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MPI-INF IRG1 Publications

MPI-INF IRG1 Publications

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Author/Editor [Non Institute]YearTitleType
Adams, McHardy
[-]
2011The 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
Journal Article
Adams, McHardy, Lundegaard, Lengauer
(Ed: Frishman, Valencia)
[-]
2009Viral Bioinformatics
In: Modern Genome Annotation : the Biosapiens Network, 429-452
Part of a Book
Gartemann, Abt, Bekel, Burger, Engemann, Flügel, Gaigalat, Goesmann, Gräfen, Kalinowski, Kaup, Kirchner, Krause, Linke, McHardy, Meyer, Pohle, Rückert, Schneiker, Zellermann, Pühler, Eichenlaub, Kaiser, Bartels
[-]
2008The 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
Journal Article
Gilbert, Steele, Caporaso, Steinbrück, Reeder, Temperton, Huse, McHardy, Knight, Joint, Somerfield, Fuhrman, Field
[-]
2012Defining seasonal marine microbial community dynamics
In: The ISME Journal [6], 298-308
Journal Article
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
[-]
2008The amphioxus genome illuminates vertebrate origins and cephalochordate biology
In: Genome Research [18], 1100-1111
Journal Article
Kalyuzhnaya, Lapidus, Ivanova, Copeland, McHardy, Szeto, Salamov, Grigoriev, Suciu, Levine, Markowitz, Rigoutsos, Tringe, Bruce, Richardson, Lidstrom, Chistoserdova
[-]
2008High-resolution metagenomics targets specific functional types in complex microbial communities
In: Nature Biotechnology [26], 1029-34
Journal Article
Konietzny, Dietz, McHardy
[-]
2011Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141
Journal Article
Lykidis, Chen, Tringe, McHardy, Copeland, Kyrpides, Hugenholtz, Macarie, Olmos, Monroy, Liu
[-]
2011Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
In: The ISME Journal [5], 122-130
Journal Article
Mavromatis, Ivanova, Barry, Shapiro, Goltsman, McHardy, Rigoutsos, Salamov, Korzeniewski, Land, Lapidus, Grigoriev, Richardson, Hugenholtz, Kyrpides
[-]
2007Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
In: Nature Methods [4], 495-500
Journal Article
McHardy
(Ed: Keith)
[-]
2008Finding genes in genome sequence
In: Bioinformatics. - Vol. 1, Data, Sequence Analysis and Evolution, 163-77
In: Methods in Molecular Biology [452], 163-77
Part of a Book
McHardy, Adams
[-]
2009The role of genomics in tracking the evolution of influenza A virus
In: PLOS Pathogens [5], e1000566:1-e1000566:6
Journal Article
McHardy, Krause, Nattkemper, Puhler, Stoye, Meyer
[-]
2007GISMO - prokaryotic gene identification using a support vector machine for ORF classification.
In: Nucleic Acids Research [32], 540-549
Journal Article
McHardy, Martin, Tsirigos, Hugenholtz, Rigoutsos
[-]
2007Accurate phylogenetic classification of variable-length DNA fragments.
In: Nature Methods [4], 63-72
Journal Article
McHardy, Patil
(Ed: de Bruijn)
[-]
2011Phylogenetic binning of metagenome sequence samples
In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358
Part of a Book
McHardy, Patil
[-]
2009Informatik für die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen
In: Tätigkeitsberichte 2009 der Institute, 1-6
Part of a Book
McHardy, Rigoutsos
[-]
2007What's in the mix? Methods for the phylogenetic classification of metagenome sequence samples.
In: Current Opinion in Microbiology [10], 499-503
Journal Article
McHardy, Steinbrück
[-]
2008Method and system for building a phylogeny from genetic sequences and using the same for recommendation of vaccine strain candidates for the influenza virusMiscellaneous
Meisinger-Henschel, Schmidt, Lukassen, Linke, Krause, Konietzny, Goesmann, Howley, Chaplin, Suter, Hausmann
[-]
2007Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara
In: Journal of General Virology [88], 3249-3259
Journal Article
Patil, Akerkar
[-]
2008Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10
Journal Article
Patil, Haider, Pope, Turnbaugh, Morrison, Scheffer, McHardy
[-]
2011Taxonomic metagenome sequence assignment with structured output models
In: Nature Methods [8], 191-192
Journal Article
Patil, Kulkarni
[-]
2007A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105
Journal Article
Patil, Roune, McHardy
[-]
2012The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences
In: PLoS ONE [7], e38581,1-e38581,9
Electronic Journal Article
Patil, Shelokar, Jayaraman, Kulkarni
[-]
2008Ant Colony Optimization in the Direct Ordering Gene Expression Data
In: Journal of Hybrid Computing Research [1], 10-10
Journal Article
Pope, Denman, Jones, Tringe, Barry, Malfatti, McHardy, Cheng, Hugenholtz, McSweeney, Morrison
[-]
2010Adaptation 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
Journal Article
Pope, Mackenzie, Gregor, Smith, Sundset, McHardy, Morrison, Eijsink
[-]
2012Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci
In: PLoS ONE [7], e38571,1-e38571,10
Electronic Journal Article
Pope, Smith, Denman, Tringe, Barry, Hugenholtz, McSweeney, McHardy, Morrison
[-]
2011Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
In: Science [333], 646-648
Journal Article
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
[-]
2007Complete genome sequence of the myxobacterium Sorangium cellulosum.
In: Nature Biotechnology [27], 281-1289
Journal Article
Schoen, Blom, Claus, Schramm-Glück, Brandt, Müller, Goesmann, Joseph, Konietzny, Kurzai, Schmitt, Friedrich, Linke, Vogel, Frosch
[-]
2008Whole-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
Journal Article
Steinbrück, McHardy
[-]
2012Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
In: PLoS Computational Biology [8], e1002492,1-e1002492,9
Electronic Journal Article
Steinbrück, McHardy
[-]
2010Allele dynamics plots for the study of evolutionary dynamics in viral populations
In: Nucleic Acids Research [39], 1-12
Electronic Journal Article
Turnbaugh, Quince, Faith, McHardy, Yatsunenko, Niazi, Affourtit, Egholm, Henrissat, Knight, Gordon
[-]
2010Organismal, 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
Journal Article
Tusche, Steinbrück, McHardy
[-]
2012Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection
In: Molecular Biology and Evolution [29], 2063-2071
Journal Article
Vieira, Cardoso, Pinto, Patil, Brazdil, Cruz, Mascarenhas, Lacerda, Gartner, Almeida, Alves, Porto
[-]
2007A 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
Journal Article
Vieira, Cardoso, Pinto, Patil, Brazdil, Cruz, Mascarenhas, Lacerda, Gartner, Almeida, Alves, Porto
[-]
2007Location 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
Journal Article
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
[-]
2007Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
In: Nature [450], 560-565
Journal Article

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