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Items: 13

1.

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment 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, Rajpert-De Meyts E, 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 Sep 13;220(8):1312-1324. doi: 10.1093/infdis/jiz318.

2.

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
3.

Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion.

Löber U, Hobbs M, Dayaram A, Tsangaras K, Jones K, Alquezar-Planas DE, Ishida Y, Meers J, Mayer J, Quedenau C, Chen W, Johnson RN, Timms P, Young PR, Roca AL, Greenwood AD.

Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):8609-8614. doi: 10.1073/pnas.1807598115. Epub 2018 Aug 6.

4.

Adaptation and conservation insights from the koala genome.

Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K.

Nat Genet. 2018 Aug;50(8):1102-1111. doi: 10.1038/s41588-018-0153-5. Epub 2018 Jul 2.

5.

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.

6.

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartman S, Greenwood AD.

PeerJ. 2016 Mar 28;4:e1847. doi: 10.7717/peerj.1847. eCollection 2016.

7.

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.

8.

An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data.

Tsangaras K, Mayer J, Alquezar-Planas DE, Greenwood AD.

Viruses. 2015 Nov 24;7(11):6089-107. doi: 10.3390/v7112927.

9.

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.

10.

Medical and molecular perspectives into a forgotten epidemic: encephalitis lethargica, viruses, and high-throughput sequencing.

Tappe D, Alquezar-Planas DE.

J Clin Virol. 2014 Oct;61(2):189-95. doi: 10.1016/j.jcv.2014.07.013. Epub 2014 Jul 30. Review.

PMID:
25129855
11.

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.

12.

Deep sequencing of RNA from ancient maize kernels.

Fordyce SL, Ávila-Arcos MC, Rasmussen M, Cappellini E, Romero-Navarro JA, Wales N, Alquezar-Planas DE, Penfield S, Brown TA, Vielle-Calzada JP, Montiel R, Jørgensen T, Odegaard N, Jacobs M, Arriaza B, Higham TF, Ramsey CB, Willerslev E, Gilbert MT.

PLoS One. 2013;8(1):e50961. doi: 10.1371/journal.pone.0050961. Epub 2013 Jan 11.

13.

Roche genome sequencer FLX based high-throughput sequencing of ancient DNA.

Alquezar-Planas DE, Fordyce SL.

Methods Mol Biol. 2012;888:109-18. doi: 10.1007/978-1-61779-870-2_7.

PMID:
22665278

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