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Folker Meyer

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentMedicine
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    Dr. Meyer builds research software to study microbial communities.

    His research interests include microbial ecology, distributed high performance computing and big data. He leads the MG-RAST project, providing what is currently the most widely used metagenomics and metatranscriptomics analysis platform which has been used to analyze over 130,000 data sets (as of 2014).

    In the past he has worked on the GenDB and RAST projects. He is a board member of the Genomics Standards Consortium and a founding member of the Earth Microbiome Project (EMP).

    His publication list can be found here: http://scholar.google.com/citations?user=XIs02Q4AAAAJ&hl=en


    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Paczian T, Trimble WL, Gerlach W, Harrison T, Wilke A, Meyer F. The MG-RAST API explorer: an on-ramp for RESTful query composition. BMC Bioinformatics. 2019 Nov 08; 20(1):561. PMID: 31703549.
      View in: PubMed
    2. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science. 2019 05 03; 364(6439):446. PMID: 31048484.
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    3. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Toward unrestricted use of public genomic data. Science. 2019 01 25; 363(6425):350-352. PMID: 30679363.
      View in: PubMed
    4. Chaterji S, Koo J, Li N, Meyer F, Grama A, Bagchi S. Federation in genomics pipelines: techniques and challenges. Brief Bioinform. 2019 01 18; 20(1):235-244. PMID: 28968781.
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    5. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol. 2018 07 06; 36(7):566-569. PMID: 29979655.
      View in: PubMed
    6. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 07 06; 36(7):660. PMID: 29979671.
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    7. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 02 06; 36(2):196. PMID: 29406516.
      View in: PubMed
    8. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017 Aug 08; 35(8):725-731. PMID: 28787424.
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    9. Howe A, Yang F, Williams RJ, Meyer F, Hofmockel KS. Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil. PLoS One. 2016; 11(11):e0166578. PMID: 27855202.
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    10. O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol. 2016 06; 18(6):2039-51. PMID: 26914164.
      View in: PubMed
    11. Keegan KP, Glass EM, Meyer F. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. Methods Mol Biol. 2016; 1399:207-33. PMID: 26791506.
      View in: PubMed
    12. Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, Paczian T, Trimble WL, Bagchi S, Grama A, Chaterji S, Meyer F. The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Res. 2016 Jan 04; 44(D1):D590-4. PMID: 26656948.
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    13. Howe A, Ringus DL, Williams RJ, Choo ZN, Greenwald SM, Owens SM, Coleman ML, Meyer F, Chang EB. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. ISME J. 2016 May; 10(5):1217-27. PMID: 26473721.
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    14. Xue H, Cordero OX, Camas FM, Trimble W, Meyer F, Guglielmini J, Rocha EP, Polz MF. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations. mBio. 2015 May 05; 6(3):e00552-15. PMID: 25944863.
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    15. Wilke A, Bischof J, Harrison T, Brettin T, D'Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F. A RESTful API for accessing microbial community data for MG-RAST. PLoS Comput Biol. 2015 Jan; 11(1):e1004008. PMID: 25569221.
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    16. Bischof J, Harrison T, Paczian T, Glass E, Wilke A, Meyer F. Metazen - metadata capture for metagenomes. Stand Genomic Sci. 2014; 9:18. PMID: 25780508.
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    17. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 2014 Aug; 12(8):e1001920. PMID: 25093819.
      View in: PubMed
    18. Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonopoulos D, Kemner KM, Meyer F. The complete genome sequence for putative H2- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol. 2014 Nov; 16(11):3443-62. PMID: 24628880.
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    19. Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch PR, Leong JA, Meyer C, Obst M, Planes S, Scholin C, Vogler AP, Gates RD, Toonen R, Berteaux-Lecellier V, Barbier M, Barker K, Bertilsson S, Bicak M, Bietz MJ, Bobe J, Bodrossy L, Borja A, Coddington J, Fuhrman J, Gerdts G, Gillespie R, Goodwin K, Hanson PC, Hero JM, Hoekman D, Jansson J, Jeanthon C, Kao R, Klindworth A, Knight R, Kottmann R, Koo MS, Kotoulas G, Lowe AJ, Marteinsson VT, Meyer F, Morrison N, Myrold DD, Pafilis E, Parker S, Parnell JJ, Polymenakou PN, Ratnasingham S, Roderick GK, Rodriguez-Ezpeleta N, Schonrogge K, Simon N, Valette-Silver NJ, Springer YP, Stone GN, Stones-Havas S, Sansone SA, Thibault KM, Wecker P, Wichels A, Wooley JC, Yahara T, Zingone A. The founding charter of the Genomic Observatories Network. Gigascience. 2014 Mar 07; 3(1):2. PMID: 24606731.
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    20. Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G. Genomic standards consortium projects. Stand Genomic Sci. 2014 Jun 15; 9(3):599-601. PMID: 25197446.
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    21. Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2014 Jan; 8(1):1-3. PMID: 24152717.
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    22. Williams D, Trimble WL, Shilts M, Meyer F, Ochman H. Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics. 2013 Aug 08; 14:537. PMID: 23924250.
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    23. Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, Chang EB, Meyer F, Antonopoulos DA. Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome. 2013 Jul 10; 1(1):20. PMID: 24450928.
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    24. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 2013 Mar 04; 1(1):9. PMID: 24451366.
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    25. Wilke A, Glass EM, Bartels D, Bischof J, Braithwaite D, D'Souza M, Gerlach W, Harrison T, Keegan K, Matthews H, Kottmann R, Paczian T, Tang W, Trimble WL, Yilmaz P, Wilkening J, Desai N, Meyer F. A metagenomics portal for a democratized sequencing world. Methods Enzymol. 2013; 531:487-523. PMID: 24060134.
      View in: PubMed
    26. Trimble WL, Phung le T, Meyer F, Gilbert JA, Silver S. Draft genome sequence of Agrobacterium albertimagni strain AOL15. J Bacteriol. 2012 Dec; 194(24):6986-7. PMID: 23209236.
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    27. Trimble WL, Phung le T, Meyer F, Silver S, Gilbert JA. Draft genome sequence of Achromobacter piechaudii strain HLE. J Bacteriol. 2012 Nov; 194(22):6355. PMID: 23105084.
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    28. Phung le T, Trimble WL, Meyer F, Gilbert JA, Silver S. Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071). J Bacteriol. 2012 Sep; 194(18):5153. PMID: 22933773.
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    29. Olivas AD, Shogan BD, Valuckaite V, Zaborin A, Belogortseva N, Musch M, Meyer F, Trimble WL, An G, Gilbert J, Zaborina O, Alverdy JC. Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak. PLoS One. 2012; 7(8):e44326. PMID: 22952955.
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    30. Trimble WL, Keegan KP, D'Souza M, Wilke A, Wilkening J, Gilbert J, Meyer F. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics. 2012 Jul 28; 13:183. PMID: 22839106.
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    31. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2012 Jul 12; 1(1):7. PMID: 23587224.
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    32. Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics. 2012 Jun 21; 13:141. PMID: 22720753.
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    33. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012 Jun 07; 30(6):513-20. PMID: 22678395.
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    34. Keegan KP, Trimble WL, Wilkening J, Wilke A, Harrison T, D'Souza M, Meyer F. A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol. 2012; 8(6):e1002541. PMID: 22685393.
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    35. Gilbert JA, Bao Y, Wang H, Sansone SA, Edmunds SC, Morrison N, Meyer F, Schriml LM, Davies N, Sterk P, Wilkening J, Garrity GM, Field D, Robbins R, Smith DP, Mizrachi I, Moreau C. Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. Stand Genomic Sci. 2012 May 25; 6(2):276-86. PMID: 22768370.
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    36. Gilbert JA, Catlett C, Desai N, Knight R, White O, Robbins R, Sankaran R, Sansone SA, Field D, Meyer F. Conceptualizing a Genomics Software Institute (GSI). Stand Genomic Sci. 2012 Mar 19; 6(1):136-44. PMID: 22675605.
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    37. Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp. 2012 Feb 09; 2(1):3. PMID: 22587947.
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    38. Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P, Vogel TM. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. 2012 Sep; 6(9):1677-87. PMID: 22297556.
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    39. Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F. From genomics to metagenomics. Curr Opin Biotechnol. 2012 Feb; 23(1):72-6. PMID: 22227326.
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    40. Meyer F, Trimble WL, Chang EB, Handley KM. Functional predictions from inference and observation in sequence-based inflammatory bowel disease research. Genome Biol. 2012; 13(9):169. PMID: 23013527.
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    41. O'Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, Meyer F. Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010. Stand Genomic Sci. 2011 Nov 30; 5(2):198-202. PMID: 22180822.
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    42. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J. The Genomic Standards Consortium. PLoS Biol. 2011 Jun; 9(6):e1001088. PMID: 21713030.
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    43. Larsen PE, Collart FR, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA. Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microb Inform Exp. 2011 Jun 14; 1(1):4. PMID: 22587810.
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    44. Lemke S, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U. BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae). BMC Genomics. 2011 May 31; 12:278. PMID: 21627820.
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    45. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 May; 29(5):415-20. PMID: 21552244.
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    46. Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Stand Genomic Sci. 2011 Apr 29; 4(2):252-6. PMID: 21677862.
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    47. Henry CS, Overbeek R, Xia F, Best AA, Glass E, Gilbert J, Larsen P, Edwards R, Disz T, Meyer F, Vonstein V, Dejongh M, Bartels D, Desai N, D'Souza M, Devoid S, Keegan KP, Olson R, Wilke A, Wilkening J, Stevens RL. Connecting genotype to phenotype in the era of high-throughput sequencing. Biochim Biophys Acta. 2011 Oct; 1810(10):967-77. PMID: 21421023.
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    48. Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S21. PMID: 21342551.
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    49. Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottmann R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O, Wooley J. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. Stand Genomic Sci. 2010 Dec 25; 3(3):225-31. PMID: 21304723.
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    50. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO, Klenk HP, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R. The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010 Dec 25; 3(3):249-53. PMID: 21304728.
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    51. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010 Dec 25; 3(3):243-8. PMID: 21304727.
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    52. 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, WA, USA August 22-27, 2010. Stand Genomic Sci. 2010 Dec 15; 3(3):235-9. PMID: 21304725.
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    53. Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O. Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010. Stand Genomic Sci. 2010 Dec 04; 3(3):232-4. PMID: 21304724.
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    54. Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A. Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci. 2010 Dec 04; 3(3):254-8. PMID: 21304729.
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    55. Davidsen T, Madupu R, Sterk P, Field D, Garrity G, Gilbert J, Glöckner FO, Hirschman L, Kolker E, Kottmann R, Kyrpides N, Meyer F, Morrison N, Schriml L, Tatusova T, Wooley J. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9. Stand Genomic Sci. 2010 Dec 04; 3(3):216-24. PMID: 21304722.
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    56. Gilbert JA, Meyer F, Bailey MJ. The future of microbial metagenomics (or is ignorance bliss?). ISME J. 2011 May; 5(5):777-9. PMID: 21107444.
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    57. Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM. Metagenomics: A foundling finds its feet. Stand Genomic Sci. 2010 Oct 27; 3(2):212-3. PMID: 21304751.
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    58. Gilbert JA, Meyer F, Schriml L, Joint IR, Mühling M, Field D. Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Stand Genomic Sci. 2010 Oct 27; 3(2):183-93. PMID: 21304748.
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    59. Wang Y, Antonopoulos DA, Zhu X, Harrell L, Hanan I, Alverdy JC, Meyer F, Musch MW, Young VB, Chang EB. Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol. 2010 Dec; 88(6):1333-42. PMID: 20931185.
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    60. Hather GJ, Haynes W, Higdon R, Kolker N, Stewart EA, Arzberger P, Chain P, Field D, Franza BR, Lin B, Meyer F, Ozdemir V, Smith CV, van Belle G, Wooley J, Kolker E. The United States of America and scientific research. PLoS One. 2010 Aug 16; 5(8):e12203. PMID: 20808949.
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    61. Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P. Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci. 2010 Jun 15; 2(3):357-60. PMID: 21304719.
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    62. Pfister CA, Meyer F, Antonopoulos DA. Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One. 2010 May 06; 5(5):e10518. PMID: 20463896.
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    63. Lemke S, Busch SE, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U. Maternal activation of gap genes in the hover fly Episyrphus. Development. 2010 May; 137(10):1709-19. PMID: 20430746.
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    64. Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010 Jan; 2010(1):pdb.prot5368. PMID: 20150127.
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    65. Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009 Dec; 5(12):e1000593. PMID: 20011103.
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    66. Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009 Nov; 37(20):6643-54. PMID: 19762480.
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    67. Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A. 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. J Biotechnol. 2009 Mar 10; 140(1-2):3-12. PMID: 19297685.
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    68. Gross R, Guzman CA, Sebaihia M, dos Santos VA, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Rückert C, Schneiker-Bekel S, Schulze K, Vorhölter FJ, Yevsa T, Engle JT, Goldman WE, Pühler A, Göbel UB, Goesmann A, Blöcker H, Kaiser O, Martinez-Arias R. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics. 2008 Sep 30; 9:449. PMID: 18826580.
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    69. Battle SE, Meyer F, Rello J, Kung VL, Hauser AR. Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals. J Bacteriol. 2008 Nov; 190(21):7130-40. PMID: 18757543.
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    70. Mela F, Fritsche K, Boersma H, van Elsas JD, Bartels D, Meyer F, de Boer W, van Veen JA, Leveau JH. Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol. 2008 Oct; 66(1):45-62. PMID: 18355297.
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    71. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008 Feb 08; 9:75. PMID: 18261238.
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    72. Gartemann KH, Abt B, Bekel T, Burger A, Engemann J, Flügel M, Gaigalat L, Goesmann A, Gräfen I, Kalinowski J, Kaup O, Kirchner O, Krause L, Linke B, McHardy A, Meyer F, Pohle S, Rückert C, Schneiker S, Zellermann EM, Pühler A, Eichenlaub R, Kaiser O, Bartels D. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. J Bacteriol. 2008 Mar; 190(6):2138-49. PMID: 18192381.
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    73. Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol. 2008 Feb; 74(4):1145-56. PMID: 18065616.
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    74. Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol. 2007 Nov; 25(11):1281-9. PMID: 17965706.
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    75. Overbeek R, Bartels D, Vonstein V, Meyer F. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev. 2007 Aug; 107(8):3431-47. PMID: 17658903.
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    76. Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F. GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Res. 2007; 35(2):540-9. PMID: 17175534.
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    77. Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Würdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann RI, Glöckner FO. Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol. 2006 Dec; 8(12):2201-13. PMID: 17107561.
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    78. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan; 35(Database issue):D347-53. PMID: 17145713.
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    79. Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hügler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT. The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol. 2006 Nov; 4(12):e383. PMID: 17105352.
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    80. Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Kärst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Pühler A, Weisshaar B, Wehland J, Liang C, Dandekar T, Lampidis R, Kreft J, Goebel W, Chakraborty T. 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. PMID: 16936040.
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    81. Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol. 2006 Aug; 24(8):997-1004. PMID: 16878126.
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    82. Krause L, Diaz NN, Bartels D, Edwards RA, Pühler A, Rohwer F, Meyer F, Stoye J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics. 2006 Jul 15; 22(14):e281-9. PMID: 16873483.
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    83. Pobigaylo N, Wetter D, Szymczak S, Schiller U, Kurtz S, Meyer F, Nattkemper TW, Becker A. Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. Appl Environ Microbiol. 2006 Jun; 72(6):4329-37. PMID: 16751548.
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    84. Linke B, McHardy AC, Neuweger H, Krause L, Meyer F. REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Appl Bioinformatics. 2006; 5(3):193-8. PMID: 16922601.
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    85. Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol. 2005 Nov; 187(21):7254-66. PMID: 16237009.
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    86. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33(17):5691-702. PMID: 16214803.
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    87. Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Pühler A. Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J Bacteriol. 2005 Jul; 187(13):4671-82. PMID: 15968079.
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    88. Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC. BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics. 2005 Apr 01; 21(7):853-9. PMID: 15514001.
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    89. Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ, Goesmann A, Meyer F, Sockett RE, Schuster SC. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004 Jan 30; 303(5658):689-92. PMID: 14752164.
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    90. Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F. EMMA: a platform for consistent storage and efficient analysis of microarray data. J Biotechnol. 2003 Dec 19; 106(2-3):135-46. PMID: 14651856.
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    91. Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F. Bioinformatics support for high-throughput proteomics. J Biotechnol. 2003 Dec 19; 106(2-3):147-56. PMID: 14651857.
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    92. Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. J Biotechnol. 2003 Dec 19; 106(2-3):157-67. PMID: 14651858.
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    93. Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F. Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique. J Biotechnol. 2003 Dec 19; 106(2-3):121-33. PMID: 14651855.
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    94. Baar C, Eppinger M, Raddatz G, Simon J, Lanz C, Klimmek O, Nandakumar R, Gross R, Rosinus A, Keller H, Jagtap P, Linke B, Meyer F, Lederer H, Schuster SC. Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20):11690-5. PMID: 14500908.
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    95. Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Krämer R, Linke B, McHardy AC, Meyer F, Möckel B, Pfefferle W, Pühler A, Rey DA, Rückert C, Rupp O, Sahm H, Wendisch VF, Wiegräbe I, Tauch A. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol. 2003 Sep 04; 104(1-3):5-25. PMID: 12948626.
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    96. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003 Apr 15; 31(8):2187-95. PMID: 12682369.
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    97. Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics. 2002 Jan; 18(1):124-9. PMID: 11836220.
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    98. Conrad KM, Lavender SA, Reichelt PA, Meyer FT. Initiating an ergonomic analysis. A process for jobs with highly variable tasks. AAOHN J. 2000 Sep; 48(9):423-9. PMID: 11760289.
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    99. Lavender SA, Conrad KM, Reichelt PA, Johnson PW, Meyer FT. Biomechanical analyses of paramedics simulating frequently performed strenuous work tasks. Appl Ergon. 2000 Apr; 31(2):167-77. PMID: 10711979.
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    100. Lavender SA, Conrad KM, Reichelt PA, Meyer FT, Johnson PW. Postural analysis of paramedics simulating frequently performed strenuous work tasks. Appl Ergon. 2000 Feb; 31(1):45-57. PMID: 10709751.
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