Folker Meyer's homepage

Folker Meyer is a computational biologist at Argonne National Laboratory and a senior fellow at the Computation Institute at the University of Chicago. He is also associate division director of the Institute of Genomics and Systems Biology.

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.

Short CV

2008 -- Associate Director, Institute for Genomics and System Biology, Argonne National Laboratory

2006 -- Scientist, Mathematics and Commputer Sciene Department, and senior fellow,Computation Institute, University of Chicago

2001 -- 2006 Executive Director, Bioinformatics Resource Facility, Bielefeld University, Germany

2002 -- PhD thesis in Dept. of Computer Science and Dept. of Biology at Bielefeld University

1999-2006 -- Designed, implemented and ran 500+ CPU high-performance bioinformatics computing facility at Bielefeld University

1996-2006 -- Started and ran applied Bioinformatics group, initially at the Department of Biology the group later moved to the Center for Biotechnology

1996 -- Diploma thesis (Master's equiv.) in Computer Science at Bielefeld University

Publications:

[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
[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. Vorhö¶lter, 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. Grä¤fe, J. Kalinowski, O. Kaup, O. Kirchner,L. Krause, B. Linke, A. McHardy, F. Meyer, S. Pohle, C. Rückert, S. Schneiker, E. M. Zellerman, A. Pü¼hler, 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 Microbiology Ecology, in print
[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 Crécy-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. Krämer, 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

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Last modified: April 06, 2009

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