Roman joined the lab in September 2008, after completing his Ph.D with Manyuan Long at the University of Chicago. Roman is starting a project new to the lab that will combine population genetic analysis and neurophysiological experiments in the periphery of the Drosophila chemosensory system. Motivated by recent outstanding advances that several cellular and neurobiology labs have made to the understanding of the molecular underpinning of fly chemosensation, Roman will be examining the contribution to variation at the level of the neurological code that is provided by variation in sequence and expression polymorphism in the genes expressed in the sensory neurons.
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Recent publication:
Shuang Yang#, J. Roman Arguello#, Xin Li, Yun Ding, Qi Zhou, Ying Chen, Yue Zhang, Ruoping Zhao, Frederic Brunet, Lixin Peng, Manyuan Long, Wen Wang. 2008. Repetitive Element-mediated Recombination as a Mechanism for New Gene Origination in Drosophila. PloS Genetics, 4(1): e3.
# Equal contributions
Clement Chow began his work in the lab in August 2008, after completing his Ph.D. in Human Genetics with Miriam Meisler at the University of Michigan. He is co-advised by Andy and Mariana Wolfner and is interested in evolutionary genetics in both Drosophila and humans. Currently, he is studying the evolutionary and population genetics of sperm competition. He is exploring the consequences of male x female genetic interactions in maintaining the high level of polymorphism in seminal proteins. He also continues to explore various issues in human genetics.
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Recent Publication:
Chow CY, Landers JE, Bergren SK, Sapp PC, Grant AE, Jones JM, Everett L, Lenk GM, McKenna-Yasek DM, Weisman LS, Figlewicz D, Brown RH, Meisler MH. Deleterious Variants of FIG4, a Phosphoinositide Phosphatase, in Patients with ALS. Am J Hum Genet. 84(1):85-8 (2009)
To understand how organisms are shaped by evolutionary forces, it is critical to know how adaptive phenotypes are produced by naturally occurring genetic variation. Rigorous answers to this question require quantitative analyses of biological networks and experimental testing of the resulting models. To identify potentially adaptive DNA sequence polymorphisms, Tony is 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 will estimate the effects of nucleotide polymorphisms on fitness, metabolic network function, and a number of physiological and stress resistance phenotypes. He will treat these associations as hypotheses to be tested by molecular genetic manipulation. The ultimate goal is to understand how the genetic network is tuned during evolution to produce phenotypic change.
Recent publication:
Greenberg, A. J., S. R. Stockwell and A. G. Clark (2008). Evolutionary constraint and adaptation in the metabolic network of Drosophila. Mol. Biol. Evol., 25:2537--2546.
Melanie 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. She is currently analyzing large arrays of tandemly repeated genes using short-read sequence data (Solexa and 454) for inferences about levels of variation and sequence divergence.
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Recent Publication:
Huntley, M.A. and A. G. Clark. (2007). Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species. Molecular Biology and Evolution. 24: 2598-2609
Jian received his BS and MS degrees in Cellular Biology and Genetics from Peking University in 1999 and 2002, respectively. He earned his PhD degree in Ecology and Evolution in 2008 from University of Chicago under the guidance of Dr. Chung-I Wu. In his Ph. D study Jian has investigated the accumulation of slightly deleterious mutations in the naturally-occurring and domesticated species. He has also used a combination of computational and experimental approaches to study the origin and subsequent evolution of microRNAs – a class of newly identified small RNAs that can regulate gene expression posttranscriptionally.
In our lab Jian is currently studying the regulatory roles of microRNAs in the innate immunity of Drosophila.
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Recent Publication:
Jian Lu, Yang Shen, Qingfa Wu, Supriya Kumar, Bin He, Richard W. Carthew,San Ming Wang and Chung-I Wu. 2008. The birth and death of microRNA genes in Drosophila. Nature Genetics 40(3):351-355.
Rich Meisel is interested in the evolution of the genic content and organization of genomes, as well as the evolution of sex chromosomes and sex-biased gene expression. Rich earned his Ph.D. working with Steve Schaeffer at Penn State University, where he studied the origin and evolution of gene duplications and chromosomal rearrangements in Drosophila. He is currently examining the evolution of gene expression on the D. willistoni neo-X chromosome to understand how sexually antagonistic selection, spermatogenic X-inactivation, and dosage compensation affect sex-biased gene expression.
Nadia Singh began her work in the 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 the 12 Drosophila genomes. She is working on a project to fine-map a region of the X chromosome, and on DNA substitution patterns of sequences in DNA transposons.
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Nancy is interested the genetic basis of adaptation in natural populations, with a focus on the evolution of disease resistance and how organisms respond to varying pathogen pressures. Her current research applies novel sequencing technologies to identify W-specific contigs in the chicken genome. Part of Nancy's dissertation research will be on population genetics and genomics of the Florida Scrub-jay (Aphelocoma coerulescens), which have experienced sporadic high mortality events putatively caused by an arbovirus. She am assembling a genome-wide SNP database for the Florida Scrub-Jay to test for disease-driven selection and to investigate the genetic consequences of recent and historical epizootics.
Recent publication:
Canfield, M.R., Greene, E., Moreau, C.S., Chen, N., Pierce, N.E. Exploring Phenotypic Plasticity in Emerald Moths: A Phylogeny of the Genus Nemoria (Lepidoptera: Geometridae). Mol. Phylogenet. Evol. 49, 477-487 (2008).
Angela Early is a second-year graduate student in the field of Ecology and Evolutionary Biology and is broadly interested in the evolution of immunity, host-pathogen interactions, and the evolution of symbiotic relationships. Currently she is addressing these interests through study of Drosophila gut bacteria. She is approaching this system from both the insect and microbe perspectives and is interested in how the microbial communities interact within themselves and with the host.
Erin is a sixth-year graduate student working on the impact of hybridization on regulation of complex gene networks, using Drosophila innate immunity as a model. She has 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 is also investigating 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.
Amanda Larracuente is a graduate student working on various projects in Drosophila genomics and population genetics, and has a special interest in sex chromosome evolution and the evolutionary advantages of recombination. Amanda's main focus to follow 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.
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Recent Publication:
Larracuente AM, Sackton TB, Greenberg AJ, Wong A, Singh ND, Sturgill D, Zhang Y, Oliver B, Clark AG. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet 24(3):114-23.
Kirk Lohmueller is 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 is co-advised by Carlos Bustamante.
Recent publication:
Lohmueller KE, Bustamante CD, Clark AG. Methods for human demographic inference using haplotype patterns from genome-wide SNP data. Genetics, in press.
Sarah is a Ph.D. candidate working on a theoretical problem centering on stability and robustness consequences of the underlying motif structure of gene regulatory networks. She is interested in studying the evolution of transcriptional networks in general, from both experimental and theoretical perspectives. She is also interested in the evolutionary accretion of complexity in gene regulatory networks, and has recently collaborated with Tony Greenberg on a network-based analysis of metabolic genes in 12 Drosophila species. 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 participated in Cornell's IGERT program in nonlinear dynamics, and was later supported by an NSF Graduate Research Fellowship. She received her B.A. from Swarthmore College, and joined the lab after several years' experience in UNIX systems administration at Qualcomm Inc.
Xu Wang is a fourth-year graduate student working on genomic imprinting in humans and mice. He recently completed a study of identifying novel imprinted gene in P2 neonatal mice brain by Illumina/Solexa sequencing the entire transcriptome, has also done inference of human gene imprinting using hybridizations of cDNA to coding SNP chips with Katie Pollard and Kelly Frazer. Xu is also examining human linkage maps, and relating them to the patterns of linkage disequilibrium using high density SNP genotype data.
Recent publication:
Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, et al. (2008) Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 3: e3839
Next to working as a technician in our lab, Conny is assisting in the Drosophila obesity project. Apart from that she is starting a project investigating novel interactions within Drosophila immunity. In the future Conny is also planning to continue along the tracks of her Master studies at Imperial College London by looking into copy number variances in humans and their distribution and association to common diseases.
