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

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary.

Hauptmann AL, Markussen TN, Stibal M, Olsen NS, Elberling B, Baelum J, Sicheritz-Ponten T, Jacobsen CS

2016 Sep 21

Front Microbiol

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

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection.

Marcatili P, Nielsen MW, Sicheritz-Ponten T, Jensen TK, Schafer-Nielsen C, Boye M, Nielsen M, Klitgaard K

2016 Dec 1

BMC Genomics

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

Structural conservation despite huge sequence diversity allows EPCR binding by the PfEMP1 family implicated in severe childhood malaria.

Lau CK, Turner L, Jespersen JS, Lowe ED, Petersen B, Wang CW, Petersen JE, Lusingu J, Theander TG, Lavstsen T, Higgins MK

2015 Jan 14

Cell host & microbe

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

Global features of the Alcanivorax borkumensis SK2 genome.

Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW

2008 Mar

Environ Microbiol

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

Trichomonas vaginalis surface proteins: a view from the genome.

Hirt RP, Noel CJ, Sicheritz-Ponten T, Tachezy J, Fiori PL

2007 Nov

Trends Parasitol

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

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

2004 May-Jun

J Proteome Res

A first glimpse into the pattern and scale of gene transfer in Apicomplexa.

Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC

2004 Mar 9

Int J Parasitol

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins.

Diella F, Cameron S, Gemund C, Linding R, Via A, Kuster B, Sicheritz-Ponten T, Blom N, Gibson TJ

2004 Jun 22

BMC Bioinformatics

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

2004 Jun

Proteomics

GenePublisher: Automated analysis of DNA microarray data.

Knudsen S, Workman C, Sicheritz-Ponten T, Friis C

2003 Jul 1

Nucleic Acids Res

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.

Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jorgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D

2003 Apr 2

BMC Genomics

A phylogenomic approach to microbial evolution.

Sicheritz-Ponten T, Andersson SG

2001 Jan 15

Nucleic Acids Res

The genome sequence of Rickettsia prowazekii and the origin of mitochondria.

Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UC, Podowski RM, Naslund AK, Eriksson AS, Winkler HH, Kurland CG

1998 Nov 12

Nature

A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae.

Sicheritz-Ponten T, Kurland CG, Andersson SG

1998 Jul 20

Biochim Biophys Acta

BioWish: a molecular biology command extension to Tcl/Tk.

Sicheritz-Ponten T

1997 Dec

Comput Appl Biosci

GRS: a graphic tool for genome retrieval and segment analysis.

Sicheritz-Ponten T, Andersson SG

1997

Microb Comp Genomics