TY - JOUR AU - Welker, F. AU - Collins, M. J. AU - Thomas, J. A. AU - Wadsley, M. AU - Brace, S. AU - Cappellini, E. PY - 2015 DA - 2015// TI - Ancient proteins resolve the evolutionary history of Darwin’s south American ungulates JO - Nature VL - 522 UR - https://doi.org/10.1038/nature14249 DO - 10.1038/nature14249 ID - Welker2015 ER - TY - JOUR AU - Buckley, M. AU - Fariña, R. A. AU - Lawless, C. AU - Tambusso, P. S. AU - Varela, L. AU - Carlini, A. A. PY - 2015 DA - 2015// TI - Collagen sequence analysis of the extinct Giant ground sloths Lestodon and Megatherium JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0144793 DO - 10.1371/journal.pone.0144793 ID - Buckley2015 ER - TY - JOUR AU - Buckley, M. PY - 2015 DA - 2015// TI - Ancient collagen reveals evolutionary history of the endemic south American “ungulates.” JO - Proc R Soc B VL - 282 UR - https://doi.org/10.1098/rspb.2014.2671 DO - 10.1098/rspb.2014.2671 ID - Buckley2015 ER - TY - JOUR AU - Welker, F. AU - Hajdinjak, M. AU - Talamo, S. AU - Jaouen, K. AU - Dannemann, M. AU - David, F. PY - 2016 DA - 2016// TI - Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne JO - Proc Natl Acad Sci U S A VL - 113 UR - https://doi.org/10.1073/pnas.1605834113 DO - 10.1073/pnas.1605834113 ID - Welker2016 ER - TY - JOUR AU - Shevchenko, A. AU - Yang, Y. AU - Knaust, A. AU - Thomas, H. AU - Jiang, H. AU - Lu, E. PY - 2014 DA - 2014// TI - Proteomics identifies the composition and manufacturing recipe of the 2500-year old sourdough bread from Subeixi cemetery in China JO - J Proteome VL - 105 UR - https://doi.org/10.1016/j.jprot.2013.11.016 DO - 10.1016/j.jprot.2013.11.016 ID - Shevchenko2014 ER - TY - JOUR AU - Hendy, J. AU - Collins, M. AU - Teoh, K. Y. AU - Ashford, D. A. AU - Thomas-Oates, J. AU - Donoghue, H. D. PY - 2016 DA - 2016// TI - The challenge of identifying tuberculosis proteins in archaeological tissues JO - J Archaeol Sci VL - 66 UR - https://doi.org/10.1016/j.jas.2016.01.003 DO - 10.1016/j.jas.2016.01.003 ID - Hendy2016 ER - TY - JOUR AU - Warinner, C. AU - Hendy, J. AU - Speller, C. AU - Cappellini, E. AU - Fischer, R. AU - Trachsel, C. PY - 2014 DA - 2014// TI - Direct evidence of milk consumption from ancient human dental calculus JO - Sci Rep VL - 4 UR - https://doi.org/10.1038/srep07104 DO - 10.1038/srep07104 ID - Warinner2014 ER - TY - JOUR AU - Warinner, C. AU - Rodrigues, J. F. M. AU - Vyas, R. AU - Trachsel, C. AU - Shved, N. AU - Grossmann, J. PY - 2014 DA - 2014// TI - Pathogens and host immunity in the ancient human oral cavity JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.2906 DO - 10.1038/ng.2906 ID - Warinner2014 ER - TY - JOUR AU - Procopio, N. AU - Chamberlain, A. T. AU - Buckley, M. PY - 2017 DA - 2017// TI - Intra- and Interskeletal proteome variations in fresh and buried bones JO - J Proteome Res VL - 16 UR - https://doi.org/10.1021/acs.jproteome.6b01070 DO - 10.1021/acs.jproteome.6b01070 ID - Procopio2017 ER - TY - JOUR AU - Rybczynski, N. AU - Gosse, J. C. AU - Harington, C. R. AU - Wogelius, R. A. AU - Hidy, A. J. AU - Buckley, M. PY - 2013 DA - 2013// TI - Mid-Pliocene warm-period deposits in the high Arctic yield insight into camel evolution JO - Nat Commun VL - 4 UR - https://doi.org/10.1038/ncomms2516 DO - 10.1038/ncomms2516 ID - Rybczynski2013 ER - TY - JOUR AU - Demarchi, B. AU - Hall, S. AU - Roncal-Herrero, T. AU - Freeman, C. L. AU - Woolley, J. AU - Crisp, M. K. PY - 2016 DA - 2016// TI - Protein sequences bound to mineral surfaces persist into deep time JO - elife VL - 5 UR - https://doi.org/10.7554/eLife.17092 DO - 10.7554/eLife.17092 ID - Demarchi2016 ER - TY - JOUR AU - Orlando, L. AU - Ginolhac, A. AU - Zhang, G. AU - Froese, D. AU - Albrechtsen, A. AU - Stiller, M. PY - 2013 DA - 2013// TI - Recalibrating Equus evolution using the genome sequence of an early middle Pleistocene horse JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12323 DO - 10.1038/nature12323 ID - Orlando2013 ER - TY - JOUR AU - Cappellini, E. AU - Collins, M. J. AU - Gilbert, M. T. P. PY - 2014 DA - 2014// TI - Unlocking ancient protein palimpsests JO - Science VL - 343 UR - https://doi.org/10.1126/science.1249274 DO - 10.1126/science.1249274 ID - Cappellini2014 ER - TY - JOUR AU - Sawafuji, R. AU - Cappellini, E. AU - Nagaoka, T. AU - Fotakis, A. K. AU - Jersie-Christensen, R. R. AU - Olsen, J. V. PY - 2017 DA - 2017// TI - Proteomic profiling of archaeological human bone JO - Royal Society Open Science VL - 4 UR - https://doi.org/10.1098/rsos.161004 DO - 10.1098/rsos.161004 ID - Sawafuji2017 ER - TY - JOUR AU - Brown, S. AU - Higham, T. AU - Slon, V. AU - Pääbo, S. AU - Meyer, M. AU - Douka, K. PY - 2016 DA - 2016// TI - Identification of a new hominin bone from Denisova cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep23559 DO - 10.1038/srep23559 ID - Brown2016 ER - TY - JOUR AU - Castellano, S. AU - Parra, G. AU - Sánchez-Quinto, F. A. AU - Racimo, F. AU - Kuhlwilm, M. AU - Kircher, M. PY - 2014 DA - 2014// TI - Patterns of coding variation in the complete exomes of three Neandertals JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1405138111 DO - 10.1073/pnas.1405138111 ID - Castellano2014 ER - TY - JOUR AU - Meyer, M. AU - Kircher, M. AU - Gansauge, M. -. T. AU - Li, H. AU - Racimo, F. AU - Mallick, S. PY - 2012 DA - 2012// TI - A high-coverage genome sequence from an archaic Denisovan individual JO - Science VL - 338 UR - https://doi.org/10.1126/science.1224344 DO - 10.1126/science.1224344 ID - Meyer2012 ER - TY - JOUR AU - Perkins, D. N. AU - Pappin, D. J. AU - Creasy, D. M. AU - Cottrell, J. S. PY - 1999 DA - 1999// TI - Probability-based protein identification by searching sequence databases using mass spectrometry data JO - Electrophoresis VL - 20 UR - https://doi.org/3.0.CO;2-2 DO - 3.0.CO;2-2 ID - Perkins1999 ER - TY - JOUR AU - Bern, M. AU - Kil, Y. J. AU - Becker, C. PY - 2012 DA - 2012// TI - Byonic: advanced peptide and protein identification software JO - Curr Protoc Bioinformatics VL - 40 ID - Bern2012 ER - TY - JOUR AU - Cox, J. AU - Mann, M. PY - 2008 DA - 2008// TI - MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification JO - Nat Biotechnol VL - 26 UR - https://doi.org/10.1038/nbt.1511 DO - 10.1038/nbt.1511 ID - Cox2008 ER - TY - JOUR AU - Frank, A. AU - Pevzner, P. PY - 2005 DA - 2005// TI - PepNovo: de novo peptide sequencing via probabilistic network modeling JO - Anal Chem VL - 77 UR - https://doi.org/10.1021/ac048788h DO - 10.1021/ac048788h ID - Frank2005 ER - TY - JOUR AU - Ma, B. AU - Zhang, K. AU - Hendrie, C. AU - Liang, C. AU - Li, M. AU - Doherty-Kirby, A. PY - 2003 DA - 2003// TI - PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry JO - Rapid Commun Mass Spectrom VL - 17 UR - https://doi.org/10.1002/rcm.1196 DO - 10.1002/rcm.1196 ID - Ma2003 ER - TY - JOUR AU - Ma, B. PY - 2015 DA - 2015// TI - Novor: real-time peptide de novo sequencing software JO - J Am Soc Mass Spectrom VL - 26 UR - https://doi.org/10.1007/s13361-015-1204-0 DO - 10.1007/s13361-015-1204-0 ID - Ma2015 ER - TY - STD TI - Muth T, Renard BY. Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? Brief Bioinform. 2017; ID - ref24 ER - TY - JOUR AU - Welker, F. AU - Smith, G. M. AU - Hutson, J. M. AU - Kindler, L. AU - Garcia-Moreno, A. AU - Villaluenga, A. PY - 2017 DA - 2017// TI - Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct middle/late Pleistocene Rhinocerotidae JO - PeerJ VL - 5 UR - https://doi.org/10.7717/peerj.3033 DO - 10.7717/peerj.3033 ID - Welker2017 ER - TY - STD TI - Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics. Proc Biol Sci. 2016;283. https://doi.org/10.1098/rspb.2016.0593. ID - ref26 ER - TY - JOUR AU - Cleland, T. P. AU - Schroeter, E. R. AU - Zamdborg, L. AU - Zheng, W. AU - Lee, J. E. AU - Tran, J. C. PY - 2015 DA - 2015// TI - Mass spectrometry and antibody-based characterization of blood vessels from Brachylophosaurus canadensis JO - J Proteome Res VL - 14 UR - https://doi.org/10.1021/acs.jproteome.5b00675 DO - 10.1021/acs.jproteome.5b00675 ID - Cleland2015 ER - TY - JOUR AU - Cleland, T. P. AU - Schroeter, E. R. AU - Schweitzer, M. H. PY - 2015 DA - 2015// TI - Biologically and diagenetically derived peptide modifications in moa collagens JO - Proc R Soc B VL - 282 UR - https://doi.org/10.1098/rspb.2015.0015 DO - 10.1098/rspb.2015.0015 ID - Cleland2015 ER - TY - JOUR AU - Schroeter, E. R. AU - DeHart, C. J. AU - Cleland, T. P. AU - Zheng, W. AU - Thomas, P. M. AU - Kelleher, N. L. PY - 2017 DA - 2017// TI - Expansion for the Brachylophosaurus canadensis collagen I sequence and additional evidence of the preservation of cretaceous protein JO - J Proteome Res VL - 16 UR - https://doi.org/10.1021/acs.jproteome.6b00873 DO - 10.1021/acs.jproteome.6b00873 ID - Schroeter2017 ER - TY - JOUR AU - Muth, T. AU - Renard, B. Y. AU - Martens, L. PY - 2016 DA - 2016// TI - Metaproteomic data analysis at a glance: advances in computational microbial community proteomics JO - Expert Rev Proteomics VL - 13 UR - https://doi.org/10.1080/14789450.2016.1209418 DO - 10.1080/14789450.2016.1209418 ID - Muth2016 ER - TY - JOUR AU - Bayram, H. L. AU - Claydon, A. J. AU - Brownridge, P. J. AU - Hurst, J. L. AU - Mileham, A. AU - Stockley, P. PY - 2016 DA - 2016// TI - Cross-species proteomics in analysis of mammalian sperm proteins JO - J Proteome VL - 135 UR - https://doi.org/10.1016/j.jprot.2015.12.027 DO - 10.1016/j.jprot.2015.12.027 ID - Bayram2016 ER - TY - JOUR AU - Wright, J. C. AU - Beynon, R. J. AU - Hubbard, S. J. PY - 2010 DA - 2010// TI - Cross species proteomics JO - Methods Mol Biol VL - 604 UR - https://doi.org/10.1007/978-1-60761-444-9_9 DO - 10.1007/978-1-60761-444-9_9 ID - Wright2010 ER - TY - JOUR AU - Salmon, C. R. AU - Tomazela, D. M. AU - Ruiz, K. G. S. AU - Foster, B. L. AU - Paes Leme, A. F. AU - Sallum, E. A. PY - 2013 DA - 2013// TI - Proteomic analysis of human dental cementum and alveolar bone JO - J Proteome VL - 91 UR - https://doi.org/10.1016/j.jprot.2013.08.016 DO - 10.1016/j.jprot.2013.08.016 ID - Salmon2013 ER - TY - JOUR AU - Wilkinson, R. D. AU - Steiper, M. E. AU - Soligo, C. AU - Martin, R. D. AU - Yang, Z. AU - Tavaré, S. PY - 2011 DA - 2011// TI - Dating primate divergences through an integrated analysis of palaeontological and molecular data JO - Syst Biol VL - 60 UR - https://doi.org/10.1093/sysbio/syq054 DO - 10.1093/sysbio/syq054 ID - Wilkinson2011 ER - TY - JOUR AU - Pozzi, L. AU - Hodgson, J. A. AU - Burrell, A. S. AU - Sterner, K. N. AU - Raaum, R. L. AU - Disotell, T. R. PY - 2014 DA - 2014// TI - Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes JO - Mol Phylogenet Evol VL - 75 UR - https://doi.org/10.1016/j.ympev.2014.02.023 DO - 10.1016/j.ympev.2014.02.023 ID - Pozzi2014 ER - TY - JOUR AU - Finstermeier, K. AU - Zinner, D. AU - Brameier, M. AU - Meyer, M. AU - Kreuz, E. AU - Hofreiter, M. PY - 2013 DA - 2013// TI - A mitogenomic phylogeny of living primates JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0069504 DO - 10.1371/journal.pone.0069504 ID - Finstermeier2013 ER - TY - JOUR AU - Cappellini, E. AU - Jensen, L. J. AU - Szklarczyk, D. AU - Ginolhac, A. AU - da Fonseca, R. A. R. AU - Stafford, T. W. PY - 2012 DA - 2012// TI - Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins JO - J Proteome Res VL - 11 UR - https://doi.org/10.1021/pr200721u DO - 10.1021/pr200721u ID - Cappellini2012 ER - TY - JOUR AU - Smedley, D. AU - Haider, S. AU - Durinck, S. AU - Pandini, L. AU - Provero, P. AU - Allen, J. PY - 2015 DA - 2015// TI - The BioMart community portal: an innovative alternative to large, centralized data repositories JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv350 DO - 10.1093/nar/gkv350 ID - Smedley2015 ER - TY - CHAP AU - Miller, M. A. AU - Pfeiffer, W. AU - Schwartz, T. PY - 2010 DA - 2010// TI - Creating the CIPRES science gateway for inference of large phylogenetic trees BT - Gateway computing environments workshop (GCE) PB - ieeexplore.ieee.org CY - New Orleans ID - Miller2010 ER - TY - JOUR AU - Lanfear, R. AU - Calcott, B. AU - Ho, S. Y. W. AU - Guindon, S. PY - 2012 DA - 2012// TI - Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss020 DO - 10.1093/molbev/mss020 ID - Lanfear2012 ER - TY - JOUR AU - Wadsworth, C. AU - Buckley, M. PY - 2014 DA - 2014// TI - Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone JO - Rapid Commun Mass Spectrom VL - 28 UR - https://doi.org/10.1002/rcm.6821 DO - 10.1002/rcm.6821 ID - Wadsworth2014 ER - TY - JOUR AU - Wadsworth, C. AU - Procopio, N. AU - Anderung, C. AU - Carretero, J. -. M. AU - Iriarte, E. AU - Valdiosera, C. PY - 2017 DA - 2017// TI - Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites JO - J Proteome VL - 158 UR - https://doi.org/10.1016/j.jprot.2017.01.004 DO - 10.1016/j.jprot.2017.01.004 ID - Wadsworth2017 ER - TY - JOUR AU - Zhang, J. AU - Xin, L. AU - Shan, B. AU - Chen, W. AU - Xie, M. AU - Yuen, D. PY - 2012 DA - 2012// TI - PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification JO - Mol Cell Proteomics VL - 111 UR - https://doi.org/10.1074/mcp.M111.010587 DO - 10.1074/mcp.M111.010587 ID - Zhang2012 ER - TY - JOUR AU - Kendall, R. AU - Hendy, J. AU - Collins, M. J. AU - Millard, A. R. AU - Gowland, R. L. PY - 2016 DA - 2016// TI - Poor preservation of antibodies in archaeological human bone and dentine JO - STAR: Science & Technology of Archaeological Research VL - 2 UR - https://doi.org/10.1080/20548923.2015.1133117 DO - 10.1080/20548923.2015.1133117 ID - Kendall2016 ER - TY - JOUR AU - Buckley, M. AU - Wadsworth, C. PY - 2014 DA - 2014// TI - Proteome degradation in ancient bone: diagenesis and phylogenetic potential JO - Palaeogeogr Palaeoclimatol Palaeoecol VL - 416 UR - https://doi.org/10.1016/j.palaeo.2014.06.026 DO - 10.1016/j.palaeo.2014.06.026 ID - Buckley2014 ER - TY - JOUR AU - Westbury, M. AU - Baleka, S. AU - Barlow, A. AU - Hartmann, S. AU - Paijmans, J. L. A. AU - Kramarz, A. PY - 2017 DA - 2017// TI - A mitogenomic timetree for Darwin’s enigmatic south American mammal Macrauchenia patachonica JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/ncomms15951 DO - 10.1038/ncomms15951 ID - Westbury2017 ER -