A snapshot of a coral "holobiont": a transcriptome assembly of the scleractinian coral, porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae.
Shinzato C, Inoue M, Kusakabe M., PLoS ONE 9(1), 2014
PMID: 24454815

Comparative genomics explains the evolutionary success of reef-forming corals.
Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutte S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG., Elife 5(), 2016
PMID: 27218454

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T., Genome Res. 24(8), 2014
PMID: 24755901

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS., Science 317(5834), 2007
PMID: 17615350

The genome of Aiptasia, a sea anemone model for coral symbiosis.
Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, Gough J, Weis VM, Aranda M, Pringle JR, Voolstra CR., Proc. Natl. Acad. Sci. U.S.A. 112(38), 2015
PMID: 26324906

Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp.
Wang X, Liew YJ, Li Y, Zoccola D, Tambutte S, Aranda M., Mol Ecol Resour 17(6), 2017
PMID: 28407448

Murray-Roberts J, Wheeler AJ, Freiwald A., 2010

Deep reefs are not universal refuges: reseeding potential varies among coral species
Bongaerts P, Riginos C, Brunner R., 2017

Metagenomic Assembly: Overview, Challenges and Applications.
Ghurye JS, Cepeda-Espinoza V, Pop M., Yale J Biol Med 89(3), 2016
PMID: 27698619

An introduction to the analysis of shotgun metagenomic data
Sharpton TJ., 2014

Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH., Nat. Biotechnol. 31(6), 2013
PMID: 23707974

Phylogenetic signals in DNA composition: limitations and prospects.
Mrazek J., Mol. Biol. Evol. 26(5), 2009
PMID: 19233962

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition.
Saeed I, Tang SL, Halgamuge SK., Nucleic Acids Res. 40(5), 2011
PMID: 22180538

MetaSort untangles metagenome assembly by reducing microbial community complexity.
Ji P, Zhang Y, Wang J, Zhao F., Nat Commun 8(), 2017
PMID: 28112173

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts.
Neave MJ, Michell CT, Apprill A, Voolstra CR., Sci Rep 7(), 2017
PMID: 28094347

Gießen: University Collections: Justus Liebig University Gießen
Diehl E, Jauker B, Albrecht C., 2018

GenomeScope: fast reference-free genome profiling from short reads.
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC., Bioinformatics 33(14), 2017
PMID: 28369201

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF., Gigascience 2(1), 2013
PMID: 23870653

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF., Science 337(6102), 2012
PMID: 23019650

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
Kang DD, Froula J, Egan R, Wang Z., PeerJ 3(), 2015
PMID: 26336640

Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects
Liu B, Shi Y, Yuan J., 2013

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.
Li Z, Chen Y, Mu D, Yuan J, Shi Y, Zhang H, Gan J, Li N, Hu X, Liu B, Yang B, Fan W., Brief Funct Genomics 11(1), 2011
PMID: 22184334

Genome size distribution in phylum Cnidaria
Adachi K, Miyake H, Kuramochi T., 2017

Sequencing depth and coverage: key considerations in genomic analyses
Sims D, Sudbery I, Ilott NE., 2014

Sequence assembly demystified.
Nagarajan N, Pop M., Nat. Rev. Genet. 14(3), 2013
PMID: 23358380

Bosch TCG, Miller DJ., 2016

Optimization of DNA extraction from a scleractinian coral for the detection of thymine dimers by immunoassay.
Banaszak AT., Photochem. Photobiol. 83(4), 2007
PMID: 17645654

Biphasic study to characterize agricultural biogas plants by high-throughput 16S rRNA gene amplicon sequencing and microscopic analysis
Maus I, Kim YS, Wibberg D., 2016

Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing.
Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M., PLoS ONE 9(8), 2014
PMID: 25144201

Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes.
Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Puhler A, Fogelqvist J, Varrelmann M, Schluter A, Dixelius C., BMC Genomics 17(), 2016
PMID: 26988094

FLASH: fast length adjustment of short reads to improve genome assemblies.
Magoc T, Salzberg SL., Bioinformatics 27(21), 2011
PMID: 21903629

Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691

UPARSE: highly accurate OTU sequences from microbial amplicon reads.
Edgar RC., Nat. Methods 10(10), 2013
PMID: 23955772

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes
Liebe S, Wibberg D, Winkler A., 2016

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome.
Theuerl S, Kohrs F, Benndorf D, Maus I, Wibberg D, Schluter A, Kausmann R, Heiermann M, Rapp E, Reichl U, Puhler A, Klocke M., Appl. Microbiol. Biotechnol. 99(18), 2015
PMID: 25998656

Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404

Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J., Genome Biol. 13(12), 2012
PMID: 23259615

Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286

BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT., Bioinformatics 27(12), 2011
PMID: 21493652

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.
Lomsadze A, Burns PD, Borodovsky M., Nucleic Acids Res. 42(15), 2014
PMID: 24990371

Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
PMID: 24427317

BEDTools: a flexible suite of utilities for comparing genomic features.
Quinlan AR, Hall IM., Bioinformatics 26(6), 2010
PMID: 20110278

InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S., Bioinformatics 30(9), 2014
PMID: 24451626

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.).
Verwaaijen B, Wibberg D, Krober M, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Puhler A, Schluter A., PLoS ONE 12(5), 2017
PMID: 28486484

AUTHOR UNKNOWN, 0

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
PMID: 23618408

ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157

ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
PMID: 27540267

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Marcais G, Kingsford C., Bioinformatics 27(6), 2011
PMID: 21217122

Eukaryotic genome size databases
Gregory TR, Nicol JA, Tamm H., 2007

Estimating the repeat structure and length of DNA sequences using L-tuples.
Li X, Waterman MS., Genome Res. 13(8), 2003
PMID: 12902383

QUAST: quality assessment tool for genome assemblies.
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM., Bioinformatics 31(19), 2015
PMID: 26059717

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

Ensembl 2016
Yates A, Akanni W, Ridwan Amode M., 2016

Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago
Shinzato C, Mungpakdee S, Arakaki N., 2015

Supporting data for “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts.”
Celis JS, Wibberg D, Ramírez-Portilla C., 2018