 | Year | | Title | BibTeX cite key | |
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 | Adams, McHardy |
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| 2011 | | The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus
In: Proceedings of the Royal Society / B, Biological Sciences [278], 2249-2256 | Adams2010 | |
| Adams, McHardy, Lundegaard, Lengauer |
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| 2009 | | Viral Bioinformatics
In: Modern Genome Annotation : the Biosapiens Network, 429-452 | Adams2008 | |
| Gartemann, Abt, Bekel, Burger, Engemann, Flügel, Gaigalat, Goesmann, Gräfen, Kalinowski, Kaup, Kirchner, Krause, Linke, McHardy, Meyer, Pohle, Rückert, Schneiker, Zellermann, Pühler, Eichenlaub, Kaiser, Bartels |
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| 2008 | | The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity
In: The Journal of Bacteriology [190], 2138-2149 | Gartemann2008 | |
| Gilbert, Steele, Caporaso, Steinbrück, Reeder, Temperton, Huse, McHardy, Knight, Joint, Somerfield, Fuhrman, Field |
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| 2012 | | Defining seasonal marine microbial community dynamics
In: The ISME Journal [6], 298-308 | MCH2011c | |
| Holland, Albalat, Azumi, Benito-Gutiérrez, Blow, Bronner-Fraser, Brunet, Butts, Candiani, Dishaw, Ferrier, Garcia-Fernàndez, Gibson-Brown, Gissi, Godzik, Hallböök, Hirose, Hosomichi, Ikuta, Inoko, Kasahara, Kasamatsu, Kawashima, Kimura, Kobayashi, Kozmik, Kubokawa, Laudet, Litman, McHardy, Meulemans, Nonaka, Olinski, Pancer, Pennacchio, Pestarino, Rast, Rigoutsos, Robinson-Rechavi, Roch, Saiga, Sasakura, Satake, Satou, Schubert, Sherwood, Shiina, Takatori, Tello, Vopalensky, Wada, Xu, Ye, Yoshida, Yoshizaki, Yu, Zhang, Zmasek, de Jong, Osoegawa, Putnam, Rokhsar, Satoh, Holland |
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| 2008 | | The amphioxus genome illuminates vertebrate origins and cephalochordate biology
In: Genome Research [18], 1100-1111 | Holland2008 | |
| Kalyuzhnaya, Lapidus, Ivanova, Copeland, McHardy, Szeto, Salamov, Grigoriev, Suciu, Levine, Markowitz, Rigoutsos, Tringe, Bruce, Richardson, Lidstrom, Chistoserdova |
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| 2008 | | High-resolution metagenomics targets specific functional types in complex microbial communities
In: Nature Biotechnology [26], 1029-34 | Kalyuzhnaya2008 | |
| Konietzny, Dietz, McHardy |
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| 2011 | | Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141 | KON2011 | |
| Lykidis, Chen, Tringe, McHardy, Copeland, Kyrpides, Hugenholtz, Macarie, Olmos, Monroy, Liu |
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| 2011 | | Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
In: The ISME Journal [5], 122-130 | mchardy2010msi | |
| Mavromatis, Ivanova, Barry, Shapiro, Goltsman, McHardy, Rigoutsos, Salamov, Korzeniewski, Land, Lapidus, Grigoriev, Richardson, Hugenholtz, Kyrpides |
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| 2007 | | Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
In: Nature Methods [4], 495-500 | Mavromatis2007 | |
| McHardy |
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| 2008 | | Finding genes in genome sequence
In: Bioinformatics. - Vol. 1, Data, Sequence Analysis and Evolution, 163-77
In: Methods in Molecular Biology [452], 163-77 | McHardy2008 | |
| McHardy, Adams |
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| 2009 | | The role of genomics in tracking the evolution of influenza A virus
In: PLOS Pathogens [5], e1000566:1-e1000566:6 | McHardy2009x | |
| McHardy, Krause, Nattkemper, Puhler, Stoye, Meyer |
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| 2007 | | GISMO - prokaryotic gene identification using a support vector machine for ORF classification.
In: Nucleic Acids Research [32], 540-549 | McHardy2007c | |
| McHardy, Martin, Tsirigos, Hugenholtz, Rigoutsos |
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| 2007 | | Accurate phylogenetic classification of variable-length DNA fragments.
In: Nature Methods [4], 63-72 | McHardy2007b | |
| McHardy, Patil |
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| 2011 | | Phylogenetic binning of metagenome sequence samples
In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358 | McHardyPatil2011 | |
| 2009 | | Informatik für die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen
In: Tätigkeitsberichte 2009 der Institute, 1-6 | MCHJahrbuch09 | |
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| 2007 | | What's in the mix? Methods for the phylogenetic classification of metagenome sequence samples.
In: Current Opinion in Microbiology [10], 499-503 | McHardy2007a | |
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| 2008 | | Method and system for building a phylogeny from genetic sequences and using the same for recommendation of vaccine strain candidates for the influenza virus | MCHSBPatent09 | |
| Meisinger-Henschel, Schmidt, Lukassen, Linke, Krause, Konietzny, Goesmann, Howley, Chaplin, Suter, Hausmann |
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| 2007 | | Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara
In: Journal of General Virology [88], 3249-3259 | Meisinger-Henschel2007 | |
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| 2008 | | Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10 | Patil2008a | |
| Patil, Haider, Pope, Turnbaugh, Morrison, Scheffer, McHardy |
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| 2011 | | Taxonomic metagenome sequence assignment with structured output models
In: Nature Methods [8], 191-192 | Patil2011 | |
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| 2007 | | A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105 | PatKulk2007 | |
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| 2012 | | The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences
In: PLoS ONE [7], e38581,1-e38581,9 | Patil2012 | |
| Patil, Shelokar, Jayaraman, Kulkarni |
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| 2008 | | Ant Colony Optimization in the Direct Ordering Gene Expression Data
In: Journal of Hybrid Computing Research [1], 10-10 | PSJK2008 | |
| Pope, Denman, Jones, Tringe, Barry, Malfatti, McHardy, Cheng, Hugenholtz, McSweeney, Morrison |
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| 2010 | | Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores
In: Proceedings of the National Academy of Sciences of the United States of America [107], 14793-14798 | mchardy2010aht | |
| Pope, Mackenzie, Gregor, Smith, Sundset, McHardy, Morrison, Eijsink |
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| 2012 | | Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci
In: PLoS ONE [7], e38571,1-e38571,10 | Pope2012 | |
| Pope, Smith, Denman, Tringe, Barry, Hugenholtz, McSweeney, McHardy, Morrison |
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| 2011 | | Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
In: Science [333], 646-648 | MCH2011b | |
| Schneiker, Perlova, Kaiser, Gerth, Alici, Altmeyer, Bartels, Bekel, Beyer, Bode, Bode, Bolten, Choudhuri, Doss, Elnakady, Frank, Gaigalat, Goesmann, Groeger, Gross, Jelsbak, Jelsbak, Kalinowski, Kegler, Knauber, Konietzny, Kopp, Krause, Krug, Linke, Mahmud, Martinez-Arias, McHardy, Merai, Meyer, Mormann, Muñoz-Dorado, Perez, Pradella, Rachid, Raddatz, Rosenau, Rückert, Sasse, Scharfe, Schuster, Suen, Treuner-Lange, Velicer, Vorhölter, Weissman, Welch, Wenzel, Whitworth, Wilhelm, Wittmann, Blöcker, Pühler, Müller |
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| 2007 | | Complete genome sequence of the myxobacterium Sorangium cellulosum.
In: Nature Biotechnology [27], 281-1289 | Schneiker2007 | |
| Schoen, Blom, Claus, Schramm-Glück, Brandt, Müller, Goesmann, Joseph, Konietzny, Kurzai, Schmitt, Friedrich, Linke, Vogel, Frosch |
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| 2008 | | Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis
In: Proceedings of the National Academy of Sciences of the United States of America [105], 3473-3478 | Schoen2008 | |
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| 2012 | | Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
In: PLoS Computational Biology [8], e1002492,1-e1002492,9 | Steinbrueck2012 | |
| 2010 | | Allele dynamics plots for the study of evolutionary dynamics in viral populations
In: Nucleic Acids Research [39], 1-12 | steinbrueck2010adp | |
| Turnbaugh, Quince, Faith, McHardy, Yatsunenko, Niazi, Affourtit, Egholm, Henrissat, Knight, Gordon |
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| 2010 | | Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
In: Proceedings of the National Academy of Sciences of the United States of America [107], 7503-7508 | mchardy2010ogt | |
| Tusche, Steinbrück, McHardy |
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| 2012 | | Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection
In: Molecular Biology and Evolution [29], 2063-2071 | Tusche2012 | |
| Vieira, Cardoso, Pinto, Patil, Brazdil, Cruz, Mascarenhas, Lacerda, Gartner, Almeida, Alves, Porto |
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| 2007 | | 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
In: International Journal of Immunogenetics [34], 359-367 | VCPP2007a | |
| 2007 | | Location of a putative gene contributing to the setting of CD8+T lymphocytes: A modifier of hereditary hemochromatosis expression?
In: American Journal of Hematology [82], 509-509 | VCPP2007 | |
| Warnecke, Luginbühl, Ivanova, Ghassemian, Richardson, Stege, Cayouette, McHardy, Djordjevic, Aboushadi, Sorek, Tringe, Podar, Martin, Kunin, Dalevi, Madejska, Kirton, Platt, Szeto, Salamov, Barry, Mikhailova, Kyrpides, Matson, Ottesen, Zhang, Hernández, Murillo, Acosta, Rigoutsos, Tamayo, Green, Chang, Rubin, Mathur, Robertson, Hugenholtz, Leadbetter |
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| 2007 | | Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
In: Nature [450], 560-565 | Richardson2007 | |
