Rosenberg lab at Stanford University

We are a mathematical, theoretical, and computational lab in genetics and evolution. Research in the lab addresses problems in evolutionary biology and human genetics through a combination of mathematical modeling, computer simulations, development of statistical methods, and inference from population-genetic data. Read more...


RECENT NEWS

  • 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 with Daniel Huson, Faculty of Computer Science, University of Tubingen
    • Paul Verdu, completing his postdoc 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!

  • Past news items


    SELECTED RECENT PUBLICATIONS

    M Jakobsson, MD Edge, NA Rosenberg (2013) The relationship between FST and the frequency of the most frequent allele. Genetics 193: 515-528. [Abstract] [PDF]

    JH Degnan, NA Rosenberg, T Stadler (2012) A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9: 1558-1568. [Abstract] [PDF]

    TJ Pemberton, D Absher, MW Feldman, RM Myers, NA Rosenberg, JZ Li (2012) Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics 91: 275-292. [Abstract] [PDF] [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]

    S Ramachandran, NA Rosenberg (2011) A test of the influence of continental axes of orientation on patterns of human gene flow. American Journal of Physical Anthropology 146: 515-529. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Tables]

    ZA Szpiech, NA Rosenberg (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [Abstract] [PDF]

    NA Rosenberg, L Huang*, EM Jewett*, ZA Szpiech*, I Jankovic*, M Boehnke (2010) Genome-wide association studies in diverse populations. Nature Reviews Genetics 11: 356-366. [Abstract] [PDF]

    JT Mosher, TJ Pemberton, K Harter, C Wang, EO Buzbas, P Dvorak, C Simon, SJ Morrison, NA Rosenberg (2010) Lack of population diversity in commonly used human embryonic stem-cell lines. New England Journal of Medicine 362: 183-185. [PDF] [Supplement]

    NM Kopelman, L Stone, C Wang, D Gefel, MW Feldman, J Hillel, NA Rosenberg (2009) Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genetics 10: 80. [Abstract] [Full text at journal website] [PDF]

    M DeGiorgio, M Jakobsson, NA Rosenberg (2009) Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proceedings of the National Academy of Sciences USA 106: 16057-16062. [Abstract] [PDF] [Supplement]

    M Jakobsson*, SW Scholz*, P Scheet*, JR Gibbs, JM VanLiere, H-C Fung, ZA Szpiech, JH Degnan, K Wang, R Guerreiro, JM Bras, JC Schymick, DG Hernandez, BJ Traynor, J Simon-Sanchez, M Matarin, A Britton, J van de Leemput, I Rafferty, M Bucan, HM Cann, JA Hardy, NA Rosenberg, AB Singleton (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003. [Abstract] [PDF] [Supplement]