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MPI-INF IRG1 Publications

MPI-INF IRG1 Publications

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#YearedocLckAuthor(s) [non member]Editor(s) [non member]TitleTypeedoc identifier
Hide details for Veröffentlichungen der MitarbeiterVeröffentlichungen der Mitarbeiter
2012[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 Article3C34442ED82EAE7AC125796B00399FA2-MCH2011c
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 ArticleE97A2F77E844B058C1257B2B0040C1D7-Tusche2012
2011[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 ArticleBFFD2B087A0D1DFDC125796600552D9D-Adams2010
2011Konietzny, Sebastian G.A.
[Dietz, Laura]
McHardy, Alice
Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141
Journal ArticleE60A4C57945406FDC125796B0038BC8F-KON2011
2011Stop sign Icon[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]
Stop sign IconMultiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
In: The ISME Journal [5], 122-130
Journal Article9CCC7E05A390C2EBC12577ED00595E00-mchardy2010msi
2011McHardy, Alice
Patil, Kaustubh R.
[de Bruijn, Frans J.]Phylogenetic binning of metagenome sequence samples
In: Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches, 353-358
Part of a Book3A66D936E9DC1DCCC125784800356078-McHardyPatil2011
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 ArticleCEC8C43625D7A791C125784800346850-Patil2011
2011[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 Article9B59790E425184D3C125796B003945EC-MCH2011b
2010[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 Article8C6EE8002010004BC12577ED005A4619-mchardy2010aht
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 Article84BAAA3033FDEA9BC12577ED005AA274-mchardy2010ogt
2009Adams, Ben
McHardy, Alice
[Lundegaard, C.]
Lengauer, Thomas
Frishman, Dmitrij
[Valencia, Alfonso]
Viral Bioinformatics
In: Modern Genome Annotation : the Biosapiens Network, 429-452
Part of a BookB4A1715B08F45B0AC125754000516BE8-Adams2008
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 Article1C9EFE44A49ED8A5C12575840044E845-McHardy2009x
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 Book9E329B79814DB7B2C125755C003AE3E5-MCHJahrbuch09
2008[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 Article3ABFD0B67D0C9CFCC1257540004F0C05-Gartemann2008
2008[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 Article3452791CFBF46FDAC1257540004CE57A-Holland2008
2008[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 Article449DDA09D41A2E2FC1257540003911DA-Kalyuzhnaya2008
2008McHardy, Alice[Keith, Jonathan M.]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 Book121B2A97396F152BC125754000397863-McHardy2008
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 virusMiscellaneousE2FBE24F31BF6320C125755C003B9A7A-MCHSBPatent09
2008Patil, Kaustubh
[Akerkar, Rajendra]
Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10
Journal ArticleFD4AAC238DFD0ED8C125773C0033CC6F-Patil2008a
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 Article0FB4ECA9E1E5147CC125758400428B8C-PSJK2008
2008[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 ArticleBBBF6A835DC9A76DC12575840044983E-Schoen2008
2007[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 Article39A42ABA1B9E9BC0C125754000412AE3-Mavromatis2007
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 Article4B8EEB6996D96333C1257540004225D1-McHardy2007c
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 Article56CA5009852B16F4C12575400041AE6B-McHardy2007b
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 ArticleDAAC69DAEAF47D95C1257540004015D5-McHardy2007a
2007[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 Article08FC50000B177748C1257584004359D5-Meisinger-Henschel2007
2007Patil, Kaustubh
[Kulkarni, Abhijit]
A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105
Journal Article3DD28201E8CA5C08C1257584004229EB-PatKulk2007
2007[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 Article81086B3B583B5992C1257584004435E3-Schneiker2007
2007[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 Article7B3006A7130F15E5C1257584004206AE-VCPP2007a
2007[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 ArticleF47DCDD8C8512584C12575840041BC7A-VCPP2007
2007[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 ArticleD2D4862F0ECC9311C12575400040392F-Richardson2007
Hide details for Publikationen im InternetPublikationen im Internet
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 ArticleB8217CD8AE542F59C1257B2B002CC4D2-Patil2012
2012[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
Electronic Journal Article1EAECC5A7307FE94C1257B2B002E1B58-Pope2012
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 ArticleF8E505A97FDE0F89C1257B2B003FC1B6-Steinbrueck2012
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 Article8FA352BBA6FEC70FC12577ED0057897A-steinbrueck2010adp

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