Rosenberg lab at Stanford University

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Comments in scientific journals on research from the lab


Past lab news

  • 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).