Publications
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Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.
Ramos-Madrigal J, Sinding MS, Caroe C, Mak SST, Niemann J, Samaniego Castruita JA, Fedorov S, Kandyba A, Germonpre M, Bocherens H, Feuerborn TR, Pitulko VV, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Larson G, Frantz LAF, Willerslev E, Meldgaard M, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP, Gopalakrishnan S
2021 Jan 11
Curr Biol
Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.
Ramos-Madrigal J, Sinding MS, Caroe C, Mak SST, Niemann J, Samaniego Castruita JA, Fedorov S, Kandyba A, Germonpre M, Bocherens H, Feuerborn TR, Pitulko VV, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Larson G, Frantz LAF, Willerslev E, Meldgaard M, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP, Gopalakrishnan S
2021 Jan 11
Curr Biol
inPhocus: A Local Perspective on Phage-Based Biocontrol in Agriculture and Aquaculture in India
Kiran Kondabagil, Thomas Sicheritz-Pontén, and Martha R.J. Clokie
2020-12-16
PHAGE
Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.
Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigo R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C
2020 Sep
Nature
Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus.
Fotakis AK, Denham SD, Mackie M, Orbegozo MI, Mylopotamitaki D, Gopalakrishnan S, Sicheritz-Ponten T, Olsen JV, Cappellini E, Zhang G, Christophersen A, Gilbert MTP, Vagene AJ
2020 Nov 23
Philos Trans R Soc Lond B Biol Sci
Dense sampling of bird diversity increases power of comparative genomics.
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sanchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro AM, Eckhart L, Fjeldsa J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jonsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, Gonzalez-Solis J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalen L, Urrutia AO, Szekely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Mila B, Ketterson ED, Fidler AE, Friis G, Parody-Merino AM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G
2020 Nov
Nature
Dense sampling of bird diversity increases power of comparative genomics.
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sanchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro AM, Eckhart L, Fjeldsa J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jonsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, Gonzalez-Solis J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalen L, Urrutia AO, Szekely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Mila B, Ketterson ED, Fidler AE, Friis G, Parody-Merino AM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G
2020 Nov
Nature
The evolutionary history of extinct and living lions.
de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Garrett Vieira F, Zepeda Mendoza ML, Liu S, Martin MD, Sinding MS, Mak SST, Caroe C, Liu S, Guo C, Zheng J, Zazula G, Baryshnikov G, Eizirik E, Koepfli KP, Johnson WE, Antunes A, Sicheritz-Ponten T, Gopalakrishnan S, Larson G, Yang H, O'Brien SJ, Hansen AJ, Zhang G, Marques-Bonet T, Gilbert MTP
2020 May 19
Proc Natl Acad Sci U S A
Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat.
Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sorensen CK, Hovmoller MS, Rathjen JP, Justesen AF
2020 May 1
Genome Biol Evol
Arctic-adapted dogs emerged at the Pleistocene-Holocene transition.
Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Caroe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jorgensen MP, Dietz R, Sonne C, Meldgaard M, Dalen L, Larson G, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Marques-Bonet T, Hansen AJ, Gilbert MTP
2020 Jun 26
Science
Arctic-adapted dogs emerged at the Pleistocene-Holocene transition.
Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Caroe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jorgensen MP, Dietz R, Sonne C, Meldgaard M, Dalen L, Larson G, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Marques-Bonet T, Hansen AJ, Gilbert MTP
2020 Jun 26
Science
Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.
Gelabert P, Sandoval-Velasco M, Serres A, de Manuel M, Renom P, Margaryan A, Stiller J, de-Dios T, Fang Q, Feng S, Manosa S, Pacheco G, Ferrando-Bernal M, Shi G, Hao F, Chen X, Petersen B, Olsen RA, Navarro A, Deng Y, Dalen L, Marques-Bonet T, Zhang G, Antunes A, Gilbert MTP, Lalueza-Fox C
2020 Jan 6
Curr Biol
Microbiota in foods from Inuit traditional hunting.
Hauptmann AL, Paulova P, Hansen LH, Sicheritz-Ponten T, Mulvad G, Nielsen DS
2020 Jan 14
PLoS One
A draft genome sequence of the elusive giant squid, Architeuthis dux.
da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro AM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazao B, Petersen B, Penaloza F, Musacchia F, Alexander GC, Osorio H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP
2020 Jan 1
Gigascience
A draft genome sequence of the elusive giant squid, Architeuthis dux.
da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro AM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazao B, Petersen B, Penaloza F, Musacchia F, Alexander GC, Osorio H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP
2020 Jan 1
Gigascience
The microbial composition of dried fish prepared according to Greenlandic Inuit traditions and industrial counterparts.
Hauptmann AL, Paulova P, Castro-Mejia JL, Hansen LH, Sicheritz-Ponten T, Mulvad G, Nielsen DS
2020 Feb
Food Microbiol
Connecting moss lipid droplets to patchoulol biosynthesis.
Peramuna A, Bae H, Quinonero Lopez C, Fromberg A, Petersen B, Simonsen HT
2020 Dec 7
PLoS One
The tuatara genome reveals ancient features of amniote evolution.
Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigo R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C
2020 Aug
Nature
Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet
Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; de Manuel, Marc; Renom, Pere; Margaryan, Ashot; Stiller, Josefin; de-Dios, Toni; Fang, Qi; Feng, Shaohong; Mañosa, Santi; Pacheco, George; Ferrando-Bernal, Manuel; Shi, Guolin; Hao, Fei; Chen, Xianqing; Petersen, Bent; Olsen, Remi-André; Navarro, Arcadi; Deng, Yuan; Dalén, Love; Marquès-Bonet, Tomàs; Zhang, Guojie; Antunes, Agostinho; Gilbert, M Thomas P; Lalueza-Fox, Carles.
2019/12/12
Current Biology
Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids
Westbury, Michael V.; Petersen, Bent; Lorenzen, Eline D
2019/09/25
PLoS ONE
Palaeogenomic insights into the origins of French grapevine diversity
Ramos-Madrigal, Jazmín; Runge, Anne Kathrine Wiborg; Bouby, Laurent; Lacombe, Thierry; Samaniego Castruita, José Alfredo; Adam-Blondon, Anne-Françoise; Figueiral, Isabel; Hallavant, Charlotte; Martínez-Zapater, José M; Schaal, Caroline; Töpfer, Reinhard; Petersen, Bent; Sicheritz-Pontén, Thomas; This, Patrice; Bacilieri, Roberto; Gilbert, M Thomas P; Wales, Nathan.
2019/06/10
Nature plants
The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi
Jorgensen, Tue Sparholt; Nielsen, Bolette Lykke Holm; Petersen, Bent; Browne, Patrick Denis; Hansen, Benni Winding; Hansen, Lars Hestbjerg
2019/05/01
G3: Genes, Genomes, Genetics
Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size
Westbury, Michael V; Petersen, Bent; Garde, Eva; Heide-Jørgensen, Mads Peter; Lorenzen, Eline D.
2019/05/01
iScience
The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia Tonsa Dana Improve the Understanding of Copepod Genome Size Evolution.
Jorgensen, Tue Sparholt; Petersen, Bent; Petersen, H. Cecilie B.; Browne, Patrick Denis; Prost, Stefan; Stillman, Jonathon H.; Hansen, Lars Hestbjerg; Hansen, Benni Winding
2019/03/27
Genome Biology and Evolution
Global Monitoring of Antimicrobial Resistance Based on Metagenomics Analyses of Urban Sewage
Hendriksen, Rene S.; Munk, Patrick; Njage, Patrick; van Bunnik, Bram; McNally, Luke; Lukjancenko, Oksana; Röder, Timo; Nieuwenhuijse, David; Pedersen, Susanne Karlsmose; Kjeldgaard, Jette; Kaas, Rolf S.; Clausen, Philip Thomas Lanken Conradsen; Vogt, Josef Korbinian; Leekitcharoenphon, Pimlapas; van de Schans, Milou G.M.; Zuidema, Tina; de Roda Husman, Ana Maria; Rasmussen, Simon; Petersen, Bent; Bego, Artan; Rees, Catherine; Cassar, Susan; Coventry, Kris; Collignon, Peter; Allerberger, Franz; Rahube, Teddie O.; Oliveira, Guilherme; Ivanov, Ivan; Vuthy, Yith; Sopheak, Thet; Yost, Christopher K.; Ke, Changwen; Zheng, Huanying; Baisheng, Li; Jiao, Xiaoyang; Donado-Godoy, Pilar; Coulibaly, Kalpy Julien; Jergović, Matijana; Hrenovic, Jasna; Karpíšková, Renáta; Villacis, Jose Eduardo; Legesse, Mengistu; Eguale, Tadesse; Heikinheimo, Annamari; Malania, Lile; Nitsche, Andreas; Brinkmann, Annika; Saba, Courage Kosi Setsoafia; Kocsis, Bela; Solymosi, Norbert; Thorsteinsdottir, Thorunn R.; Hatha, Abdulla Mohamed; Alebouyeh, Masoud; Morris, Dearbhaile; Cormican, Martin; O’Connor, Louise; Moran-Gilad, Jacob; Alba, Patricia; Battisti, Antonio; Shakenova, Zeinegul; Kiiyukia, Ciira; Ng’eno, Eric; Raka, Lul; Avsejenko, Jeļena; Bērziņš, Aivars; Bartkevics, Vadims; Penny, Christian; Rajandas, Heraa; Parimannan, Sivachandran; Haber, Malcolm Vella; Pal, Pushkar; Jeunen, Gert Jan; Gemmell, Neil; Fashae, Kayode; Holmstad, Rune; Hasan, Rumina; Shakoor, Sadia; Rojas, Maria Luz Zamudio; Wasyl, Dariusz; Bosevska, Golubinka; Kochubovski, Mihail; Radu, Cojocaru; Gassama, Amy; Radosavljevic, Vladimir; Wuertz, Stefan; Zuniga-Montanez, Rogelio; Tay, Moon Y.F.; Gavačová, Dagmar; Pastuchova, Katarina; Truska, Peter; Trkov, Marija; Esterhuyse, Kerneels; Keddy, Karen; Cerdà-Cuéllar, Marta; Pathirage, Sujatha; Norrgren, Leif; Örn, Stefan; Larsson, D. G.Joakim; Heijden, Tanja Van der; Kumburu, Happiness Houka; Sanneh, Bakary; Bidjada, Pawou; Njanpop-Lafourcade, Berthe Marie; Nikiema-Pessinaba, Somtinda Christelle; Levent, Belkis; Meschke, John Scott; Beck, Nicola Koren; Van, Chinh Dang; Phuc, Nguyen Do; Tran, Doan Minh Nguyen; Kwenda, Geoffrey; Tabo, Djim adjim; Wester, Astrid Louise; Cuadros-Orellana, Sara; Amid, Clara; Cochrane, Guy; Sicheritz-Ponten, Thomas; Schmitt, Heike; Alvarez, Jorge Raul Matheu; Aidara-Kane, Awa; Pamp, Sünje J.; Lund, Ole; Hald, Tine; Woolhouse, Mark; Koopmans, Marion P.; Vigre, Håkan; Petersen, Thomas Nordahl; Aarestrup, Frank M
2019/03/08
Nature Communication
NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning
Klausen, Michael Schantz; Jespersen, Martin Closter; Nielsen, Henrik; Jensen, Kamilla Kjærgaard; Jurtz, Vanessa Isabell; Sønderby, Casper Kaae; Sommer, Morten Otto Alexander; Winther, Ole; Nielsen, Morten; Petersen, Bent; Marcatili, Paolo
2019/02/02
Proteins: Structure, Function, and Bioinformatics
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Prost, Stefan; Armstrong, Ellie E.; Nylander, Johan; Thomas, Gregg W. C.; Suh, Alexander; Petersen, Bent; Dalen, Love; Benz, Brett W.; Blom, Mozes P. K.; Palkopoulou, Eleftheria; Ericson, Per G. P.; Irestedt, Martin
2019/01/24
GigaScience
Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids.
Westbury MV, Petersen B, Lorenzen ED
2019 Sep 25
PLoS One
High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.
Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdottir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Hogdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Ponten T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ
2019 Sep 13
J Infect Dis
Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries.
Asplund M, Kjartansdottir KR, Mollerup S, Vinner L, Fridholm H, Herrera JAR, Friis-Nielsen J, Hansen TA, Jensen RH, Nielsen IB, Richter SR, Rey-Iglesia A, Matey-Hernandez ML, Alquezar-Planas DE, Olsen PVS, Sicheritz-Ponten T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ
2019 Oct
Clin Microbiol Infect
The Whole Genome Sequence and mRNA Transcriptome of the Tropical Cyclopoid Copepod Apocyclops royi.
Jorgensen TS, Nielsen BLH, Petersen B, Browne PD, Hansen BW, Hansen LH
2019 May 7
G3 (Bethesda)
The Third Annual Meeting of the European Virus Bioinformatics Center.
Hufsky F, Ibrahim B, Modha S, Clokie MRJ, Deinhardt-Emmer S, Dutilh BE, Lycett S, Simmonds P, Thiel V, Abroi A, Adriaenssens EM, Escalera-Zamudio M, Kelly JN, Lamkiewicz K, Lu L, Susat J, Sicheritz T, Robertson DL, Marz M
2019 May 5
Viruses
Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size.
Westbury MV, Petersen B, Garde E, Heide-Jorgensen MP, Lorenzen ED
2019 May 31
iScience
The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution.
Jorgensen TS, Petersen B, Petersen HCB, Browne PD, Prost S, Stillman JH, Hansen LH, Hansen BW
2019 May 1
Genome Biol Evol
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
Prost S, Armstrong EE, Nylander J, Thomas GWC, Suh A, Petersen B, Dalen L, Benz BW, Blom MPK, Palkopoulou E, Ericson PGP, Irestedt M
2019 May 1
Gigascience
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.
Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Roder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM
2019 Mar 8
Nat Commun
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.
Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Roder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM
2019 Mar 8
Nat Commun
Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India.
Chatterjee A, Sicheritz-Ponten T, Yadav R, Kondabagil K
2019 Mar 6
Sci Rep
MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements.
Rey-Iglesia A, Gopalakrishan S, Caroe C, Alquezar-Planas DE, Ahlmann Nielsen A, Roder T, Bruhn Pedersen L, Naesborg-Nielsen C, Sinding MS, Fredensborg Rath M, Li Z, Petersen B, Gilbert MTP, Bunce M, Mourier T, Hansen AJ
2019 Mar
Mol Ecol Resour
Palaeogenomic insights into the origins of French grapevine diversity.
Ramos-Madrigal J, Runge AKW, Bouby L, Lacombe T, Samaniego Castruita JA, Adam-Blondon AF, Figueiral I, Hallavant C, Martinez-Zapater JM, Schaal C, Topfer R, Petersen B, Sicheritz-Ponten T, This P, Bacilieri R, Gilbert MTP, Wales N
2019 Jun
Nat Plants
Palaeogenomic insights into the origins of French grapevine diversity.
Ramos-Madrigal J, Runge AKW, Bouby L, Lacombe T, Samaniego Castruita JA, Adam-Blondon AF, Figueiral I, Hallavant C, Martinez-Zapater JM, Schaal C, Topfer R, Petersen B, Sicheritz-Ponten T, This P, Bacilieri R, Gilbert MTP, Wales N
2019 Jun
Nat Plants
NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.
Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sonderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcatili P
2019 Jun
Proteins
Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial.
Roager HM, Vogt JK, Kristensen M, Hansen LBS, Ibrugger S, Maerkedahl RB, Bahl MI, Lind MV, Nielsen RL, Frokiaer H, Gobel RJ, Landberg R, Ross AB, Brix S, Holck J, Meyer AS, Sparholt MH, Christensen AF, Carvalho V, Hartmann B, Holst JJ, Rumessen JJ, Linneberg A, Sicheritz-Ponten T, Dalgaard MD, Blennow A, Frandsen HL, Villas-Boas S, Kristiansen K, Vestergaard H, Hansen T, Ekstrom CT, Ritz C, Nielsen HB, Pedersen OB, Gupta R, Lauritzen L, Licht TR
2019 Jan
Gut
Interspecific Gene Flow Shaped the Evolution of the Genus Canis.
Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Caroe C, de Manuel Montero M, Kuderna L, Serres A, Gonzalez-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jorgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP
2019 Dec 2
Curr Biol
Interspecific Gene Flow Shaped the Evolution of the Genus Canis.
Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Caroe C, de Manuel Montero M, Kuderna L, Serres A, Gonzalez-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jorgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP
2019 Dec 2
Curr Biol
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements
Rey-Iglesia, Alba; Gopalakrishan, Shyam; Carøe, Christian; Alquezar-Planas, David E.; Ahlmann Nielsen, Anne; Röder, Timo; Pedersen, Lene Bruhn; Næsborg-Nielsen, Christina; Sinding, Mikkel-Holger S.; Rath, Martin Fredensborg; Li, Zhipeng; Petersen, Bent; Gilbert, M Thomas P; Bunce, Michael; Mourier, Tobias; Hansen, Anders Johannes
2018/12/21
Molecular Ecology Resources
Population genomics of grey wolves and wolf-like canids in North America
Sinding, Mikkel Holger S.; Gopalakrishan, Shyam; Vieira, Filipe G.; Samaniego Castruita, Jose A.; Raundrup, Katrine; Heide Jørgensen, Mads Peter; Meldgaard, Morten; Petersen, Bent; Sicheritz-Ponten, Thomas; Mikkelsen, Johan Brus; Marquard-Petersen, Ulf; Dietz, Rune; Sonne, Christian; Dalén, Love; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, M. Thomas P
2018/11/12
PLOS Genetics
Interspecific gene flow shaped the evolution of the genus Canis
Gopalakrishnan, Shyam; Sinding, Mikkel Holger S.; Ramos-Madrigal, Jazmín; Niemann, Jonas; Samaniego Castruita, Jose A.; Vieira, Filipe G.; Carøe, Christian; Montero, Marc de Manuel; Kuderna, Lukas; Serres, Aitor; González-Basallote, Víctor Manuel; Liu, Yan Hu; Wang, Guo Dong; Marques-Bonet, Tomas; Mirarab, Siavash; Fernandes, Carlos; Gaubert, Philippe; Koepfli, Klaus Peter; Budd, Jane; Rueness, Eli Knispel; Heide-Jørgensen, Mads Peter; Petersen, Bent; Sicheritz-Ponten, Thomas; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, M. Thomas P
2018/10/18
Current Biology
“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus
Machado, André M.; Tørresen, Ole K.; Kabeya, Naoki; Couto, Alvarina; Petersen, Bent; Felicio, Mónica; Campos, Paula F.; Fonseca, Elza; Bandarra, Narcisa; Lopes-Marques, Mónica; Ferraz, Renato; Ruivo, Raquel; Fonseca, Miguel M.; Jentoft, Sissel; Monroig, Óscar; da Fonseca, Rute R.; Castro, L. Filipe C
2018/10/09
Genes
Improved ontology for eukaryotic single-exon coding sequences in biological databases
Jorquera, Roddy; González, Carolina; Clausen, Philip Thomas Lanken Conradsen; Petersen, Bent; Holmes, David S
2018/09/18
Database
Antibodies to intercellular adhesion molecule 1-binding Plasmodium falciparum erythrocyte membrane protein 1-DBLβ are biomarkers of protective immunity to malaria in a cohort of young children from Papua New Guinea
Tessema, Sofonias K; Utama, Digjaya; Chesnokov, Olga; Hodder, Anthony N; Lin, Clara S; Harrison, G L Abby; Jespersen, Jakob S; Petersen, Bent; Tavul, Livingstone; Siba, Peter; Kwiatkowski, Dominic; Lavstsen, Thomas; Hansen, Diana S; Oleinikov, Andrew V; Mueller, Ivo; Barry, Alyssa E
2018/07/23
Infection and immunity
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios
Matey-Hernandez, Maria Luisa; Danish Pan Genome Consortium ; Brunak, Søren; Izarzugaza, Jose M.G.; Sørensen, Lasse Maretty; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Belling, Kirstine G; Have, Christian Theil; Bork-Jensen, Jette; Sun, Jihua; Hansen, Torben; Krogh, Anders; Sørensen, Thorkild I.A.; Pedersen, Oluf Borbye; Wang, Jun; Eiberg, Hans Rudolf Lytchoff; Kristiansen, Karsten
2018/06/25
BMC Bioinformatics
Accurate genotyping across variant classes and lengths using variant graphs
Sibbesen, Jonas Andreas; Maretty, Lasse; Krogh, Anders; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Have, Christian Theil; Bork-Jensen, Jette; Guo, Xiaosen; Hansen, Torben; Krogh, Anders; Sørensen, Thorkild I.A.; Pedersen, Oluf Borbye; Wang, Jun; Brunak, Søren
2018/06/18
Nature Genetics
Improved de novo genomic assembly for the domestic donkey
Renaud, Gabriel; Petersen, Bent; Seguin-orlando, Andaine; Bertelsen, Mads Frost; Waller, Andrew; Newton, Richard; Paillot, Romain; Bryant, Neil; Vaudin, Mark; Librado, Pablo; Orlando, Ludovic.
2018/04/04
Science Advances
"Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus.
Machado AM, Torresen OK, Kabeya N, Couto A, Petersen B, Felicio M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig O, da Fonseca RR, C Castro LF
2018 Oct 9
Genes (Basel)
Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.
Zepeda Mendoza ML, Roggenbuck M, Manzano Vargas K, Hansen LH, Brunak S, Gilbert MTP, Sicheritz-Ponten T
2018 Oct 11
Acta Vet Scand
Interspecific Gene Flow Shaped the Evolution of the Genus Canis.
Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Caroe C, Montero MM, Kuderna L, Serres A, Gonzalez-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jorgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP
2018 Nov 5
Curr Biol
Interspecific Gene Flow Shaped the Evolution of the Genus Canis.
Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Caroe C, Montero MM, Kuderna L, Serres A, Gonzalez-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jorgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP
2018 Nov 5
Curr Biol
A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.
Hansen LBS, Roager HM, Sondertoft NB, Gobel RJ, Kristensen M, Valles-Colomer M, Vieira-Silva S, Ibrugger S, Lind MV, Maerkedahl RB, Bahl MI, Madsen ML, Havelund J, Falony G, Tetens I, Nielsen T, Allin KH, Frandsen HL, Hartmann B, Holst JJ, Sparholt MH, Holck J, Blennow A, Moll JM, Meyer AS, Hoppe C, Poulsen JH, Carvalho V, Sagnelli D, Dalgaard MD, Christensen AF, Lydolph MC, Ross AB, Villas-Boas S, Brix S, Sicheritz-Ponten T, Buschard K, Linneberg A, Rumessen JJ, Ekstrom CT, Ritz C, Kristiansen K, Nielsen HB, Vestergaard H, Faergeman NJ, Raes J, Frokiaer H, Hansen T, Lauritzen L, Gupta R, Licht TR, Pedersen O
2018 Nov 13
Nat Commun
Population genomics of grey wolves and wolf-like canids in North America.
Sinding MS, Gopalakrishan S, Vieira FG, Samaniego Castruita JA, Raundrup K, Heide Jorgensen MP, Meldgaard M, Petersen B, Sicheritz-Ponten T, Mikkelsen JB, Marquard-Petersen U, Dietz R, Sonne C, Dalen L, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP
2018 Nov 12
PLoS Genet
Population genomics of grey wolves and wolf-like canids in North America.
Sinding MS, Gopalakrishan S, Vieira FG, Samaniego Castruita JA, Raundrup K, Heide Jorgensen MP, Meldgaard M, Petersen B, Sicheritz-Ponten T, Mikkelsen JB, Marquard-Petersen U, Dietz R, Sonne C, Dalen L, Bachmann L, Wiig O, Hansen AJ, Gilbert MTP
2018 Nov 12
PLoS Genet
Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira.
Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Ponten T, Smets BF
2018 Jun
ISME J
Antibodies to Intercellular Adhesion Molecule 1-Binding Plasmodium falciparum Erythrocyte Membrane Protein 1-DBLbeta Are Biomarkers of Protective Immunity to Malaria in a Cohort of Young Children from Papua New Guinea.
Tessema SK, Utama D, Chesnokov O, Hodder AN, Lin CS, Harrison GLA, Jespersen JS, Petersen B, Tavul L, Siba P, Kwiatkowski D, Lavstsen T, Hansen DS, Oleinikov AV, Mueller I, Barry AE
2018 Jul 23
Infect Immun
Improved ontology for eukaryotic single-exon coding sequences in biological databases.
Jorquera R, Gonzalez C, Clausen P, Petersen B, Holmes DS
2018 Jan 1
Database (Oxford)
Improved de novo genomic assembly for the domestic donkey.
Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L
2018 Apr 4
Sci Adv
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.
Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, Runge AK, Theze J, Streicker D, Frank HK, Loza-Rubio E, Liu S, Ryder OA, Samaniego Castruita JA, Katzourakis A, Pacheco G, Taboada B, Lober U, Pybus OG, Li Y, Rojas-Anaya E, Bohmann K, Carmona Baez A, Arias CF, Liu S, Greenwood AD, Bertelsen MF, White NE, Bunce M, Zhang G, Sicheritz-Ponten T, Gilbert MPT
2018 Apr
Nat Ecol Evol
The first draft reference genome of the American mink (Neovison vison)
Cai, Zexi; Petersen, Bent; Sahana, Goutam; Madsen, Lone B.; Larsen, Knud; Thomsen, Bo; Bendixen, Christian; Lund, Mogens Sandø; Guldbrandtsen, Bernt; Panitz, Frank
2017/11/06
Scientific Reports
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion
Danish Pan Genome Consortium; Sørensen, Lasse Maretty; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Belling, Kirstine G; Have, Christian Theil; Bork-Jensen, Jette; Hansen, Torben; Krogh, Anders; Sørensen, Thorkild I.A.; Pedersen, Oluf Borbye; Rasmussen, Simon; Kristiansen, Karsten; Brunak, Søren.
2017/08/28
PLoS Genetics
Assembly and analysis of 100 full MHC haplotypes from the Danish population
Jensen, Jacob M.; Villesen, Palle; Friborg, Rune M.; Mailund, Thomas; Besenbacher, Søren; Sørensen, Lasse Maretty; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Skov, Laurits; Belling, Kirstine G; Have, Christian Theil; Izarzugaza, Jose M. G.; Grosjean, Marie; Bork-Jensen, Jette; Grove, Jakob; Als, Thomas D.; Huang, Shujia; Chang, Yuqi; Xu, Ruiqi; Ye, Weijian; Rao, Junhua; Guo, Xiaosen; Sun, Jihua; Cao, Hongzhi; Ye, Chen; Beusekom, Johan V.; Espeseth, Thomas; Flindt, Esben; Halager, Anders E.; Hellard, Stephanie Le; Hultman, Christina M.; Lescai, Francesco; Li, Shengting; Lund, Ole; Løngren, Peter; Matey-Hernandez, Maria Luisa; Mors, Ole; Pedersen, Christian N. S.; Sicheritz-Pontén, Thomas; Sullivan, Patrick; Syed, Ali; Westergaard, David; Yadav, Rachita; Li, Ning; Xu, Xun; Hansen, Torben; Bolund, Lars; Krogh, Anders; Sørensen, Thorkild I. A.; Pedersen, Oluf Borbye; Gupta, Ramneek; Rasmussen, Simon; Børglum, Anders D.; Wang, Jun; Eiberg, Hans Rudolf Lytchoff; Kristiansen, Karsten; Brunak, Søren; Schierup, Mikkel Heide.
2017/08/03
Genome research
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Sørensen, Lasse Maretty; Jensen, Jacob Malte; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Villesen, Palle; Skov, Laurits; Belling, Kirstine G; Have, Christian Theil; Izarzugaza, Jose M. G.; Grosjean, Marie; Bork-Jensen, Jette; Grove, Jakob; Als, Thomas D.; Huang, Shujia; Chang, Yuqi; Xu, Ruiqi; Ye, Weijian; Rao, Junhua; Guo, Xiaosen; Sun, Jihua; Cao, Hongzhi; Ye, Chen; van Beusekom, Johan; Espeseth, Thomas; Flindt, Esben; Friborg, Rune M.; Halager, Anders E.; Le Hellard, Stephanie; Hultman, Christina M.; Lescai, Francesco; Li, Shengting; Lund, Ole; Løngren, Peter; Mailund, Thomas; Matey-Hernandez, Maria Luisa; Mors, Ole; Pedersen, Christian N. S.; Sicheritz-Pontén, Thomas; Sullivan, Patrick; Syed, Ali; Westergaard, David; Yadav, Rachita; Li, Ning; Xu, Xun; Hansen, Torben; Krogh, Anders; Bolund, Lars; Sørensen, Thorkild I. A.; Pedersen, Oluf Borbye; Gupta, Ramneek; Rasmussen, Simon; Besenbacher, Søren; Børglum, Anders D.; Wang, Jun; Eiberg, Hans Rudolf Lytchoff; Kristiansen, Karsten; Brunak, Søren; Schierup, Mikkel Heide
2017/07/26
Nature
The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
Gopalakrishnan, Shyam; Samaniego Castruita, Jose Alfredo; Sinding, Mikkel Holger Strander; Kuderna, Lukas F. K.; Räikkönen, Jannikke; Petersen, Bent; Sicheritz-Pontén, Thomas; Larson, Greger; Orlando, Ludovic Antoine Alexandre; Marques-Bonet, Tomas; Hansen, Anders Johannes; Dalén, Love; Gilbert, Tom
2017/06/29
BMC Genomics
Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Mak, Sarah; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas F. K.; Zhang, Wenwei; Fu, Shujin; Garrett Vieira, Filipe Jorge; Germonpré, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Tom
2017/06/26
Gigascience
Diversity, Prevalence, and Longitudinal Occurrence of Type II Toxin-Antitoxin Systems of Pseudomonas aeruginosa Infecting Cystic Fibrosis Lungs
Andersen, Sandra B.; Ghoul, Melanie; Griffin, Ashleigh S.; Petersen, Bent; Johansen, Helle K.; Molin, Søren
2017/06/23
Frontiers in Microbiology
Gene expression plasticity across hosts of an invasive scale insect species
Christodoulides, Nicholas; Van Dam, Alex R.; Peterson, Daniel A.; Frandsen, Rasmus John Normand; Mortensen, Uffe Hasbro; Petersen, Bent; Rasmussen, Simon; Normark, Benjamin B.; Hardy, Nate B
2017/05/04
PLOS ONE
Genome Sequence of Talaromyces atroroseus, Which Produces Red Colorants for the Food Industry
Thrane, Ulf; Rasmussen, Kasper Bøwig; Petersen, Bent; Rasmussen, Simon; Sicheritz-Pontén, Thomas; Mortensen, Uffe Hasbro
2017/03/02
Genome Announcements
Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)
Haddad, Nizar Jamal; Al-Nakeeb, Kosai Ali Ahmed; Petersen, Bent; Dalén, Love; Blom, Nikolaj; Sicheritz-Pontén, Thomas
2017/03/01
Mitochondrial DNA Part B
The first draft reference genome of the American mink (Neovison vison).
Cai Z, Petersen B, Sahana G, Madsen LB, Larsen K, Thomsen B, Bendixen C, Lund MS, Guldbrandtsen B, Panitz F
2017 Nov 6
Sci Rep
Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.
Al-Nakeeb K, Petersen TN, Sicheritz-Ponten T
2017 Nov 21
BMC Bioinformatics
Gene expression plasticity across hosts of an invasive scale insect species.
Christodoulides N, Van Dam AR, Peterson DA, Frandsen RJN, Mortensen UH, Petersen B, Rasmussen S, Normark BB, Hardy NB
2017 May 4
PLoS One
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads.
Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Moller Aarestrup F, Sicheritz-Ponten T
2017 May 3
PLoS One
Genome Sequence of Talaromyces atroroseus, Which Produces Red Colorants for the Food Industry.
Thrane U, Rasmussen KB, Petersen B, Rasmussen S, Sicheritz-Ponten T, Mortensen UH
2017 Mar 2
Genome Announc
Genome Sequence of Talaromyces atroroseus, Which Produces Red Colorants for the Food Industry.
Thrane U, Rasmussen KB, Petersen B, Rasmussen S, Sicheritz-Ponten T, Mortensen UH
2017 Mar 2
Genome Announc
Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).
Haddad NJ, Al-Nakeeb K, Petersen B, Dalen L, Blom N, Sicheritz-Ponten T
2017 Mar 1
Mitochondrial DNA B Resour
Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).
Haddad NJ, Al-Nakeeb K, Petersen B, Dalen L, Blom N, Sicheritz-Ponten T
2017 Mar 1
Mitochondrial DNA B Resour
The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.
Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, Kuderna LFK, Raikkonen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen AJ, Dalen L, Gilbert MTP
2017 Jun 29
BMC Genomics
The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.
Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, Kuderna LFK, Raikkonen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen AJ, Dalen L, Gilbert MTP
2017 Jun 29
BMC Genomics
Diversity, Prevalence, and Longitudinal Occurrence of Type II Toxin-Antitoxin Systems of Pseudomonas aeruginosa Infecting Cystic Fibrosis Lungs.
Andersen SB, Ghoul M, Griffin AS, Petersen B, Johansen HK, Molin S
2017 Jun 23
Front Microbiol
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.
Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Longren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Ponten T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sorensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Borglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH
2017 Aug 3
Nature
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.
Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Longren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Ponten T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sorensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Borglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH
2017 Aug 3
Nature
Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae).
Haddad N, Adjlane N, Loucif-Ayad W, Dash A, S N, Rajashekar B, Al-Nakeeb K, Sicheritz-Ponten T
2017 Aug 22
Mitochondrial DNA B Resour
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.
Mak SST, Gopalakrishnan S, Caroe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpre M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Ponten T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP
2017 Aug 1
Gigascience
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.
Mak SST, Gopalakrishnan S, Caroe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpre M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Ponten T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP
2017 Aug 1
Gigascience
Plasmodium falciparum var genes expressed in children with severe malaria encode CIDRα1 domains
Jespersen, Jakob S; Wang, Christian W; Mkumbaye, Sixbert I; Minja, Daniel Tr; Petersen, Bent; Turner, Louise; Petersen, Jens Ev; Lusingu, John Pa; Theander, Thor G; Lavstsen, Thomas
2016/06/27
EMBO Molecular Medicine
Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data
Rask, Thomas S; Petersen, Bent; Chen, Donald S; Day, Karen P; Pedersen, Anders Gorm
2016/04/22
BMC Bioinformatics
Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.
Palomo A, Jane Fowler S, Gulay A, Rasmussen S, Sicheritz-Ponten T, Smets BF
2016 Nov
ISME J
Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis.
Walter S, Ali S, Kemen E, Nazari K, Bahri BA, Enjalbert J, Hansen JG, Brown JK, Sicheritz-Ponten T, Jones J, de Vallavieille-Pope C, Hovmoller MS, Justesen AF
2016 Mar 20
Ecol Evol
Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut.
Roager HM, Hansen LB, Bahl MI, Frandsen HL, Carvalho V, Gobel RJ, Dalgaard MD, Plichta DR, Sparholt MH, Vestergaard H, Hansen T, Sicheritz-Ponten T, Nielsen HB, Pedersen O, Lauritzen L, Kristensen M, Gupta R, Licht TR
2016 Jun 27
Nat Microbiol
Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.
Friis-Nielsen J, Kjartansdottir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Ponten T, Lund O, Hansen AJ, Izarzugaza JM, Brunak S
2016 Feb 19
Viruses
Transcriptional interactions suggest niche segregation among microorganisms in the human gut.
Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Dore J, Machado AM, de Evgrafov MC, Hansen T, Jorgensen T, Bork P, Guarner F, Pedersen O, Sommer MO, Ehrlich SD, Sicheritz-Ponten T, Brunak S, Nielsen HB
2016 Aug 26
Nat Microbiol
Plasmodium falciparum var genes expressed in children with severe malaria encode CIDRalpha1 domains.
Jespersen JS, Wang CW, Mkumbaye SI, Minja DT, Petersen B, Turner L, Petersen JE, Lusingu JP, Theander TG, Lavstsen T
2016 Aug 1
EMBO Mol Med
Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data.
Rask TS, Petersen B, Chen DS, Day KP, Pedersen AG
2016 Apr 22
BMC Bioinformatics
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
Sanz, Pablo Librado; Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel; Jónsson, Hákon; Albrechtsen, Anders; Fumagalli, Matteo; Yang, Melinda A.; Gamba, Cristina; Seguin-Orlando, Andaine; Mortensen, Cecilie D.; Petersen, Bent; Hoover, Cindi A.; Lorente-Galdos, Belen; Nedoluzhko, Artem; Boulygina, Eugenia; Tsygankova, Svetlana; Neuditschko, Markus; Jagannathan, Vidhya; Theves, Catherine; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A. S.; Sicheritz-Pontén, Thomas; Popov, Ruslan; Grigoriev, Semyon; Alekseev, Anatoly N.; Rubin, Edward M.; McCue, Molly; Rieder, Stefan; Leeb, Tosso; Tikhonov, Alexei; Crubézy, Eric; Slatkin, Montgomery; Marques-Bonet, Tomas; Nielsen, Rasmus; Willerslev, Eske; Kantanen, Juha; Prokhortchouk, Egor; Orlando, Ludovic Antoine Alexandre
2015/12/15
Proceedings of the National Academy of Sciences
Within-host microevolution of Pseudomonas aeruginosa in Italian cystic fibrosis patients
Marvig, Rasmus Lykke; Dolce, Daniela; Sommer, Lea M.; Petersen, Bent; Ciofu, Oana; Campana, Silvia; Molin, Soren; Taccetti, Giovanni; Johansen, Helle Krogh
2015/10/19
BMC microbiology
Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse
Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel; Yang, Melinda A.; Sanz, Pablo Librado; Fumagalli, Matteo; Jónsson, Hákon; Bar-Gal, Gila Kahila; Albrechtsen, Anders; Garrett Vieira, Filipe Jorge; Petersen, Bent; Ginolhac, Aurélien; Seguin-Orlando, Andaine; Magnussen, Kim; Fages, Antoine Alphonse; Gamba, Cristina; Lorente-Galdos, Belen; Polani, Sagi; Steiner, Cynthia; Neuditschko, Markus; Jagannathan, Vidhya; Feh, Claudia; Greenblatt, Charles L.; Ludwig, Arne; Abramson, Natalia I.; Zimmermann, Waltraut; Schafberg, Renate; Tikhonov, Alexei; Sicheritz-Ponten, Thomas; Willerslev, Eske; Marques-Bonet, Tomas; Ryder, Oliver A.; McCue, Molly; Rieder, Stefan; Leeb, Tosso; Slatkin, Montgomery; Orlando, Ludovic Antoine Alexandre
2015/09/24
Current Biology
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses.
Zepeda Mendoza ML, Sicheritz-Ponten T, Gilbert MT
2015 Sep
Brief Bioinform
Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.
Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jonsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L
2015 Oct 5
Curr Biol
Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.
Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jonsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L
2015 Oct 5
Curr Biol
Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.
Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjogren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Ponten T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E
2015 Oct 22
Cell
Within-host microevolution of Pseudomonas aeruginosa in Italian cystic fibrosis patients.
Marvig RL, Dolce D, Sommer LM, Petersen B, Ciofu O, Campana S, Molin S, Taccetti G, Johansen HK
2015 Oct 19
BMC Microbiol
Reads2Type: a web application for rapid microbial taxonomy identification.
Saputra D, Rasmussen S, Larsen MV, Haddad N, Sperotto MM, Aarestrup FM, Lund O, Sicheritz-Ponten T
2015 Nov 25
BMC Bioinformatics
Traces of ATCV-1 associated with laboratory component contamination.
Kjartansdottir KR, Friis-Nielsen J, Asplund M, Mollerup S, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Sicheritz-Ponten T, Nielsen LP, Brunak S, Willerslev E, Izarzugaza JM, Hansen AJ
2015 Mar 3
Proc Natl Acad Sci U S A
Population genomics of Bronze Age Eurasia.
Allentoft ME, Sikora M, Sjogren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlstrom T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, Harvig L, Baron J, Della Casa P, Dabrowski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V, Kolar J, Kriiska A, Lasak I, Longhi C, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan R, Moiseyev V, Paja L, Palfi G, Pokutta D, Pospieszny L, Price TD, Saag L, Sablin M, Shishlina N, Smrcka V, Soenov VI, Szeverenyi V, Toth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Ponten T, Brunak S, Nielsen R, Kristiansen K, Willerslev E
2015 Jun 11
Nature
Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance.
Nordahl Petersen T, Rasmussen S, Hasman H, Caroe C, Baelum J, Schultz AC, Bergmark L, Svendsen CA, Lund O, Sicheritz-Ponten T, Aarestrup FM
2015 Jul 10
Sci Rep
Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients.
Wesolowska-Andersen A, Borst L, Dalgaard MD, Yadav R, Rasmussen KK, Wehner PS, Rasmussen M, Orntoft TF, Nordentoft I, Koehler R, Bartram CR, Schrappe M, Sicheritz-Ponten T, Gautier L, Marquart H, Madsen HO, Brunak S, Stanulla M, Gupta R, Schmiegelow K
2015 Feb
Leukemia
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jonsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Theves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubezy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L
2015 Dec 15
Proc Natl Acad Sci U S A
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jonsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Theves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubezy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L
2015 Dec 15
Proc Natl Acad Sci U S A
Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing.
Vinner L, Mourier T, Friis-Nielsen J, Gniadecki R, Dybkaer K, Rosenberg J, Langhoff JL, Cruz DF, Fonager J, Izarzugaza JM, Gupta R, Sicheritz-Ponten T, Brunak S, Willerslev E, Nielsen LP, Hansen AJ
2015 Aug 19
Sci Rep
Transcriptome and genome size analysis of the Venus flytrap.
Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Ponten T, Mundy J
2015 Apr 17
PLoS One
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, Mikkel; Jónsson, Hákon; Chang, Dan; Der Sarkissian, Clio; Ermini, Luca; Ginolhac, Aurélien; Albrechtsen, Anders; Dupanloup, Isabelle; Foucal, Adrien; Petersen, Bent; Fumagalli, Matteo; Raghavan, Maanasa; Seguin-Orlando, Andaine; Korneliussen, Thorfinn Sand; Velazquez, Amhed M.V.; Stenderup, Jesper; Hoover, Cindi A; Rubin, Carl-Johan; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; MacHugh, David E; Kalbfleisch, Ted; MacLeod, James N; Rubin, Edward M; Sicheritz-Ponten, Thomas; Andersson, Leif; Hofreiter, Michael; Marques-Bonet, Tomas; Gilbert, M. Thomas P.; Nielsen, Rasmus; Excoffier, Laurent; Willerslev, Eske; Shapiro, Beth; Orlando, Ludovic Antoine Alexandre
2014/12/30
Proceedings of the National Academy of Sciences
Speciation with gene flow in equids despite extensive chromosomal plasticity
Jónsson, Hákon; Schubert, Mikkel; Seguin-Orlando, Andaine; Ginolhac, Aurélien; Petersen, Lillian; Fumagalli, Matteo; Albrechtsen, Anders; Petersen, Bent; Korneliussen, Thorfinn Sand; Mouatt, Julia Thidamarth Vilstrup; Lear, Teri; Myka, Jennifer Leigh; Lundquist, Judith; Miller, Donald C.; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A.S.; Stagegaard, Julia; Strauss, Günter; Bertelsen, Mads Frost; Sicheritz-Ponten, Thomas; Antczak, Douglas F.; Bailey, Ernest; Nielsen, Rasmus; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre.
2014/12/30
Proceedings of the National Academy of Sciences
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y W; Faircloth, Brant C.; Nabholz, Benoit; Howard, Jason T.; Suh, Alexander; Weber, Claudia C.; Rodrigues da Fonseca, Rute Andreia; Li, Jianwen; Zhang, Fang; Li, Hui; Zhou, Long; Narula, Nitish; Liu, Liang; Ganapathy, Ganesh; Boussau, Bastien; Bayzid, Md Shamsuzzoha; Zavidovych, Volodymyr; Subramanian, Sankar; Gabaldón, Toni; Capella-Gutiérrez, Salvador; Huerta-Cepas, Jaime; Rekepalli, Bhanu; Terkelsen, Kasper Munch; Schierup, Mikkel Heide; Lindow, Bent Erik Kramer; Warren, Wesley C.; Ray, David; Green, Richard E.; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Li, Shengbin; Li, Ning; Huang, Yinhua; Derryberry, Elizabeth P.; Bertelsen, Mads Frost; Sheldon, Frederick H.; Brumfield, Robb T.; Mello, Claudio V.; Lovell, Peter V.; Wirthlin, Morgan; Schneider, Maria Paula Cruz; Prosdocimi, Francisco; Samaniego Castruita, Jose Alfredo; Velazquez, Amhed Missael Vargas; Alfaro Nuñez, Luis Alonso; Campos, Paula; Petersen, Bent; Sicheritz-Ponten, Thomas; Pas, An; Bailey, Tom; Scofield, Paul; Bunce, Michael; Lambert, David M.; Zhou, Qi; Perelman, Polina; Driskell, Amy C.; Shapiro, Beth; Xiong, Zijun; Zeng, Yongli; Liu, Shiping; Li, Zhenyu; Liu, Binghang; Wu, Kui; Xiao, Jin; Yinqi, Xiong; Zheng, Qiuemei; Zhang, Yong; Yang, Huanming; Wang, Jian; Smeds, Linnea; Rheindt, Frank E.; Braun, Michael; Fjeldså, Jon; Orlando, Ludovic Antoine Alexandre; Barker, F. Keith; Jønsson, Knud Andreas; Johnson, Warren; Koepfli, Klaus Peter; O'Brien, Stephen; Haussler, David; Ryder, Oliver A.; Rahbek, Carsten; Willerslev, Eske; Graves, Gary R.; Glenn, Travis C.; McCormack, John; Burt, Dave; Ellegren, Hans; Alström, Per; Edwards, Scott V.; Stamatakis, Alexandros; Mindell, David P.; Cracraft, Joel; Braun, Edward L.; Warnow, Tandy; Wang, Jun; Gilbert, M Thomas P; Zhang, Guojie
2014/12/12
Science
Structural conservation despite huge sequence diversity allows EPCR binding by the PfEMP1 family implicated in severe childhood malaria
Lau, Clinton K Y; Turner, Louise; Jespersen, Jakob S; Lowe, Edward D; Petersen, Bent; Wang, Christian W; Petersen, Jens E V; Lusingu, John; Theander, Thor G; Lavstsen, Thomas; Higgins, Matthew K
2014/12/04
Cell host & microbe
Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank).
Tsangaras K, Wales N, Sicheritz-Ponten T, Rasmussen S, Michaux J, Ishida Y, Morand S, Kampmann ML, Gilbert MT, Greenwood AD
2014 Oct 2
PLoS One
Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.
Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Goncalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SD, Willerslev E
2014 Nov 3
Curr Biol
The microbiome of New World vultures.
Roggenbuck M, Baerholm Schnell I, Blom N, Baelum J, Bertelsen MF, Sicheritz-Ponten T, Sorensen SJ, Gilbert MT, Graves GR, Hansen LH
2014 Nov 25
Nat Commun
Bacterial diversity in snow on North Pole ice floes.
Hauptmann AL, Stibal M, Baelum J, Sicheritz-Ponten T, Brunak S, Bowman JS, Hansen LH, Jacobsen CS, Blom N
2014 Nov
Extremophiles
Benchmarking of methods for genomic taxonomy.
Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Ponten T, Aarestrup FM, Ussery DW, Lund O
2014 May
J Clin Microbiol
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
Wesolowska-Andersen A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Ponten T, Gupta R, Licht TR
2014 Jun 5
Microbiome
Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.
Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW Jr, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Magi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E
2014 Jan 2
Nature
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.
Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Moller N, Aarestrup FM
2014 Jan
J Clin Microbiol
The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E
2014 Feb 13
Nature
Speciation with gene flow in equids despite extensive chromosomal plasticity.
Jonsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L
2014 Dec 30
Proc Natl Acad Sci U S A
Prehistoric genomes reveal the genetic foundation and cost of horse domestication.
Schubert M, Jonsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L
2014 Dec 30
Proc Natl Acad Sci U S A
Prehistoric genomes reveal the genetic foundation and cost of horse domestication.
Schubert M, Jonsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L
2014 Dec 30
Proc Natl Acad Sci U S A
Speciation with gene flow in equids despite extensive chromosomal plasticity.
Jonsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L
2014 Dec 30
Proc Natl Acad Sci U S A
Whole-genome analyses resolve early branches in the tree of life of modern birds.
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldon T, Capella-Gutierrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Nunez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jonsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alstrom P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G
2014 Dec 12
Science
Whole-genome analyses resolve early branches in the tree of life of modern birds.
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldon T, Capella-Gutierrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Nunez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jonsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alstrom P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G
2014 Dec 12
Science
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Dore J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Leonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sorensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD
2014 Aug
Nat Biotechnol
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Johnson, Philip L. F.; Fumagalli, Matteo; Mouatt, Julia Thidamarth Vilstrup; Raghavan, Maanasa; Korneliussen, Thorfinn Sand; Malaspinas, Anna Sapfo; Vogt, Josef; Szklarczyk, Damian Milosz; Kelstrup, Christian; Vinther, Jakob; Dolocan, Andrei; Stenderup, Jesper; Velazquez, Amhed M. V.; Cahill, James; Rasmussen, Morten; Wang, Xiaoli; Min, Jiumeng; Zazula, Grant D.; Seguin-Orlando, Andaine; Mortensen, Cecilie; Magnussen, Kim; Thompson, John F.; Weinstock, Jacobo; Gregersen, Kristian; Røed, Knut H.; Eisenmann, Véra; Rubin, Carl J.; Miller, Donald C.; Antczak, Douglas F.; Bertelsen, Mads F.; Brunak, Søren; Al-Rasheid, Khaled A. S.; Ryder, Oliver; Andersson, Leif; Mundy, John; Krogh, Anders; Gilbert, Tom; Kjær, Kurt H.; Sicheritz-Pontén, Thomas; Jensen, Lars Juhl; Olsen, Jesper Velgaard; Hofreiter, Michael; Nielsen, Rasmus; Shapiro, Beth; Wang, Jun; Willerslev, Eske
2013/06/26
Nature
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, Roed 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, Kjaer K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E
2013 Jul 4
Nature
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, Roed 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, Kjaer K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E
2013 Jul 4
Nature
Complete genes may pass from food to human blood.
Spisak S, Solymosi N, Ittzes P, Bodor A, Kondor D, Vattay G, Bartak BK, Sipos F, Galamb O, Tulassay Z, Szallasi Z, Rasmussen S, Sicheritz-Ponten T, Brunak S, Molnar B, Csabai I
2013 Jul 30
PLoS One
Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.
Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Martin Embley T, Hirt RP
2013 Feb 25
Genome Biol
Bacterial natural transformation by highly fragmented and damaged DNA.
Overballe-Petersen S, Harms K, Orlando LA, Mayar JV, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, Inselmann S, de Vries J, Wackernagel W, Pybus OG, Nielsen R, Johnsen PJ, Nielsen KM, Willerslev E
2013 Dec 3
Proc Natl Acad Sci U S A
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, Jorgensen 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, Clement K, Dore J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, Bork P, Wang J, Ehrlich SD, Pedersen O
2013 Aug 29
Nature
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
2013 Apr
ISME J
Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs).
Udatha DB, Rasmussen S, Sicheritz-Ponten T, Panagiotou G
2013
Methods Mol Biol
Novel inhibitory activity of the Staphylococcus aureus NorA efflux pump by a kaempferol rhamnoside isolated from Persea lingue Nees.
Holler JG, Christensen SB, Slotved HC, Rasmussen HB, Guzman A, Olsen CE, Petersen B, Molgaard P
2012 May
J Antimicrob Chemother
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
2012 Jan
ISME J
Multilocus sequence typing of total-genome-sequenced bacteria.
Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Ponten T, Ussery DW, Aarestrup FM, Lund O
2012 Apr
J Clin Microbiol
An Aboriginal Australian genome reveals separate human dispersals into Asia.
Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Avila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Ponten T, Villems R, Nielsen R, Wang J, Willerslev E
2011 Oct 7
Science
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, Dore J, Antolin 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, Merieux 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
2011 May 12
Nature
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
2011 Jun
Leukemia
NetTurnP–neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features
Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl
2010/11/30
PLoS One
NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.
Petersen B, Lundegaard C, Petersen TN
2010 Nov 30
PLoS One
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, Le 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, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J
2010 Mar 4
Nature
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
2010 Feb 8
BMC Genomics
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 MT, 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, Gronnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E
2010 Feb 11
Nature
A generic method for assignment of reliability scores applied to solvent accessibility predictions
Petersen, Bent; Petersen, Thomas Nordahl; Andersen, Pernille; Nielsen, Morten; Lundegaard, Claus
2009/07/31
BMC structural biology
A generic method for assignment of reliability scores applied to solvent accessibility predictions.
Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C
2009 Jul 31
BMC Struct Biol
InterMap3D: predicting and visualizing co-evolving protein residues.
Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Molgaard A, Pedersen AG
2009 Aug 1
Bioinformatics
The genus burkholderia: analysis of 56 genomic sequences.
Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM
2009
Genome Dyn
Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis.
Alsmark UC, Sicheritz-Ponten T, Foster PG, Hirt RP, Embley TM
2009
Methods Mol Biol
Linear motif atlas for phosphorylation-dependent signaling.
Miller ML, Jensen LJ, Diella F, Jorgensen 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
2008 Sep 2
Sci Signal
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
2008 Jul
Antimicrob Agents Chemother
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, Muller 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
2007 Jan 12
Science
Structure and content of the Entamoeba histolytica genome.
Clark CG, Alsmark UC, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noel CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillen N, Duchene M, Nozaki T, Hall N
2007
Adv Parasitol
Genome update: sigma factors in 240 bacterial genomes.
Kill K, Binnewies TT, Sicheritz-Ponten T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW
2005 Oct
Microbiology
Genome update: distribution of two-component transduction systems in 250 bacterial genomes.
Kiil K, Ferchaud JB, David C, Binnewies TT, Wu H, Sicheritz-Ponten T, Willenbrock H, Ussery DW
2005 Nov
Microbiology
Genome update: prediction of secreted proteins in 225 bacterial proteomes.
Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Ponten T, Ussery DW
2005 Jun
Microbiology
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-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N
2005 Feb 24
Nature
GRS: a graphic tool for genome retrieval and segment analysis.
Sicheritz-Ponten T, Andersson SG
1997
Microb Comp Genomics