Rosenberg lab at Stanford University

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Comments in scientific journals on research from the lab

Past lab news

  • 10-31-2018 — Congratulations to Ilana Arbisser on defending her thesis "Mathematical investigations into fundamental population genetics statistics and models." Ilana's thesis examines the joint distribution of the height and length of coalescent trees, the relationship of the population-genetic statistic FST to the triangle inequality, and the state space of a discrete-state coalescent model with recombination and migration. Dr. Arbisser's wise words about making hard decisions, such as square root transformation vs. Cailliez constant in multidimensional scaling: "it's important to consider what choices we're making and the consequences of those choices." Congrats Ilana!

  • 10-18-2018 — The lab examines the potential for determining that relatives genotyped with nonoverlapping marker sets are in fact relatives. This analysis demonstrates that people typed with microsatellites used in forensic genetics can be connected to close relatives typed with single-nucleotide polymorphisms used in biomedical, genealogical, personal-genomic, and population-genetic studies. Lead author is Jaehee Kim with former lab members Doc Edge and Bridget Algee-Hewitt also contributing. [CNN] [Nature] [New Scientist] [Science] [Scientific American] [Stanford Report] [Wired]

  • 9-14-2018 — A new study characterizes all (gene tree, species tree) pairs with exactly one coalescent history. The characterization of these "lonely" pairs relies on the way in which the taxa contained in cherries of the gene tree are placed with respect to the root of the species tree.

  • 8-30-2018Rohan Mehta has defended his PhD thesis "Mathematical modeling of genetic and cultural traits." Rohan's thesis studies a variety of mathematical modeling problems in diverse areas of population genetics and evolutionary biology. He examines combinatorial and probabilistic aspects of genealogical lineages along the branches of species trees, mathematical properties of FST statistics in relation to homozygosities and haploypes, and a gene-culture coevolutionary model of health-related behaviors. Congrats Rohan!

  • 8-30-2018 — Three articles from the lab have recently appeared.
    • Alan Aw reports a study in the Journal of Mathematical Biology, on the bounds on homozygosity and entropy statistics that measure genetic diversity in terms of the frequency of the most frequent allele. Alan uses the theory of majorization to obtain the bounds, generalizing previous mathematical results from the lab [52] [87].

    • Amy Goldberg and Lawrence Uricchio report an overview of the literature on natural selection in human populations in an Oxford Bibliographies article.

    • A commentary on Anthony Edwards's 2003 essay of multivariate classification of individuals into populations on the basis of genetic markers appears in a new book edited by Rasmus Winther about Edwards's career and contributions. Among other topics, the commentary discusses the influence of Edwards's model on a phenotypic model from the lab [129].

  • 7-18-2018Ilana Arbisser reports a mathematical investigation of the relationship between two of the most frequently used features of gene genealogies, the height and length of coalescent trees. The study also includes simulations describing the effect of population growth and population subdivision on the relationship between tree height and tree length. PhD graduate Ethan Jewett contributed to the project.

  • 7-11-2018 — Check out the Stanford X-Tree Project! The lab visualizes concepts in phylogenetics using photos of trees on the Stanford campus.

  • 5-30-2018 — We congratulate Jonathan Kang on the defense of his PhD thesis "Analysis and application of linkage disequilibrium in population and statistical genetics." In his thesis, Jonathan focuses on three questions concerning linkage disequilibrium (LD) and genomic sharing: the identification of optimal subsamples to prioritize for sequencing in order to enhance LD-based imputation, the relationship of runs of homozygosity to consanguinity in Jewish populations, and mathematical properties of measures of LD. Congrats to Jon!

  • 9-14-2017 — The lab reports a study of consanguinity and runs of homozygosity in Jewish populations. PhD student Jonathan Kang compares runs of homozygosity in contemporary Jewish populations to estimates of consanguinity measured in the 1950s from interviews with mothers in maternity wards. The study finds that the demographic consanguinity rates predict the fraction of the genome that resides in long runs of homozygosity. PhD graduates Amy Goldberg and Doc Edge contributed to the study.

  • 9-8-2017Filippo Disanto reports a study of the number of ancestral configurations possessed by matching gene trees and species trees. Ancestral configurations represent a combinatorial structure useful in producing probability formulas for gene trees given species trees, and they are hence connected to coalescent histories. Filippo's work is the latest in his series of combinatorial enumerations of structures that arise in the study of gene trees and species trees [123] [135] [142].

  • 8-21-2017 — A new study from the lab shows that in the admixed population of Cape Verde, genetic admixture is correlated with a measure of linguistic admixture evaluated by tabulating words of Portuguese and African origin in individuals' speech in the Cape Verde Kriolu lnaguage. The analyses suggest a mechanism of cotransmission of genetic and linguistic admixture during the descent of a creole-speaking admixed population. We congratulate lab alumni Paul Verdu*, Ethan Jewett*, and Trevor Pemberton on the study.

  • 8-5-2017Olga Kamneva reports a phylogenetic study of 20 worldwide species of strawberries (Fragaria) on the basis of next-generation sequencing data assembled via a bioinformatics pipeline designed specifically for polyploids of mixed ploidy. The study suggests new hypotheses for the diploid progenitors of polyploid species of Fragaria.

  • 7-6-2017Nicolas Alcala has obtained mathematical bounds on population-genetic statistic FST in the case of a biallelic marker whose mean frequency across a set of populations is fixed. His bounds provide an explanation of a frequently observed dependence of FST on the number of populations under consideration. Nicolas's paper expands on two earlier studies from the lab concerning bounds on FST [102] [121].

  • 5-30-2017 — Recent PhD graduate Doc Edge reports in a new study that on the basis of correlations between genotypes at neighboring markers, profiles containing nonoverlapping sets of genetic markers can be connected to the same individual. This "record-matching" is demonstrated using genomic and forensic genetic markers, and it has implications for forensic genetics and genomic privacy. Postdoc Bridget Algee-Hewitt and former postdoc Trevor Pemberton contributed to the project. [Stanford Report news story]

  • 5-8-2017 — Congratulations to Amy Goldberg on the defense of her thesis "Mathematical and statistical approaches to elucidate recent human evolutionary history." Amy's thesis considers mechanistic mathematical models of admixture, including the effect of sex-biased admixture on autosomes and on the X chromosome, and the inference from ancient autosomes and X chromosomes of sex-biased migration during prehistoric admixture events in Europe. She also examines the human population size history of South America on the basis of the density and location of archaeological sites. Congratulations Amy!

  • 4-24-2017 — We congratulate Amy Goldberg on receiving the 2017 Sherwood Washburn Prize from the American Association of Physical Anthropologists! This prize recognizes the best student presentation at the AAPA annual meeting. Amy spoke about her work on the contrast between Neolithic and Bronze Age migrations in Europe in their levels of male and female migration. [Read the paper]

  • 3-15-2017Amy Goldberg reports that two ancient migration events in Europe involved different proportions of male and female migrants, the earlier Neolithic migration from Anatolia having similar numbers of males and females and the later Pontic-Caspian migration having a greater proportion of males. The result, relying on comparisons of ancient DNA patterns from the X chromosome and the autosomes, builds on Amy's earlier work on sex bias in genetic admixture models [122] [133]. [Science news story]

  • 3-10-2017 — A new simulation study by postdoc alum Olga Kamneva evaluates the behavior of several methods for inferring species networks when the evolutionary process includes hybridization. The paper provides much-needed information on the comparative performance of the various approaches.

  • 2-27-2017 — Postdoc alum Olga Kamneva reports in PLoS Computational Biology a study of the relationship between genome composition of microbes and the co-occurrence of microbes in the environment. She finds that comparisons of microbial genomes can contribute to predictions about whether microbes are associated ecologically. Congrats Olga!

  • 2-22-2017 — We wish several members of the lab well in their new positions.
    • Nicolas Alcala — Postdoc with Matthieu Foll, International Agency for Research on Cancer, World Health Organization, Lyon.
    • Filippo Disanto — Junior faculty, Department of Mathematics, University of Pisa (sponsored by the Rita Levi Montalcini researcher program).
    • Doc Edge — Postdoc with Graham Coop, Department of Evolution and Ecology, University of California, Davis.
    • Olga Kamneva — Bioinformatics Scientist, Affymetrix, Inc.

  • 11-14-2016 — Postdoc Lawrence Uricchio has reported an upper bound on the size of gene tree sets required before all splits of a species tree appear in a gene tree set with a specified probability. His upper bound depends on a single parameter — the shortest internal branch in the species tree. The computation extends the lab's work on methods for species tree inference from gene trees.

  • 10-14-2016 — Recent PhD graduate Doc Edge has devised a general mathematical model to understand how genotypic differences between populations contribute to phenotypic differences between populations. He uses the model to analyze the relationship of genetics to "health disparities," concluding that health disparities that all trend in the same direction are incompatible with neutral genetic explanations. The work extends a simpler model of Doc's [129], allowing for diploidy, genetic drift, and general distributions of allele frequencies.

  • 10-7-2016 — Postdoc Filippo Disanto continues the lab's work on coalescent histories with a study of the number of coalescent histories for matching gene trees in caterpillar-like families of species trees. Filippo's work solves an open problem from earlier work in the lab [111], showing that the number of coalescent histories is asymptotic to a constant multiple of the Catalan numbers. He uses clever iterative enumerations and techniques of analytic combinatorics to obtain the result. See also [41], [68], and [135] for related work.

  • 7-27-2016 — We are pleased to announce that the software MONOPHYLER is now available. MONOPHYLER computes probabilities that sets of lineages are monophyletic, both for general species trees and for trees of small size. MONOPHYLER is reported by PhD student Rohan Mehta. The software encodes formulas from Rohan's recent Proceedings of the National Academy of Sciences paper.

  • 7-22-2016 — We congratulate PhD student Doc Edge on his thesis defense, "Pick up the pieces: combining information from multiple genetic loci." Doc's thesis examines several problems in the mathematical modeling of the genotype-to-phenotype relationship in structured populations, mathematical properties of the Fst measure of genetic differentiation, and population-genetic aspects of forensic DNA testing and genetic association studies. Doc has been recognized with the Samuel Karlin Prize in Mathematical Biology, awarded by the Department of Biology. Congratulations Doc!

  • 7-19-2016 — PhD student Rohan Mehta reports a computation of the probability that a set of gene lineages on an arbitrary species tree. The work generalizes earlier studies from the lab that considered trees of only two or three species. Rohan illustrates the new formula with an application in maize. The study is a contribution to the Comparative Phylogeography volume of the "In the Light of Evolution" special issue series of Proceedings of the National Academy of Sciences USA.

  • 6-27-2016 — We congratulate biology MS student Brian Donovan on the completion of his PhD in science education "An experimental exploration of how text-based instruction in school biology affects belief in genetic essentialism of race in adolescent populations." Brian defended his PhD in the Graduate School of Education on May 26. He is continuing his studies as a postdoctoral fellow at the Biological Sciences Curriculum Study in Colorado Springs.

  • 6-17-2016 — The lab reports a study examining the predicted distribution of gene tree shape under a birth-death model of species divergence. The work suggests that gene trees are expected to be more imbalanced than species trees, potentially providing part of the explanation for an excess of imbalance observed in inferred phylogenies.

  • 6-15-2016 — Congratulations to Amy Goldberg and Jaehee Kim, who have received fellowships for 2016-2017 from the Stanford Center for Computational, Evolutionary, and Human Genomics!

  • 5-12-2016 — Lab alumnus Mike DeGiorgio reports on the consistency properties of species tree inference methods in a model with ancestral population structure. By introducing a model that includes population subdivision in ancestral species, his paper introduces a new direction for studying consistency in species tree inference. The work is related to several recent papers from the lab on consistency of species tree methods ([85], [88], [89], [97], [109])

  • 4-22-2016 — Several projects from the lab have been in the news:

  • 4-5-2016 — We congratulate PhD student Amy Goldberg on the publication of her Nature article entitled "Post-invasion demography of prehistoric humans in South America." In this work, Amy and her colleagues use the locations and dates of South American archaeological sites to estimate the time trajectory of the human population size history of the continent. Read the news story here.

  • 4-4-2016 — Lab members Bridget Algee-Hewitt, Doc Edge, and Jaehee Kim report that forensic genetic markers selected for their use in individual identification possess a surprising level of information about genetic ancestry. Moreover, their study finds that a general correlation holds for genetic markers between their information about individual identity and ancestry information. The result makes use of theory from the lab on the connection between measures of genetic diversity and genetic differentiation ([102], [121]).

  • 1-5-2016 — The lab helps celebrate the centennial of the journal Genetics!

    When PhD student Amy Goldberg develops a model for sex-biased admixture on the X-chromosome, a curious mathematical sequence leads to an unexpected connection deep in the Genetics archive.

    Read about the oscillatory functions and coupled recursions encountered in this scholarly adventure — with a surprise appearance of the Fibonacci numbers.

  • 10-7-2015 — PhD student Jonathan Kang has analyzed a new approach for prioritizing individuals for whole-genome sequencing. This approach, based on minimizing a quantity the average distance to the closest leaf, seeks to identify a set of samples that will provide optimal templates for imputing genotypes in additional individuals. He compares the method to an earlier algorithm, also from the lab: maximizing phylogenetic diversity ([108]). Jonathan's article has been selected for Genetics issue highlights.

  • 9-30-2015 — Postdoc Filippo Disanto reports a study of the number of coalescent histories for gene trees and species trees in the lodgepole family. He uses connections with other combinatorial structures from theoretical computer science to derive exact results in the context of a new problem arising from biology. The term "lodgepole" for the tree shape he considers is based on a resemblance to the pattern in which lodgepole pine needles branch off the main twig. The work follows earlier studies from the lab on coalescent histories ([41], [68], [111]).

  • 9-24-2015 — We report an article on detecting selective sweeps using a new statistic, the haplotype allele frequency (HAF) score. This statistic tabulates the frequencies of alleles on a haplotype, and it has distinctive patterns of change during a selective sweep. The approach is related to previous articles from the lab that examined haplotype properties for detecting a deviation from null population-genetic models ([23] [127]).

  • 9-9-2015 — The lab reports two articles in this month's issue of Genetics.
    • PhD student Amy Goldberg reports a study of the effect of sex-biased admixture on the X chromosome. The study has a number of surprises: (1) The admixture level on the X chromosome is not simply a 2/3-and-1/3 linear combination of female and male parameters. (2) A difference in X chromosomal and autosomal levels of admixture need not imply male bias entering the admixed population from one source and female bias from a second source: the bias can be in the same direction in both source populations, but with different magnitudes. (3) A third surprise involves the appearance of a sequence related to the Fibonacci numbers! The paper follows two previous articles from the lab on mechanistic models of admixture ([82], [122]).

    • We report a review of three cases in which differences in levels of genetic diversity across populations contribute to population differences in societal variables — related to forensic testing, transplantation matching, and genome-wide association. The study also considers a fourth scenario, performing a reanalysis that contests a claim that within-population genetic diversity has influenced global economic development. PhD student Jonathan Kang contributed to the project. [Genes to Genomes blog post from the Genetics Society of America]

  • 8-11-2015 — Our program note reporting the software CLUMPAK is now available. What does the program do? It clumps and packages results from Structure and related programs. What does it produce? A pack of CLUMPPed Distruct plots — a clumpak! CLUMPAK is reported by PhD graduate Naama Kopelman. Former postdoc Mattias Jakobsson contributed to the project.

  • 7-24-2015 — PhD student Doc Edge uses a mathematical model to interpret the implications of two computations in population genetics---the partition of genetic variance, and the genetic assignment of individual ancestry---for human phenoypic differentiation. He concludes that a typical selectively neutral quantitative phenotype is comparable to a single genetic locus in terms of its ancestry information. The study is part of a special issue of Studies in History and Philosophy of Biological and Biomedical Sciences on Genomics and Philosophy of Race.

  • 5-22-2015 — We congratulate three lab members who have recently been awarded competitive fellowships!
    • Nicolas Alcala — Swiss National Science Foundation Early Postdoc.Mobility Fellowship (2015-2017).
    • Amy Goldberg — Achievement Rewards for College Scientists Fellowship from the Northern California Chapter of the ARCS Foundation (2015-2016).
    • Lawrence Uricchio — Stanford Center for Computational, Evolutionary, and Human Genomics Postdoctoral Fellowship (2015-2016).

  • 5-15-2015 — PhD student Nandita Garud from Dmitri Petrov's lab next door reports on the mathematical properties of statistics used in detecting soft selective sweeps. Nandita provides an improvement to the use of proposed statistics H12 and H2/H1, applying the modified statistics to analyze selection in Drosophila. The work relies on the lab's mathematical analysis of homozygosity and the frequency of the most frequent allele ([52], [87]).

  • 5-14-2015 — We are pleased to congratulate the lab's Administrative Associate Elena Yujuico on receiving the Humanities & Sciences Dean's Award of Merit! This award recognizes staff members who make outstanding contributions in the School of Humanities & Sciences.

  • 2-19-2015 — A news story in the Stanford Medicine SCOPE blog discusses with Noah the journal Theoretical Population Biology, for which he serves as the Editor-in-Chief.

  • 2-3-2015 — A new study by Nicole Creanza et al. performs the largest joint analysis of genetic variation and phonemic variation in populations worldwide. The study uncovers a number of new coevolutionary patterns in genes and languages, including correspondences in spatial axes of genetic and linguistic diversity, and a difference for genes and languages in the effects of population isolation. Former postdoc Trevor Pemberton contributed to the project. [\ Ars Technica] [The Atlantic] [] [Quar\ tz] [Stanford Report] [Nature Reviews Genetics] [PNAS commentary by Keith Hunley]

  • 12-10-2014Filippo Disanto reports a probabilistic result about anomalous ranked gene trees (ARGTs), demonstrating that as the number of species increases, the fraction of ranked species trees that produces ARGTs approaches 1. The work extends earlier existence results on ARGTs ([85], [97]).

  • 12-3-2014 — Approximate Bayesian Computation (ABC) provides a way of performing statistical inference from complex models that can be simulated but for which likelihoods are difficult to evaluate. Former postdoc Erkan Buzbas reports a new advance in ABC techniques for scenarios in which even simulating from the model is challenging — Approximate Approximate Bayesian Computation. Read about it here!

  • 11-7-2014 — PhD student Amy Goldberg reports a surprising result, that properties of admixture obtained from autosomal loci alone can be informative about sex bias in the history of admixture. The result is obtained in a new article in the November 2014 issue of Genetics. It builds on an earlier model studied by former postdoc Paul Verdu, who is also a contributor to the project.

  • 10-1-2014Nicolas Alcala joins us as a new postdoc. Nicolas completed his PhD in ecology and evolution at the University of Lausanne, performing several studies in the population-genetic modeling of demography and population structure. We are pleased to welcome Nicolas to the group!

  • 9-12-2014 — PhD student Doc Edge reports a new paper on the mathematical properties of population-genetic statistic FST. Doc has refined the bounds on FST as functions of the frequency of the most frequent allele and homozygosity obtained in an earlier study from the lab, considering a finitely-many-alleles case instead of the less constrained infinitely-many-alleles case. The work extends the lab's line of work on mathematical properties of population-genetic statistics.

  • 8-28-2014 — We welcome Ilana Arbisser as a PhD student in the lab. Ilana completed her BA at the University of Pennsylvania, where she majored in biology with a concentration in biological mathematics. Ilana rotated through the lab during the spring quarter, working on problems in coalescent theory. Welcome Ilana!

  • 8-15-2014 — A new study in PLoS Genetics led by former postdoc Paul Verdu reports on admixture in Native American and First Nation populations of the Pacific Northwest. The study describes recent European admixture in coastal and inland populations from British Columbia and Alaska, also uncovering evidence of recent East Asian admixture in the inland groups. It is the first genomic investigation focused on the Pacific Northwest region. Former postdoc Trevor Pemberton was a contributor to the project.

  • 8-8-2014 — We congratulate PhD student Ethan Jewett on the defense of his thesis, "Models, tools, and approaches for studying genetic and cultural variation." Ethan's thesis examines a series of problems on coalescent lineage distributions, with applications to the study of population growth and migration, inference of species trees, and genotype imputation. He also conducts analyses of variation in word usage, both in the United States and in Cape Verde, posing questions about cultural evolution. Ethan's work has been recognized with the Department of Biology's Samuel Karlin Prize in Mathematical Biology. Congratulations Ethan!

  • 7-22-2014 — Former postdoc Trevor Pemberton reports a study of population-genetic factors that affect worldwide variation in the inbreeding coefficent, showing that the value of this popular population-genetic statistic increases with increased consanguinty — but also with measures that reflect decreasing genetic diversity and increasing genetic isolation. The study is part of a special issue of Human Heredity on Consanguinity and Genomics.

  • 6-25-2014 — We congratulate co-mentored graduate student Dr. Naama Kopelman, on the completion of her PhD! Naama's thesis, conducted at Tel Aviv University on "The complex genealogy of Jewish populations," examines the genetic relationships of Jewish populations using both microsatellite loci [63] and genome-wide single nucleotide polymorphisms [114]. She also performs a theoretical investigation of the effect of admixture on tree-reconstruction algorithms, inspired by the placement of Jewish populations in a neighbor-joining tree [99]. Naama has begun a postdoc with Itay Mayrose, Department of Molecular Biology and Ecology of Plants, Tel Aviv University.

  • 6-22-2014 — A new special issue of Human Biology focuses on the genetics of Jewish populations. The lab contributes to two research studies in the special issue:
    • In a study of Y-chromosomal lineages in the Samaritans, Oefner et al. find that most Samaritans have a distinctive Y chromosome similar to that of Jewish Cohen lineages. Curiously, among the Samaritans, the only exception distant from the Cohen model haplotype is that of the Samaritan Cohen lineage.
    • An international team including graduate student Naama Kopelman studies genetic relationships with the Ashkenazi Jewish population in a large genome-wide data set, finding considerable shared ancestry with other Jewish populations and tracing more distant relationships to other populations of Europe and the Middle East.
    • Read the introduction to the special issue, by Noah Rosenberg and Steven Weitzman.

  • 6-5-2014 — A new paper by former postdoc Cuong Than determines the mean of the deep coalescence cost, measuring the fit of a gene tree to a species tree, under probability distributions for the shapes of gene trees and species trees. This paper extends Cuong's previous analysis focusing on the maximum deep coalescence cost rather than the mean [103]. The work advances knowledge of an important concept in estimation of species trees.

  • 3-29-2014 — Former graduate student Mike DeGiorgio has compared the properties of several different methods for species tree inference, using sequence data from eight species of North American pines. The paper and data support theoretical work from the lab on properties of the deep coalescence cost [75] [103] and extend the lab's work on gene trees and species trees.

  • 3-14-2014 — Graduate student Ethan Jewett has summarized and enhanced results on the properties of the number of lineages in genealogies obtained under the coalescent model. His work produces new approximations that can facilitate uses of the coalescent in large samples and complex demographies. The article appears in the May 2014 issue of Theoretical Population Biology.

  • 2-5-2014 — A new paper in the IEEE/ACM Transactions on Computational Biology and Bioinformatics describes the properties of coalescent histories for gene trees and species trees that resemble the "caterpillar" shape. The work extends earlier projects from the lab on coalescent histories [41] [68], and it advances the lab's research program on the combinatorics of evolutionary trees.

  • 1-2-2014 — Former graduate student Mike DeGiorgio has started a lab as Assistant Professor of Biology at Pennsylvania State University. We wish him all the best in his new position!

  • 11-26-2013 — A new article describes a unifying principle that underlies the production of anomalous gene trees (AGTs), gene trees that are more probable under an evolutionary model than the gene tree that matches the species tree. The new principle, identifying pairs of consecutive short branches as key to AGT production, refines earlier work from the lab on AGTs [30] [47].

  • 11-18-2013 — We welcome postdoc Filippo Disanto! Filippo joins us from the University of Cologne, where he completed an earlier postdoctoral fellowship in population genetics and bioinformatics.

  • 11-8-2013 — A report by Doc Edge et al. appears online in Evolution, Medicine, and Public Health, on surprises that occur in the application of population-genetic principles to association mapping. The article describes windfalls arising from population genetics—and pitfalls.

  • 10-3-2013 — A new article in Genetics reports an algorithm for optimizing the choice of samples to include in sequencing studies, when the goal is accurate genotype imputation. The algorithm is based on "phylogenetic diversity," the extent to which a subset of lineages captures the genealogical structure underlying an evolutionary tree. The work extends a line of investigation in the lab on genotype imputation [55] [62] [83] [92] [95] [106].

  • 9-29-2013 — We welcome several new members!
    • Bridget Algee-Hewitt; Bridget joins us as a postdoc from the University of Tennessee, where she completed an earlier postdoctoral fellowship in forensic anthropology.
    • Arbel Harpak; Arbel joins us as a PhD student after having completed his MS in ecology, evolution, and behavior at the Hebrew University of Jerusalem.
    • Jonathan Kang; Jonathan joins us a PhD student. His undergraduate degree is in applied mathematics and biology from Brown University, and most recently he has been performing research at the Bioinformatics Institute of Singapore.
    • Rohan Mehta; Rohan joins us as a PhD student after having completed his BS in biology and mathematics at the University of California, San Diego.

  • 9-5-2013 — We report a comment in Genetics in Medicine on strategies for improving the identification of recent parental relatedness as an incidental outcome in samples sent for clinical genomic testing. The comment highlights several principles for detection of runs of homozygosity that we previously reported in the work of Trevor Pemberton et al.

  • 8-13-2013 — This month we say goodbye to postdoc Lars Andersen. Lars's work in the lab has focused on coalescent theory, migration models, and Markov chains in population genetics. Lars returns to the Department of Mathematics at the University of Aarhus, where he will be starting a faculty position. We wish Lars all the best in his reversible jump.

  • 7-21-2013 — PhD graduate Lucy Huang and former postdoc Erkan Buzbas report a study of a population-genetic model of genotype imputation. The model complements a previous paper of Ethan Jewett et al., focusing on the role of mutation rather than sample size. Both models provide insight into the contribution of population-genetic parameters to the performance of genotype imputation methods for disease association studies.

  • 7-16-2013 — A paper by recent Ph.D. graduate Zach Szpiech contributes to the ongoing discussion on the population genetics of deleterious variation in humans. Zach finds that long runs of homozygosity (ROH) have a high level of recessive deleterious variation, reflecting a cumulative effect of recent parental relatedness in elevating the frequency of deleterious homozygotes. Former postdoc Trevor Pemberton is also a contributor to the work.

  • 5-28-2013 — A comprehensive dataset on worldwide human microsatellite variation is reported in a new paper in G3: Genes, Genomes, Genetics. Former postdoc Trevor Pemberton and PhD graduate Mike DeGiorgio have assembled eight major datasets, producing a collection of >5000 individuals from >250 populations, and using the collection to identify new features of human population structure. The data are available for future studies of human genetic variation.

  • 5-21-2013 — A new paper in IEEE/ACM Transactions on Computational Biology and Bioinformatics by former postdoc Cuong Than reports on mathematical properties of the deep coalescence cost, a quantity useful in inferring species trees from gene trees. Cuong's work explains an observation that deep coalescence algorithms tend to produce estimated trees with a high degree of balance. The paper builds upon Cuong's earlier work on deep coalescence [75].

  • 3-15-2013 — Lab alumnus Mattias Jakobsson has been awarded the 2013 Tage Erlanders Prize for Science and Technology in the field of biology. The prize, awarded every five years by the Royal Swedish Academy of Sciences to a young investigator in Sweden, recognizes Mattias's contributions to large-scale genetic studies of human demographic history. Congrats to Mattias!

  • 3-4-2013From Generation to Generation: Scientific and Cultural Approaches to Jewish Genetics, a course held in the autumn quarter of 2012, is profiled in Stanford Report.

  • 2-8-2013 — In this month's issue of Genetics, former postdoc Mattias Jakobsson and PhD student Doc Edge report the exact constraint on the FST measure of population structure at a locus as a function of the frequency of the locus's most frequent allele. The result can be used to explain comparatively low values of FST in diverse African human populations and lower values of FST for rare variants than for common variants. The work builds upon related studies reported by the lab [52] [87]. The cover image illustrates the work. Read the article. [Genetics issue highlights note] [Genetics commentary by F Rousset]

  • 1-19-2013 — In a new article reported in Molecular Biology and Evolution, recent graduate Mike DeGiorgio seeks to explain why it is possible under a range expansion for the first principal component of genetic variation to be either parallel or perpendicular to the direction of the expansion. The explanation involves the connection between coalescence times, Fst, and principal components.

  • 1-14-2013 — Noah takes on the role of Editor-in-Chief of Theoretical Population Biology! Read the welcome editorial.

  • 12-11-2012 — The second installment of the coalescent theory of ranked gene trees has appeared, in a paper jointly written with former postdoc James Degnan and Tanja Stadler (IEEE/ACM Trans Comp Biol Bioinformat 9: 1558-1568). The paper proves a surprising result, that most species trees have a ranking that gives rise to anomalous ranked gene trees. The paper extends earlier work from the lab on unranked gene trees.

  • 12-6-2012Trevor Pemberton is leaving the lab to begin work as Assistant Professor of Biochemistry and Medical Genetics at the University of Manitoba. We wish Trevor success in his new position!

  • 10-27-2012 — In a letter to the editor of Molecular Phylogenetics and Evolution, Erkan Buzbas comments that an approximate Bayesian computation (ABC) method proposed by Fan and Kubatko for species tree inference is not technically an ABC method. While Erkan does not claim that the method does not work well in practice, he finds that it fails to be a proper ABC method for quite interesting reasons. Read Erkan's ABC blog!

  • 10-22-2012 — A new theoretical paper from the lab, by Naama Kopelman et al., reports on the behavior of admixed populations in the neighbor-joining algorithm for constructing evolutionary trees. The theory provides explanations for a variety of patterns seen in actual neighbor-joining trees involving admixed populations. The paper will be presented at a session on Phylogenomics and Population Genomics at the Pacific Symposium on Biocomputing.

  • 10-2-2012 — In a new paper, Chaolong Wang and collaborator Kari Schroeder report a new method for estimating allelic dropout rates in microsatellite data. The method is novel in that it is designed explicitly for the case in which no replicate genotypes are available. Chaolong has written MicroDrop, a program that implements the new approach.

  • 9-19-2012 — This month, we welcome new members:
    • Lars Andersen; Lars joins us as a postdoc from the University of Aarhus, where he received his PhD in probability theory and performed postdoctoral work in population genetics.
    • Doc Edge; Doc returns as a PhD student to Stanford, where he previously completed his BA in human biology. He joins us after earning his MA in statistics at the University of California at Berkeley.
    • Amy Goldberg; Amy rejoins us as a PhD student. She was previously at the University of Michigan, where she completed her BS in biological anthropology and mathematics and was an undergraduate in the lab in its former home.

    We say goodbye to:

    • Erkan Buzbas, completing his postdoc and joining the faculty of \ the University of Idaho as Assistant Professor of Statistical Science
    • Zach Szpiech, receiving his PhD and starting a\ postdoc with Ryan Hernandez, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
    • Cuong Than, continuing in his postdoctoral studies wit\ h Daniel Huson, Faculty of Computer Science, University of Tubingen
    • Paul Verdu, completing his post\ doc and joining the faculty of the Natural History Museum of Paris as CNRS Associate Scientist
    • Chaolong Wang, receiving his PhD and starting a postdoc \ with Liming Liang and Xihong Lin, Department of Biostatistics, Harvard School of Public Health

    We wish everyone all the best in their new positions!

  • 8-24-2012 — In a paper in PLoS Genetics, Chaolong Wang reports on the pattern of similarity between genes and geography in human populations. His work standardizes analyses of genes and geography across different data sets from geographic regions, producing visualizations of the agreement between genetic variation and geographic maps of population sampling locations. Interestingly, the similarity between genes and geography is greater in Asia, rather than in Europe, where a similarity between genes and geography has been more widely known. [Science Editor's Choice note]

  • 8-17-2012 — A new paper by Trevor Pemberton et al. in the American Journal of Physical Anthropology examines patterns of variation in a distinctive endogamous group consisting of of six Gujarati villages. Trevor finds a genetic signature of the patrilocal practice in which marriages occur between villages, with wives moving to the husband's village.

  • 8-14-2012 — The lab reports on the worldwide distribution of runs of homozygosity (ROH) in the human genome in a recent paper by Trevor Pemberton et al. in the American Journal of Human Genetics. Trevor's paper also provides a new approach to categorizing ROH by the processes that have likely generated them, and reveals a variety of interesting geographic patterns in ROH lengths and frequencies. [Stanford Report article]

  • 8-10-2012 — Graduate students Zach Szpiech and Chaolong Wang have successfully defended their PhD dissertations in bioinformatics!
    Chaolong, Noah, and Zach at the University of Michigan Department of Computational Medicine and Biology, with graduate program director Margit Burmeister and founding center director Gil Omenn

    Zach's thesis on "Human migration, population divergence, and the accumulation of deleterious alleles: insights from private genetic variation and whole-exome sequencing" considers several perspectives on private alleles, including a model of microsatellite private alleles, a method for counting private alleles in uneven samples, and a study of connections among rare, private, and deleterious variants.

    Chaolong's thesis on "Statistical methods for analyzing human genetic variation in diverse populations" considers new approaches for studying spatial population-genetic variation, and develops a new method for circumventing allelic dropout in microsatellite data without requiring replicate genotypes.

  • 8-9-2012 — A paper by Ethan Jewett et al. describes a population-genetic model for genotype imputation. The paper links the framework of the coalescent to an important topic in the implementation of genome-wide association studies, producing new results that can help guide association study design.

  • 6-15-2012 — Two recent papers from the lab develop improved methods for estimating species trees from gene trees. In the first paper in the series, Ethan Jewett has developed iGLASS, which improves upon the method known as GLASS.

    In the second paper, Laura Helmkamp and Ethan Jewett have developed three more methods in the same family of approaches: iSD, iSTEAC, and iMAC. Laura and Ethan's paper appears in a special issue of the Journal of Computational Biology in honor of Simon Tavaré and Mike Waterman.

  • 5-7-2012 — We have moved into a newly renovated space on the third floor of Herrin Labs! [Photos (courtesy of MEI architects)]

  • 4-5-2012 — Undergraduate Amy Goldberg has been awarded a National Science Foundation Graduate Research Fellowship. Amy will be joining us at Stanford this autumn as a PhD student. Congrats Amy!

  • 3-6-2012 — Recent PhD graduate Mike DeGiorgio received an Honorable Mention for the ProQuest Distinguished Dissertation Award. The award recognizes outstanding dissertations across all PhD programs at the University of Michigan. Congrats Mike!

  • 1-1-2012 — A recently published paper of Shashir Reddy reports upper and lower bounds on the frequency of the most frequent allele at a locus, conditional on the homozygosity and number of distinct alleles of the locus (J Math Biol 64: 87-108). This paper refines an earlier study that did not condition on the number of alleles, and it is one of several articles in the lab to feature undergraduate research.

  • 12-28-2011 — Two papers from the lab investigate properties of human haplotype variation. Former postdoc Paul Scheet and his student Anthony San Lucas have developed Haploscope, a visualization tool for examining haplotypes in populations (Genet Epidemiol 36: 17-21). Graduate student Lucy Huang, former postdoc Mattias Jakobsson, postdoc Trevor Pemberton and collaborators have studied patterns of haplotype variation in African populations, interpreting them in light of models of human evolution and investigating their implications for imputation-based association studies of disease (Genet Epidemiol 35: 766-780).

  • 12-20-2011 — A paper from the lab has appeared on the properties of ranked gene trees conditional on species trees (Math Biosci 235: 45-55). In contrast to previous work from the lab on gene trees and species trees, this study takes into consideration not only the gene tree topology, but also the sequences of events involved in producing gene trees. The project is a collaboration with former postdoc James Degnan and Tanja Stadler.

  • 12-17-2011 — Postdoc Paul Verdu's paper on a mathematical model of admixture has appeared in Genetics. This work uses a mechanistic evolutionary model to examine the properties of admixture predicted for an admixed population, as a function of parameters that describe the way in which admixture takes place over time.

  • 10-13-2011 — Three recent papers from the lab provide new developments in population-genetic theory. Zach Szpiech has investigated the properties of private alleles at microsatellite loci in a two-population model (Theor Pop Biol 80: 100-113). Simina Boca has evaluated population divergence measures involving admixed populations in a model of admixture between two source groups (Theor Pop Biol 80: 208-216). Mike DeGiorgio and James Degnan have analyzed gene genealogies in a model designed for considering human migrations out of Africa (Genetics 189: 579-593).

  • 10-11-2011 — Work from the lab on human genetic variation and genome-wide association studies is featured in the October 2011 cover story of Genome Technology. [Genome Technology article]

  • 9-27-2011 — Graduate student Lucy Huang successfully defended her PhD dissertation in bioinformatics on "Genotype imputation in worldwide human populations: empirical and theoretical approaches." Lucy's thesis studies genotype imputation accuracy in diverse human populations, including African populations, as a function of different ways of selecting imputation reference panels; it also considers investigations of sample-size inflation for maintaining power in imputation studies, and coalescent models for genotype imputation. Congrats Lucy!

  • 9-22-2011 — "A test of the influence of continental axes of orientation on patterns of human gene flow" by Sohini Ramachandran and Noah Rosenberg has appeared online in the American Journal of Physical Anthropology. This paper provides a test on the basis of genetics of Jared Diamond's hypothesis in Guns, Germs, and Steel that differences in contintental orientation contributed to differences in the speed of technological diffusion in Eurasia and the Americas. [Abstract] [PDF] [Science news story] [Discovery News story] [Scientific American news story] [Brown Daily Herald news story]

  • 8-5-2011 — Graduate student Chaolong Wang has been awarded a Howard Hughes Medical Institute International Student Research Fellowship. The fellowship provides support to international students in the third to fifth years of their PhD work. Congrats Chaolong! [HHMI press release]

  • 7-1-2011The Rosenberg Lab has moved from the University of Michigan to Stanford University!

  • 4-25-2011 — Graduate student Mike DeGiorgio successfully defended his PhD dissertation in bioinformatics on "Genetic variation and modern human origins." Mike's thesis includes investigations of models of human origins on the basis of simulations and analytical summary statistics; mathematical work on the estimation of heterozygosity in cases in which samples contain related individuals; and development of phylogenetic methods for inferring species trees in the setting in which gene trees are discordant. Mike will be joining the lab of Rasmus Nielsen at the University of California, Berkeley, supported by an NSF Postdoctoral Fellowship in Biology. Congrats Mike!

  • 4-7-2011 — Graduate student Chaolong Wang has been awarded a Rackham Predoctoral Fellowship from the Rackham Graduate School. The fellowship provides a year of support to graduate students nearing the conclusion of their PhD work.

  • 2-11-2011 — This month's cover of the American Journal of Human Genetics is inspired by the work of Mike DeGiorgio and Ivana Jankovic on estimating heterozygosity in samples with relatives, published in Genetics last December. [AJHG, February 2011]

  • 12-3-2010 — Graduate student Chaolong Wang has been named a winner of a Delill Nasser travel award from the Genetics Society of America. Chaolong will use the award to attend the 12th International Congress of Human Genetics, which will be held in Montreal in October 2011. Congrats Chaolong! [GSA Reporter news story]

  • 10-7-2010 — The work of postdoc Trevor Pemberton et al. on identifying unexpected close relatives in the newly reported individuals from Phase 3 of the HapMap project has been published in the American Journal of Human Genetics. Trevor's paper will be informative for researchers working closely with the HapMap 3 samples who require knowledge of relatedness in their analyses. [Genome Technology news story]

  • 9-20-2010 — Graduate student Mike DeGiorgio is one of two recipients of this year's Program in Biomedical Sciences Graduate Student Award for Excellence in Research. Congratulations Mike!

  • 9-17-2010 — Graduate student Mike DeGiorgio and postdoc Erkan Buzbas will be speaking about their work at the upcoming meeting of the American Society of Human Genetics in Washington, DC. Mike will speak about coalescence time distributions in a serial founder model of human evolutionary history, and his trip is sponsored by a FASEB Minority Access to Research Careers travel award. Erkan will speak about balancing selection on human immune system genes, with travel support from a Delill Nasser travel award from the Genetics Society of America. Graduate students Lucy Huang, Ethan Jewett, Zach Szpiech, and Chaolong Wang, as well as postdocs Trevor Pemberton and Paul Verdu, will be presenting posters at the meeting.

  • 7-28-2010Ivana Jankovic's work on genetic diversity in the Yellowstone wolves has been reported in Molecular Ecology. Ivana has found that genetic diversity in the reintroduced population is relatively stable, supporting field observations that the wolves are effective at avoiding inbreeding.

  • 6-28-2010 — Graduate students Mike DeGiorgio, Ethan Jewett, and Zach Szpiech have been awarded fellowships from the University of Michigan Genome Science Training Program. The fellowships provide 1-2 years of support for graduate training.

  • 5-19-2010 — Postdoc Trevor Pemberton was awarded a University of Michigan Center for Genetics in Health and Medicine postdoctoral fellowship. The fellowship will support Trevor's work on genomic patterns of homozygosity in worldwide human populations.

  • 5-1-2010 — Undergraduate Ivana Jankovic will be leaving for the University of California, Los Angeles to begin her MD/PhD. Congrats Ivana!

  • 4-7-2010 — Graduate student Lucy Huang has been awarded a Rackham Predoctoral Fellowship from the Rackham Graduate School. The fellowship provides a year of support to graduate students nearing the conclusion of their PhD work.

  • 1-27-2010Chaolong Wang et al. have developed an approach for quantitatively comparing the similarity of statistical maps of population-genetic variation with geographic maps of sampling variation. The paper is available here.

  • 12-17-2009 — In collaboration with Sean Morrison's group, the lab has conducted a study that finds that the most widely used human embryonic stem cell lines derive from donors with European ancestry. The limited population diversity in widely used lines has important implications for ongoing work on human embryonic stem cells. [UM news release] [UPI news story]

  • 10-20-2008ADZE is available for download. This program examines alleles private to combinations of populations, correcting for sample size differences across populations. A description of ADZE is reported in Bioinformatics 24: 2498-2504 (2008).

  • 2-26-2008 — "Genotype, haplotype, and copy-number variation in worldwide human populations" has appeared in Nature. This work was featured in several news stories.
    [Washington Post]

  • 12-3-2007 — "Genetic variation and population structure in Native Americans" is now available online in PLoS Genetics. This work was featured in Science News.

  • 10-10-2007CLUMPP version 1.1.1 is now available for download. A description of CLUMPP is reported in Bioinformatics 23: 1801-1806 (2007).

  • 6-28-2007distruct version 1.1 is now available for download. The new version includes color schemes from ColorBrewer.

    A description of distruct appears in Molecular Ecology Notes 4: 137-138 (2004).