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Thomas Rattei

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Enterobacter sakazakii

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TOP 3
Yuliang Jin; Thomas Rattei; Dmitrij Turaev; Thomas Weinmaier; Hernán A Makse
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.
Sebastian Lücker; Boris Nowka; Thomas Rattei; Eva Spieck; Holger Daims
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer.
Thomas Weinmaier; Carolina Arguedas-Villa; Jacques Bille; Thomas Rattei; Martin Riesing; Roger Stephan; Taurai Tasara
Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland.

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All Publications

2013: Yuliang Jin; Thomas Rattei; Dmitrij Turaev; Thomas Weinmaier; Hernán A Makse
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.
PloS one 2013;8(3):e58134.
2013: Sebastian Lücker; Boris Nowka; Thomas Rattei; Eva Spieck; Holger Daims
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer.
Frontiers in microbiology 2013;4():27.
2013: Thomas Weinmaier; Carolina Arguedas-Villa; Jacques Bille; Thomas Rattei; Martin Riesing; Roger Stephan; Taurai Tasara
Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland.
Genome announcements 2013;1(1):.
2012: Kerstin Hochwind; Thomas Rattei; Michael Schmid; Saskia van Hemert; Thomas Weinmaier; Anton Hartmann; Michael Rothballer
Draft genome sequence of Lactobacillus casei W56.
Journal of bacteriology 2012;194(23):6638.
2012: Anja Spang; Eva Spieck; Wolfgang R. Streit; Thomas Weinmaier; Sabine Zumbrägel; Christoph Böhm; Rolf Daniel; Alexander Galushko; Susanne Haider; Roland Hatzenpichler; Elena V Lebedeva; Boris Nowka; Pierre Offre; Anja Poehlein; Thomas Rattei; Nicolas Rychlik; Christa Schleper; Christel Schmeisser; Markus Schmid; Michael Wagner
The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations.
Environmental microbiology 2012;14(12):3122-45.
2012: Melanie Kuffner; Christelle Melodelima; Thomas Rattei; Andreas Schindlbacher; Michael Schloter; Brigitte Hai; Robert Jandl; Sophie Zechmeister-Boltenstern; Angela Sessitsch
Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing.
FEMS microbiology ecology 2012;82(3):551-62.
2012: Mirjami Mattila; Thomas Rattei; Panu Somervuo; Roger Stephan; Hannu Korkeala; Taurai Tasara
Phenotypic and transcriptomic analyses of Sigma L-dependent characteristics in Listeria monocytogenes EGD-e.
Food microbiology 2012;32(1):152-64.
2012: Regina Radax; Hans Tore Rapp; Thomas Rattei; Christoph Bayer; Anders Lanzen; Tim Urich; Christa Schleper
Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community.
Environmental microbiology 2012;14(5):1308-24.
2012: Regina Dick; Alfons Gierl; Martin Haslbeck; Thomas Rattei; Wilfried Schwab; Monika Frey
Comparative analysis of benzoxazinoid biosynthesis in monocots and dicots: independent recruitment of stabilization and activation functions.
The Plant cell 2012;24(3):915-28.
2012: Michael Pester; Thomas Rattei; Barbara Reinhold-Hurek; Andreas Richter; Stefan Flechl; Alexander Gröngröft; Alexander Loy; Jörg Overmann; Michael Wagner
amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions.
Environmental microbiology 2012;14(2):525-39.
2012: Elena R Toenshoff; Michael Wagner; Thomas Weinmaier; Astrid Collingro; Waltraud Klepal; Thomas Narzt; Thomas Penz; Stefan Pfeiffer; Thomas Rattei; Stephan Schmitz-Esser; Matthias Horn
Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae).
The ISME journal 2012;6(2):384-96.
2012: Eva Heinz; Robert P Hirt; John M Lucocq; Stephanie Markert; Sirintra Nakjang; Christophe J Noël; Thomas Rattei; Thomas Schweder; Daniel C Swan; Thomas Weinmaier; Tom A Williams; Dörte Becher; Jörg Bernhardt; Tal Dagan; Alina V Goldberg; Christian Hacker; Neil Hall; Simon R Harris; T Martin Embley
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution.
PLoS pathogens 2012;8(10):e1002979.
2012: André M Comeau; Henry M Krisch; Alla I Kushkina; Sylvain Moineau; Thomas Rattei; FI Tovkach; Denise Tremblay; Hans-Wolfgang Ackermann
Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses.
PloS one 2012;7(7):e40102.
2012: Sean Powell; Thomas Rattei; Alexander Roth; Damian Szklarczyk; Kalliopi Trachana; Christian von Mering; Tobias Doerks; Lars Jensen; Michael Kuhn; Ivica Letunic; Jean Muller; Roland Arnold; Peer Bork
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic acids research 2012;40(Database issue):D284-9.
2011: Astrid Collingro; Maureen G Friedman; Eva Heinz; Patrik M Bavoil; Robert C Brunham; Simona Kahane; Garry S A Myers; Thomas Penz; Thomas Rattei; Timothy D Read; Konrad Sachse; Patrick Tischler; Thomas Weinmaier; Matthias Horn
Unity in variety--the pan-genome of the Chlamydiae.
Molecular biology and evolution 2011;28(12):3253-70.
2011: Franz Bergmann; Drazenka Selesi; Thomas Weinmaier; Patrick Tischler; Thomas Rattei; Rainer U Meckenstock
Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47.
Environmental microbiology 2011;13(5):1125-37.
2011: Stefan Götz; Roland Arnold; Patricia Sebastián-León; Samuel Martín-Rodríguez; Patrick Tischler; Marc-André Jehl; Joaquín Dopazo; Thomas Rattei; Ana Conesa
B2G-FAR, a species-centered GO annotation repository.
Bioinformatics (Oxford, England) 2011;27(7):919-24.
2011: Monika R Nuk; Andreas Reisner; Martina Neuwirth; Katrin Schilcher; Roland Arnold; Andre Jehl; Thomas Rattei; Ellen L Zechner
Functional analysis of the finO distal region of plasmid R1.
Plasmid 2011;65(2):159-68.
2011: Thilo M Fuchs; Katharina Brandt; Mandy Starke; Thomas Rattei
Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals.
BMC genomics 2011;12():168.
2011: Hans-Werner Mewes; Andreas Ruepp; Fabian J Theis; Thomas Rattei; Mathias Walter; Dmitrij Frishman; Karsten Suhre; Manuel Spannagl; Klaus F X Mayer; Volker Stümpflen; Alexey Antonov
MIPS: curated databases and comprehensive secondary data resources in 2010.
Nucleic acids research 2011;39(Database issue):D220-4.
2011: Marc-André Jehl; Roland Arnold; Thomas Rattei
Effective--a database of predicted secreted bacterial proteins.
Nucleic acids research 2011;39(Database issue):D591-5.
2011: Roger Stephan; Angelika Lehner; Patrick Tischler; Thomas Rattei
Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates.
Journal of bacteriology 2011;193(1):309-10.
2010: Silvia Lang; Karl Gruber; Sanja Mihajlovic; Roland Arnold; Christian J Gruber; Sonja Steinlechner; Marc-Andre Jehl; Thomas Rattei; Kai-Uwe Fröhlich; Ellen L Zechner
Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases.
Molecular microbiology 2010;78(6):1539-55.
2010: Zheng Yu; Georg Haberer; Michaela Matthes; Thomas Rattei; Klaus F X Mayer; Alfons Gierl; Ramon A Torres-Ruiz
Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(41):17809-14.
2010: Nidal Abu Laban; Drazenka Selesi; Thomas Rattei; Patrick Tischler; Rainer U Meckenstock
Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture.
Environmental microbiology 2010;12(10):2783-96.
2010: Thomas Kriehuber; Thomas Rattei; Thomas Weinmaier; Alexander Bepperling; Martin Haslbeck; Johannes Buchner
Independent evolution of the core domain and its flanking sequences in small heat shock proteins.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2010;24(10):3633-42.
2010: Nicole S Webster; Stephen Whalan; Faris Behnam; Matthias Horn; Sebastian Lücker; Thomas Rattei; Michael W Taylor; Michael Wagner
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.
Environmental microbiology 2010;12(8):2070-82.
2010: Anja Spang; Roland Hatzenpichler; Céline Brochier-Armanet; Thomas Rattei; Patrick Tischler; Eva Spieck; Wolfgang R. Streit; David A Stahl; Michael Wagner; Christa Schleper
Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota.
Trends in microbiology 2010;18(8):331-40.
2010: Sebastian Lücker; Michael Wagner; Frank Maixner; Eric Pelletier; Hanna Koch; Benoit Vacherie; Thomas Rattei; Jaap S Sinninghe Damsté; Eva Spieck; Denis Le Paslier; Holger Daims
A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(30):13479-84.
2010: Roland Arnold; Andre Jehl; Thomas Rattei
Targeting effectors: the molecular recognition of Type III secreted proteins.
Microbes and infection / Institut Pasteur 2010;12(5):346-58.
2010: Stephan Schmitz-Esser; Patrick Tischler; Roland Arnold; Jacqueline Montanaro; Michael Wagner; Thomas Rattei; Matthias Horn
The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria.
Journal of bacteriology 2010;192(4):1045-57.
2010: Pawel Smialowski; Philipp Pagel; Philip Wong; Barbara Brauner; Irmtraud Dunger; Gisela Fobo; Goar Frishman; Corinna Montrone; Thomas Rattei; Dmitrij Frishman; Andreas Ruepp
The Negatome database: a reference set of non-interacting protein pairs.
Nucleic acids research 2010;38(Database issue):D540-4.
2010: Thomas Rattei; Patrick Tischler; Stefan Götz; Marc-André Jehl; Jonathan Hoser; Roland Arnold; Ana Conesa; Hans-Werner Mewes
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
Nucleic acids research 2010;38(Database issue):D223-6.
2010: Drazenka Selesi; Nico Jehmlich; Martin von Bergen; Frank Schmidt; Thomas Rattei; Patrick Tischler; Tillmann Lueders; Rainer U Meckenstock
Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47.
Journal of bacteriology 2010;192(1):295-306.
2009: Roland Arnold; Stefan Brandmaier; Frederick Kleine; Patrick Tischler; Eva Heinz; Sebastian Behrens; Antti Niinikoski; Hans-Werner Mewes; Matthias Horn; Thomas Rattei
Sequence-based prediction of type III secreted proteins.
PLoS pathogens 2009;5(4):e1000376.
2009: Eva Heinz; Patrick Tischler; Thomas Rattei; Garry S A Myers; Michael Wagner; Matthias Horn
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae.
BMC genomics 2009;10():634.
2008: Thomas Rattei; Jürgen Engel; Wolfgang Naumann; Alexander Lang; Matthias Rischer
Modification of the in vitro release profile of Cetrorelix by complexation with biophilic partners.
Current drug delivery 2008;5(4):319-23.
2008: Alexander Loy; roland arnold; Patrick Tischler; Thomas Rattei; Michael Wagner; Matthias Horn
probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity.
Environmental microbiology 2008;10(10):2894-8.
2008: Igor V Tetko; Igor V Rodchenkov; Mathias Walter; Thomas Rattei; Hans-Werner Mewes
Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information.
Bioinformatics (Oxford, England) 2008;24(5):621-8.
2008: Maya Grimm; Roger Stephan; Carol Iversen; Giuseppe G G Manzardo; Thomas Rattei; Kathrin Riedel; Andreas Ruepp; Dmitrij Frishman; Angelika Lehner
Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms.
Journal of food protection 2008;71(1):13-8.
2008: Hans-Werner Mewes; Sabine Dietmann; Dmitrij Frishman; R Gregory; Gertrud Mannhaupt; Klaus F X Mayer; Martin Münsterkötter; Andreas Ruepp; Manuel Spannagl; Volker Stümpflen; Thomas Rattei
MIPS: analysis and annotation of genome information in 2007.
Nucleic acids research 2008;36(Database issue):D196-201.
2008: Thomas Rattei; Patrick Tischler; roland arnold; Franz Hamberger; Jörg Krebs; Jan Krumsiek; Benedikt Wachinger; Volker Stümpflen; Werner Mewes
SIMAP--structuring the network of protein similarities.
Nucleic acids research 2008;36(Database issue):D289-92.
2007: Jan Krumsiek; roland arnold; Thomas Rattei
Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Bioinformatics (Oxford, England) 2007;23(8):1026-8.
2007: Thomas Rattei; Stephan Ott; Michaela Gutacker; Jan Rupp; Matthias Maass; Stefan Schreiber; Werner Solbach; Thierry Wirth; Jens Gieffers
Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure.
BMC genomics 2007;8():355.
2006: Angelika Lehner; Maya Grimm; Thomas Rattei; Andreas Ruepp; Dmitrij Frishman; Giuseppe G G Manzardo; Roger Stephan
Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment.
FEMS microbiology letters 2006;265(2):244-8.
2006: Angelika Lehner; Kathrin Riedel; Thomas Rattei; Andreas Ruepp; Dmitrij Frishman; Pieter Breeuwer; Benjamin Diep; Leo Eberl; Roger Stephan
Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism.
Systematic and applied microbiology 2006;29(8):609-25.
2006: Andreas Ruepp; Octave Noubibou Doudieu; Jos van den Oever; Barbara Brauner; Irmtraud Dunger-Kaltenbach; Gisela Fobo; Goar Frishman; Corinna Montrone; Christine Skornia; Steffi Wanka; Thomas Rattei; Philipp Pagel; Louise Riley; Dmitrij Frishman; Dimitrij Surmeli; Igor V Tetko; Matthias Oesterheld; Volker Stümpflen; Hans-Werner Mewes
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context.
Nucleic acids research 2006;34(Database issue):D568-71.
2006: Thomas Rattei; roland arnold; Patrick Tischler; Dominik Lindner; Volker Stümpflen; Hans-Werner Mewes
SIMAP: the similarity matrix of proteins.
Nucleic acids research 2006;34(Database issue):D252-6.
2006: Hans-Werner Mewes; Dmitrij Frishman; Klaus F X Mayer; Martin Münsterkötter; O Noubibou; Philipp Pagel; Thomas Rattei; Matthias Oesterheld; Andreas Ruepp; Volker Stümpflen
MIPS: analysis and annotation of proteins from whole genomes in 2005.
Nucleic acids research 2006;34(Database issue):D169-72.
2005: roland arnold; Thomas Rattei; Patrick Tischler; Minh-Duc Truong; Volker Stümpflen; Werner Mewes
SIMAP--the similarity matrix of proteins.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii42-6.
2004: Ralf Rabus; Andreas Ruepp; Tancred Frickey; Thomas Rattei; Berthold Fartmann; M Stark; Margarete Bauer; Arne Zibat; Thierry Lombardot; I Becker; J Amann; K Gellner; Hanno Teeling; W D Leuschner; Frank Oliver Glöckner; A N Lupas; Rudolf Amann; Hans-Peter Klenk
The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.
Environmental microbiology 2004;6(9):887-902.
2004: Matthias Horn; Astrid Collingro; Stephan Schmitz-Esser; Cora L Beier; Ulrike Purkhold; Berthold Fartmann; Petra Brandt; Gerald Nyakatura; Marcus Droege; Dmitrij Frishman; Thomas Rattei; Hans-Werner Mewes; Michael Wagner
Illuminating the evolutionary history of chlamydiae.
Science (New York, N.Y.) 2004;304(5671):728-30.