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YearAuthor/EditorTitleType
2012Gilbert, 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
2012Patil, 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		Electronic Journal Article
2012Pope, 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		Electronic Journal Article
2012Steinbrück, 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		Electronic Journal Article
2012Tusche, 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
2011Adams, 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
2011Konietzny, Sebastian G.A.
Dietz, Laura
McHardy, Alice		Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141		Journal Article
2011Lykidis, 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
2011McHardy, Alice
Patil, Kaustubh R.		Phylogenetic binning of metagenome sequence samples
In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358		Part of a Book
2011Patil, 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
2011Pope, 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
2010Pope, 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
2010Steinbrück, Lars
McHardy, Alice		Allele dynamics plots for the study of evolutionary dynamics in viral populations
In: Nucleic Acids Research [39], 1-12		Electronic Journal Article
2010Turnbaugh, 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
2009Adams, Ben
McHardy, Alice
Lundegaard, C.
Lengauer, Thomas		Viral Bioinformatics
In: Modern Genome Annotation : the Biosapiens Network, 429-452		Part of a Book
2009McHardy, 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
2009McHardy, Alice
Patil, Kaustubh		Informatik für die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen
In: Tätigkeitsberichte 2009 der Institute, 1-6		Part of a Book
2008Gartemann, 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
2008Holland, 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
2008Kalyuzhnaya, 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
2008McHardy, AliceFinding 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
2008McHardy, 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 virusMiscellaneous
2008Patil, Kaustubh
Akerkar, Rajendra		Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10		Journal Article
2008Patil, 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
2008Schoen, 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
2007Mavromatis, 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
2007McHardy, 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
2007McHardy, 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
2007McHardy, 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
2007Meisinger-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
2007Patil, Kaustubh
Kulkarni, Abhijit		A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105		Journal Article
2007Schneiker, 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
2007Vieira, 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
2007Vieira, 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
2007Warnecke, 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

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