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| BibTeX cite key | Author/Editor | Year | Title | Type | |
|---|---|---|---|---|---|
| Holland2008 | 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. | 2008 | The amphioxus genome illuminates vertebrate origins and cephalochordate biology In: Genome Research [18], 1100-1111 | Journal Article | |
| Kalyuzhnaya2008 | 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. | 2008 | High-resolution metagenomics targets specific functional types in complex microbial communities In: Nature Biotechnology [26], 1029-34 | Journal Article | |
| KON2011 | Konietzny, Sebastian G.A. Dietz, Laura McHardy, Alice | 2011 | Inferring functional modules of protein families with probabilistic topic models In: BMC Bioinformatics [12], 141 | Journal Article | |
| Mavromatis2007 | 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. | 2007 | Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. In: Nature Methods [4], 495-500 | Journal Article | |
| MCH2011b | Pope, P. B. Smith, W. Denman, S. E. Tringe, S. G. Barry, K. Hugenholtz, P. McSweeney, C. S. McHardy, Alice Morrison, M. | 2011 | Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies In: Science [333], 646-648 | Journal Article | |
| MCH2011c | 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 | 2012 | Defining seasonal marine microbial community dynamics In: The ISME Journal [6], 298-308 | Journal Article | |
| McHardy2007a | McHardy, Alice Rigoutsos, I. | 2007 | What's in the mix? Methods for the phylogenetic classification of metagenome sequence samples. In: Current Opinion in Microbiology [10], 499-503 | Journal Article | |
| McHardy2007b | McHardy, Alice Martin, H. G. Tsirigos, A. Hugenholtz, P. Rigoutsos, I. | 2007 | Accurate phylogenetic classification of variable-length DNA fragments. In: Nature Methods [4], 63-72 | Journal Article | |
| McHardy2007c | McHardy, Alice Krause, L. Nattkemper, T. W. Puhler, A. Stoye, J. Meyer, F. | 2007 | GISMO - prokaryotic gene identification using a support vector machine for ORF classification. In: Nucleic Acids Research [32], 540-549 | Journal Article | |
| McHardy2008 | McHardy, Alice | 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 | Part of a Book | |
| McHardy2009x | McHardy, Alice Adams, Ben | 2009 | The role of genomics in tracking the evolution of influenza A virus In: PLOS Pathogens [5], e1000566:1-e1000566:6 | Journal Article | |
| mchardy2010aht | 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. | 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 | Journal Article | |
| mchardy2010msi | 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 | 2011 | Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium In: The ISME Journal [5], 122-130 | Journal Article | |
| mchardy2010ogt | 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. | 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 | Journal Article | |
| McHardyPatil2011 | McHardy, Alice Patil, Kaustubh R. | 2011 | Phylogenetic binning of metagenome sequence samples In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358 | Part of a Book | |
| MCHJahrbuch09 | McHardy, Alice Patil, Kaustubh | 2009 | Informatik für die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen In: Tätigkeitsberichte 2009 der Institute, 1-6 | Part of a Book | |
| MCHSBPatent09 | McHardy, Alice Steinbrück, Lars | 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 | Miscellaneous | |
| Meisinger-Henschel2007 | Meisinger-Henschel, Christine Schmidt, Michaela Lukassen, Susanne Linke, Burkhard Krause, Lutz Konietzny, Sebastian Goesmann, Alexander Howley, Paul Chaplin, Paul Suter, Mark Hausmann, Jürgen | 2007 | Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara In: Journal of General Virology [88], 3249-3259 | Journal Article | |
| Patil2008a | Patil, Kaustubh Akerkar, Rajendra | 2008 | Tackling Traveling Salesman Problem with Random Key Genetic Algorithm In: Journal of Hybrid Computing Research [1], 10-10 | Journal Article | |
| Patil2011 | Patil, Kaustubh R. Haider, Peter Pope, Philip B. Turnbaugh, Peter J. Morrison, Mark Scheffer, Tobias McHardy, Alice | 2011 | Taxonomic metagenome sequence assignment with structured output models In: Nature Methods [8], 191-192 | Journal Article | |
| Patil2012 | Patil, Kaustubh Raosaheb Roune, Linus McHardy, Alice Carolyn | 2012 | The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences In: PLoS ONE [7], e38581,1-e38581,9 | Electronic Journal Article | |
| PatKulk2007 | Patil, Kaustubh Kulkarni, Abhijit | 2007 | A simple visualization technique to understand the system dynamics in bioreactors In: Biotechnology Progress [23], 1101-1105 | Journal Article | |
| Pope2012 | Pope, Phillip B. Mackenzie, Alasdair K. Gregor, Ivan Smith, Wendy Sundset, Monica A. McHardy, Alice C. Morrison, Mark Eijsink, Vincent G.H. | 2012 | Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci In: PLoS ONE [7], e38571,1-e38571,10 | Electronic Journal Article | |
| PSJK2008 | Patil, Kaustubh Shelokar, P. S. Jayaraman, V. K. Kulkarni, B. D. | 2008 | Ant Colony Optimization in the Direct Ordering Gene Expression Data In: Journal of Hybrid Computing Research [1], 10-10 | Journal Article | |
| Richardson2007 | 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. | 2007 | Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite In: Nature [450], 560-565 | Journal Article | |
| Schneiker2007 | 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 | 2007 | Complete genome sequence of the myxobacterium Sorangium cellulosum. In: Nature Biotechnology [27], 281-1289 | Journal Article | |
| Schoen2008 | 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 | 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 | Journal Article | |
| steinbrueck2010adp | Steinbrück, Lars McHardy, Alice | 2010 | Allele dynamics plots for the study of evolutionary dynamics in viral populations In: Nucleic Acids Research [39], 1-12 | Electronic Journal Article | |
| Steinbrueck2012 | Steinbrück, Lars McHardy, Alice Carolyn | 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 | Electronic Journal Article | |
| Tusche2012 | Tusche, Christina Steinbrück, Lars McHardy, Alice Carolyn | 2012 | Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection In: Molecular Biology and Evolution [29], 2063-2071 | Journal Article | |
| VCPP2007 | Vieira, J Cardoso, CS Pinto, JP Patil, Kaustubh Brazdil, P Cruz, E Mascarenhas, C Lacerda, R Gartner, A Almeida, S Alves, H Porto, G | 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 | Journal Article | |
| VCPP2007a | Vieira, J Cardoso, CS Pinto, JP Patil, Kaustubh Brazdil, P Cruz, E Mascarenhas, C Lacerda, R Gartner, A Almeida, S Alves, H Porto, G | 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 | Journal Article |
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