Research graph
References from PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins. Local targets link to admitted publications; unresolved targets remain external evidence.
Detection of Mature Collagen in Human Dental Enamel
10.1007/s00223-004-0122-0 · 2005 · External reference
Unraveling the Human Bone Microenvironment beyond the Classical Extracellular Matrix Proteins: A Human Bone Protein Library
10.1021/pr200522n · 2011 · External reference
Anaconda Software Distribution
2020 · External reference
Detecting and Correcting Misclassified Sequences in the Large-Scale Public Databases
10.1093/bioinformatics/btaa586 · 2020 · External reference
CRAM 3.1: Advances in the CRAM File Format
10.1093/bioinformatics/btac010 · 2022 · External reference
Palaeoproteomics Identifies Beaver Fur in Danish High-Status Viking Age Burials-Direct Evidence of Fur Trade
10.1371/journal.pone.0270040 · 2022 · External reference
Identification of a New Hominin Bone from Denisova Cave, Siberia Using Collagen Fingerprinting and Mitochondrial DNA Analysis
10.1038/srep23559 · 2016 · External reference
The Earliest Denisovans and Their Cultural Adaptation
10.1038/s41559-021-01581-2 · 2022 · External reference
Ancient Collagen Reveals Evolutionary History of the Endemic South American `Ungulates'
10.1098/rspb.2014.2671 · 2015 · External reference
Species Identification by Analysis of Bone Collagen Using Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry
10.1002/rcm.4316 · 2009 · External reference
Collagen Sequence Analysis of Fossil Camels, Camelops and Cf Paracamelus, from the Arctic and Sub-Arctic of Plio-Pleistocene North America
10.1016/j.jprot.2018.11.014 · 2019 · External reference
Distinguishing between Archaeological Sheep and Goat Bones Using a Single Collagen Peptide
10.1016/j.jas.2009.08.020 · 2010 · External reference
High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
10.1101/2021.02.06.430068 · 2021 · External reference
Unlocking Ancient Protein Palimpsests
10.1126/science.1249274 · 2014 · External reference
Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins
10.1021/pr200721u · 2012 · External reference
Early Pleistocene Enamel Proteome from Dmanisi Resolves Stephanorhinus Phylogeny
10.1038/s41586-019-1555-y · 2019 · External reference
Identification of Proteins from Human Permanent Erupted Enamel
10.1111/eos.12214 · 2015 · External reference
A Late Middle Pleistocene Denisovan Mandible from the Tibetan Plateau
10.1038/s41586-019-1139-x · 2019 · External reference
Open-pFind Enables Precise, Comprehensive and Rapid Peptide Identification in Shotgun Proteomics
10.1101/285395 · 2018 · External reference
MaxQuant Enables High Peptide Identification Rates, Individualized Ppb-Range Mass Accuracies and Proteome-Wide Protein Quantification
10.1038/nbt.1511 · 2008 · External reference
The Variant Call Format and VCFtools
10.1093/bioinformatics/btr330 · 2011 · External reference
Protein Sequences Bound to Mineral Surfaces Persist into Deep Time
10.7554/elife.17092 · 2016 · External reference
Ancient Proteins Resolve Controversy over the Identity of Genyornis Eggshell
10.1073/pnas.2109326119 · 2022 · External reference
DIA-NN: Neural Networks and Interference Correction Enable Deep Coverage in High-Throughput Proteomics
10.1038/s41592-019-0638-x · 2018 · External reference
Direct Dating of Neanderthal Remains from the Site of Vindija Cave and Implications for the Middle to Upper Paleolithic Transition
10.1073/pnas.1709235114 · 2017 · External reference
Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach
10.1007/bf01734359 · 1981 · External reference
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
10.1093/sysbio/syq010 · 2010 · External reference
Taxon Sampling and the Accuracy of Phylogenetic Analyses
10.3724/sp.j.1002.2008.08016 · 2008 · External reference
Ancient Protein Analysis in Archaeology
10.1126/sciadv.abb9314 · 2021 · External reference
An Open-Source Pipeline to Reconstruct Phylogenies with Paleoproteomic Data.
10.24072/pci.paleo.100220 · 2023 · External reference
MRBAYES: Bayesian inference of phylogenetic trees
10.1093/bioinformatics/17.8.754 · 2001 · External reference
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
10.1080/10618600.1997.10474731 · 2016 · External reference
Comprehensive Proteomic Analysis of Human Dentin
10.1111/j.1600-0722.2012.00977.x · 2012 · External reference
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
10.1093/molbev/mst010 · 2013 · External reference
The Genome 10K Project: A Way Forward
10.1146/annurev-animal-090414-014900 · 2015 · External reference
MSFragger: Ultrafast and Comprehensive Peptide Identification in Mass Spectrometry–Based Proteomics
10.1038/nmeth.4256 · 2017 · External reference
Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA
10.1007/13836_2018_54 · 2018 · External reference
Multi-Protease Analysis of Pleistocene Bone Proteomes
10.1016/j.jprot.2020.103889 · 2020 · External reference
Earth BioGenome Project: Sequencing Life for the Future of Life
10.1073/pnas.1720115115 · 2018 · External reference
The Sequence Alignment/Map Format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
Rapid and Sensitive Protein Similarity Searches
10.1126/science.2983426 · 1985 · External reference
PEAKS: Powerful Software for Peptide de Novo Sequencing by Tandem Mass Spectrometry
10.1002/rcm.1196 · 2003 · External reference
A High-Coverage Neandertal Genome from Chagyrskaya Cave
10.1073/pnas.2004944117 · 2020 · External reference
Ensembl 2023
2023 · External reference
Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo
10.1080/10618600.1997.10474731 · 1997 · External reference
MPI: A Message-Passing Interface Standard Version 4.0
2021 · External reference
Sustainable Data Analysis with Snakemake
10.12688/f1000research.29032.2 · 2021 · External reference
The Proteome Landscape of the Kingdoms of Life
10.1038/s41586-020-2402-x · 2020 · External reference
Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
10.1016/j.cub.2017.09.047 · 2017 · External reference
Genome
2004 · External reference
Extraction and Sequencing of Human and Neanderthal Mature Enamel Proteins Using MALDI-TOF/TOF MS
10.1016/j.jas.2009.04.004 · 2009 · External reference
Ancient Enamel Peptides Recovered from the South American Pleistocene Species Notiomastodon Platensis and Myocastor Cf. Coypus
10.1016/j.jprot.2021.104187 · 2021 · External reference
Phylogenetic Analysis Using Protein Sequences
10.1017/cbo9780511819049.011 · 2003 · External reference
New Strategies for Characterizing Ancient Proteins Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
10.1016/s0016-7037(99)00381-6 · 2000 · External reference
Proteomics Analysis of Human Dentin Reveals Distinct Protein Expression Profiles
10.1021/pr801065s · 2009 · External reference
Hominid Palaeoproteomic Reference Dataset - v1.0.1
10.5281/zenodo.7728060 · 2022 · External reference
Palaeoprophyler - Public Release v1.0.1
10.5281/zenodo.10122365 · 2023 · External reference
EAGER: Efficient Ancient Genome Reconstruction
10.1186/s13059-016-0918-z · 2016 · External reference
Probability-based protein identification by searching sequence databases using mass spectrometry data
10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2 · 1999 · External reference
New Techniques for the Recovery of Small Amounts of Mature Enamel Proteins
10.1016/j.jas.2011.08.030 · 2011 · External reference
Great Ape Genetic Diversity and Population History
10.1038/nature12228 · 2013 · External reference
Data from: Palaeoproteomics Resolves Sloth Phylogeny
10.1038/s41559-019-0909-z · 2019 · External reference
A high-coverage Neandertal genome from Vindija Cave in Croatia
10.1126/science.aao1887 · 2017 · External reference
Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
10.1007/bf02338839 · 1996 · External reference
Taxon Sampling, Bioinformatics, and Phylogenomics
10.1080/10635150390132894 · 2003 · External reference
Mid-Pliocene Warm-Period Deposits in the High Arctic Yield Insight into Camel Evolution
10.1038/ncomms2516 · 2013 · External reference
SPIN Enables High Throughput Species Identification of Archaeological Bone by Proteomics
10.1038/s41467-022-30097-x · 2022 · External reference
Global Proteome Profiling of Dental Cementum under Experimentally-Induced Apposition
10.1016/j.jprot.2016.03.036 · 2016 · External reference
Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic Analysis Using PALEOMIX
10.1038/nprot.2014.063 · 2014 · External reference
Enhanced Global Post-Translational Modification Discovery with MetaMorpheus
10.1021/acs.jproteome.7b00873 · 2018 · External reference
UniProt Readme file
2021 · External reference
Paleoproteomics
10.1021/acs.chemrev.1c00703 · 2022 · External reference
Pathogens and Host Immunity in the Ancient Human Oral Cavity
10.1038/ng.2906 · 2014 · External reference
Palaeoproteomic Evidence Identifies Archaic Hominins Associated with the Châtelperronian at the Grotte Du Renne
10.1073/pnas.1605834113 · 2016 · External reference
The Dental Proteome of Homo Antecessor
10.1038/s41586-020-2153-8 · 2020 · External reference
Enamel Proteome Shows That Gigantopithecus Was an Early Diverging Pongine
10.1038/s41586-019-1728-8 · 2019 · External reference
Middle Pleistocene Protein Sequences from the Rhinoceros Genus Stephanorhinus and the Phylogeny of Extant and Extinct Middle/Late Pleistocene Rhinocerotidae
10.7717/peerj.3033 · 2017 · External reference
The Ensembl REST API: Ensembl Data for Any Language
10.1093/bioinformatics/btu613 · 2015 · External reference
Comparative genomics reveals insights into avian genome evolution and adaptation
10.1126/science.1251385 · 2014 · External reference
