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Items: 46

1.

High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach.

Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir 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, De Meyts ER, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ.

J Infect Dis. 2019 Jun 28. pii: jiz318. doi: 10.1093/infdis/jiz318. [Epub ahead of print]

PMID:
31253993
2.

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries.

Asplund M, Kjartansdóttir 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-Pontén T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ.

Clin Microbiol Infect. 2019 May 4. pii: S1198-743X(19)30206-X. doi: 10.1016/j.cmi.2019.04.028. [Epub ahead of print]

3.

Correction: Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii.

Salunke R, Mourier T, Banerjee M, Pain A, Shanmugam D.

PLoS Biol. 2019 Mar 6;17(3):e3000176. doi: 10.1371/journal.pbio.3000176. eCollection 2019 Mar.

4.

MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements.

Rey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, Röder T, Bruhn Pedersen L, Naesborg-Nielsen C, Sinding MS, Fredensborg Rath M, Li Z, Petersen B, Gilbert MTP, Bunce M, Mourier T, Hansen AJ.

Mol Ecol Resour. 2019 Mar;19(2):512-525. doi: 10.1111/1755-0998.12984. Epub 2019 Feb 6.

PMID:
30575257
5.

Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii.

Salunke R, Mourier T, Banerjee M, Pain A, Shanmugam D.

PLoS Biol. 2018 Jul 13;16(7):e2006128. doi: 10.1371/journal.pbio.2006128. eCollection 2018 Jul. Erratum in: PLoS Biol. 2019 Mar 6;17(3):e3000176.

6.

3D high resolution imaging for microelectronics: A multi-technique survey on copper pillars.

Fraczkiewicz A, Lorut F, Audoit G, Boller E, Capria E, Cloetens P, Da Silva J, Farcy A, Mourier T, Ponthenier F, Bleuet P.

Ultramicroscopy. 2018 Oct;193:71-83. doi: 10.1016/j.ultramic.2018.04.012. Epub 2018 Jun 15.

PMID:
29957329
7.

Correction to: Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin.

Omland SH, Wettergren EE, Mollerup S, Asplund M, Mourier T, Hansen AJ, Gniadecki R.

BMC Cancer. 2018 Jan 30;18(1):111. doi: 10.1186/s12885-018-3987-4.

8.

Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin.

Omland SH, Wettergren EE, Mollerup S, Asplund M, Mourier T, Hansen AJ, Gniadecki R.

BMC Cancer. 2017 Oct 7;17(1):675. doi: 10.1186/s12885-017-3663-0. Erratum in: BMC Cancer. 2018 Jan 30;18(1):111.

9.

Cutavirus in Cutaneous Malignant Melanoma.

Mollerup S, Fridholm H, Vinner L, Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Herrera JA, Steiniche T, Mourier T, Brunak S, Willerslev E, Izarzugaza JM, Hansen AJ, Nielsen LP.

Emerg Infect Dis. 2017 Feb;23(2):363-365. doi: 10.3201/eid2302.161564.

10.

Transposable elements and circular DNAs.

Mourier T.

Mob Genet Elements. 2016 Sep 26;6(6):e1240748. doi: 10.1080/2159256X.2016.1240748. eCollection 2016.

11.

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.

Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15066-15071. doi: 10.1073/pnas.1615819114. Epub 2016 Dec 12.

12.

High diversity of picornaviruses in rats from different continents revealed by deep sequencing.

Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR, Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, Nielsen LP, Vinner L, Hansen AJ.

Emerg Microbes Infect. 2016 Aug 17;5(8):e90. doi: 10.1038/emi.2016.90.

13.

Potential movement of transposable elements through DNA circularization.

Mourier T.

Curr Genet. 2016 Nov;62(4):697-700. Epub 2016 Mar 15. Review.

PMID:
26979517
14.

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.

Friis-Nielsen J, Kjartansdóttir 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-Pontén T, Lund O, Hansen AJ, Izarzugaza JM, Brunak S.

Viruses. 2016 Feb 19;8(2). pii: E53. doi: 10.3390/v8020053.

15.

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing.

Mollerup S, Friis-Nielsen J, Vinner L, Hansen TA, Richter SR, Fridholm H, Herrera JA, Lund O, Brunak S, Izarzugaza JM, Mourier T, Nielsen LP, Hansen AJ.

J Clin Microbiol. 2016 Apr;54(4):980-7. doi: 10.1128/JCM.02723-15. Epub 2016 Jan 27.

16.

Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae.

Møller HD, Larsen CE, Parsons L, Hansen AJ, Regenberg B, Mourier T.

G3 (Bethesda). 2015 Dec 17;6(2):453-62. doi: 10.1534/g3.115.025858.

17.

Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads.

Mourier T, Mollerup S, Vinner L, Hansen TA, Kjartansdóttir KR, Guldberg Frøslev T, Snogdal Boutrup T, Nielsen LP, Willerslev E, Hansen AJ.

Sci Rep. 2015 Oct 23;5:15644. doi: 10.1038/srep15644.

18.

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.

Sci Rep. 2015 Aug 19;5:13201. doi: 10.1038/srep13201.

19.

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites.

Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A.

Elife. 2015 Jul 15;4:e06974. doi: 10.7554/eLife.06974.

20.

Draft Genome Sequence of the First Human Isolate of the Ruminant Pathogen Mycoplasma capricolum subsp. capricolum.

Seersholm FV, Fischer A, Heller M, Jores J, Sachse K, Mourier T, Hansen AJ.

Genome Announc. 2015 Jun 18;3(3). pii: e00583-15. doi: 10.1128/genomeA.00583-15.

21.

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features.

Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, Panigrahi A, Vermont SJ, Otto TD, Wastling J, Pain A.

PLoS One. 2015 Apr 13;10(4):e0124473. doi: 10.1371/journal.pone.0124473. eCollection 2015.

22.

Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery.

Jensen RH, Mollerup S, Mourier T, Hansen TA, Fridholm H, Nielsen LP, Willerslev E, Hansen AJ, Vinner L.

PLoS One. 2015 Apr 8;10(4):e0122636. doi: 10.1371/journal.pone.0122636. eCollection 2015.

23.

The genomic and phenotypic diversity of Schizosaccharomyces pombe.

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J.

Nat Genet. 2015 Mar;47(3):235-41. doi: 10.1038/ng.3215. Epub 2015 Feb 9.

24.

Traces of ATCV-1 associated with laboratory component contamination.

Kjartansdóttir 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-Pontén T, Nielsen LP, Brunak S, Willerslev E, Izarzugaza JM, Hansen AJ.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):E925-6. doi: 10.1073/pnas.1423756112. Epub 2015 Feb 5. No abstract available.

25.

Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J.

Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.

26.

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A.

Genome Res. 2014 Oct;24(10):1676-85. doi: 10.1101/gr.168955.113. Epub 2014 Jul 11.

27.

Transposable elements in cancer as a by-product of stress-induced evolvability.

Mourier T, Nielsen LP, Hansen AJ, Willerslev E.

Front Genet. 2014 May 30;5:156. doi: 10.3389/fgene.2014.00156. eCollection 2014.

28.

Fifty thousand years of Arctic vegetation and megafaunal diet.

Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergård M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Bråthen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sønstebø JH, Murton J, Sher A, Rasmussen M, Rønn R, Mourier T, Cooper A, Austin J, Möller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RD, Gilbert MT, Kjær KH, Orlando L, Brochmann C, Taberlet P.

Nature. 2014 Feb 6;506(7486):47-51. doi: 10.1038/nature12921.

PMID:
24499916
29.

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing.

Alquezar-Planas DE, Mourier T, Bruhn CA, Hansen AJ, Vitcetz SN, Mørk S, Gorodkin J, Nielsen HA, Guo Y, Sethuraman A, Paxinos EE, Shan T, Delwart EL, Nielsen LP.

Sci Rep. 2013;3:2468. doi: 10.1038/srep02468.

30.

Probable transmission of coxsackie B3 virus from human to chimpanzee, Denmark.

Nielsen SC, Mourier T, Baandrup U, Søland TM, Bertelsen MF, Gilbert MT, Nielsen LP.

Emerg Infect Dis. 2012 Jul;18(7):1163-5. doi: 10.3201/eid1807.111689.

31.

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.

Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A, Wastling JM.

PLoS Pathog. 2012;8(3):e1002567. doi: 10.1371/journal.ppat.1002567. Epub 2012 Mar 22.

32.

Statistical guidelines for detecting past population shifts using ancient DNA.

Mourier T, Ho SY, Gilbert MT, Willerslev E, Orlando L.

Mol Biol Evol. 2012 Sep;29(9):2241-51. doi: 10.1093/molbev/mss094. Epub 2012 Mar 16.

PMID:
22427706
34.

Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons.

Mourier T, Willerslev E.

BMC Genomics. 2010 Mar 12;11:167. doi: 10.1186/1471-2164-11-167.

35.

Retrotransposons and non-protein coding RNAs.

Mourier T, Willerslev E.

Brief Funct Genomic Proteomic. 2009 Nov;8(6):493-501. doi: 10.1093/bfgp/elp036. Epub 2009 Sep 3. Review.

PMID:
19729447
36.

Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes?

Mourier T, Willerslev E.

PLoS One. 2008;3(11):e3760. doi: 10.1371/journal.pone.0003760. Epub 2008 Nov 19.

37.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG, Berriman M.

Nature. 2008 Oct 9;455(7214):799-803. doi: 10.1038/nature07306.

38.

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.

Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A.

Genome Res. 2008 Feb;18(2):281-92. Epub 2007 Dec 20.

39.

The biology of intron gain and loss.

Jeffares DC, Mourier T, Penny D.

Trends Genet. 2006 Jan;22(1):16-22. Epub 2005 Nov 14.

PMID:
16290250
40.

Reverse transcription in genome evolution.

Mourier T.

Cytogenet Genome Res. 2005;110(1-4):56-62. Review.

PMID:
16093658
41.

The genome of the social amoeba Dictyostelium discoideum.

Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A.

Nature. 2005 May 5;435(7038):43-57.

42.

A selenocysteine tRNA and SECIS element in Plasmodium falciparum.

Mourier T, Pain A, Barrell B, Griffiths-Jones S.

RNA. 2005 Feb;11(2):119-22.

43.

Eukaryotic intron loss.

Mourier T, Jeffares DC.

Science. 2003 May 30;300(5624):1393. No abstract available.

44.

Contamination in the draft of the human genome masquerades as lateral gene transfer.

Willerslev E, Mourier T, Hansen AJ, Christensen B, Barnes I, Salzberg SL.

DNA Seq. 2002 Apr;13(2):75-6. No abstract available.

PMID:
12180348
45.

The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus.

Mourier T, Hansen AJ, Willerslev E, Arctander P.

Mol Biol Evol. 2001 Sep;18(9):1833-7. No abstract available.

PMID:
11504863
46.

Statistical evidence for miscoding lesions in ancient DNA templates.

Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P.

Mol Biol Evol. 2001 Feb;18(2):262-5. No abstract available.

PMID:
11158385

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