| [1] | Hawass Z, Gad YZ, Ismail S, Khairat R, Fathalla D, et al. (2010) Ancestry and Pathology in King Tutankhamun’s Family. Journal of the American Medical Association 303: 638–647.
|
| [2] | Raoult D, Aboudharam G, Crubezy E, Larrouy G, Ludes B, et al. (2000) Molecular identification by “suicide PCR” of Yersinia pestis as the agent of Medieval Black Death. Proceedings of the National Academy of Sciences 97: 12800–12803.
|
| [3] | Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478: 506–510.
|
| [4] | Gilbert MTP, Bandelt H-J, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends in Ecology & Evolution 20: 541–544.
|
| [5] | Cooper A, Poinar HN (2000) Ancient DNA: do it right or not at all. Science 289: 1139–1139.
|
| [6] | Timmann C, Meyer CG (2010) King Tutankhamun’s Family and Demise. Journal of the American Medical Association 303: 2473–.
|
| [7] | Marlowe EM, Wolk DM (2006) Pathogen Detection in the Genomic Era. Advanced Techniques in Diagnostic Microbiology. pp. 505–523.
|
| [8] | Relman DA (1999) The Search for Unrecognized Pathogens. Science 284: 1308–1310.
|
| [9] | Ye Y, Mar E-C, Tong S, Sammons S, Fang S, et al. (2010) Application of proteomics methods for pathogen discovery. Journal of Virological Methods 163: 87–95.
|
| [10] | Drancourt M, Raoult D (2005) Palaeomicrobiology: current issues and perspectives. Nature Reviews Microbiology 3: 23–35.
|
| [11] | Kricka LJ (2000) Interferences in Immunoassay–Still a Threat. Clinical Chemistry 46: 1037–1038.
|
| [12] | Washburn MP (2011) Driving biochemical discovery with quantitative proteomics. Trends in Biochemical Sciences 36: 170–177.
|
| [13] | Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry. Science 316: 280–285.
|
| [14] | Schweitzer MH, Zheng W, Organ CL, Avci R, Suo Z, et al. (2009) Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis. Science 324: 626–631.
|
| [15] | Lubec G, Afjehi-Sadat L (2007) Limitations and Pitfalls in Protein Identification by Mass Spectrometry. Chemical Reviews 107: 3568–3584.
|
| [16] | Spivey A (2009) Amplify, amplify: shotgun proteomics boosts the signal for biomarker discovery. Environmental Health Perspectives 117: A206–209.
|
| [17] | Ceruti MC (2003) Llullaillaco: Sacrificios y Ofrendas en un Santuario Inca de Alta Monta？a. Salta: EUCASA.
|
| [18] | Reinhard J (2005) The Ice Maiden: Inca Mummies, Mountain Gods, and Sacred Sites in the Andes. Washington, D.C.: National Geographic Society.
|
| [19] | Wilson AS, Taylor T, Ceruti MC, Chavez JA, Reinhard J, et al. (2007) Stable isotope and DNA evidence for ritual sequences in Inca child sacrifice. Proceedings of the National Academy of Sciences 104: 16456–16461.
|
| [20] | Previgliano CH, Ceruti C, Reinhard J, Araoz FA, Diez JG (2003) Radiologic Evaluation of the Llullaillaco Mummies. American Journal of Roentgenology 181: 1473–1479.
|
| [21] | Besson M-T, Soustelle L, Birman S (2000) Selective high-affinity transport of aspartate by a Drosophila homologue of the excitatory amino-acid transporters. Current Biology 10: 207–210.
|
| [22] | Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods 4: 207–214.
|
| [23] | Eng JK, McCormack AL, Yates JR III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5: 976–989.
|
| [24] | Tabb DL, McDonald WH, Yates JR (2002) DTA Select and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics. Journal of Proteome Research 1: 21–26.
|
| [25] | Sokal RR, Rohlf FJ (1995) Biometry: The principles and practice of statistics in biological research. New York: Freeman.
|
| [26] | Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, Hettich RL, et al. (2006) Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics. Journal of Proteome Research 5: 2909–2918.
|
| [27] | Mann HB, Whitney DR (1947) On a test of whether one of two random variables is stochastically larger than the other. Annals of Mathematical Statistics 18: 50–60.
|
| [28] | Hothorn T, Hornik K, Wiel MAvd, Zeileis A (2011) coin: Conditional Inference Procedures in a Permutation Test Framework. 1.0–20 ed.
|
| [29] | R Development Core Team (2010) R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
|
| [30] | Konomi N, Lebwohl E, Mowbray K, Tattersall I, Zhang D (2002) Detection of mycobacterial DNA in Andean mummies. Journal of Clinical Microbiology 40: 4738–4740.
|
| [31] | Park H, Jang H, Kim C, Chung B, Chang CL, et al. (2000) Detection and Identification of Mycobacteria by Amplification of the Internal Transcribed Spacer Regions with Genus- and Species-Specific PCR Primers. Journal of Clinical Microbiology 38: 4080–4085.
|
| [32] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.
|
| [33] | Katoh K, Kuma K-i, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511–518.
|
| [34] | Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286–298.
|
| [35] | Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.
|
| [36] | Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456–463.
|
| [37] | Tavaré S (1986) Some probabilistic and statistical problems on the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17: 57–86.
|
| [38] | Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39: 306–314.
|
| [39] | Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
|
| [40] | Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51: 492–508.
|
| [41] | Shimodaira H, Hasegawa M (2001) Consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246–1247.
|
| [42] | Yang Z (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution 24: 1586–1591.
|
| [43] | Bangalore N, Travis J, Onunka VC, Pohl J, Shafer WM (1990) Identification of the primary antimicrobial domains in human neutrophil cathepsin G. Journal of Biological Chemistry 265: 13584–13588.
|
| [44] | Hiemstra PS, van Wetering S, Stolk J (1998) Neutrophil serine proteinases and defensins in chronic obstructive pulmonary disease: effects on pulmonary epithelium. European Respiratory Journal 12: 1200–1208.
|
| [45] | Korkmaz B, Moreau T, Gauthier F (2008) Neutrophil elastase, proteinase 3 and cathepsin G: Physicochemical properties, activity and physiopathological functions. Biochimie 90: 227–242.
|
| [46] | Sommerhoff CP, Nadel JA, Basbaum CB, Caughey GH (1990) Neutrophil elastase and cathepsin G stimulate secretion from cultured bovine airway gland serous cells. Journal of Clinical Investigation 85: 682–689.
|
| [47] | Travis J (1988) Structure, function, and control of neutrophil proteinases. American Journal of Medicine 84: 37–42.
|
| [48] | Van Wetering S, Mannesse-Lazeroms SP, Dijkman JH, Hiemstra PS (1997) Effect of neutrophil serine proteinases and defensins on lung epithelial cells: modulation of cytotoxicity and IL-8 production. Journal of Leukocyte Biology 62: 217–226.
|
| [49] | Brinkmann V, Reichard U, Goosmann C, Fauler B, Uhlemann Y, et al. (2004) Neutrophil Extracellular Traps Kill Bacteria. Science 303: 1532–1535.
|
| [50] | Fertakis A, Archimandritis A, Tsourapas A, Douratsos A, Angelopoulos B (1977) Serum levels and alpha1-antitrypsin phenotypes in active pulmonary tuberculosis. Acta Geneticae Medicae et Gemellologiae 26: 97–99.
|
| [51] | Masala C, Amendolea MA, Bonini S (1976) Mucus antibodies in pulmonary tuberculosis and chronic obstructive lung disease. The Lancet 2: 821–824.
|
| [52] | Poh SC, Seet AM (1975) Alpha1 antitrypsin levels in chronic obstructive lung disease and pulmonary tuberculosis in Singapore. Singapore Medical Journal 16: 89–91.
|
| [53] | Ugajin M, Miwa S, Shirai M, Ohba H, Eifuku T, et al. (2011) Serum alpha-1-antitrypsin levels in pulmonary tuberculosis. The European Respiratory Journal 77: 371–375.
|
| [54] | Ganz T (2003) Defensins: antimicrobial peptides of innate immunity. Nature Reviews Immunology 3: 710–720.
|
| [55] | de Torre C, Ying S-X, Munson PJ, Meduri GU, Suffredini AF (2006) Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage. Proteomics 6: 3949–3957.
|
| [56] | Lau ATY, Chiu J-F (2009) Biomarkers of lung-related diseases: Current knowledge by proteomic approaches. Journal of Cellular Physiology 221: 535–543.
|
| [57] | Seth M, Lamont EA, Janagama HK, Widdel A, Vulchanova L, et al. (2009) Biomarker Discovery in Subclinical Mycobacterial Infections of Cattle. PLoS ONE 4: e5478.
|
| [58] | Bannalikar AS, Verma R (2006) Detection of Mycobacterium avium & M. tuberculosis from human sputum cultures by PCR-RFLP analysis of hsp65 gene & pncA PCR. Indian Journal of Medical Research 123: 165–172.
|
| [59] | Hernandez-Pando R, Jeyanathan M, Mengistu G, Aguilar D, Orozco H, et al. (2000) Persistence of DNA from Mycobacterium tuberculosis in superficially normal lung tissue during latent infection. The Lancet 356: 2133–2138.
|
| [60] | Demissie A, Abebe M, Aseffa A, Rook G, Fletcher H, et al. (2004) Healthy Individuals That Control a Latent Infection with Mycobacterium tuberculosis Express High Levels of Th1 Cytokines and the IL-4 Antagonist IL-4Δ2. Journal of Immunology 172: 6938–6943.
|
| [61] | Wittram C, Weisbrod GL (2002) Mycobacterium avium complex lung disease in immunocompetent patients: radiography-CT correlation. British Journal of Radiology 75: 340–344.
|
| [62] | Ismail AAA, Walker PL, Cawood ML, Barth JH (2002) Interference in immunoassay is an underestimated problem. Annals of Clinical Biochemistry 39: 366–373.
|
| [63] | Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, et al. (2006) Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes. Genetics 172: 733–741.
|
