Papers:
Weber CC, Perron U, Casey D, Yang Z, Goldman N. 2020. Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space. Systematic Biology (link | previously available as preprint)
Weber CC, Whelan S. 2019. Physicochemical amino acid properties better describe substitution rates in large populations. Molecular Biology and Evolution (link | previously available as preprint).
Platt A*, Weber CC*, Liberles DA. 2018. Protein Evolution Depends On Multiple Distinct Population Size Parameters. BMC Evolutionary Biology 18 (17) (link | previously available as preprint) *Authors contributed equally. Names in alphabetical order.
Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA. 2018. A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution. Proteins 86:2 (link)
Arenas M, Weber CC, Liberles DA, Bastolla U. 2017. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology 66:6, 1054-1064
Mugal CF, Weber CC, Ellegren H (2015) GC-biased gene conversion links the recombination landscape and demography to genomic base composition. BioEssays doi:10.1002/bies.201500058 (link)
Weber CC, Boussau B, Romiguier J, et al. 2014. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biology 15:549 (link) (appeared as #1 "most forwarded" on Genome Biology's site on Dec 17th 2014)
Weber CC, Nabholz B, Romiguier J, et al. 2014. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biology 15:542 (link)
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331 (link)
Suh A, Weber CC, Kehlmaier C, et al. 2014. Early Mesozoic coexistence of amniotes and Hepadnaviridae. PLoS Genetics 10:e1004559 (link)
Weber CC, Pink CJ, Hurst LD. 2012. Late-replicating domains have higher divergence and diversity in Drosophila melanogaster. Molecular Biology and Evolution 29:873–82 (link)
Weber CC, Hurst LD. 2011. Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation. Genome Biology 12:R23 (link)
Weber CC, Hurst LD. 2010. Intronic AT Skew is a Defendable Proxy for Germline Transcription but does not Predict Crossing-Over or Protein Evolution Rates in Drosophila melanogaster. Journal of Molecular Evolution: 415–426 (link | free PDF)
Weber CC, Hurst LD. 2009. Protein rates of evolution are predicted by double-strand break events, independent of crossing-over rates. Genome Biology and Evolution 1:340–9 (link)
Warnecke T, Weber CC, Hurst LD. 2009. Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence. Biochemical Society transactions 37:756–61 (link | PDF)
Data notes:
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, et al. Phylogenomic Analyses Data of the Avian Phylogenomics Project. GigaScience
PhD Thesis:
Weber, CC. 2011. Genome structure and determinants of rates of evolution. Thesis (Doctor of Philosophy (PhD)). University of Bath (link)