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MPI-INF IRG1 Publications

MPI-INF IRG1 Publications

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Journal Full Title / ISSNYearAuthor/EditorTitle
Hide details for PNASPNAS
Proceedings of the National Academy of Sciences of the United States of America
0027-8424
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
Proceedings of the National Academy of Sciences of the United States of America
0027-8424
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
Proceedings of the National Academy of Sciences of the United States of America
1091-6490
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
Hide details for (Not Categorized)(Not Categorized)
The ISME Journal
1751-7362
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
Molecular Biology and Evolution
0737-4038
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
Proceedings of the Royal Society / B, Biological Sciences
0950-1193
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
BMC Bioinformatics
-
2011Konietzny, Sebastian G.A.
Dietz, Laura
McHardy, Alice
Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141
The ISME Journal
1751-7362
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
Nature Methods
1548-7091
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
Science
-
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
PLOS Pathogens
1553-7366
2009McHardy, Alice
Adams, Ben
The role of genomics in tracking the evolution of influenza A virus
In: PLOS Pathogens [5], e1000566:1-e1000566:6
The Journal of Bacteriology
0021-9193
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
Genome Research
1088-9051
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
Nature Biotechnology
1087-0156
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 of Hybrid Computing Research
-
2008Patil, Kaustubh
Akerkar, Rajendra
Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10
Journal of Hybrid Computing Research
0974-5858
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
Nature Methods
-
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
Nucleic Acids Research
-
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
Nature Methods
-
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
Current Opinion in Microbiology
-
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 of General Virology
-
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
Biotechnology Progress
-
2007Patil, Kaustubh
Kulkarni, Abhijit
A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105
Nature Biotechnology
-
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
International Journal of Immunogenetics
-
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
American Journal of Hematology
-
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
Nature
-
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

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