MPI-INF IRG1 Publications

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.

2008

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

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

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

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

Konietzny, Sebastian G.A.
Dietz, Laura
McHardy, Alice

2011

Inferring functional modules of protein families with probabilistic topic models
In: BMC Bioinformatics [12], 141

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

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

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

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

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

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

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

Patil, Kaustubh
Akerkar, Rajendra

2008

Tackling Traveling Salesman Problem with Random Key Genetic Algorithm
In: Journal of Hybrid Computing Research [1], 10-10

Patil, Kaustubh
Kulkarni, Abhijit

2007

A simple visualization technique to understand the system dynamics in bioreactors
In: Biotechnology Progress [23], 1101-1105

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

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

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

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

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

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

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

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

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

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

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

Electronic Journal Article

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

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

Steinbrück, Lars
McHardy, Alice

2010

Allele dynamics plots for the study of evolutionary dynamics in viral populations
In: Nucleic Acids Research [39], 1-12