Margarida Moreira Cardoso After completing her Ph.D. resarch in teh Manyuan Long lab at the University of Chicago, Margarida joined the Clark lab in June 2009 studying the mutational and selective forces shaping copy number variation as well as the functional consequences of copy number variants. Margarida left the Clark lab at the end of 2012 to continue her research at UNIL's Center for Integrative Genomics.
Roman Arguello Roman joined the lab in September 2008 after completing his Ph.D. with Manyuan Long at the University of Chicago. His research involved population genomics projects that involve analysis of a whole genome resequencing effort for five geographically diverse populations of D. melanogaster. Roman left the Clark Lab at the end of 2012 continuing his research with Dr. Richard Benton's group at UNIL's Center for Integrative Genomics. Roman's webpage: http://neptuneelixir.net
Li Ma Li joined the Clark lab in August 2010 after finishing his Ph.D. in Animal Science at the University of Minnesota. Li's research interests include developing statistical methods and computational tools for mapping genetic factors associated with complex diseases and traits. Li's work continues in the Keinan lab at Cornell.
Alexander Coventry After receiving his Ph.D. from Massachusetts Institute of Technology, Alex joined the Clark Lab in July 2008. While at Cornell Alex worked on the NIH funded projects Genomic Approaches to Common Chronic Disease as well as Modeling DNA Diversity in Reverse Cholesterol Transport.
Anthony Greenberg joined the Clark Lab in August 2008. Tony worked to identify potentially adaptive DNA sequence polymorphisms, fitting models of the metabolic network to quantitative genetic data from two behaviorally isolated populations of Drosophila melanogaster and combining them with a large-scale population-genetic survey. The models estimate the effects of nucleotide polymorphisms on fitness, metabolic network function, and a number of physiological and stress resistance phenotypes. His ultimate goal was to understand how the genetic network is tuned during evolution to produce phenotype change. Tony transferred to the lab of Assistant Professor, Jason Mezey, in January 2011.
Andre Lehovich joined the Clark lab in March 2009 coming from the radiology department at the University of Massachusetts Medical School. Andres research involved the genetic correlates of mental illness in humans by combining functional magnetic resonance imaging (FMRI) brain scans with genotype data. He also worked on a project to analyze brain scans for activity patterns linked with genetic markers.
Danielle Presgraves began her wok with Dr. Clark and Dr. Carlos Bustamante in October 2009, after finishing her Ph.D. in Biology with John Wakeley at Harvard University. Her Ph.D. research focused on modeling gene conversion and crossing-over events using Identity-By-Descent in a retrospective coalescent framework with and without selection. While with the Clark lab, she contributed to the anyalysis on the 1000 genomes project.
Lumi Viljakainen After completing her Ph.D. with Pekka Pamilo at the University of Oulu, Finland in November 2009, Lumi joined the Clark lab. Her principal research interests lie in evolutionary genetics of insect immunity. Her objective, in collaboration with Dr. Gene Robinson, (University of Illinois,) was to elucidate the evolution of insect immune genes with a focus on social insects. Investigating the role of sociality by comparing closely related social and non-social (solitary) organisms using extensive sequence data from immune genes of 12 bee species.
Nadia Singh joined the Clark lab in September 2006 after completing her Ph.D. with Dmitri Petrov at Stanford University. Nadia completed an analysis of the contrasting evolutionary forces acting on X-linked and autosomal protein-coding genes in teh 12 Drosophila geomes. While with the lab, she worked on a project to fine-map a region of the X chromosome, and on DNA substitution patterns of sequences in DNA transposons. Nadia left the Clark lab during the summer of 2010 to join the faculty at North Carolina State University.
Melanie Huntley joined the Clark lab in August 2006, after completing her Ph.D. with Brian Golding at McMaster University. Her interests in unusual sequences and the evolutionary and mechanistic processes that contribute to their formation and persistence have motivated much of her research on repetitive sequences in eukaryotic proteins. During her time with the Clark lab Melanie has completed an analysis of amino-acid repeats within the proteomes of the 12 Drosophila species, finding that flies are exceptional in their tolerance of repeats in proteins. Melanie left the Clark lab in January 2010 for a position in the Bioinformatics Department at Genentech in South San Francisco. You may find Melanie on the web at http://www.melaniehuntleyphd.com/ .
Dara Torgerson started with us in January 2005, after completing her Ph.D. with Rama Singh at McMaster University. Dara's thesis covered aspects of the comparative molecular evolution of sex-related genes, including inference of positive selection, accelerated evolution of X-linked sperm genes over autosomal ones, and duplication and subfunctionalization of the testes-specific alpha4 proteasome subunits. She is working on evolutionary processes on candidate cis-regulatory sequences using flanking SNP data from 39 humans (the Applera SNP collection).
Aida Andres started in the lab in Fall 2004 after completing her Ph.D. work on primate neurological genes in the lab of Jaume Bertranpetit in Barcelona. Aida is working on our collaborative project on the genetics of cardiovascular disease risk, with an emphasis on understanding the role of haplotype phase in testing associations between genetic variants and complex traits. Aida is now a postdoctoral researcher with Eric Green at the NIH genome center.
Sergi Castellano was a student with Roderic Guigo in Barcelona working on selenoprotein molecular evolution. He recently completed a study showing that the exchangeability of selenocysteine codons across the mammalian phylogeny is very low, implying that selenocysteine and cysteine are not equivalent from an evolutionary perspective, and are probably maintained by specific purifying selection. Sergi is now at Janelia Farm in Rockville, MD working with Sean Eddy.
Kurt McKean joined the lab in August 2003 to work on aspects of the evolution of innate immunity in Drosophila. He is taking a broad perspective by considering how initiation of an immune response might have fitness costs, particularly with respect to reproductive fitness. Kurt got his Ph.D. working with Len Nunney at UC Riverside. Kurt is now on the faculty at Albany University.
Jian Li came to the lab with a Ph.D. in Statistics from N.C. State University. He worked on problems of testing association between segregating variation in the reverse cholesterol transport pathway and cardiovascular risk. Jian now has a position on the faculty at the University of Missouri in Kansas City.
Anthony Fiumera came to us from the University of Georgia to work on the evolutionary biology of sperm competition in Drosophila. He was continuously engaged in large association studies, testing the influence of SNPs in accessory gland proteins on sperm competition phenotypes. Anthony got his Ph.D. with John Avise and at the University of Georgia, and he is now on the faculty at Binghamton University. We continue to collaborate on problems of sperm competition, especially inference of the parameters of sperm competition from wild-caught females.
Kristi Montooth was a graduate student, the briefly stayed on as a postdoc working on the evolutionary genetics of physiological systems, particular energy metabolism. She has extensive mapping data on the genetic basis for variation in enzyme activities, and finds that fairly simple regression models can explain large portions of the variance in metabolic rate and flight power. These models are being further developed to find the limit of prediction of such complex systems. Kristi had a fellowship from the Howard Hughes Medical Institute and support from an NSF Dissertation Improvement Award. She is currently a postdoc with Dr. David Rand at Brown, and will soon move to Indiana University for a faculty position there.
Daven Presgraves joined the lab in August 2004 after a short postdoctoral study with Wolfgang Stephan at the University of Munich. Daven's Ph.D. degree from the University of Rochester (with Allen Orr) resulted in the discovery that a component of the nuclear pore complex is involved in hybrid male inviability between D. melanogaster and D. simulans. He is now working on several problems in Drosophila comparative genomics. Daven began a faculty appointment at the University of Rochester in Fall 2005.
Todd Schlenke joined the lab in August 2002, after completing a Ph.D. on innate immunity in Drosophila with David Begun at the University of California at Davis. Todd pursued research on the cellular immune system in Drosophila, with particular focus on variation in the ability of Drosophila to encapsulate eggs of parasitoid wasps. Todd's wonderful work on the differences in expression profiles of Drosophila larvae after oviposition by generalist vs. specialist parasitoid wasps recently came out in PLoS Pathogens. He now has a faculty position at Emory University.
Trisha Wittkopp joined the lab in August 2002, having completed her graduate work with Sean Carroll at the University of Wisconsin. Trisha is interested in the evolution of developmental processes and the use of bioinformatics tools to understand genome function and evolution. She developed an excellent method for quantifying allele-specific expression in F1 hybrids, and has used it to ascertain the balance of cis- vs trans-regulation in hybrids. Trisha had a fellowship from the Damon Runyon foundation. She is now on the faculty at the University of Michigan, and we continue to collaborate on the evolution of cis and trans regulation of gene expression.
Kevin Thornton joined the lab in November 2003 after finishing his Ph.D. work on Drosophila duplications with Manyuan Long at the University of Chicago. Kevin jumped right in to helping with the analysis of the Drosophila pseudoobscura genome, and went on to develop approximate Bayesian methods for inference of Drosophila demography from genetic data. Kevin is now on the faculty at the University of California at Irvine.
Bret Payseur joined the lab in January 2004 to work on the genetic basis for variation in cardiovascular disease risk. He has experience working on population genetic analysis of genome-scale data sets, and is eager to get to work on more chimpanzee comparative genomics. He got his degree with Michael Nachman at the University of Arizona and is now on the faculty at the University of Wisconsin.
Doris Bachtrog was in the lab from October 2003 until August 2004 to work on the origination of dosage compensation on the neo-Y chromosome of Drosophila miranda. She had just finished her Ph.D. work with Brian Charlesworth at Edinburgh, where she developed the neo-X/neo-Y system of D. miranda for testing many theoretical predictions about the evolution of the Y chromosome. Doris is now on the faculty at the University of California at San Diego.
Brian Lazzaro was a postdoctoral fellow briefly after he completed his graduate work in December 2002. For his degree he did a series of association tests to identify segregating polymorphism in natural populations of Drosophila that contribute to variation in immune competence. He developed methods for establishing stable infections in flies and for querying the expression status of components of the immune system. Brian is currently an Assistant Professor in the Department of Entomology at Cornell, and we continue to collaborate on problems of innate immunity in Drosophila.
Brian Bettencourt came to us from the University of Chicago to work on the analysis of genetic variation underlying pathogen defense in Drosophila. He has extensive experience with the molecular population genetics of heat shock proteins, the subject of his Ph.D. thesis with Dr. Martin Feder. Brian is on the faculty at the University of Massachusetts Lowell.
Alberto Civetta was a postdoctoral fellow from June 1996 until July 2000 working on aspects of sperm competition and the molecular evolution of genes related to sexual reproduction. He did some exciting work using transgenic flies that produce green fluorescent sperm thanks to the sperm-specific expression of Green Fluorescent protein. This line was useful in establishing that sperm are actually removed from storage by subsequent matings. Beto also did a study of sperm competition in a set of interspecific introgression lines, mapping genes involved in conspecific sperm precedence. Beto is now on the faculty at the University of Alberta in Winnipeg.
Malia Fullerton came to us from Oxford University and the University of Chicago to work on the analysis of DNA sequence variation in candidate genes for cardiovascular disease. She has extensive experience with the analysis of linkage phase of multiple-site heterozygotes, and with applying this information to make inferences about the function of candidate genes. Malia has also done some creative analysis of polymorphism in origins of DNA replication, and she has found that these regions appear to be evolving rapidly. She is now at the University of Washington.
David Goldstein was in the lab from Sept 1994 until August 1996 studying microsatellite variation in Drosophila and applying the methods to understand the basis for interspecific divergence among Drosophila species. His Nucleic Acids Research paper was the first study applying microsatellite variation to Drosophila. David is now on the faculty at Duke University.
Brenda Leicht was with us from January 1990 until August 1993 working on the evolution of alternative splicing in the myosin alkali light chain gene. This gene produces two isoforms, one for the indirect flight muscle and one for other somatic muscles, and the two differ only in the presence/absence of exon 5. We found a striking dependence of the substitution process upon the secondary structure of the pre-mRNA, such that substitutions that favor excessive stem formation were improbable. Brenda is now on the faculty at the University of Iowa.
Spencer Muse was in the lab from January 1994 until August 1996 working on statistical models of DNA sequence evolution. He devised a model for testing the significance of stem formation in DNA sequences by estimating the parameters of a model having all possible base pairings. This idea was extended to consider the full 61 x 61 transition matrix among non-stop codons to estimate rates of synonymous and nonsynonymous substitution. Spencer is now on the faculty in the Statistics Department at North Carolina State University
Sarah Tishkoff was a postdoctoral fellow from November 1996 until August 2000 working on analysis of linked stable polymorphisms and microsatellites in human populations. She has studied CD4, PLAT, DM, and most recently G6PD, with a focus on African populations and a special interest in the question of African origins. The study of G6PD polymorphisms centers on the idea that G6PD deficiencies are associated with malarial resistance, and this natural selection has left a strong signature in the standing variation at G6PD. Sarah is now on the faculty at the University of Maryland.
Conny Scheitz Joining the Clark lab in 2009, Conny assisted in the Drosophila obesity project. She also started a project investigaing novel interactions within Drosophila immunity. After her gradation in January, 2013, Conny headed to the west coast for a position at Transcriptic.
Sarah Stockwell As a Ph.D. candidate after receiving her B.A. from Swarthmore College, Sarah joined the Clark lab bringing several years' experience in UNIX systems administration at Qualcomm Inc. Sarah worked on a theoretical problem centering on stability and robustness consequences of the underlying structure of gene regulatory networks. She has developed an arsenal of computational tools for generating regulatory networks, simulating their dynamics, and comparing their dynamics to that of related logical systems. Sarah left the Clark lab in September 2010 for a Post Doctoral position at UC San Diego.
Kirk Lohmueller joined the lab as a fourth-year graduate student working on human population genetics. He is specifically interested in the interplay of demographic history and its effect on the efficacy of natural selection. His work has shown that the out-of-Africa bottleneck of non-African populations resulted in an increased frequency of variants that are inferred to be damaging to protein function. This is a result entirely consistent with population genetics theory, as confirmed by extensive simulations. Kirk has also developed methods to estimate parameters in population genetic models from haplotype patterns in genome-wide SNP datasets. Kirk left the Clark lab to join the Dr. R. Nielsen lab as a Postdoctoral Fellow at the University of Califonia, Berkeley, in the Department of Integrative Biology.
Amanda Larracuente joined the lab as a graduate student, and until her graduation in Fall of 2009, worked on various projects in Drosophila genomics and population genetics. She had a special interest in sex chromosome evolution and the evolution advantages of recombination. Her main focus was in following up on the exciting discovery that the Drosophila pseudoobscura Y chromosome seems to have arisen from the Muller D element, and that genes that are normally Y-linked in most Drosophila species, have been translocated to the autosomes in D. pseudoobscura and its close relatives.
Erin Hill Burns Between Fall 2008 and until her graduation in August 2009, Erin contributed to the lab as a graduate student, working on the impact of hybridization on regulation of complex gene networks, using Drosophila innate immunity as a model. She made extensive use of our custom illumina BeadChip, along with short-read sequencing, for quantifying expression levels in interspecific hybrids of D. melanogaster and D. simulans. She also investigated the effects of mutations in genes throughout the innate immune pathways in the context of a hybrid genetic background. Erin received her undergraduate degree from the University of Delaware .
Tim Sackton worked on problems relating to innate immunity in Drosophila. He completed a collaborative project that examined patterns of gene duplication and sequence divergence in the genes encoding components of the Drosophila innate immune system. In collaboration with Brian Lazzaro, he has infected a series of Drosophila lines with a series of different naturally-occurring Drosophila pathogens to determine the specificity of the immune response. Tim got his B.S. degree from Brown University where he worked with David Rand.
Kristi Montooth worked on the evolutionary genetics of physiological systems, particular energy metabolism. She has extensive mapping data on the genetic basis for variation in enzyme activities, and finds that fairly simple regression models can explain large portions of the variance in metabolic rate and flight power. These models are being further developed to see what is the limit of prediction of such complex systems. Kristi had a fellowship from the Howard Hughes Medical Institute and support from an NSF Dissertation Improvement Award
Brian Lazzaro was a graduate student working on Drosophila immunity. He has identified some new genes that play a role in pathogen defense, and characterized the levels of polymorphism and divergence in immune system genes. He also has developed methods for establishing stable infections in flies and for querying the expression status of components of the immune system. Brian was supported by an NIH grant and an NSF Dissertation Improvement Award.
Manolis Dermitzakis was a graduate student working on the evolution of pattern formation genes, especially bicoid, Hunchback, caudal, and pumilio. These genes play a key role in establishing orientation and cell fates of the Drosophila embryo, and the interplay of their maternal and zygotic roles poses evolutionary questions that he pursued. Regulation of these genes is well understood, and analysis of the DNA sequence polymorphism and divergence in promoters is underway. Manolis developed Hidden Markov models to identify binding sites for transcription factors that incorporate interspecific divergences. Manolis was successful in getting an NSF Dissertation Improvement Award for his project.
Eva Lyckegaard did an analysis of the rDNA array on the X and Y chromosomes of D. melanogaster. She did a careful quantitation of rDNA gene copy number variation, and discovered an over 7-fold variation on the Y chromosome. She went on to work in the research division of Astra Zeneca in Lund, Sweden.
Andy Merriwether did a Masters thesis which involved a massive assembly of published mtDNA data from over 3200 individuals and a retrospective analysis of population demographics. He went on to earn his Ph.D. at the University of Pittsburgh in human genetics. Andy is now on the faculty at the University of Michigan.
Lei Wang worked on regulation of metabolic enzymes in Drosophila, and did massive studies to quantify the distribution of mutational effects caused by spontaneous mutations (in mutation-accumulation lines) and by P-element insertion. Lei is developing new drugs and generally saving the world by working at Myriad Genetics in Salt Lake City.
Denis O'Meally received his Ph.D. from the Australian National University. While visiting the Clark lab during the summer of 2012, Denis worked on computational analysis of snake chromosomes. In collaboration with Denis, we are sequencing, assembling and annotating the tiger snake genome, one of the species with cryptic sex chromosomes.
Bernardo Carvalho is on the faculty at the University of Rio de Janeiro where he has been working on the genetic basis for sex ratio distortion in Drosophila mediopunctata. In this species there are segregating Y chromosomes that suppress the effects of X-linked drivers, and restore normal sex ratio. Bernardo has obtained sequences from the Y dyneins of D. mediopunctata, and investigated several Y-linked genes in D. melanogaster as well. We have an ongoing collaborative project on evolution of the Y chromosome. Bernardo also played an important role in the final assembly of the Y chromosome sequences for the 12 Drosophila genomes project.
Yoko Hatta-Ohashi visited the lab with her husband Jun, and immediately found a home in improving the efficiency of our SNP genotyping operations. Yoko had experience in the microarray division of Olympus Inc, in Japan, so she is very familiar with hybridization technologies. She worked primarily on the Drosophila innate immunity projects.
Jun Ohashi was a visiting scholar from the University of Tokyo, where he holds a faculty position in human genetics. Jun has demonstrated a striking spread of the hemoglobin E variant in Southeast Asia in a manner consistent with its role in resistance to malaria. He is also interested in whole genome LD mapping, and modeled the factors that limit the power of these methods.