Research Topics
| MONTGOMERY W SLATKINSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundaryJohannes Krause
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
BMC Evol Biol 8:220. 2008..Widely divergent topologies have been suggested based on various data sets and methods...- The sampling distribution of disease-associated allelesM Slatkin
Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
Genetics 147:1855-61. 1997..In particular, roughly the same population growth rate appears consistent with both data sets... - A population-genetic test of founder effects and implications for Ashkenazi Jewish diseasesMontgomery Slatkin
Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
Am J Hum Genet 75:282-93. 2004.... - A vectorized method of importance sampling with applications to models of mutation and migrationMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Theor Popul Biol 62:339-48. 2002..The analysis of eight low-frequency allozyme alleles found in the glaucous-winged gull, Larus glaucescens, illustrates how geographically restricted dispersal can be detected... - Estimating allele ageM Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Annu Rev Genomics Hum Genet 1:225-49. 2000..We emphasize that estimates of allele age depend on assumptions about demographic history and natural selection... - Simulating genealogies of selected alleles in a population of variable sizeM Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Genet Res 78:49-57. 2001..This method was used to estimate the intensity of selection affecting the delta 32 allele at the CCR5 locus in Europeans and a mutant at the MLH1 locus associated with colorectal cancer in the Finnish population... - The use of intraallelic variability for testing neutrality and estimating population growth rateM Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Genetics 158:865-74. 2001..027 per generation with a support interval of (0.017-0.037). Four of the relatively common alleles at CFTR also appear to be neutral but DeltaF508 appears to be significantly advantageous to heterozygous carriers... - Allele age and a test for selection on rare allelesM Slatkin
Department of lntegrative Biology, University of California, Berkeley 94720 3140, USA
Philos Trans R Soc Lond B Biol Sci 355:1663-8. 2000..The test is applied to the locus, BRCA1, associated with early-onset breast cancer in humans and shows that two common disease-associated alleles (5382insC and 185delAG) appear to have been subject to natural selection... - Genetic hitch-hiking in a subdivided populationM Slatkin
Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
Genet Res 71:155-60. 1998.... - Disequilibrium mapping of a quantitative-trait locus in an expanding populationM Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Am J Hum Genet 64:1764-72. 1999..The tests also provide a basis for defining a measure of association, gamma, between a low-frequency allele at a putative QTL and a low-frequency allele at a marker locus... - Overdominant alleles in a population of variable sizeM Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Genetics 152:775-81. 1999..Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class... - Balancing selection at closely linked, overdominant loci in a finite populationM Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Genetics 154:1367-78. 2000..The model can reproduce many of the observed patterns at DQA1 and DQB1 provided that the recombination rate is assumed to be very small... - A method for estimating the intensity of overdominant selection from the distribution of allele frequenciesM Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Genetics 156:2119-26. 2000..A comparison of two types of data for DQA1 and DRB1 showed that serotyping led to generally lower estimates of S... - Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populationsMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Mol Ecol 14:67-73. 2005..The apparent migration matrix determined by the method described in this paper probably represents the upper bound on the effect of ghost populations... - On selecting markers for association studies: patterns of linkage disequilibrium between two and three diallelic lociChad Garner
Department of Medicine, University of California, Irvine, California 92697 7550, USA
Genet Epidemiol 24:57-67. 2003..Haplotypes of two or more SNPs generally have a higher probability than individual SNPs of showing useful LD with a disease mutation, although exceptions are described... - The loss of statistical power to distinguish populations when certain samples are ambiguousMontgomery Slatkin
Department of Integrative Biology, University of California, 3060 Valley Life Sciences, Bldg. 3140 (4151-4155 VLSB, Berkeley, CA 94720-3140, USA
Theor Popul Biol 64:177-92. 2003..For the special situation of two di-allelic marker loci, we obtain a simple expression for R and its upper bound... - A graphical approach to multi-locus match probability computation: revisiting the product ruleYun S Song
Department of Computer Science, University of California, Davis, CA 95616, USA
Theor Popul Biol 72:96-110. 2007..We show that monogamy increases the probabilities of genotypic matches at unlinked loci and that the effect of monogamy increases with the number L of loci. We conjecture a sharp upper bound on the effect of monogamy for a given L... - Multiplex relative risk and estimation of the number of loci underlying an inherited diseasePaul Schliekelman
Department of Integrative Biology, University of California, Berkeley, USA
Am J Hum Genet 71:1369-85. 2002..This method avoids the potential inconsistencies of the Risch method and has greater precision. We apply our method to data on cleft lip/cleft palate and schizophrenia... - The joint allele-frequency spectrum in closely related speciesHua Chen
Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Genetics 177:387-98. 2007.... - General epistatic models of the risk of complex diseasesYun S Song
Department of Electrical Engineering, University of California, Berkeley, California 94720 3140, USA
Genetics 186:1467-73. 2010.... - A Bayesian method for jointly estimating allele age and selection intensityMontgomery Slatkin
Department of Integrative Biology, 3060 VLSB, University of California at Berkeley, Berkeley, CA 94720 3140, USA
Genet Res (Camb) 90:129-37. 2008..The method is illustrated with an application to the A-allele of G6PD in Africa. Because changes in allele frequency and recombination are both intrinsically stochastic, there are limits to the accuracy achievable with any method... - Linkage disequilibrium--understanding the evolutionary past and mapping the medical futureMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Nat Rev Genet 9:477-85. 2008..At present, linkage disequilibrium is used much more extensively in the study of humans than in non-humans, but that is changing as technological advances make extensive genomic studies feasible in other species... - Genotype-specific recurrence risks as indicators of the genetic architecture of complex diseasesMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Am J Hum Genet 83:120-6. 2008..If there is saturation of risk with increasing numbers of causative alleles, then observed GSRs for individuals with high-risk genotypes will be lower than predicted by the multiplicative model... - Likelihood-based disequilibrium mapping for two-marker haplotype dataChad Garner
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Theor Popul Biol 61:153-61. 2002..Haplotype configurations exist for which the composite likelihood will fail to place the disease locus in the correct marker interval... - Subdivision in an ancestral species creates asymmetry in gene treesMontgomery Slatkin
Department of Integrative Biology, University of California at Berkeley, USA
Mol Biol Evol 25:2241-6. 2008..We show that substantial levels of persistent ancestral subdivision are needed to account for the observed levels of asymmetry found in these two studies... - Exchangeable models of complex inherited diseasesMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Genetics 179:2253-61. 2008..If causative alleles are in relatively high frequency, then the combined effects of numerous causative loci are necessary to substantially elevate disease risk... - An investigation of the statistical power of neutrality tests based on comparative and population genetic dataWeiwei Zhai
Department of Integrative Biology, University of California, Berkeley, USA
Mol Biol Evol 26:273-83. 2009..We discuss our findings in the light of the discordant results obtained in several recently published genomic scans... - Epigenetic inheritance and the missing heritability problemMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Genetics 182:845-50. 2009..The model highlights the need for empirical estimates of the persistence times of heritable epialleles... - Inference of microbial recombination rates from metagenomic dataPhilip L F Johnson
Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America
PLoS Genet 5:e1000674. 2009..The method itself makes no assumption specific to microbial populations, opening the door for application to any mixed population sample where the number of individuals sampled is much greater than the number of fragments sequenced... - Accounting for bias from sequencing error in population genetic estimatesPhilip L F Johnson
Biophysics Graduate Group, University of California, Berkeley, USA
Mol Biol Evol 25:199-206. 2008..We propose a rule of thumb to judge when a given threshold will lead to significant bias and suggest alternative approaches that reduce bias... - Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virusWeiwei Zhai
Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720 3140, USA
J Mol Evol 65:340-8. 2007..Our results suggest that it may be more difficult to use inferences regarding the strength of selection on mutations to make predictions regarding viral epidemics than previously thought... - Intense selection in an age-structured populationAlison P Galvani
Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Proc Biol Sci 271:171-6. 2004..We relate our model and results to selection for disease resistance, although the results have broader implications for inferences about past selection pressures in general... - Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineageMark W Neff
Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
Proc Natl Acad Sci U S A 101:11725-30. 2004.... - The geographic spread of the CCR5 Delta32 HIV-resistance alleleJohn Novembre
Department of Integrative Biology, University of California, Berkeley, California, United States of America
PLoS Biol 3:e339. 2005..Our results describe the evolutionary history of the Delta32 allele and establish a general methodology for studying the geographic distribution of selected alleles... - The concordance of gene trees and species trees at two linked lociMontgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Genetics 172:1979-84. 2006..Both balancing selection and selective sweeps can result in much longer genomic regions having concordant gene trees... - Non-equilibrium theory of the allele frequency spectrumSteven N Evans
Department of Statistics 3860, University of California at Berkeley, 367 Evans Hall, Berkeley, CA 94720 3860, USA
Theor Popul Biol 71:109-19. 2007..For example, it is shown that approximately 30% of the expected total heterozygosity of neutral loci is attributable to mutations that arose since the onset of population growth in roughly the last 150,000 years... - Inference of population genetic parameters in metagenomics: a clean look at messy dataPhilip L F Johnson
Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
Genome Res 16:1320-7. 2006..We illustrate the use of our technique on a new project analyzing activated sludge from a lab-scale bioreactor seeded by a wastewater treatment plant... - Evaluating plague and smallpox as historical selective pressures for the CCR5-Delta 32 HIV-resistance alleleAlison P Galvani
Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 100:15276-9. 2003..By using a population genetic framework that takes into account the temporal pattern and age-dependent nature of specific diseases, we find that smallpox is more consistent with this historical role... - Average probability that a "cold hit" in a DNA database search results in an erroneous attributionYun S Song
Departments of EECS and Statistics, University of California, Berkeley, CA 94720 3140, USA
J Forensic Sci 54:22-7. 2009.... - Estimating the number of founder lineages from haplotypes of closely linked SNPsRaphael Leblois
Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 9472 3140, USA
Mol Ecol 16:2237-45. 2007..We illustrate the use of our method by applying it to a previously published data set from a recently founded population of wolves (Canis lupus) in Scandinavia... - Population-genetic basis of haplotype blocks in the 5q31 regionEric C Anderson
Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 94720, USA
Am J Hum Genet 74:40-9. 2004..Estimates of local recombination rates for the Daly et al. data do not indicate the presence of recombination hotspots... - Multilocus self-recognition systems in fungi as a cause of trans-species polymorphismChristina A Muirhead
Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
Genetics 161:633-41. 2002....