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2013
Richness of human gut microbiome correlates with metabolic markers.
Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M\\\'Rini C, Mérieux A, Yamada T
Nature. 2013, 2013 |
PubMed
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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E
Nature. 2013, 2013 |
PubMed
Relevant URL
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Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs).
Udatha DB, Rasmussen S, Sicheritz-Pontén T, Panagiotou G
Methods Mol Biol. 2013;985:409-28. doi: 10.1007/978-1-62703-299-5_20., 2013 |
PubMed
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Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP
Genome Biol, 2013 |
PubMed
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2012
The chemical interactome space between the human host and the genetically defined gut metabotypes
Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G
The ISME Journal advance online publication, 22 November 2012; doi:10.1038/ismej.2012.141, 2012 |
Relevant URL
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2011
Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia
Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Helt LR, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R
Leukemia, June 25th, 2011 |
PubMed
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Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene
Bowman JS, Rasmussen S, Blom N, Deming JW, Rysgaard S, Sicheritz-Ponten T
ISME J, Jun 30, 2011 |
PubMed
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Enterotypes of the human gut microbiome
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M\'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P
Nature, May 12, 2011 |
PubMed
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2010
A human gut microbial gene catalogue established by metagenomic sequencing
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich DS & Wang J
Nature, Volume 464 Number 7285 pp7-132, 2010 |
PubMed
Nature frontpage
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Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics
Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori PL, Hirt RP
BMC Genomics 11:99doi:10.1186/1471-2164-11-99, 2010 |
PubMed
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Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E
Nature 11 Feb;463(7282):757-62, 2010 |
PubMed
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2009
InterMap3D: predicting and visualizing co-evolving protein residues
Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG
Bioinformatics, 2009 |
PubMed
PDF
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2008
Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, Bonnal RJ, Sicheritz-Ponten T, De Bellis G, Visca P, Cassone A, Carattoli A
Antimicrobial agents and chemotherapy, 2008 Jul;52(7):2616-25. Epub 2008 Apr 14, 2008 |
PubMed
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Linear motif atlas for phosphorylation-dependent signaling.
Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
Science Signaling, 2008 Sep 2;1(35):ra2, 2008 |
PubMed
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Global features of the Alcanivorax borkumensis SK2 genome
Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW
Environ Microbiol. 2008 Mar;10(3):614-25 and Mol Genet Genomics, 279:523-534, (2008), 2008 |
PubMed
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2007
Structure and Content of the Entamoeba histolytica Genome
Clark CG, Alsmark UCM, Tazreiter M, Saito Y, Nakano, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya S, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N
Advances in Parasitology, 65, 51-190, 2007 |
PubMed
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Trichomonas vaginalis surface proteins: a view from the genome
Hirt RP, Noel CJ, Sicheritz-Ponten T, Tachezy J, Fiori PL
Trends Parasitol., 23(11):540-7, 2007 |
PubMed
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Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ
Science. Jan 12;315(5809):207-12, 2007 |
PubMed
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2005
Genome update: Prediction of secreted proteins in 225 bacterial proteomes
Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW
Microbiology, 151, 1725-1727, 2005 |
PubMed
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Genome update: Sigma factors in 240 bacterial genomes
Kiil K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaart TM, Ussery DW
Microbiology-SGM, 151, 3147-3150, 2005 |
PubMed
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Genome update: Distribution of two.component trensduction systems in 250 bacterial genomes
Kiil K, Ferchaud JB, David C, Binnewies T, Wu H, Sicheritz-Pontén T, Willenbrock H, Ussery DW
Microbiology, 151, 3447-3452, 2005 |
PubMed
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The genome of the protist parasite Entamoeba histolytica
Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Pontén T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N
Nature, 24;433, 865-8, 2005 |
PubMed
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2004
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ
BMC Bioinformatics. Jun 22;5:79, 2004 |
PubMed
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Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry
Hjerrild M, Stensballe A, Rasmussen TE, Kofoed CB, Blom N, Sicheritz-Ponten T, Larsen MR, Brunak S, Jensen ON, Gammeltoft S
J Proteome Research 426-33, 2004 |
PubMed
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Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S
Proteomics, 4, 1633-49, 2004 |
PubMed
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A first glimpse into the pattern and scale of gene transfer in Apicomplexa
Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC
International Journal of Parasitology, 34, 265-74, 2004 |
PubMed
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2003
GenePublisher: Automated analysis of DNA microarray data
Knudsen S, Workman C, Sicheritz-Ponten T, Friis C
Nucleic Acids Res, 31, 3471-76, 2003 |
PubMed
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Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D
BMC Genomics, 4, 12, 2003 |
PubMed
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2002
Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, REP Elements and Oligonucleotide Motif Signatures
Weinel C, Ussery DW, Ohlsson H, Sicheritz-Ponten T, Kiewitz C, Tümmler B
Genome Letters, 1, 175-187, 2002 |
Genome Letters website
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2001
A phylogenomic approach to microbial evolution
Sicheritz-Pontén T, Andersson SGE
Nucleic Acids Res., 29, 545-552, 2001 |
PubMed
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Books
The Genome of Trichomonas vaginalis
Carlton JM, Malik SB, Sullivan SA, Sicheritz-Ponten T, Tang P, Hirt RP
Anaerobic Parasitic Protozoa: Genomics and Molecular Biology, Chapter 3, 2010 |
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The genus Burkholderia: analysis of 56 genomic sequences
Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM
Microbial Pathogenomics,Karger AG publishers, Basel, 2009 |
PubMed
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