Publications

2010

Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS,Morrison M
Adaptation to herbivory by the Tammar Wallaby includes bacterial and glycoside hydrolases profiles different to other herbivores.
Proc Natl Acad Sci U S A, 2010; accepted.
Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.
Proc Natl Acad Sci U S A, 2010; 107:7503-8.

2009

McHardy AC and Adams B
The role of genomics in tracking the evolution of influenza A virus.
PLoS Pathogens 2009, October;5(10): e1000566. doi:10.1371/journal.ppat.1000566

2008

Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L.
High-resolution metagenomics targets specific functional types in complex microbial communities.
Nat Biotechnol. 2008 Sep;26(9):1029-34.
McHardy AC.
Finding genes in genome sequence.
Methods Mol Biol. 2008;452:163-77. Review.
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW.
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Genome Res. 2008 Jul;18(7):1100-11. Epub 2008 Jun 18. Erratum in: Genome Res. 2008 Aug;18(8):1380.
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. Epub 2008 Jan 11.
Schoen C, Blom J, Claus H, Schramm-Glück A, Brandt P, Müller T, Goesmann A, Joseph B, Konietzny S, Kurzai O, Schmitt C, Friedrich T, Linke B, Vogel U, Frosch M.
Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3473-8. Epub 2008 Feb 27.
Patil, Kaustubh, Shelokar P.S., Jayaraman V.K., and Kulkarni B.D.
Ant Colony Optimization in the Direct Ordering Gene Expression Data.
To appear in Journal of Hybrid Computing Research.
B. Adams, A.C. McHardy, C. Lundegaard, T. Lengauer
Viral Bioinformatics
Modern Genome Annotation, D. Frishman, A. Valencia (Editors), Springer Verlag, NY

2007

F. Warnecke, P. Luginbühl, N. Ivanova, M. Ghassemian, T.H. Richardson, J.T. Stege, M. Cayouette, A.C. McHardy, G. Djordjevic, N. Aboushadi, R. Sorek, S.G. Tringe, M. Podar, H.G. Martin, V. Kunin, D. Dalevi, J. Madejska, E. Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N.C. Kyrpides, E.G. Matson, E.A. Ottesen, X. Zhang, M. Hernández, C. Murillo, L.G. Acosta, I. Rigoutsos, G. Tamayo, B.D. Green, C. Chang, E.M. Rubin, E.J. Mathur, D.E. Robertson, P. Hugenholtz, J.R. Leadbetter
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.
Nature 2007, 450(7169):560-565
S. Schneiker,O. Perlova,O. Kaiser,K. Gerth,A. Alici, M.O. Altmeyer, D. Bartels, T. Bekel, S. Beyer, E. Bode, H.B. Bode, C.J. Bolten, J.V. Choudhuri, S. Doss, Y.A. Elnakady, B. Frank, L. Gaigalat, A. Goesmann, C. Groeger, F. Gross, L. Jelsbak,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. Muñoz-Dorado, J. Perez, S. Pradella, 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. Vorhölter, K.J. Weissman, R.D. Welch, S.C. Wenzel, D.E. Whitworth, S. Wilhelm, C. Wittmann, H. Blöcker, A. Pühler,R. Müller
Complete genome sequence of the myxobacterium Sorangium cellulosum.
Nature Biotechnology 2007, 25(11):1281-1289
A.C. McHardy and I. Rigoutsos
What's in the mix? Methods for the phylogenetic classification of metagenome sequence samples.
Current Opinion in Microbiology 2007, 10(5):499-503
K. Mavromatis, N. Ivanova, K. Barry, H. Shapiro, E. Goltsman, A.C. McHardy, I. Rigoutsos, A. Salamov, F. Korzeniewski, M. Land, A. Lapidus, I. Grigoriev, P. Richardson, P. Hugenholtz, N.C. Kyrpides
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
Nature Methods 2007, 4(6):495-500
A.C. McHardy, H.Garcia Martin, A. Tsirigos, P. Hugenholtz, I. Rigoutsos
Accurate phylogenetic classification of variable-length DNA fragments.
Nature Methods 2007, 4(1):63-72
A.C. McHardy*, L. Krause*, J. Stoye, T. Nattkemper, A. Puehler, F. Meyer (*joint first authors)
GISMO -- prokaryotic gene identification using a support vector machine for ORF classification.
Nucleic Acids Research 2007, 35(2):540-9
Meisinger-Henschel C, Schmidt M, Lukassen S, Linke B, Krause L, Konietzny S, Goesmann A, Howley P, Chaplin P, Suter M, Hausmann J.
Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara.
J Gen Virol. 2007 Dec;88(Pt 12):3249-59.
Vieira J, Cardoso CS, Pinto JP, Patil K, Brazdil P, Cruz E, Mascarenhas C, Lacerda R, Gartner A, Almeida S, Alves H and Porto G
A Putative Gene Located at the MHC-CLASS I Region Around the D6S105 Marker Contributes to the Setting of CD8+ T Lymphocyte Numbers in Humans.
Int. J. of Immunogenetics, Volume 34 Issue 5 Page 359-367, October 2007.
J. Vieira, C. S. Cardoso, J. Pinto, K. Patil, P. Brazdil, E. Cruz, C. Mascarenhas, R. Lacerda, A. Gartner, S. Almeida, H. Alves, G. Porto
Location of a putative gene contributing to the setting of CD8+T lymphocytes: A modifier of hereditary hemochromatosis expression?
American Journal of Hematology, 82(6), p. 509-509, June, 2007. (abstract from IBIS 2007)
Patil, Kaustubh and Brazdil, Pavel
SumGraph: Text Summarization using Centrality in the Pathfinder Network.
International Journal on Computer Science and Information Systems, 2(1), 2007, pp. 18--32. Weblink
Patil, Kaustubh and Kulkarni, Abhijit
A simple visualization technique to understand the system dynamics in bioreactors.
Biotechnology Progress, 23(5), pp. 1101-1105, 2007.

2006

A. Krause, A. Ramakumar, D. Bartels, F. Battistoni, T. Bekel, J. Boch, M. Bohm, F. Friedrich, T. Hurek, L. Krause, B. Linke, A.C. McHardy, A. Sarkar, S. Schneiker, A. A. Syed, R. Thauer, F. Vorholter, S. Weidner, Alfred Puhler, B. Reinhold-Hurek, O. Kaiser, A. Goesmann
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
Nature Biotechnology 2006, 24(11):1385-91
H. Garcia Martin, N. Ivanova, V. Kunin, F. Warnecke, K. Barry, A.C. McHardy, C. Yeates, S. He, A. Salamov, E. Szeto, E. Dalin, N. Putnam, I. Rigoutsos, N.C. Kyrpides, L.L. Blackall, K.D. McMahon, P. Hugenholtz
Metagenomic analysis of phosphorus removing sludge communities.
Nature Biotechnology 2006, 24(10):1263-9
S. Schneiker, A.P. dos Santos, D. Bartels, T. Bekel, M. Brecht, J. Buhrmester, T.N. Chernikova, M. Ferrer, C. Gertler, A. Goesmann, O.V. Golyshina, F. Kaminski, A.N. Khachane, S. Lang, B. Linke, A.C. McHardy, F. Meyer, T. Nechitaylo, A. Puhler, D. Regenhardt, O. Rupp, J.S. Sabirova, W. Selbitschka, M.M. Yakimov, K.N. Timmis, F. Vorholter, S. Weidner, O. Kaiser, P.N. Golyshin
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
Nature Biotechnology 2006, 24(8):997-1004
I. Rigoutsos, T. Huynh, K. Miranda, A. Tsirigos, A.C. McHardy, D. Platt
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.
PNAS 2006,103(17):6605-10
A.C. McHardy*, B. Linke*, H. Neuwege, L. Krause, F. Meyer (*joint first authors)
REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes.
Applied Bioinformatics 2006, 5(3):193-8

2005

F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch,D. Buttner,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-Klosgen, T. Patschkowski, C. Ruckert, O. Rupp, S. Schneiker, S.C. Schuster, F.J. Vorholter, E. Weber, A. Puhler, U. Bonas, D. Bartels, O. Kaiser
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Journal of Bacteriology 2005, 187(21):7254-66
R. Overbeek, T. Begley, R.M. Butler, J.V. Choudhuri, H.Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E.D. Frank, S. Gerdes, E.M. Glass,A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M.Kubal, N. Larsen, B. Linke, A.C. McHardy, F. Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman,V. Portnoy, G.D. Pusch, D.A. Rodionov, C. Ruckert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva,Y.Ye,O. Zagnitko, V. Vonstein
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Nucleic Acids Research 2005, 33(17):5691-702

2004

A.C. McHardy, A. Goesmann, A. Puhler, F. Meyer
Development of joint application strategies for two microbial gene finders.
Bioinformatics 2004, 20(10):1622-31
A.C. McHardy, J. Kalinowski, A. Puhler, F. Meyer
Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'.
Proteomics 2004, 4(1):46-58

2003

A. Wilke, C. Ruckert, D. Bartels, M. Dondrup, A. Goesmann, A. Huser, S. Kespohl, B. Linke, M. Mahne, A.C. McHardy, A. Puhler, F. Meyer
Bioinformatics support for high-throughput proteomics.
Journal of Biotechnology 2003, 106(2-3):147-56
A. Goesmann, B. Linke, O. Rupp, L. Krause, D. Bartels, M. Dondrup, A.C.McHardy, A. Wilke, A. Puhler, F. Meyer
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Journal of Biotechnology 2003, 106(2-3):157-67
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. Kramer, B. Linke, A.C. McHardy, F. Meyer, B. Mockel, W. Pfefferle, A. Puhler, D.A. Rey, C. R¨uckert, O. Rupp, H. Sahm, V.F. Wendisch, I. Wiegrabe, A. Tauch
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 2003, 104(1-3):5-25
A.C. McHardy, A. Tauch, C. Ruckert, A. Puhler, J. Kalinowski
Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum.
Journal of Biotechnology 2003, 104(1-3):229-40
F. Meyer, A. Goesmann, A.C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, A. Puhler
GenDB--an open source genome annotation system for prokaryote genomes.
Nucleic Acids Research 2003, 31(8):2187-95