ABOUT THE LAB. 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

• 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!

• 3-4-2013 — From 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 F_ST 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 F_ST in diverse African human populations and lower values of F_ST for rare variants than for common variants. The work builds upon related studies [52] [87] reported by the lab. The cover image illustrates the work. Read the article. [Genetics issue highlights note]

• 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, F_st, 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.

• 12-6-2012 — Trevor 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!

• 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.

• Past news items

SELECTED RECENT PUBLICATIONS

M Jakobsson, MD Edge, NA Rosenberg (2013) The relationship between F_ST 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]