Folker Meyer's homepage

Folker Meyer is a computational biologist at Argonne National Laboratory, a Professor at the Department of Medicine, University of Chicago and a senior fellow at the Computation Institute at the University of Chicago. He is also deputy division director of the Biology Division at Argonne National Laboratory and a senior fellow at the Institute of Genomics and Systems Biology (a joint Argonne National Laboratory and University of Chicago Institute).

He trained as a computer scientists and started to work with biologists early on in his career. It was that exposure to interesting biological problems that sparked his interest in building software systems to tackle biological problems, mostly in the field of genomics or post-genomics. In the past he has been best known for his leadership role in the development of the GenDB genome annotation system, he has also played an active role in the design and implementation of several high-performance computing platforms.

His current work focuses on the analysis of shotgun metagenomics data sets and on the MG-RAST community resource for metagenomics. Shotgun metagenomics is benefitting directly from the current advances in sequencing technology, leading to dramatic growth in the number scientists using this approach and the number and size of the data sets being produced. He also has an interest in microbial genomics and the analysis of complete microbial genomes and is a member of the RAST project.

He is a founding member of the Earthmicrobiome project (EMP). He is a member of the Genomics Standards Consortium (GSC).

Folker's google scholar page



Folker Meyer
Mathematics and Computer Science Division
and
Institute for Genomics and Systems Biology
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
U.S.A.
Phone: 630 252-3261
eMail: folker@anl.gov
Picture of Folker Meyer Folker Meyer
University of Chicago
Computation Institute
Searle Chemistry Laboratory
5735 South Ellis Avenue
Chicago, IL 60637
U.S.A.

Short CV


Selected Publications:

Please use google scholar for a more complete list.

[78] J. Gilbert, F. Meyer
Modeling the Earth Microbiome -- Careful planning can reduce sampling and measurement biases while building data sets describing microbes across multiple ecosystems
ASM Microbe 2012
[77] T. Thomas, J. Gilbert and F. Meyer Metagenomics - a guide from sampling to data analysis
BMC Microbial Informatics and Experimentation 2012
[76] T. O. Delmont, E. Prestat, K. P Keegan, M. Faubladier, P. Robe, a. M. Clark, E. Pelletier, P. R. Hirsch, F. Meyer, J. A. Gilbert, D. Le Paslier, P. Simonet and T. M Vogel
Structure, fluctuation and magnitude of a natural grassland soil metagenome
The ISME Journal (2012), 1–11
[75] N. Desai, D. Antonopoulos, J. A Gilbert, E. M Glass and F. Meyer
From genomics to metagenomics
Current Opinions in Biotechnology, 2012
[74] D. A. Antonopoulos, E. M. Glass, and F. Meyer
Analyzing Metagenomic data: inferring microbial community function with MG-RAST
Metagenomics and its applications in agriculture, biomedicine, and environmental studies
publisher: Nova Science Publishers, 2011
editor: Robert W. Li
ISBN: 978-1-61668-682-6
[73] E. M. Glass and F. Meyer
Analysis of Metagenomics Data
Bioinformatics for High Throughput Sequencing
publisher: Springer 2012
editors: Rodríguez-Ezpeleta, Naiara; Hackenberg, Michael; Aransay, Ana M. (Eds.)
ISBN: 978-1-4614-0781-2
[72] D. Field, L. Amaral-Zettler, G, Cochrane, J. R Cole, P. Dawyndt, G. M Garrity, J. Gilbert, F. O. Glöckner, L. Hirschman, I. Karsch-Mizrachi, H.-P. Klenk, R. Knight, R. Kottmann, N. Kyrpides, F. Meyer, I. San Gill, S.-A. Sansone, L. M Schriml, P. Sterk, T. Tatusova, D. W Ussery, O. White, J. Wooley
The Genomic Standards Consortium
PLoS Biology2011 June; 9(6): e1001088.
[71] A. Wilke, J. Wilkening, E. M. Glass, N. L. Desai, and F. Meyer
Porting the MG-RAST metagenomic data analysis pipeline to the cloud
Concurrency and Computation2011, DOI: 10.1002/cpe.1799
[70] C. S. Henry, R. Overbeek, F. Xia, A. A. Best, E. Glass, J. Gilbert, P. Larsen, R. Edwards, T. Disz, F. Meyer, V. Vonstein, M. DeJongh, D. Bartels, N. Desai, M. D'Souza, S. Devoid, K. P. Keegan, R. Olson, A. Wilke, J. Wilkening, and R. L. Stevens
Connecting Genotype to Phenotype in the Era of High-throughput Sequencing
Biochim Biophys Acta. 2011 Oct;1810(10):967-77
[69] E. M. Glass and Folker Meyer
The metagenomics RAST server --- a public resource for the automatic phylogenetic and functional analysis of metagenomes
Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats
publisher: Wiley/Blackwell
Editor: Frans J. de Bruin
[68] P.E. Larsen, F. Collart, D. Field,F. Meyer, K.P. Keegan, C.S. Henry, J. McGrath,J. Quinn, J.A. Gilbert
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset.
BMC Microbial Informatics and Experimentation. , 2011, 1:4
[67] S. Lemke, D. A Antonopoulos, F. Meyer, M. H Domanus, U. Schmidt-Ott
BMP Signaling Components in Embryonic Transcriptomes of the Hover Fly Episyrphus balteatus (Syrphidae)
BMC Genomics 2011, 12:278doi:10.1186/1471-2164-12-278
[66] J. A. Gilbert,F. Meyer, L. Schriml, I.R. Joint, M. Mühling, D. Field
Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel
Standards in Genomic Sciences 3 (2): 183-193 2010
[65] P. Yilmaz, R. Kottmann, D. Field, R. Knight, J. R. Cole, L. Amaral-Zettler, J. A. Gilbert, I. Karsch-Mizrachi, A. Johnston, G. Cochrane, R. Vaughan, C. Hunter, J. Park, N. Morrison, P. Rocca-Serra, P. Sterk, M. Arumugam, M. Bailey, L. Baumgartner, B. W. Birren, M. J. Blaser, V. Bonazzi, T. Booth, P. Bork, F. D. Bushman, P. L. Buttigieg, P. S. G. Chain, E. Charlson, E. K. Costello, H. Huot-Creasy, P. Dawyndt, T. DeSantis, N. Fierer, J. A. Fuhrman, R. E. Gallery, D. Gevers, R. A. Gibbs, M. Gwinn Giglio, I. San Gil, A. Gonzalez, J. I. Gordon, R. Guralnick, W. Hankeln, S. Highlander, P. Hugenholtz, J. Jansson, S. T. Kelley, J. Kennedy, D. Knights, O. Koren, J. Kuczynski, N. Kyrpides, R. Larsen, C. L. Lauber, T. Legg, R. E. Ley, C. A. Lozupone, W. Ludwig, D. Lyons, E. Maguire, B. A. Methé, F. Meyer, S. Nakielny, K. E. Nelson, D. Nemergut, J. D. Neufeld, L. K. Newbold, A. E. Oliver, N. R. Pace, G. Palanisamy, J. Peplies, J. Peterson, J. Petrosino, L. Proctor, E. Pruesse, C. Quast, J. Raes, S. Ratnasingham, J. Ravel, D. A. Relman, S. Assunta-Sansone, P. D. Schloss, L. Schriml, R. Sinha, E. Sodergren, A. Spor, J. Stombaugh, J. M. Tiedje, D. V. Ward, G. M. Weinstock, D. Wendel, O. White, A. Whiteley, A. Wilke, J. R. Wortman, F. O. Glöckner
The “Minimum Information about a MARKer gene Sequence” (MIMARKS) specification
Nature Biotechnology 2011
[64] S.Mitra, P. Rupek, D. C. Richter, T. Urich, J. A. Gilbert, F. Meyer, A. Wilke, D. H.Huson
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
BMC Bioinformatics 12(Suppl 1):S21doi:10.1186/1471-2105-12-S1-S21
[63] D. Field, S. Sansone, E. F. DeLong, P. Sterk, I. Friedberg, R. Kottmann, L. Hirschman, G. Garrity, G. Cochrane, J. Wooley, F. Meyer, S. Hunter, O. White
Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010
Standards in Genomic Science (SIGS), Vol 3 (3)
[62] J.A. Gilbert, F. Meyer, D. A. Antonoploulos, P. Balaji, C.T. Brown, N. Desai, J.A. Eisen, D. Evers, W. Feng, D. Huson, J. Jasson, R. Knight, J. Knight, E. Kolker, K. Kostantindis, J. Kostka, N. Kyrpides, R. Mackelprang, A.C. McHardy, C. Quince, J. Raes, A. Sczyrba, A. Shade, R. Stevens
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
Standards in Genomics Science (SIGS), Vol 3 (3), 2010
[61] Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glockner F-O, Klenk H-P, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R.
Microbiome Project: Meeting report of the 1st EMP meeting on sample selection and acquisition at Argonne National Laboratory October 6th 2010
Standards in Genomics Science (SIGS), Vol 3 (3), 2010
[60] Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottman R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O , Wooley J.
Meeting report from the Genomics Satndards Consortium (GSC) workshop 10
Standards in Genomics Science (SIGS), Vol 3 (3), 2010
[59] Gilbert JA, Meyer F, Knight R, Field D, Kyrpides N, Yilmaz P, Wooley J.
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle
Standards in Genomic Science (SIGS) Vol 3 (3), 2010
[58] Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM.
Metagenomics: A foundling finds its feet.
Standards in Genomic Science (SIGS) , Vol 3 (2) , 2010
[57] Y. Wang, D. A. Antonopoulos, X. Zhu, L. Harrell, I. Hanan, J. C. Alverdy, F. Meyer, M. Musch, V. B. Young, E. B. Chang
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon
Applied Microbiology and Biotechnology, 2010
[56] Hather, G. J., Haynes, W., Higdon, R., Kolker, N., Stewart, E. A., Arzberger, P., Chain, P., Field, D., Franza, B. R., Lin, B., Meyer, F., Ozdemir, V., Smith, C. V., Van Belle, G., Wooley, J., and Kolker, E.
The United States of America and Scientific Research.
PLoS ONE 5, no. 8: 9. http://dx.plos.org/10.1371/journal.pone.0012203., 2010
[55] J. A. Gilbert, F. Meyer, M. J. Bailey
The Future of microbial metagenomics (or is ignorance bliss?)
The ISME Journal , (25 November 2010) | doi:10.1038/ismej.2010.178, 2010
[54] C. Pfister, F. Meyer, D. Antonopoulos
Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling
PLoS One 2010
[53] S. Lemke, S. E. Busch, D. A Antonopoulos, F. Meyer, M. H Domanus, and U. Schmidt-Ott
Maternal activation of gap genes in the hover fly Episyrphus
Development 137, (2010) doi:10.1242/dev.046649
[52] F. E. Angly, D. Willner, A. Prieto-Dav, R. A. Edwards, R. Schmieder, R. Vega-Thurber, D. A. Antonopoulos, K. Barott, M. T. Cottrell, C. Desnues, E. A. Dinsdale, M. Furlan, M. Haynes, M. R. Henn, Y. Hu, D. L. Kirchman, T. McDole, J. D. McPherson, F. Meyer, R. M. Miller, E. Mundt, R. K. Naviaux, B. Rodriguez-Mueller, R. Stevens, L. Wegley, L. Zhang, B. Zhu, F. Rohwer
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
PLOS Computational Biology 2010
[51] E. M. Glass, J. Wilkening, A. Wilke, D. Antonopoulos, and F. Meyer
Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes
Cold Spring Harbor Protocols 2010, Cold Spring Harb. Protoc.; 2010; doi:10.1101/pdb.prot5368
[50] J. Wilkening, A. Wilke, N. Desai, F. Meyer
Using Clouds for Metagenomics: A Case Study
IEEE International Conference on Cluster Computing (Cluster 2009), AUG 31-SEP 04, 2009 New Orleans, LA 2009 (preprint) ( PDF)
[49] F. Meyer, R. Overbeek, A. Rodriguez
FIGfams: Yet another set of protein families
Nucleic Acids Res. Volume: 37 Issue: 20 Pages: 6643-6654 , 2009
[48] T. Bekel, K. Henckel, H. Küster, F. Meyer V. Mittard Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Pühler, J. Stoye, A. Goesmann
The Sequence Analysis and Management System SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
Journal of Biotechnology, 2009
[47] R. Gross, C. A Guzman., M. Sebaihia, V.AP Martins dos Santos, D. H Pieper, R. Koebnik, M. Lechner, D. Bartels, J. Buhrmester, J. V Choudhuri, T. Ebensen, L. Gaigalat, S. Herrmann, C. Larisch, S. Link, B. Linke, F. Meyer, S. Mormann, D. Nakunst, C. Rückert, S. Schneiker-Bekel, K. Schulze, F.-J. Vorhölter, T. Yevsa, J. T Engle, W. E Goldman, A. Pühler, U. B Göbel, H. Blöcker, A. Goesmann, O. Kaiser & R. Martinez-Arias
The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae
BMC Genomics, 9:449
[46] S. E. Battle, F. Meyer, J. Rello, V.L. Kung and A. R. Hauser
The Hybrid Pathogenicity Island PAGI-5 Contributes to the Highly Virulent Phenotype of a Pseudomonas aeruginosa Isolate in Mammals
J Bacteriol. 2008 Aug 29. [Epub ahead of print]
[45] F. Meyer, D. Paarmann, M. D'Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian , A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, R. A. Edwards
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
BMC Bioinformatics 2008, 9:386.
[44] K.H. Gartemann, B. Abt, T. Bekel, A. Burger A, J. Engemann, M. Flügel, L. Gaigalat, A. Goesmann, I. Gräfe, J. Kalinowski, O. Kaup, O. Kirchner,L. Krause, B. Linke, A. McHardy, F. Meyer, S. Pohle, C. Rückert, S. Schneiker, E. M. Zellerman, A. Pühler, R. Eichenlaub, O. Kaiser, D. Bartels (2008)
The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity.
J Bacteriol. 2008 Jan 11; [Epub ahead of print]
[43] R. K. Aziz, D. Bartels, A. A. Best, M. DeJongh, T. Disz, R. A. Edwards, K. Formsma, S. Gerdes, E. M. Glass, M. Kubal, F. Meyer, G. J. Olsen, R. Olson, A. L. Osterman, R. A. Overbeek, L. K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, O. Zagnitko (2008)
The RAST Server: Rapid Annotations using Subsystems Technology
BMC Genomics, 2008 Feb 8;9(1):75
[42] F. Mela, K. Fritsche, H. Kathrin, J.; van Elsas, D. Bartels, F. Meyer, W. de Boer, J. van Veen, J. Leveau
Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331
FEMS Microbial Ecology, 2008 Oct;66(1):45-62. Epub 2008 Mar 19.
[41] S. M. Sievert, K. M. Scott, M. G. Klotz, P. S. G. Chain, L. J. Hauser, J. Hemp, M. Hüler, M. Land, A. Lapidus, F. W. Larimer, S. Lucas, S. A. Malfatti, F. Meyer, I. T. Paulsen, Q. Ren, J. Simon, and the USF Genomics Class (2008)
The genome of epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans
Applied and Environmental Microbiology, 2008 74: p. 1145-1156
[40] S. Schneiker, O. Perlova, A. Alici, M. O. Altmeyer, D. Bartels, T. Bekel, S. Beyer, H. Blöcker, E. Bode, H. B. Bode, C. Bolten, J. V. Choudhuri, S. Doss, Y. A. Elnakady, B. Frank, L. Gaigalat, K. Gerth, A. Goesmann, C. Groeger, F. Gross, L. Jelsbak, L. Jelsbak, O. Kaiser, J. Kalinowski, C. Kegler, T. Knauber, S. Konietzny, M. Kopp, L. Krause, D. Krug, B. Linke, T. Mahmud, R. Martinez-Arias, A. C. McHardy, M. Merai, F. Meyer, S. Mormann, J. Munoz-Dorado, J. Perez, S. Rachid, G. Raddatz, F. Rosenau, C. Rückert, F. Sasse, M. Scharfe, S. C. Schuster, G. Suen, A. Treuner-Lange, G. J. Velicer, F.-J. Vorhöter, K. J. Weissman, R. D. Welch, S. C. Wenzel, D. Whitworth, S. Wilhelm, C. Wittmann, A. Pühler and Rolf Müller (2007)
Complete sequence of the largest known bacterial genome from the myxobacterium Sorangium cellulosum
Nature Biotechnology, Nov;25(11):1281-9
[39] R. Overbeek, D. Bartels, V. Vonstein and F. Meyer
Annotation of Bacterial and Archaeal Genomes: Improving Accuracy and Consistency
Chemical Reviews, 2007 Aug;107(8):3431-47
[38] F. Meyer
Genome Sequencing vs. Moores Law: Cyber Challenges for the Next Decade
Cyberinfrastructure Technology Watch, 2006
[37] M. Bauer, M. Kube, H. Teeling, M. Richter, T. Lombardot, E. Allers, C. A. Würdemann, C. Quast, H. Kuhl, F. Knaust, D. Woebken, K. Bischof, M. Mussmann, J. V. Choudhuri, F. Meyer, R. Reinhardt, R. I. Amann, F. O. Glöckner
Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter
Environmental Microbiology, 2006 Dec;8(12):2201-13
[36] L. K. McNeil, C. Reich, R. M. Aziz, D. Bartels, M. Cohoon, T. Disz, R. A. Edwards, S. Gerdes, K. Hwang, M. Kubal, G. R. Margaryan, F. Meyer, W. Mihalo, G. J. Olsen, R. Olson, A. Osterman, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, D. A. Rodionov, X. Shi, O. Vassieva, V. Vonstein, O. Zagnitko, F. Xia, J. Zinner, R. Overbeek and R. Stevens
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53
[35] L. Krause, A. C. McHardy, T. Nattkemper, A. Pühler, J. Stoye and F. Meyer
GISMO - Gene Identification using a Support Vector Machine for ORF classification (2007)
Nucleic Acids Res, Nucleic Acids Res. 2007;35(2):540-9
[34] H. Küster, A. Becker, C. Firnhaber, N. Hohnjec, K. Manthey, A. M. Perlick, T. Bekel, M. Dondrup, K. Henckel, A. Goesmann, F. Meyer, D. Wipf, N. Requena, U. Hildebrandt, R. Hampp, U. Nehls, F. Krajinski, P. Franken, A. Pühler (2007)
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses
Phytochemistry, 2007 Jan;68(1):19-32
[33] K. M. Scott, S. Sievert, F. N. Abril, L. A. Ball, C. J. Barrett, R. A. Blake, A. J. Boller, P. S. Chain, J. A. Clark, C. R. Davis, C. Detter, K. F. Do, K. P. Dobrinski, B. I. Faza, K. A. Fitzpatrick, S. K. Freyermuth, T. L. Harmer, L. J. Hauser, C. A. Kerfeld, W. W. Kong, M. Land, A. Lapidus, F. W. Larimer, D. L. Longo, S. Lucas, S. A. Malfatti, S. E. Massey, D. D. Martin, Z. McCuddin, F. Meyer, J. L. Moore, L. H. Ocampo, J. H. Paul, I. T. Paulsen, D. K. Reep, R. L. Ross, P. Y. Sato, P. Thomas, L. E. Tinkham, and G. T. Zeruth
The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2
PLOS Biology, 2006 Nov;4(12):e383
[32] T. Hain, C. Steinweg, C. T. Kuenne, A. Billion, R. Ghai, S. S. Chatterjee, E. Domann, U. Karst, A. Goesmann, T. Bekel, D. Bartels, O. Kaiser, F. Meyer, A. Pühler, B. Weisshaar, J. Wehland, C. Liang, T. Dandekar, R. Lampidis, J. Kreft, W. Goebel and T. Chakraborty (2006)
Whole genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes
J Bacteriol, 2006 Nov;188(21):7405-15.
[31] S. Schneiker, VAP. Martins dos Santos, D. Bartels, T. Bekel, M. Brecht, J. Buhrmester, TN Chernikova, R. Denaro, M. Ferrer, C. Gertler, A. Goesmann, OV. Golyshina, F. Kaminski, AN. Khachane, S. Lang, B. Linke, AC. McHardy, F. Meyer, T. Nechitaylo, A. Pühler, D. Regenhardt, O. Rupp, J. S Sabirova, W. Selbitschka, MM. Yakimov, K. N. Timmis, F.J. Vorhölter, S. Weidner, O. Kaiser, P. N. Golyshin (2006)
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
Nature Biotechnology, Aug;24(8):997-1004
[30] N. Pobigaylo, D. Wetter, S. Szymczak, U. Schiller, S. Kurtz, F. Meyer, T.W. Nattkemper, A. Becker (2006)
Construction of a Large Signature-Tagged Mini-Tn5 Transposon Library and Its Application to Mutagenesis of Sinorhizobium meliloti.
Appl Environ Microbiol 72(6): 4329-4337
[29] H. Küster, A. Becker, C. Firnhaber, N. Hohnjec, K. Manthey, A.M. Perlick, T. Bekel, M. Dondrup, K. Henckel, A. Goesmann, F. Meyer, D. Wipf, N. Requena, U. Hildebrandt, R. Hampp, U. Nehls, F. Krajinski, P. Franken, A. Pühler (2006)
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Phytochemistry, 2007 Jan;68(1):19-32
[28] L.Krause, N. N. Diaz, D. Bartels, R. A. Edwards, A. Pühler, F. Rohwer, F. Meyer, J. Stoye (2006)
Finding novel genes in bacterial communities isolated from the environment
ISMB 2006 (Proc Int Conf Intell Syst Mol Biol) 14 and Bioinformatics 2006 Jul 15;22(14):e281-9
[27] B. Linke, A.C. McHardy, H. Neuweger, L. Krause, F. Meyer (2006)
The REGANOR gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes.
Applied Bioinformatics, 5(3):193-8
[26] F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Büttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, O. Kirchner, C. Lanz, B. Linke, A.C. McHardy, F. Meyer, G. Mittenhuber, D.H. Nies, U. Niesbach-Klösgen, T. Patschkowski, C. Rückert, O. Rupp, S. Schneiker, S.C. Schuster, F.-J. Vorhölter, E. Weber, A. Pühler, U. Bonas, D. Bartels, O. Kaiser (2005)
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Journal of Bacteriology 187(21): 7254-66
[25] R. Overbeek, T. Begley, R.M. Butler, J.V. Choudhuri, N. Diaz, H.-Y. Chuang, M. Cohoon, V. de Crecy-Lagard, T. Disz, R. Edwards, M. Fonstein, E.D. Frank, S. Gerdes, E.M. Glass, A. Goesmann, L. Krause, B. Linke, A.C. McHardy, F. Meyer, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, M. Kubal, N. Larsen, H. Neuweger, C. Rückert, G. Olsen, R. Olson, A. Osterman, V. Portnoy, G.D. Pusch, D.A. Rodionov, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, V. Vonstein (2005)
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Nucleic Acids Res 33(17)
[24]A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, F. Meyer (2005)
BRIGEP - The BRIDGE-based Genome-Transcriptome-Proteome Browser.
Nucleic Acids Res 33: W710-W160
[23] A. Frenzel, K. Manthey, A.M. Perlick, F. Meyer, A. Pühler, H. Küster, F. Krajinski (2005)
Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes.
Mol Plant-Microbe Interact 18( 8): 771-782
[22] A. Tauch, O. Kaiser, T. Hain, A. Goesmann, B. Weisshaar, A. Albersmeier, T. Bekel, N. Bischoff, I. Brune, T. Chakraborty, J. Kalinowski, F. Meyer, O. Rupp, S. Schneiker, P. Viehoever, A. Pühler (2005)
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
J Bacteriol 187(13): 4671-82
[21] D. Bartels, S. Kespohl, S. Albaum, T. Drüke, A. Goesmann, J. Herold, O. Kaiser, A. Pühler, F. Pfeiffer, G. Raddatz, J. Stoye, F. Meyer, S.C. Schuster (2005)
BACCardI -- A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bioinformatics 21(7): 853-9
[20] A.C. McHardy, A. Goesmann, A. Pühler, F. Meyer (2004)
Development of joint application strategies for two microbial gene finders
Bioinformatics 20(10): 1622-31
[19] S. Rendulic, P. Jagtap, A. Rosinus, M. Eppinger, C. Baar, C. Lanz, H. Keller, C. Lambert, K.J. Evans, A. Goesmann, F. Meyer, R.E. Sockett, S.C. Schuster (2004)
A Predator Unmasked: The Lifecycle of Bdellovibrio bacteriovorus from a Genomic Perspective
Science 303: 689-692
[18] H. Küster, N. Hohnjec, F. Krajinski, F. El Yahyaoui, K. Manthey, J. Gouzy, M. Dondrup, F. Meyer, J. Kalinowski, L. Brechenmacher, D. van Tuinen, V. Gianinazzi-Pearson, A. Pühler, P. Gamas, A. Becker (2004)
Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula
Journal of Biotechnology 108(2): 95-113
[17] A.C. McHardy, J. Kalinowski, A. Pühler, F. Meyer (2004)
Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics
Proteomics 4(1): 46-58 (DOI 10.1002/pmic.200300501)
[16] O. Nyamsuren, F. Colditz, S. Rosendahl, M. Tamasloukht, T. Bekel, F. Meyer, H. Küster, P. Franken, F. Krajinski (2003)
Transcriptional profiling of Medicago truncatula roots after infection with Aphanomyces euteiches (oomycota) identifies novel genes upregulated during this pathogenic interaction.
Physiological and Molecular Plant Pathology 63(1): 17-26
[15] M. Dondrup, A. Goesmann, D. Bartels, J. Kalinowski, L. Krause, B. Linke, O. Rupp, A. Sczyrba, A. Pühler, F. Meyer (2003)
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Journal of Biotechnology 106(2-3): 135-46
[14] F.-J. Vorhölter, T. Thias, F. Meyer, T. Bekel, O. Kaiser, A. Pühler, K. Niehaus (2003)
Comparison of two Xanthomonas campestris pathovar campestris genomes revealed differences in their gene composition.
Journal of Biotechnology 106(2-3): 193-202
[13] A. Goesmann, B. Linke, O. Rupp, L. Krause, D. Bartels, M. Dondrup, A.C. McHardy, A. Wilke, A. Pühler, F. Meyer (2003)
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Journal of Biotechnology 106(2-3): 157-67
[12] A. Wilke, C. Rückert, D. Bartels, M. Dondrup, A. Goesmann, A.T. Hüser, S. Kespohl, B. Linke, M. Mahne, A.C. McHardy, A. Pühler, F. Meyer (2003)
Bioinformatics support for high-throughput proteomics.
Journal of Biotechnology 106(2-3): 147-56 -
[11] O. Kaiser, D. Bartels, T. Bekel, A. Goesmann, S. Kespohl, A. Pühler, F. Meyer (2003)
Whole genome shotgun sequencing guided by bioinformatics pipelines-an optimized approach for an established technique.
Journal of Biotechnology 106(2-3): 121-33
[10] S. Rüberg, Z.X. Tian, E. Krol, B. Linke, F. Meyer, Y. Wang, A. Pühler, S. Weidner, A. Becker (2003)
Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.
Journal of Biotechnology 106(2-3): 255-68
[9] C. Baar, M. Eppinger, G. Raddatz, J. Simon, C. Lanz, O. Klimmek, R. Nandakumar, R. Gross, A. Rosinus, H. Keller, P. Jagtap, B. Linke, F. Meyer, H. Lederer, S. Schuster (2003)
Complete genome sequence and analysis of Wolinella succinogenes.
PNAS (Proc Natl Acad Sci U S A) 100(20): 11690-5
[8] J. Kalinowski, B. Bathe, D. Bartels, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B.J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Krömer, B. Linke, A.C. McHardy, F. Meyer, B. Möckel, W. Pfefferle, A. Pühler, D.A. Rey, C. Rückert, O. Rupp, H. Sahm, V.F. Wendisch, I. Wiegräbe, A. Tauch (2003)
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Journal of Biotechnology 104(1-3): 5-25
[7] F. Meyer, A. Goesmann, A.C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, A. Pühler (2003)
GenDB--an open source genome annotation system for prokaryote genomes.
Nucleic Acids Res 31(8): 2187-95
[6] A. Wulf, K. Manthey, J. Doll, A.M. Perlick, B. Linke, T. Bekel, F. Meyer, P. Franken, H. Küster, F. Krajinski (2003)
Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula.
Mol Plant Microbe Interact 16(4): 306-314
[5] A. Tauch, A. Schlüter, N. Bischoff, A. Goesmann, F. Meyer, A. Pühler (2003)
The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family.
Mol Genet Genomics 268(5): 570-84
[4] A. Goesmann, M. Haubrock, F. Meyer, J. Kalinowski, R. Giegerich (2002)
PathFinder: reconstruction and dynamic visualization of metabolic pathways.
Bioinformatics 18(1): 124-9
[3] J. Stoye, D. Evers, F. Meyer (1998)
Rose: generating sequence families.
Bioinformatics 14(2): 157-63
[2]J. Stoye, D. Evers, F. Meyer (1997)
Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions.
ISMB1997 (Proc Int Conf Intell Syst Mol Biol) 5: 303-6
[1] R. Giegerich, F. Meyer, C. Schleiermacher (1996)
GeneFisher--software support for the detection of postulated genes.
ISMB1996 (Proc Int Conf Intell Syst Mol Biol) 4: 68-77