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#	Y		Author/Editor		Title
5	2012
2		Journal Article
			Gilbert, Jack A. Steele, Joshua A. Caporaso, J. Gregory Steinbrück, Lars Reeder, Jens Temperton, Ben Huse, Susan McHardy, Alice C. Knight, Rob Joint, Ian Somerfield, Paul Fuhrman, Jed A. Field, Dawn		Defining seasonal marine microbial community dynamics In: The ISME Journal [6], 298-308
			Tusche, Christina Steinbrück, Lars McHardy, Alice Carolyn		Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection In: Molecular Biology and Evolution [29], 2063-2071
3		Electronic Journal Article
			Patil, Kaustubh Raosaheb Roune, Linus McHardy, Alice Carolyn		The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences In: PLoS ONE [7], e38581,1-e38581,9
			Pope, Phillip B. Mackenzie, Alasdair K. Gregor, Ivan Smith, Wendy Sundset, Monica A. McHardy, Alice C. Morrison, Mark Eijsink, Vincent G.H.		Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci In: PLoS ONE [7], e38571,1-e38571,10
			Steinbrück, Lars McHardy, Alice Carolyn		Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses In: PLoS Computational Biology [8], e1002492,1-e1002492,9
6	2011
1		Part of a Book
			McHardy, Alice Patil, Kaustubh R.		Phylogenetic binning of metagenome sequence samples In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358
5		Journal Article
			Adams, Ben McHardy, Alice		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
			Konietzny, Sebastian G.A. Dietz, Laura McHardy, Alice		Inferring functional modules of protein families with probabilistic topic models In: BMC Bioinformatics [12], 141
			Lykidis, Athanasios Chen, Chia-Lung Tringe, Susannah G. McHardy, Alice Copeland, Alex Kyrpides, Nikos C. Hugenholtz, Philip Macarie, Hervé Olmos, Alejandro Monroy, Oscar Liu, Wen-Tso		Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium In: The ISME Journal [5], 122-130
			Patil, Kaustubh R. Haider, Peter Pope, Philip B. Turnbaugh, Peter J. Morrison, Mark Scheffer, Tobias McHardy, Alice		Taxonomic metagenome sequence assignment with structured output models In: Nature Methods [8], 191-192
			Pope, P. B. Smith, W. Denman, S. E. Tringe, S. G. Barry, K. Hugenholtz, P. McSweeney, C. S. McHardy, Alice Morrison, M.		Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies In: Science [333], 646-648
3	2010
2		Journal Article
			Pope, P. B. Denman, S. E. Jones, M. Tringe, S. G. Barry, K. Malfatti, S. A. McHardy, Alice Cheng, J.-F. Hugenholtz, P. McSweeney, C. S. Morrison, M.		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
			Turnbaugh, Peter J. Quince, Christopher Faith, Jeremiah J. McHardy, Alice Yatsunenko, Tanya Niazi, Faheem Affourtit, Jason Egholm, Michael Henrissat, Bernhard Knight, Rob Gordon, Jeffrey I.		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
1		Electronic Journal Article
			Steinbrück, Lars McHardy, Alice		Allele dynamics plots for the study of evolutionary dynamics in viral populations In: Nucleic Acids Research [39], 1-12
3	2009
2		Part of a Book
			Adams, Ben McHardy, Alice Lundegaard, C. Lengauer, Thomas		Viral Bioinformatics In: Modern Genome Annotation : the Biosapiens Network, 429-452
			McHardy, Alice Patil, Kaustubh		Informatik für die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen In: Tätigkeitsberichte 2009 der Institute, 1-6
1		Journal Article
			McHardy, Alice Adams, Ben		The role of genomics in tracking the evolution of influenza A virus In: PLOS Pathogens [5], e1000566:1-e1000566:6
8	2008
1		Part of a Book
			McHardy, Alice		Finding genes in genome sequence In: Bioinformatics. - Vol. 1, Data, Sequence Analysis and Evolution, 163-77 In: Methods in Molecular Biology [452], 163-77
6		Journal Article
			Gartemann, K. H. 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, Alice Meyer, F. Pohle, S. Rückert, C. Schneiker, S. Zellermann, E. M. 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 In: The Journal of Bacteriology [190], 2138-2149
			Holland, L. Z. Albalat, R. Azumi, K. Benito-Gutiérrez, E. Blow, M. J. Bronner-Fraser, M. Brunet, F. Butts, T. Candiani, S. Dishaw, L. J. Ferrier, D. E. Garcia-Fernàndez, J. Gibson-Brown, J. J. 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, G. W. McHardy, Alice Meulemans, D. Nonaka, M. Olinski, R. P. Pancer, Z. Pennacchio, L. A. Pestarino, M. Rast, J. P. 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, J. K. Zhang, Q. Zmasek, C. M. de Jong, P. J. Osoegawa, K. Putnam, N. H. Rokhsar, D. S. Satoh, N. Holland, P. W.		The amphioxus genome illuminates vertebrate origins and cephalochordate biology In: Genome Research [18], 1100-1111
			Kalyuzhnaya, M. G. Lapidus, A. Ivanova, N. Copeland, A. C. McHardy, Alice Szeto, E. Salamov, A. Grigoriev, I. V. Suciu, D. Levine, S. R. Markowitz, V. M. Rigoutsos, I. Tringe, S. G. Bruce, D. C. Richardson, P. M. Lidstrom, M. E. Chistoserdova, L.		High-resolution metagenomics targets specific functional types in complex microbial communities In: Nature Biotechnology [26], 1029-34
			Patil, Kaustubh Akerkar, Rajendra		Tackling Traveling Salesman Problem with Random Key Genetic Algorithm In: Journal of Hybrid Computing Research [1], 10-10
			Patil, Kaustubh Shelokar, P. S. Jayaraman, V. K. Kulkarni, B. D.		Ant Colony Optimization in the Direct Ordering Gene Expression Data In: Journal of Hybrid Computing Research [1], 10-10
			Schoen, Christoph Blom, Jochen Claus, Heike Schramm-Glück, Anja Brandt, Petra Müller, Tobias Goesmann, Alexander Joseph, Biju Konietzny, Sebastian Kurzai, Oliver Schmitt, Corinna Friedrich, Torben Linke, Burkhard Vogel, Ulrich Frosch, Matthias		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
1		Miscellaneous
			McHardy, Alice Steinbrück, Lars		Method and system for building a phylogeny from genetic sequences and using the same for recommendation of vaccine strain candidates for the influenza virus
10	2007
10		Journal Article
			Mavromatis, K. Ivanova, N. Barry, K. Shapiro, H. Goltsman, E. McHardy, Alice Rigoutsos, I. Salamov, A. Korzeniewski, F. Land, M. Lapidus, A. Grigoriev, I. Richardson, P. Hugenholtz, P. Kyrpides, N. C.		Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. In: Nature Methods [4], 495-500
			McHardy, Alice Krause, L. Nattkemper, T. W. Puhler, A. Stoye, J. Meyer, F.		GISMO - prokaryotic gene identification using a support vector machine for ORF classification. In: Nucleic Acids Research [32], 540-549
			McHardy, Alice Martin, H. G. Tsirigos, A. Hugenholtz, P. Rigoutsos, I.		Accurate phylogenetic classification of variable-length DNA fragments. In: Nature Methods [4], 63-72
			McHardy, Alice Rigoutsos, I.		What's in the mix? Methods for the phylogenetic classification of metagenome sequence samples. In: Current Opinion in Microbiology [10], 499-503
			Meisinger-Henschel, Christine Schmidt, Michaela Lukassen, Susanne Linke, Burkhard Krause, Lutz Konietzny, Sebastian Goesmann, Alexander Howley, Paul Chaplin, Paul Suter, Mark Hausmann, Jürgen		Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara In: Journal of General Virology [88], 3249-3259
			Patil, Kaustubh Kulkarni, Abhijit		A simple visualization technique to understand the system dynamics in bioreactors In: Biotechnology Progress [23], 1101-1105
			Schneiker, Susanne Perlova, Olena Kaiser, Olaf Gerth, Klaus Alici, Aysel Altmeyer, Matthias Bartels, Daniela Bekel, Thomas Beyer, Stefan Bode, Edna Bode, Helge Bolten, Christoph Choudhuri, Jomuna Doss, Sabrina Elnakady, Yasser Frank, Bettina Gaigalat, Lars Goesmann, Alexander Groeger, Carolin Gross, Frank Jelsbak, Lars Jelsbak, Lotte Kalinowski, Jörn Kegler, Carsten Knauber, Tina Konietzny, Sebastian Kopp, Maren Krause, Lutz Krug, Daniel Linke, Bukhard Mahmud, Taifo Martinez-Arias, Rosa McHardy, Alice Merai, Michelle Meyer, Folker Mormann, Sascha Muñoz-Dorado, Jose Perez, Juana Pradella, Silke Rachid, Shwan Raddatz, Günter Rosenau, Frank Rückert, Christian Sasse, Florenz Scharfe, Maren Schuster, Stephan C. Suen, Garret Treuner-Lange, Anke Velicer, Gregory Vorhölter, Frank-Jörg Weissman, Kira J. Welch, Roy D. Wenzel, Silke C. Whitworth, David E. Wilhelm, Susanne Wittmann, Christoph Blöcker, Helmut Pühler, Alfred Müller, Rolf		Complete genome sequence of the myxobacterium Sorangium cellulosum. In: Nature Biotechnology [27], 281-1289
			Vieira, J Cardoso, CS Pinto, JP Patil, Kaustubh Brazdil, P Cruz, E Mascarenhas, C Lacerda, R Gartner, A Almeida, S Alves, H 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 In: International Journal of Immunogenetics [34], 359-367
			Vieira, J Cardoso, CS Pinto, JP Patil, Kaustubh Brazdil, P Cruz, E Mascarenhas, C Lacerda, R Gartner, A Almeida, S Alves, H Porto, G		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
			Warnecke, F. Luginbühl, P. Ivanova, N. Ghassemian, M. Richardson, T. H. Stege, J. T. Cayouette, M. McHardy, Alice Djordjevic, G. Aboushadi, N. Sorek, R. Tringe, S. G. Podar, M. Martin, H. G. Kunin, V. Dalevi, D. Madejska, J. Kirton, E. Platt, D. Szeto, E. Salamov, A. Barry, K. Mikhailova, N. Kyrpides, N. C. Matson, E. G. Ottesen, E. A. Zhang, X. Hernández, M. Murillo, C. Acosta, L. G. Rigoutsos, I. Tamayo, G. Green, B. D. Chang, C. Rubin, E. M. Mathur, E. J. Robertson, D. E. Hugenholtz, P. Leadbetter, J. R.		Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite In: Nature [450], 560-565
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