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MPI-INF IRG1 Publications

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BibTeX cite keyAuthor/EditorYearTitleType
Adams2008Adams, Ben
McHardy, Alice
Lundegaard, C.
Lengauer, Thomas
2009Viral Bioinformatics
In: Modern Genome Annotation : the Biosapiens Network, 429-452
Part of a Book
Adams2010Adams, Ben
McHardy, Alice
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
Gartemann2008Gartemann, 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.
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
Holland2008Holland, 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.
2008The amphioxus genome illuminates vertebrate origins and cephalochordate biology
In: Genome Research [18], 1100-1111
Journal Article
Kalyuzhnaya2008Kalyuzhnaya, 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.
2008High-resolution metagenomics targets specific functional types in complex microbial communities
In: Nature Biotechnology [26], 1029-34
Journal Article
KON2011Konietzny, Sebastian G.A.
Dietz, Laura
McHardy, Alice
2011Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141
Journal Article
Mavromatis2007Mavromatis, 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.
2007Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
In: Nature Methods [4], 495-500
Journal Article
MCH2011bPope, P. B.
Smith, W.
Denman, S. E.
Tringe, S. G.
Barry, K.
Hugenholtz, P.
McSweeney, C. S.
McHardy, Alice
Morrison, M.
2011Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
In: Science [333], 646-648
Journal Article
MCH2011cGilbert, 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
2012Defining seasonal marine microbial community dynamics
In: The ISME Journal [6], 298-308
Journal Article
McHardy2007aMcHardy, Alice
Rigoutsos, I.
2007What's in the mix? Methods for the phylogenetic classification of metagenome sequence samples.
In: Current Opinion in Microbiology [10], 499-503
Journal Article
McHardy2007bMcHardy, Alice
Martin, H. G.
Tsirigos, A.
Hugenholtz, P.
Rigoutsos, I.
2007Accurate phylogenetic classification of variable-length DNA fragments.
In: Nature Methods [4], 63-72
Journal Article
McHardy2007cMcHardy, Alice
Krause, L.
Nattkemper, T. W.
Puhler, A.
Stoye, J.
Meyer, F.
2007GISMO - prokaryotic gene identification using a support vector machine for ORF classification.
In: Nucleic Acids Research [32], 540-549
Journal Article
McHardy2008McHardy, Alice2008Finding 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
McHardy2009xMcHardy, Alice
Adams, Ben
2009The role of genomics in tracking the evolution of influenza A virus
In: PLOS Pathogens [5], e1000566:1-e1000566:6
Journal Article
mchardy2010ahtPope, 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.
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
mchardy2010msiLykidis, 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
2011Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
In: The ISME Journal [5], 122-130
Journal Article
mchardy2010ogtTurnbaugh, Peter J.
Quince, Christopher
Faith, Jeremiah J.
McHardy, Alice
Yatsunenko, Tanya
Niazi, Faheem
Affourtit, Jason
Egholm, Michael
Henrissat, Bernhard
Knight, Rob
Gordon, Jeffrey I.
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
McHardyPatil2011McHardy, Alice
Patil, Kaustubh R.
2011Phylogenetic binning of metagenome sequence samples
In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358
Part of a Book
MCHJahrbuch09McHardy, Alice
Patil, Kaustubh
2009Informatik für die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen
In: Tätigkeitsberichte 2009 der Institute, 1-6
Part of a Book
MCHSBPatent09McHardy, Alice
Steinbrück, Lars
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-Henschel2007Meisinger-Henschel, Christine
Schmidt, Michaela
Lukassen, Susanne
Linke, Burkhard
Krause, Lutz
Konietzny, Sebastian
Goesmann, Alexander
Howley, Paul
Chaplin, Paul
Suter, Mark
Hausmann, Jürgen
2007Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara
In: Journal of General Virology [88], 3249-3259
Journal Article
Patil2008aPatil, Kaustubh
Akerkar, Rajendra
2008Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10
Journal Article
Patil2011Patil, Kaustubh R.
Haider, Peter
Pope, Philip B.
Turnbaugh, Peter J.
Morrison, Mark
Scheffer, Tobias
McHardy, Alice
2011Taxonomic metagenome sequence assignment with structured output models
In: Nature Methods [8], 191-192
Journal Article
Patil2012Patil, Kaustubh Raosaheb
Roune, Linus
McHardy, Alice Carolyn
2012The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences
In: PLoS ONE [7], e38581,1-e38581,9
Electronic Journal Article
PatKulk2007Patil, Kaustubh
Kulkarni, Abhijit
2007A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105
Journal Article
Pope2012Pope, Phillip B.
Mackenzie, Alasdair K.
Gregor, Ivan
Smith, Wendy
Sundset, Monica A.
McHardy, Alice C.
Morrison, Mark
Eijsink, Vincent G.H.
2012Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci
In: PLoS ONE [7], e38571,1-e38571,10
Electronic Journal Article
PSJK2008Patil, Kaustubh
Shelokar, P. S.
Jayaraman, V. K.
Kulkarni, B. D.
2008Ant Colony Optimization in the Direct Ordering Gene Expression Data
In: Journal of Hybrid Computing Research [1], 10-10
Journal Article
Richardson2007Warnecke, 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.
2007Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
In: Nature [450], 560-565
Journal Article
Schneiker2007Schneiker, 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
2007Complete genome sequence of the myxobacterium Sorangium cellulosum.
In: Nature Biotechnology [27], 281-1289
Journal Article
Schoen2008Schoen, 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
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
steinbrueck2010adpSteinbrück, Lars
McHardy, Alice
2010Allele dynamics plots for the study of evolutionary dynamics in viral populations
In: Nucleic Acids Research [39], 1-12
Electronic Journal Article
Steinbrueck2012Steinbrück, Lars
McHardy, Alice Carolyn
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
Tusche2012Tusche, Christina
Steinbrück, Lars
McHardy, Alice Carolyn
2012Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection
In: Molecular Biology and Evolution [29], 2063-2071
Journal Article
VCPP2007Vieira, J
Cardoso, CS
Pinto, JP
Patil, Kaustubh
Brazdil, P
Cruz, E
Mascarenhas, C
Lacerda, R
Gartner, A
Almeida, S
Alves, H
Porto, G
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
VCPP2007aVieira, J
Cardoso, CS
Pinto, JP
Patil, Kaustubh
Brazdil, P
Cruz, E
Mascarenhas, C
Lacerda, R
Gartner, A
Almeida, S
Alves, H
Porto, G
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

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