Publications 2011 – University of Copenhagen

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GeoGenetics > Publications > Publications 2011

Publications 2011

Allentoft ME, Oskam C, Houston J, Hale ML, Gilbert MTP, Rasmussen M, Spencer P, Jacomb C, Willerslev E, Holdaway RN, Bunce M. Profiling the dead: Generating microsatellite data from fossil bones of extinct megafauna - protocols, problems and prospects. PLoS ONE 6:e16670, (2011)

Arnold L, Roberts RG, MacPhee RDE, Haile JS, Brock F, Möller P, Froese DG, Tikhonov AN, Chivas AR, Gilbert MTP, Willerslev E. Dirt, dates and DNA: OSL and radiocarbon chronologies of perennially-frozen sediments in Siberia, and their implications for sedimentary ancient DNA studies. Boreas 40:417-445, (2011)

Arppe L, Aaris-Sørensen K, Daugnora L, Lõugas L, Wojtal P, Zupins I. The palaeoenvironmental delta13C record in European woolly mammoth. Quaternary International 245:285-290, (2011)

Ávila-Arcos MC, Cappellini E, Romero-Navarro JA, Wales N, Moreno-Mayar JV, Rasmussen M, Fordyce SL, Montiel R, Vielle-Calzada J-P, Willerslev E, Gilbert MTP. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Scientific Reports 1:74, (2011)

Baret F, Bringer F, Busti D, Carpentier A, Caudron N, Charrier C, Celle F, Daoust G, Froissart H, Geray L, Jalabert S, Mauffrey A, Olive C, Picoche J-M, Rebulard S, Salomon L, Seguin-Orlando A, Seyed R, Thébault P-O, Vigier S, Woerle A. SVT 1re S. (Editor: Belin ). A French textbook for before-last year of high-school (scientific sections) on natural and earth sciences, 335 pages, April 2011

Barrett JH, Orton D, Johnstone C, Harland J, Van Neer W, Ervynck A, Roberts C, Locker A, Amundsen C, Enghoff IB, Hamilton-Dyer S, Heinrich D, Hufthammer A, Jones A, Jonsson L, Makowiecki D, Pope P, O'Connell T, de Roo T, Richards M. Interpreting the expansion of sea fishing in Medieval Europe using stable isotope analysis of archaeological cod bones. Journal of Archaeological Science 36: 1516-1524. (2011)

Bjørk AA, Björck S, Cronholm A, Haile J, Ljung K, Porter C. Possible Late Pleistocene volcanic activity on Nightingale Island, South Atlantic Ocean, based on geoelectrical resistivity measurements, sediment corings and 14C dating. GFF, vol. 133, Issue 3-4, pp. 141-147, (2011)

Bohmann K, Monadjem A, Noer C, Rasmussen M, Zeale M, Clare E, Jones G, Willerslev E, Gilbert MTP. Molecular diet analysis of two African free-tailed bats (Molossidae) using high throughput sequencing. PLoS ONE 6:e21441, (2011)

Bou Kheir T, Futoma-Kazmierczak A, Jacobsen A, Krogh A, Bardram L, Hother C, Grønbæk K, Federspiel B, Lund AH, Friis-Hansen L. miR-449 inhibits cell proliferation and is down-regulated in gastric cancer. Mol. cancer, 10:29, 2011

Brandt LØ, Tranekjer LD, Mannering U, Ringgaard M, Frei KM, Willerslev E, Gleba M, Gilbert MTP. Characterising the potential of sheep wool for ancient DNA analyses. Arch. Anth. Sci. 3:209-221, (2011)

Bruhn CAW, Gilbert MTP. HIV-2 down, HIV-1 to go? - Understanding the possibilities of treatment as prevention. Lancet Infectious Diseases 11:260-261, (2011)

Cheung C, Schroeder H, Hedges REM. Diet, social differentiation and cultural change in Roman Britain: new isotopic evidence from Gloucestershire. Arch. Anth. Sci. 4(1), 61–73. doi:10.1007/s12520-011-0083-y, (2011)

Deecke VB, Nykänen M, Foote AD, Janik VM. Vocal behavior and feeding ecology of killer whales (Orcinus orca) around Shetland, UK. Aquatic Biology 13:79-88, (2011)

Duchene S, Archer FI, Vilstrup J, Caballero S, and Morin PA. Mitogenome phylogenetics: The impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS ONE 6(11): e27138, (2011)

Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG, Shapiro B. Multiple hybridizations between ancient brown and polar bears and an Irish origin for the modern polar bear matriline. Curr. Biol. 21, 1251-1258, (2011)

Enghoff IB. Regionality and biotope exploitation in Danish Ertebølle and adjoining periods. Scientia Danica. Series B, Biologica 1: 1-394. (2011)

Foote AD, Morin PA, Durban JW, Willerslev E, Orlando L, Gilbert MTP. Out of the Pacific and back again: insights into the matrilineal history of Pacific killer whale ecotypes. PLoS ONE 6:e24980, (2011)

Foote AD, Morin PA, Durban JW, Pitman RL, Wade P, Willerslev E, Gilbert MTP, da Fonseca RR. Positive selection on the killer whale mitogenome. Biology Letters 1:116-118, (2011)

Foote AD, Vilstrup JT, de Stephanis R, Verborgh P, Abel Nielsen SC, Deaville R, Kleivane L, Martin V, Miller PJO, Øien N, Perez-Gil M, Rasmussen M, Reid RJ, Robertson KM, Rogan E, Simla T, Tejedor ML, Vester H, Vikingsson GA, Willerslev E, Gilbert MTP, Piertney SB. Genetic differentiation among North Atlantic killer whale populations. Mol. Ecol. 20:629-641, (2011)

Fordyce SL, Avila-Arcos MC, Rockenbauer E, Børsting C, Frank-Hansen R, Torp Petersen F, Willerslev E, Hansen AJ, Morling N, Gilbert MTP. High-throughput sequencing of core STR loci for forensic genetic investigation using the Roche Genome Sequencer FLX platform. Biotechniques 51:127-133, (2011)

Frankel LB, Wen J, Lees M, Høyer-Hansen M, Farkas T, Krogh A, Ja ̈a ̈ttela M, Lund AH. microRNA-101 is a potent inhibitor of autophagy. EMBO Journal, 30(22):4628–4641, Nov 2011

Funder S, Gosse H, Jepsen HF, Kaas E, Kjær KH, Korsgaard NJ, Larsen NK, Linderson H, Lyså A, Möller P, Olsen J, Willerslev E. A 10,000-year record of Arctic Ocean sea ice variability - View from the beach. Science 333, 747-750 (2011) (PR)(CO)

Funder S, Kjeldsen KK, Kjær KH, Cofaigh CO. The Greenland Ice Sheet During the Past 300,000 Years: A Review. Natural History, 699-713, (2011), doi:10.1016/B978-0-444-53447-7.00050-7 (PR)(CO)

Gilbert MTP. News and Perspectives: The Mummy Returns...and sheds new light on old questions. Mol. Ecol. 20: 4195-4198, (2011)

Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 15:2153-2155, (2011)

Glykou A, Heinrich D, Enghoff IB. Bearbeitete Wirbel von Thunfischen, Thunnus thynnus (L. 1758). Frühneuzeitliche objekte unbekannter function. Offa 63/64, 2006/07 (2011):  209-215

Grønnow B, Gulløv HC, Jakobsen BH, Gotfredsen AB, Kauffmann LH, Kroon A, Pedersen JT, Sørensen M. At the Edge: High Arctic Walrus Hunters during the Little Ice Age. Antiquity 85 (329) September 2011: 960-977

Harvey DJ, Gange AC, Hawes CJ, Rink M,.......Thomsen PF,.......(48 authors total). Bionomics and distribution of the stag beetle, Lucanus cervus (L.) across Europe. Insect Conservation and Diversity 4, 23-38, (2011)

Heide-Jørgensen MP, Garde,E. Fetal growth of narwhals (Monodon monoceros). Marine Mammal Science 27:659-664, (2011)Til toppen

Houmark-Nielsen M. Pleistocene Glaciations in Denmark: A Closer Look at Chronology, Ice Dynamics and Landforms. In Ehlers J, Gibbard PL, Hughes PD (eds.). Developments in Quaternary Science, Vol. 15, 47-58, (2011)

Houmark-Nielsen M. Geologien i Odsherred, Odsherredbuerne: Et istidslandskab skabt i krydsfeltet mellem tre isstrømme. & Sites: Lavningerne i Odsherred, Nakke-Rørvig Halvøen, Vejrhøjbuen, Gniben, Klint-Ebbeløkke, Korevle og Ordrup Næs. http://www.geopark-odsherred.dk/page5341.aspx (2011)

Kampmann ML, Fordyce SL, Avila-Arcos MC, Rasmussen M, Willerslev E, Nielsen LP, Gilbert MTP. A simple method for the parallel deep sequencing of full influenza A genomes. J. Virological Methods 178:243-248, (2011)

Lalueza-Fox C, Gilbert MTP. Paleogenomics of archaeic hominins. Curr. Biol. 21, R1002–R1009, (2011)

Lalueza-Fox C, Rosas A, Estalrrich A, Gigli E, Campos PF, Garcia-Tabernero A, Garcia-Vargas S, Sanchez-Quinto F, Ramirez O, Civit S, Bastir M, Huguet R, Santamaria D, Gilbert MTP, Willerslev E, de la Rasilla M. Genetic evidence for patrilocal mating behaviour among Neandertal groups. Proc. Natl. Acad. Sci. USA. 108:250-253, (2011)

Lalueza-Fox C, Rosas A, de la Rasilla M, Gilbert MTP, Willerslev E. Reply to Vigilant and Langergraber: Patrilocality in Neandertals is still the most plausible explanation. Proc. Natl. Acad. Sci. USA. 108, E88-E88, (2011)

Larsen N, Kjær KH, Funder S, Möller P, van der Meer JJ, Schomacker A, Linge H, & Darby DA, (2011). Late Quaternary glaciation history of northernmost Greenland - Evidence of shelf-based ice. Quaternary Science Reviews 29, 3399-3414. (PR)(CO)

Larsen NK, Kjær KH, Olsen J, Funder S, Kjeldsen KK, Nørgaard-Pedersen N. Restricted impact of Holocene climate variations on the southern Greenland Ice Sheet. Quat. Sci. Rev. 1-10, (2011). doi:10.1016/j.quascirev.2011.07.022 (PR)(CO)

Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper, A, Weinstock J, Willerslev E, Shapiro B. Hofreiter M. Rediscovering the lost diversity of paternal horse lineages using ancient DNA. Nature Communications, 2, 450pp. 2011

Lorenzen ED, Nogués-Bravo, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R, Ho SYW, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli K-P, Froese D, Zazula G, Stafford Jr. TW, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbeck C, Willerslev E. Individualistic species responses to climate and humans determinate Late Quaternary megafaunal extinction and survival. Nature 479:359-364, (2011)

Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A. IMPACT: integrated multiprogram platform for analyses in ConTest. J Hered. 2011 May-Jun;102(3):366-9. Epub 2011 Mar 16

Mourier T. Retrotransposon-Centered Analysis of piRNA Targeting Shows a Shift from Active to Passive Retrotransposon Transcription in Developing Mouse Testes. BMC Genomics 12:440, (2011)

Nygaard S, Zhang G, Schiøtt M, Li C, Wurm Y, Hu Y, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJ, Wang J, Boomsma JJ. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res. 21(8):1339–1348, 2011

Olmi L, Maria Mercuri AM, Gilbert MPT, Biagetti S, Fordyce S, Cappellini E, Massamba N’siala I, di Lernia S. Morphological and genetic analyses of early-mid Holocene wild cereals from the Takarkori rockshelter (central Sahara, Libya): first results and prospects. In Reports in African Archaeology; Windows on the African Past; Current approaches to African archaeobotany. Pp. 175-184. 2011. Editor: Catherine D'Andrea

Olsen ME, Bengtsson CF, Bertelsen MF, Willerslev E, Gilbert MTP. DNA from keratinous tissue, part II: Feather. Ann Anat 194:31-35, (2011)Til toppen

Orton DC, Makowiecki D, de Roo T, Johnstone C, Harland J, Jonsson L, Heinrich D, Enghoff IB, Lougas L, Van Neer W, Ervynck A, Hufthammer AK, Amundsen C, Jones AK, Locker A, Hamilton-Dyer S, Pope P, MacKenzie B, Richards M, O'Connell TC, Barrett JH. Stable isotope evidence for Late Medieval (14th-15th C) origin of the eastern Baltic cod (Gadus morhua) fishery. PloS One 6(11): 1-15. (2011)

Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KAS, Gilbert MTP, Willerslev E. True single-molecule DNA sequencing of a Pleistocene horse bone. Genome Res. 21: 1705-1719, (2011)

Pantmann P, Enghoff IB. På dybt vand. Skalk 2011(1): 12-15

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 F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weiner LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut F-X, 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 C, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94-98, (2011)

Razgour O, Clare EL, Zeale MRK, Schnell IB, Rasmussen M, Gilbert MTP, Jones. High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species. Ecology and Evolution, 1, 556-70 (2011)

Rehn N, Filatova OA, Durban JW, Foote AD. Cross-cultural and cross-ecotype production of a killer whale ‘excitement' call suggests universality. Naturwissenschaften 98:1-6, (2011)

Stouge S, Christiansen JL, Harper, DAT, Houmark-Nielsen M, Kristiansen K, MacNiocaill C, Buchardt-Westergaard, B. Neoproterozoic (Cryogenian-Ediacaran) deposits in East and North-East Greenland. Geological Society, London, Memoirs 2011; v. 36; p. 581-592, doi: 10.1144/M36.56

Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert MTP, Ussery DW, Knøchel S. Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse. Std. gen. sci., 4, 113-122, 2011

Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert MTP, Ussery DW, Knøchel S. Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099. J. Bacterology, 193, 5546-7. 2011

Tange O. GNU Parallel - The Command-Line Power Tool. ;login: The USENIX Magazine, February 2011:42-47

Tange O. GNU SQL - A Command Line Tool for Accessing Different Databases Using DBURLs. ;login: The USENIX Magazine, April 2011:29-32

Ukkonen P, Aaris-Sørensen K, Arppe L, Clark PU, Daugnora L, Lister AM, Lõugas L, Seppä H, Sommer RS, Stuart AJ, Wojtal P, Zupins I. Woolly mammoth (Mammuthus primigenius Blum.) and its environment in northern Europe during the last glaciation. Quat. Sci. Rev. 30: 693-712, (2011)

Van Doorn N, Wilson A, Willerslev E, Gilbert MTP. Bone marrow and bone as a source for post-mortem RNA. J. Forensic Science 56:720-725, (2011)

Vilstrup JT, Ho SYW, Foote AD, Morin PA, Kreb D, Krützen M, Parra GJ, Robertson KM, de Stephanis R, Verborgh P, Willerslev E, Orlando L, Gilbert MTP. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol. Biol. 11:65, (2011)

Waters MR, Stafford Jr. TW, McDonald GH, Gustafson C, Rasmussen M, Cappellini E, Olsen JV, Szklarczyk D, Juhl Jensen L, Gilbert MTP, Willerslev E. Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington: Implications for explaining the extinction of megafauna at the end of the Pleistocene. Science 334:351-353, (2011)

White NE, Phillips MJ, Gilbert MTP, Alfaro-Nuñes A, Willerslev E, Mawson PR, Spencer PBS, Bunce M. The evolutionary history of Cockatoos (Psittaciformes: Cacatuidae). Mol. Phyl. Evol. 59:615-622, (2011)

Wen J, Parker BJ, Jacobsen A, Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA, 17(5):820–834, May 2011

Wiig Ø, Heide-Jørgensen MP, Laidre KL, Garde E, Reeves RR. Geographic variation in cranial morphology of narwhals (Monodon monoceros) from Greenland and the eastern Canadian Arctic. Polar Biology 35:63-71