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#	Y			Author/Editor		Title	Type	Editor(s) [non member]	ISSN / Coden	Year
2	2012
1		Molecular Biology and Evolution
1			Oxford University Press [Oxford]
				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	Journal Article		0737-4038	2012
1		The ISME Journal
1			Nature Publishing Group [Basingstoke]
				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	Journal Article		1751-7362	2012
5	2011
1		BMC Bioinformatics
1			(Not Categorized)
				Konietzny, Sebastian G.A. Dietz, Laura McHardy, Alice		Inferring functional modules of protein families with probabilistic topic models In: BMC Bioinformatics [12], 141	Journal Article			2011
1		Nature Methods
1			Nature Publishing Group [London]
				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	Journal Article		1548-7091	2011
1		Proceedings of the Royal Society / B, Biological Sciences
1			The Royal Society [London]
				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	Journal Article		0950-1193	2011
1		Science
1			AAAS
				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	Journal Article			2011
1		The ISME Journal
1			Nature Publishing Group [London]
				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	Journal Article		1751-7362	2011
2	2010
2		Proceedings of the National Academy of Sciences of the United States of America
2			National Academy of Sciences [Washington, DC]
				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	Journal Article		0027-8424	2010
				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	Journal Article		0027-8424	2010
1	2009
1		PLOS Pathogens
1			Public Library of Science (PLoS) [San Francisco, CA]
				McHardy, Alice Adams, Ben		The role of genomics in tracking the evolution of influenza A virus In: PLOS Pathogens [5], e1000566:1-e1000566:6	Journal Article		1553-7366	2009
6	2008
1		Genome Research
1			Cold Spring Harbour Lab. Press [Cold Spring Harbour, USA]
				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	Journal Article		1088-9051	2008
2		Journal of Hybrid Computing Research
2			(Not Categorized)
				Patil, Kaustubh Akerkar, Rajendra		Tackling Traveling Salesman Problem with Random Key Genetic Algorithm In: Journal of Hybrid Computing Research [1], 10-10	Journal Article			2008
				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	Journal Article		0974-5858	2008
1		Nature Biotechnology
1			Nature American Pub. [New York, USA]
				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	Journal Article		1087-0156	2008
1		Proceedings of the National Academy of Sciences of the United States of America
1			NAS [Washington, DC]
				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	Journal Article		1091-6490	2008
1		The Journal of Bacteriology
1			American Society for Microbiology [Washington, USA]
				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	Journal Article		0021-9193	2008
10	2007
1		American Journal of Hematology
1			(Not Categorized)
				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	Journal Article			2007
1		Biotechnology Progress
1			(Not Categorized)
				Patil, Kaustubh Kulkarni, Abhijit		A simple visualization technique to understand the system dynamics in bioreactors In: Biotechnology Progress [23], 1101-1105	Journal Article			2007
1		Current Opinion in Microbiology
1			Elsevier
				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	Journal Article			2007
1		International Journal of Immunogenetics
1			(Not Categorized)
				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	Journal Article			2007
1		Journal of General Virology
1			(Not Categorized)
				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	Journal Article			2007
1		Nature
1			(Not Categorized)
				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	Journal Article			2007
1		Nature Biotechnology
1			(Not Categorized)
				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	Journal Article			2007
2		Nature Methods
2			(Not Categorized)
				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	Journal Article			2007
				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	Journal Article			2007
1		Nucleic Acids Research
1			(Not Categorized)
				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	Journal Article			2007
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