A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
2009
Computer applications in the biosciences : CABIOS
Preserved Fulltext
the ascertainment bias from the functional characterization of non-coding elements. ...
We introduce a set of correction coefficients for the probabilities of the GO categories that accounts for the variability in the length of the non-coding DNA across different loci and effectively eliminates ...
ACKNOWLEDGEMENTS We thank Adam Woolfe for his helpful comments on the article, as well as three anonymous reviewers. ...
doi:10.1093/bioinformatics/btp043
pmid:19168912
pmcid:PMC2647827
fatcat:wmdwto7agzh4djjmbvut4epome
Genome-Wide Analysis of Natural Selection on Human Cis-Elements
2008
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
It has been speculated that the polymorphisms in the non-coding portion of the human genome underlie much of the phenotypic variability among humans and between humans and other primates. ...
However, the non-coding region is a heterogeneous mix of functional and non-functional regions. ...
However, only recently has it become possible to infer natural selection on entire classes of non-coding elements due to the availability of genome-wide validated single nucleotide polymorphism (SNP) data ...
doi:10.1371/journal.pone.0003137
pmid:18781197
pmcid:PMC2522239
fatcat:bj244i4ppjdtxabhqcqfiudmvy
Abundant Raw Material for Cis-Regulatory Evolution in Humans
2002
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. ...
Ordinary smallscale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation. ...
Acknowledgments We thank the National Science Foundation and NASA for support and E. Davidson ...
doi:10.1093/oxfordjournals.molbev.a004023
pmid:12411608
fatcat:p4mtgongtzfczodz6j35yenkli
Elevated Basal Slippage Mutation Rates among the Canidae
2007
Journal of Heredity
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
of polymorphism, but the fragmentary nature of the available dog genome sequence thwarted attempts to distinguish between locus-specific and genome-wide origins of this disparity. ...
Building on the approach that gave rise to the initial observation in dogs, we sequenced 55 coding repeat regions in 42 species representing 10 major carnivore clades and found that a genome-wide elevated ...
This will result in an ascertainment bias toward longer repeat length in primates, and no ascertainment bias among any members of a taxon with a common ancestor separating them from primates, as is the ...
doi:10.1093/jhered/esm017
pmid:17437958
fatcat:snqzubaijrbe5d6v2cjkx7ol7i
Comparative Genetics of Functional Trinucleotide Tandem Repeats in Humans and Apes
2004
Journal of Molecular Evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
The aims of our study are to infer the comparative pattern of variation and evolution of this set of loci in order to show species-specific features in this group of STRs and on their potential for expansion ...
Humans present slightly larger alleles than the rest of species but a more relevant difference appears in variability levels: Humans are the species with the largest vari-ance, although only for the expanding ...
disease) but do not try to generalize our observations to infer traits for the rest of STRs, which would produce a strong ascertainment bias. ...
doi:10.1007/s00239-004-2628-5
pmid:15553088
fatcat:hgwp5ffpbrdc7ku6chhctzv3xa
SNPs in ecology, evolution and conservation
2004
Trends in Ecology & Evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
Inferences drawn from mtDNA sequences are further limited by the fact that the mtDNA genome comprises a single maternally inherited locus. ...
By contrast, mutations observed as SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) are abundant and widespread in many species' genomes (coding and non-coding regions), and they evolve in a manner well described ...
We are grateful to Pascal Gagneux and three anonymous reviewers for helpful comments. Members of the SNP workshop group contributed extensively and nearly equally to the ideas presented here. ...
doi:10.1016/j.tree.2004.01.009
fatcat:obsmh4wenvhf3mkxpctjrnjs6y
Recent and ongoing selection in the human genome
2007
Nature reviews genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
| The recent availability of genome-scale genotyping data has led to the identification of regions of the human genome that seem to have been targeted by selection. ...
These findings have increased our understanding of the evolutionary forces that affect the human genome, have augmented our knowledge of gene function and promise to increase our understanding of the genetic ...
Acknowledgements We would like to thank D. Reich, M. Przeworski and two anonymous reviewers for their helpful comments on earlier versions of this manuscript. ...
doi:10.1038/nrg2187
pmid:17943193
pmcid:PMC2933187
fatcat:eqvyx7e6yvbordyjhp5lvx4nmm
Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing
2012
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between ...
However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. ...
Acknowledgments The authors would like to thank Gareth Highnam, Phillip Whisenhunt, and the Human Genome Sequencing Center at BCM (particularly Dianhui Zhu) for helpful comments and suggestions. ...
doi:10.1371/journal.pone.0033036
pmid:22427938
pmcid:PMC3299726
fatcat:itir32odb5astimu44h3hrtagi
Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans
2005
PLoS Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2012; you can also visit the original URL.
The file type is application/pdf.
The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution. ...
Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. ...
Acknowledgments We thank Lisa Bukovnik, Manny Lopez, and Anjali Patel for assistance in the lab and Cliff Cunningham, Greg Gibson, Fred Nijhout, and Mark Rausher for helpful comments. ...
doi:10.1371/journal.pbio.0030387
pmid:16274263
pmcid:PMC1283535
fatcat:hkjw4mp5affxzijzstjkomwdsy
Mobile DNA elements in primate and human evolution
2007
American Journal of Physical Anthropology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human- ...
Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. ...
ACKNOWLEDGMENTS The authors thank the editor and the three anonymous reviewers for their constructive and valuable comments. ...
doi:10.1002/ajpa.20722
pmid:18046749
fatcat:g4h3sd5p6bgkbiprdydb5psgg4
The current excitement about copy-number variation: how it relates to gene duplications and protein families
2008
Current Opinion in Structural Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Acknowledgements Funding was provided by a Marie Curie Fellowship (J.O.K.) and the NIH (Yale Center of Excellence in Genomic Science grant). ...
The authors thank Pedro Alves and Jeroen Raes for valuable comments on the manuscript. ...
For instance, recent studies have revealed that protein-coding genes, and also other genomic elements including highly conserved non-coding regions, tend to be depleted among CNVs, indicating purifying ...
doi:10.1016/j.sbi.2008.02.005
pmid:18511261
pmcid:PMC2577873
fatcat:wuers2lucrdy3o34pm7lxucrha
PopHumanScan: the online catalog of human genome adaptation
2018
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of the Phase III of the 1000 Genomes Project to detect selective sweeps at ...
as a response to changes in the environment or lifestyle of human populations. ...
ACKNOWLEDGEMENTS We thank Carla Giner for helpful comments on the PopHu-manScan data and implementation, and Esteve Sanz for help with the informatics infrastructure in which PopHu-manScan is implemented ...
doi:10.1093/nar/gky959
pmid:30335169
pmcid:PMC6323894
fatcat:fepixczm3vdtxm7cphrqe26gzi
A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data
2015
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The GenoCanyon web server is available at http://genocanyon.med.yale.edu Annotating functional elements in the human genome is a major goal in human genetics. ...
Identifying functional regions in the human genome is a major goal in human genetics. ...
and Development, and the Yale World Scholars Program sponsored by the China Scholarship Council. ...
doi:10.1038/srep10576
pmid:26015273
pmcid:PMC4444969
fatcat:jeup7aoaf5flnltxvx7c4l6ogu
Alu repeats increase local recombination rates
2009
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2011; you can also visit the original URL.
The file type is application/pdf.
The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density) that could influence recombination rate estimates. ...
If individual Alu insertions have even modest effects on local recombination rates, they could collectively have a significant impact on the pattern of linkage disequilibrium in the human genome and on ...
Acknowledgements This work was supported by a grant to MAB and LBJ from the National Institutes of Health (GM-59290). ...
doi:10.1186/1471-2164-10-530
pmid:19917129
pmcid:PMC2785838
fatcat:j4qut5346vfsvdubgmsrv5xywq
Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations
[article]
2016
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species. 2 ...
The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. ...
We want to thank two anonymous reviewers, Stephane Boissinot, Joris Bertrand and Anne Roulin for their insightful comments on previous versions of the manuscript. ...
doi:10.1101/052761
fatcat:hxnpz3gwkbfnrpx7pmxszaknb4
« Previous
Showing results 1 — 15 out of 1,777 results