Inaugural Article: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

By David G. Hwang. 2004

410 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c80bb6149175f5eb339916c6f83d31dbb89679d5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma (2014, unknown): “A similar signature is dominant in myeloid malignancies 23,24 , a major contributor to early mutations in breast cancer 11,22 and seen at high rates in the germline 25 .”
Distribution and intensity of constraint in mammalian genomic sequence. (2005, methodology): “generation of both “observed” and “expected” rates (Hwang and Green 2004; Siepel and Haussler 2004b) might eventually be used to improve the methodology, as the conceptual framework we have described is not dependent on the particulars of rate estimation.”
Most mammalian mRNAs are conserved targets of microRNAs. (2008, methodology): “Human UTR boundaries were used to acquire orthologous UTRs from the 28-genome vertebrate sequence alignments from the UCSC genome browser (Karolchik et al. 2008).”
Genome sequence, comparative analysis and haplotype structure of the domestic dog (2005, background): “The lineage-speciﬁc divergence rates (human , dog , mouse) are probably explained by differences in metabolic rates 50,51 or generation times 52,53 , but the relative contributions of these factors remain unclear 49 .”
When Is Selection Effective? (2014, background): “If we consider the 24 Mb of exome covered by the 1000 Genomes project, and assume that 70% of mutations are coding in that region [33], the model predicts a non-synonymous load difference of 0.”
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome (2008, methodology): “To determine what proportion of new nonsynonymous mutations PolyPhen classifies as benign, possibly damaging, or probably damaging, we randomly mutated coding sequences from RefSeq 18 using a context-dependent substitution model [45].”
Relaxed Phylogenetics and Dating with Confidence (2006, unknown): “The primate dataset was a subset of a 2,160,276 bp alignment of non-coding DNA from 19 mammals [41,42].”
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data (2009, methodology): “We statistically corrected the AFS for ancestral misidentification [17], using a context-dependent substitution model [44].”
Widespread Genomic Signatures of Natural Selection in Hominid Evolution (2009, methodology): “We then grouped alignment columns into categories based upon their ancestral purine and pyrimidine contexts because these contexts have previously been shown to capture a substantial proportion of mutation rate variation [74].”
The Life History of 21 Breast Cancers (2012, background): “…variants is a default mutation spectrum, closely mirroring that seen in tumor types such as blood, pancreatic, and brain cancers (Greenman et al., 2007; Jones et al., 2008; Papaemmanuil et al., 2011; Puente et al., 2011) and indeed in germline nucleotide substitutions (Hwang and Green, 2004).”