Selected media coverage
Coverage by university news
explore how disease dynamics change when cultural behaviors spread
like a pathogen (Stanford Report, September 8, 2020)
scientists commemorate 50 years of a "famously obscure" field
(Stanford Report, June 1, 2020)
for an "aha moment": pair up with your spouse (Stanford Medicine
Scope, February 13, 2020)
scientists link Neanderthal extinction to human diseases (Stanford
Report, November 7, 2019)
researchers discover a new way to find relatives from forensic DNA
(Stanford Report, October 17, 2018)
- Cape Verde creole, DNA, speech data reveal history of
genetic, linguistic evolution (University of Michigan Global
Michigan, August 28, 2017)
fish in a pond or a needle in a haystack? DNA tool rasises promise,
privacy concerns (University of Michigan Health Lab Report,
May 18, 2017)
patterns could aid scientists and police, but raise privacy
concerns, Stanford scientists say (Stanford Report, May
DNA reveals more than we thought, and that's both good and
bad (Stanford Medicine Scope, May 15, 2017)
benefit of mathematical models in medicine (Stanford
Medicine Scope, February 19, 2015)
dispersal and the evolution of languages show strong link, Stanford
biologists find (Stanford Report, January 30, 2015)
the deep history of human genes and language (Brown
University News From Brown, January 19, 2015)
- Noah Rosenberg and Fiorenza Micheli named to endowed chairs
(Stanford Department of Biology news, October 10, 2014)
humanities and science scholars join forces for groundbreaking
research on Jewish genetics (Stanford Report, March 1, 2013)
launches new center to advance 'information age of genomics'
(Stanford Report, December 3, 2012)
chromosomes agree, Stanford researchers find signatures of human
migrations and marriage practices (Stanford Report,
August 14, 2012)
bolsters migration theory (Brown Daily Herald, October
- U-M study reveals
surprising lack of genetic diversity in the most widely used human
embryonic stem cell lines (University of Michigan News
Service, December 16, 2009)
Native Americans Descended From a Single Ancestral Group, DNA Study
Confirms (UC Davis News and Information, April 28, 2009)
- U-M researchers
release most detailed global study of genetic variation
(University of Michigan News Service, February 20, 2008)
Gene study adds weight to theory that native people of the Americas
arrived in a single main migration across the Bering Strait
(University of Michigan Health System Newsroom, November 27, 2007)
of Genetic Traits Makes Progress (USC News, December
- One small snip from
man; one giant leap for the genome (University of Michigan
News Service, December 7, 2006)
All in the Family (USC News, December 19, 2003)
DNA suggests humans descend from small ancestral population
(Stanford Report, May 28, 2003)
(USC News, December 19, 2002)
More media coverage...
Comments in scientific journals on research from the lab
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!
7-1-2011 The 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!
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
DeGiorgio and Ivana Jankovic on estimating heterozygosity
in samples with relatives, published in Genetics last December.
Past lab news
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
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
, 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
 for related
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
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
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.
and Jaehee Kim, who have received fellowships for
2016-2017 from the Stanford Center for Computational, Evolutionary, and
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,
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
4-22-2016 Several projects from the lab have been in
4-5-2016 We congratulate PhD
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
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
1-5-2016 The lab helps celebrate the centennial of the
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
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
Jonathan's article has been selected
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 (,
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 (
The lab reports two articles in this month's issue of Genetics.
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
Distruct plots a
clumpak! CLUMPAK is reported by PhD
graduate Naama Kopelman. Former
Jakobsson contributed to the
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.
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
- 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
5-22-2015 We congratulate three lab members who have
recently been awarded competitive fellowships!
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
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
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 &
- 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
- Lawrence Uricchio Stanford Center for Computational,
Evolutionary, and Human Genomics Postdoctoral Fellowship (2015-2016).
story in the Stanford Medicine SCOPE blog discusses with
Noah the journal Theoretical Population Biology, for which he
serves as the Editor-in-Chief.
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
Pemberton contributed to the project.
commentary by Keith Hunley]
12-10-2014 Filippo Disanto reports a
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
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!
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
studied by former postdoc Paul Verdu, who is also a contributor
to the project.
10-1-2014 Nicolas 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!
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
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
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!
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
 and genome-wide single
nucleotide polymorphisms . 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
. 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:
new paper by
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 . The
work advances knowledge of an important concept in estimation of species
3-29-2014 Former graduate
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
support theoretical work from the lab on properties of the deep
coalescence cost 
 and extend the
lab's work on
trees and species trees.
- 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.
to the special issue, by Noah
Rosenberg and Steven Weitzman.
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
, and it advances
the lab's research program on the
combinatorics of evolutionary
1-2-2014 Former graduate
DeGiorgio has started a lab as Assistant Professor of
Biology at Pennsylvania State University. We wish him all the best
in his new position!
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
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 geneticsand pitfalls.
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
9-29-2013 We welcome several new members!
9-5-2013 We report
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
Pemberton et al.
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
- 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.
7-21-2013 PhD graduate Lucy Huang and former
postdoc Erkan Buzbas
study of a
population-genetic model of genotype imputation. The model
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.
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
reflecting a cumulative effect of recent parental relatedness in
elevating the frequency of deleterious homozygotes. Former
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
Pemberton and PhD
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
for future studies of human genetic variation.
5-21-2013 A new paper in IEEE/ACM Transactions on
Computational Biology and Bioinformatics by former
Than reports on mathematical properties of the deep
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
3-15-2013 Lab alumnus
Jakobsson has been awarded the 2013
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!
Generation to Generation: Scientific and Cultural Approaches to Jewish
Genetics, a course held in the autumn quarter of 2012, is profiled
2-8-2013 In this month's issue of Genetics,
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
The cover image illustrates the work.
Read the article.
issue highlights note]
commentary by F Rousset]
1-19-2013 In a new
reported in Molecular Biology and Evolution, recent
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
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
(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.
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
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
10-22-2012 A new
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
on Phylogenomics and Population Genomics at the Pacific Symposium on
10-2-2012 In a
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
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 \
University of Idaho as Assistant Professor of Statistical Science
Szpiech, receiving his PhD and starting a\
postdoc with Ryan
Hernandez, Department of Bioengineering and Therapeutic Sciences,
California, San Francisco
- Cuong Than,
continuing in his postdoctoral studies wit\
h Daniel Huson,
Faculty of Computer Science, University of Tubingen
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 \
Liang and Xihong Lin, Department of Biostatistics, Harvard School of
We wish everyone all the best in their new positions!
8-24-2012 In a paper
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
Editor's Choice note]
8-17-2012 A new paper
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
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
8-10-2012 Graduate students
Zach Szpiech and
Wang have successfully defended their PhD dissertations in
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
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.
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
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
3-6-2012 Recent PhD
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.
1-1-2012 A recently published
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
12-28-2011 Two papers from the lab investigate
properties of human haplotype variation. Former
Scheet and his student Anthony San Lucas have
a visualization tool for examining haplotypes in populations (Genet
Epidemiol 36: 17-21). Graduate student
postdoc Mattias Jakobsson,
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
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.
has investigated the properties of private alleles at microsatellite loci
in a two-population model (Theor Pop Biol 80:
Boca has evaluated population divergence measures involving
admixed populations in a model of admixture between two source groups
(Theor Pop Biol 80:
DeGiorgio and James
Degnan have analyzed gene genealogies in a model designed for
considering human migrations out of Africa (Genetics 189:
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
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"
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.
news story] [Discovery
American news story]
Daily Herald news story]
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
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.
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
Pemberton and Paul Verdu, will be presenting posters at
7-28-2010 Ivana 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.
1-27-2010 Chaolong 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.
news release] [UPI
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
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.
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.
10-10-2007 CLUMPP version 1.1.1 is now available
for download. A description of CLUMPP is reported in Bioinformatics
23: 1801-1806 (2007).
6-28-2007 distruct 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: