Primary Faculty

Paul Adler

PAUL ADLER

William R. Kenan, Jr. Professor of Biology

Email: pna@virginia.edu
Office: (434) 982-5475
Lab: (434) 982-5476
Office: 420 PLSB

EDUCATION

B.A., Carnegie Mellon University, 1969
M.A., Boston University, 1971
Ph.D., Massachusetts Institute of Technology, 1975
Postdoctoral Research, University of California, Irvine, 1975-77

RESEARCH INTERESTS

Research in the Adler lab is focused on aspects of cell and tissue polarity. For many years we have studied planar polarity using the wing of Drosophila as a model system. This tissue polarity is manifested by each cell in the wing forming a distally pointing hair. Early work from the lab established that a genetic regulatory pathway (the frizzled pathway) controlled this by restricting the activation of the cytoskseleton to grow the hair to the most distal part of the cell. Work from a number of laboratories has shown that the proteins encoded by frizzled pathway genes accumulate in protein complexes located on either the proximal or distal sides of wing cells. In recent years our research has primarily been focused on downstream members of the pathway, such as frizt, inturned and multiple wing hairs and how these proteins interact and function to locally activate the cytoskeleton.

RECENT PUBLICATIONS

Janis Antonovics

JANIS ANTONOVICS

Lewis and Clark Professor of Biology

Email: ja8n@virginia.edu
Office: (434) 243-5076
Lab: (434) 982-5462
Office: 051 Gilmer Hall

Laboratory Website

EDUCATION

B.A., Cambridge University, 1963
Ph.D., University of Wales, 1966

RESEARCH INTERESTS

Research in my lab is on the evolution and epidemiology of infectious disease in natural populations. Current research questions focus on the role of diseases in determining species range limits, host-pathogen co-evolution, and the evolutionary dynamics of sexually transmitted diseases. The research combines theoretical modeling with empirical research on sexually transmitted diseases of plants (the anther smuts) and analysis of datasets involving diseases of organisms ranging from bumble-bees to humans.

For more information about research interests, please visit my lab website.

REPRESENTATIVE PUBLICATIONS

Benjamin Blackman

BENJAMIN BLACKMAN

Assistant Professor of Biology
Email: bkb2f@virginia.edu
Office: (434)924-1930
Lab: (434)924-2332
Office: GIL 063

Laboratory Website

EDUCATION

B.S., Stanford University, 2001
Ph.D, Indiana University, 2009

RESEARCH INTERESTS

My research focuses on the diversification in the phenotypic plasticity of developmental timing. Because environments fluctuate daily and seasonally, the onsets of major life history events--e.g. germination, flowering, hibernation--are responses partly or wholly cued by environmental signals. These responses are often the products of adaptive evolution because as species expand their ranges, colonize new environments, or adjust to historical and recent anthropogenic changes, the combination of environmental cues predictive for the optimal timing of developmental transitions may change dramatically. In my lab, we seek to address three major questions: 1) how do organisms integrate environmental cues to trigger developmental transitions, 2) through what mechanisms does this plasticity evolve and 3) what natural or anthropogenic factors have driven or maintain this variation?

By connecting genetic variation to phenotypes to survival and reproduction, my lab's work aims to understand all levels of the evolutionary process, and consequently our studies range from molecular genetics to population and quantitative genomics to ecological studies in natural environments. We work predominantly in two systems, sunflowers and monkeyflowers, that exhibit tremendous variation across broad geographic transects in how flowering responds to photoperiod and other environmental cues. Characterizing the genetic architecture and ecological pressures involved in adaptation of these species to diverse environments will allow us to develop improved functional models that predict how species may adapt to future global change. In sunflower, my work also examines the genetics of how flowering time and other traits evolved during its domestication because we seek to understand the dynamics of how novel and complex trait syndromes evolve.

RECENT PUBLICATIONS

Blackman B.K., Scascitelli M., Kane N.C., Luton H.H., Rasmussen D.A., Bye R.A., Lentz D.L., and Rieseberg L.H. 2011. Sunflower domestication alleles support single domestication center in eastern North America.Proceedings of the National Academy of Sciences USA 108: 14350-14365 (2011).

Blackman B.K., Rasmussen D.A., Strasburg J.L., Raduski A.R., Burke J.M., Knapp S.J., Michaels S.D., and Rieseberg L.H. 2011. Contributions of flowering time genes to sunflower domestication and improvement.Genetics 187: 271-287.

Blackman B.K., Michaels S.D., and Rieseberg L.H. 2011. Connecting the sun to flowering in sunflower adaptation. Molecular Ecology 20: 3503-3512.

Blackman B.K., Strasburg J.L., Raduski A.R., Michaels S.D., and Rieseberg L.H. 2010. The role of recently derived FT paralogs in sunflower domestication. Current Biology 20: 629-635.

George Bloom

GEORGE BLOOM

Professor of Biology and Cell Biology

Email: gsb4g@virginia.edu
Office: (434) 243-3543
Lab: (434) 243-3544
Office: 216 PLSB

Laboratory Website

EDUCATION

B.A., University of Pennsylvania, 1973
Ph.D., University of Pennsylvania, 1979

RESEARCH INTERESTS

Research in our laboratory is now focused primarily on Alzheimer’s disease (AD). The histopathological hallmark of AD is the presence in brain of extracellular plaques of ß-amyloid peptide fibrils, and intraneuronal neurofibrillary tangles, which are filaments composed of the protein, tau. Despite the conspicuous appearance of plaques and tangles, a growing body of evidence points to their building blocks, ß-amyloid and tau oligomers, as being the toxic molecular species that cause AD. For example, we have found that tau expression is required for several adverse effects of ß-amyloid oligomers on neurons, including microtubules loss, ectopic re-rentry into the cell cycle and cytotoxicity. The goals of our work are to decipher the metabolic links that connect ß-amyloid and tau to damage neurons, to define the structures and pathological properties of various types of ß-amyloid and tau oligomers, and to develop effective therapeutic and diagnostic tools for AD.

For more information about research interests, visit my lab website.

REPRESENTATIVE PUBLICATIONS

Edmund D. Brodie, III

EDMUND D. BRODIE, III

B.F.D. Runk Professor in Botany, Director of Mountain Lake Biological Station
Email: bbrodie@virginia.edu
Office: (434) 243-1068
Lab: (434) 243-4338
Office: 223 Gilmer Hall

Laboratory Website

EDUCATION

B.A., Princeton University (honors), 1985
M.S., University of Chicago, 1987
Ph.D., University of Chicago, 1991

RESEARCH INTERESTS

I strive to understand both the selective forces shaping biodiversity and the genetic processes that translate natural selection into evolutionary changes. My research focuses on interactions at different levels of biological organization that promote phenotypic and genetic integration, from epistasis between loci within individuals to ecological interactions between different species. The results of interaction can range from genetic coadaptation (the evolution of coadapted gene complexes), to developmental integration, to phenotypic coadaptation of species engaged in coevolutionary interactions. My lab employs a wide variety of approaches to addressing these problems, including quantitative genetics, basic fieldwork, behavioral observations, manipulative experiments, mathematical modeling, and molecular genetics. Much of my work concentrates on the predatory and antipredator adaptations of reptiles and amphibians and the coevolutionary arms races between them. I also explore the evolutionary importance of interactions among conspecifics through studies of indirect genetic effects and social selection, primarily using insect systems.

For more information on research interests, see my lab website.

REPRESENTATIVE PUBLICATIONS

Barry Condron

BARRY CONDRON

Professor of Biology
Email: bc4f@virginia.edu
Office: (434) 243-6593
Lab: (434) 243-6794
Office: 310 PLSB

Laboratory Website

EDUCATION

B.S., University College, Cork, Ireland, 1985
Ph.D., University of Utah, 1991

RESEARCH INTERESTS

My lab is interested in how the cellular architecture of neurons dictates their function. We mostly focus on one serotonergic neuron, a type of cell that plays a critical role in diseases of human emotion. We have built a large repertoire of biological information about one point in the life of this cell in a model organism, and are using this to develop a systems-level understanding of its function. In order to further apply this structural approach, we are developing methods to scan the structures of all neurons in a part of the CNS. We are using this to assay global community-type changes in the nervous system is response to various insults.

For more information about research interests, visit my lab website.

REPRESENTATIVE PUBLICATIONS

Robert Cox

ROBERT COX

Assistant Professor of Biology
Email: rmc3u@virginia.edu
Office: (434) 982-1987
Office: 047 Gilmer Hall
Lab: (434) 243-3399

Laboratory Website

EDUCATION

B.A., College of the Holy Cross, 1999

Ph.D., Rutgers University, 2005

RESEARCH INTERESTS

My research lies at the interface of two topics: (1) the evolutionary dynamics associated with the divergent reproductive roles of males and females, and (2) the ecological factors that shape natural selection on physiology, morphology, and life history. Current projects in my lab are addressing causes and consequences of sexual conflict, the evolutionary and endocrine basis of sexual dimorphism, and the physiological and ecological mechanisms that shape life-history trade-offs. All of these projects involve vertebrates (usually reptiles) and most combine both laboratory and field components, with an emphasis on experimental approaches. I conduct the field portions of these studies in diverse natural habitats ranging from eastern ponds and forests to the deserts and mountains of Arizona and the islands of the Bahamas. In any study, my overarching goal is to understand both how a particular phenomenon is regulated (physiology, genetics) and why it has evolved (ecology, evolution).

For more information on research interests, see my lab website.

REPRESENTATIVE PUBLICATIONS

Cox, R.M., and R. Calsbeek. 2010. Cryptic sex-ratio bias provides indirect genetic benefits despite sexual conflict. Science 328: 92-94.

Cox, R.M., and R. Calsbeek. 2010. Severe costs of reproduction persist in Anolis lizards despite the evolution of a single-egg clutch. Evolution 64: 1321-1330.

Cox, R.M., and R. Calsbeek. 2009. Sexually antagonistic selection, sexual dimorphism, and the resolution of intralocus sexual conflict. American Naturalist 173: 176-187.

Cox, R.M., D.S. Stenquist, and R. Calsbeek. 2009. Testosterone, growth, and the evolution of sexual size dimorphism. Journal of Evolutionary Biology 22: 1586-1598.

Claire Cronmiller

CLAIRE CRONMILLER

Professor of Biology, Director of Undergraduate Studies
Email: crc2s@virginia.edu
Office: (434) 982-5484
Lab: (434) 982-5485
Office: 260 Gilmer Hall

EDUCATION

A.B., Bryn Mawr College, 1974
Ph.D., Princeton University, 1986
Postdoctoral Research, Princeton University, 1986-1989

RESEARCH INTERESTS

My research interests focus on understanding how complex sequences of differentiation are genetically regulated during development. My primary research uses Drosophila oogenesis as an experimental model fordiscovering basic genetic and cell biological mechanisms that shape multicellular tissues. My lab has taken several experimental approaches to study this process of morphogenesis. Genetically, we identified an extra-ovarian regulatory pathway that we have recently shown involves the function of a metalloprotease, which could be required to activate a long-range signaling molecule. Through a novel pharmacological approach, we uncovered the participation of neural signaling in both follicle formation and maturation. Our current work is aimed at elucidating specific molecular components of these pathways, as well as their biochemical/cellular functions. In addition to my study of tissue morphogenesis, I have established an ongoing collaboration with the laboratory of Dr. David Brautigan (UVA, Center for Cell Signaling) to pursue a related interest in the genetic control of cell division during development. In this work Drosophila genetics is being used to identify cellular functions of important vertebrate regulatory proteins.

REPRESENTATIVE PUBLICATIONS

Christopher Deppmann

CHRISTOPHER DEPPMANN

Assistant Professor of Biology
Email: deppmann@virginia.edu
Office & Lab: (434) 260-1572
Office: 314 PLSB

Laboratory Website

EDUCATION

B.S., Western Michigan University, 1997
Ph.D., Biochemistry & Molecular Biology, Purdue University, 2003
Postdoctoral, Johns Hopkins University, SOM, 2003-2009

RESEARCH INTERESTS

Our research centers around understanding the molecular basis by which the nervous system is sculpted during development. We use a combination of genetic, biochemical, and mathematical modeling techniques to determine how competition defines proper cell number and synaptic connectivity.

We are also interested in how these competitive developmental programs that are used to assemble the nervous system might be exploited by pathologies such as Alzheimer's and Lou Gerhig's Disease to disassemble the nervous system.

There are several projects that are available which will be scaled for undergrad students, grad students, or post-docs. To learn more about potential research projects for people to work on, visit my lab webpage.

REPRESENTATIVE PUBLICATIONS

Wolfgang Otto Friesen

WOLFGANG OTTO FRIESEN

Professor of Biology
Email: wof@virginia.edu
Office: (434) 982-5493
Lab: (434) 982-5609
Office: 283 Gilmer Hall

Laboratory Website

EDUCATION

B.A., Bethel College, Kansas, 1964
M.A., University of California, Berkeley, 1966
Ph.D., University of California, San Diego, 1974

RESEARCH INTERESTS

Our research goal is to identify and describe neuronal mechanisms that underlie animal behavior. We concentrate on rhythmic movements, which are particularly tractable for such studies. The neuronal systems that control animal movement comprise neuronal oscillator circuits, usually interneurons located within the central nervous system; motor neurons to coordinate muscle tensions; and sensory receptors that modify and adapt the central neuronal pattern to the specific structure of the animal and to its environment. We study the relatively simple movements (swimming) of one favorable invertebrate, the medicinal leech. Currently we are investigating 1) mechanisms by which brief sensory input evokes prolonged behavioral motor patterns and 2) the roles of sensory input in shaping neuronal activity patterns to generate effective locomotion. In addition, we are continuing to develop NeuroDynamix II , a graphical suite of computer models, to simulate dynamic properties of complex neuronal circuits, therewith to explore the behavioral implications of identified neuronal circuits and to investigate conceptual models. Our primary techniques include electrophysiological recording from identified neurons, pharma-cological manipulations, and computer modeling.

For more information about research interests, see my lab website

REPRESENTATIVE PUBLICATIONS

Laura Galloway

LAURA GALLOWAY

Professor and Chair of Biology

Email: lg8b@virginia.edu
Office: (434) 982-5010
Lab: (434) 982-5599
Office: 255 Gilmer Hall

Laboratory Website

EDUCATION

B.A., Oberlin College, 1984
Ph.D., University of California, Davis, 1994
Postdoctoral, University of Maryland, 1994-1996

RESEARCH INTERESTS

My research uses ecological and genetical approaches to explore mechanisms of adaptation and patterns of evolutionary change in natural plant populations. Plants are sedentary and therefore can not directly choose their growth environment or mates, they vary in their gender and potential for inbreeding, and many species are polyploid having more than two copies of each chromosome and gene. I study the consequences of these plant attributes for evolution using a combination of field and greenhouse studies, quantitative genetics, and molecular techniques.

My current research focuses on the adaptive role of maternal effects, cross-generation influences of the environment and maternal genes. In addition, I am investigating how the multiple gene copies in polyploids affect the accumulation of reproductive isolation that leads to speciation as well as the consequences of inbreeding.

My students and I incorporate studies of invasive species, altered habitats, and climate change into our research because these novel conditions permit insight into mechanisms of evolution.

For more information on research interests, see my lab webpage.

REPRESENTATIVE PUBLICATIONS

Reginald Garrett

REGINALD GARRETT

Professor of Biology
Email: rhg@virginia.edu
Office: (434) 982-5494
Office: 204 PLSB

EDUCATION

B.S., The Johns Hopkins University, 1964
Ph.D., The Johns Hopkins University, 1964
Postdoctoral Research, The Johns Hopkins University, 1968

RESEARCH INTERESTS

Together with my colleague, Mitchell Smith of the Center for Food Safety and Applied Nutrition (CFSAN) in the Food and Drug Administration (FDA), we have taken a systems analysis approach to discover the relationship between a number of inflammatory disease conditions and the consumption of various drugs and/or dietary supplements. A prominent example is eosinophilia-myalgia syndrome ( EMS ) and the consumption of L-tryptophan-containing dietary supplements (LTCDS). The belief that microimpurities found in mass-produced LTCDS caused EMS in individuals consuming such supplements remains widespread in the epidemiological, medical, and nutritional communities, even though no impurity with such toxicity has ever been identified. At least three dozen deaths are attributed to EMS and the ingestion of LTCDS. Our systems analysis of EMS based on Boolean-logic, keyword-based computer searches of peer-reviewed literature disclosed correlations between eosinophilia (elevated circulating eosinophil levels), myalgia (muscle pain), and compromised histamine degradation. Both eosinophilia and myalgia are conditions associated with excessive histamine activity. Our search revealed that consumption of tryptophan supplements leads to enhanced levels of formate and indolyl compounds, several of which impair histamine degradation and thus have the potential to prolong the latent effect of histamine. In light of our findings, the assumption that microimpurities in LTCDS cause EMS is unwarranted.

REPRESENTATIVE PUBLICATIONS

Robert Grainger

ROBERT GRAINGER

W.L. Lyons Brown Professor of Biology
Email: rmg9p@virginia.edu
Office: (434) 982-5495
Lab: (434) 982-5605
Office: PLSB 306

REPRESENTATIVE PUBLICATIONS

Melissa Henriksen

MELISSA HENRIKSEN

Assistant Professor of Biology
Email: mah2hx@virginia.edu
Office: (434) 243-4945
Lab: (434) 243-4946
Office: 212 PLSB

Laboratory Website

EDUCATION

B.A., The College of Holy Cross, 1990
Ph.D., The University of Pennsylvania, 1996
Postdoc, The Rockefeller University, 2000

RESEARCH INTERESTS

My laboratory studies the epigenetic mechanisms that contribute to gene expression. A human cell contains about two meters of DNA in its tiny nucleus, presenting a phenomenal packaging problem. To manage, the cell relies on chromatin to organize its genome. Chromatin's operational structure is the nucleosome, consisting of 146 bp of DNA wrapped around a bundle of eight core histone proteins (H3, H4, H2A and H2B). The packing of nucleosomes into increasingly complex structures explains how the DNA fits. But when genes are expressed, the chromatin template must alter its structure, unpacking itself to make those genes accessible to the scores of proteins involved in transcription. Epigenetics, then, is the study of how modifications to the chromatin template establish and propagate differences in gene expression. We aim to define the epigenetic controls that contribute to tumorigenesis and cancer stem cell plasticity in Neuroblastoma, as well as the histone modifications that regulate inducible gene expression downstream of the STAT signaling pathway. For more information about our research, visit our laboratory page.

REPRESENTATIVE PUBLICATIONS

Jay Hirsh

JAY HIRSH

Professor of Biology
Email: jh6u@virginia.edu
Office: (434) 982-5608
Lab: (434) 982-5607
Office: 416 PLSB

Laboratory Website

EDUCATION

B.A., Northwestern University, 1971
Ph.D., Brandeis University, 1976
Postdoc Research, California Inst. of Technology, 1976-1979

RESEARCH INTERESTS

We study behavioral roles of biogenic amine neurotransmitters in the fruit fly, Drosophila melanogaster. These transmitters, including the well studied molecules dopamine and serotonin, have roles in the fly that parallel those found in higher animals, validating use of this important genetic model. We study these roles with pharmacological, physiological and genetic approaches. Drugs such as aerosolized free base cocaine directly target this system, and can be used as probes to study its statein vivo. Studies using cocaine as a probe identified an intriguing connection with circadian genes, a connection under intensive study. These transmitters also have roles in circadian rhythmicity, and in setting motor activity levels and light sensitivity of motor activation and circadian entrainment. We have developed assays to study the effects of dim light that have identified specific roles for these transmitters. Tools under development will allow these roles to be localized to small neuronal subsets, and ultimately, the brain circuitry responsible for behavioral outputs.

Link to videos showing cocaine-induced fly behaviors>>

REPRESENTATIVE PUBLICATIONS

Masashi Kawasaki

MASASHI KAWASAKI

Professor of Biology

Email: mk3u@virginia.edu
Office: (434) 982-5763
Lab: (434) 243-5494
Office: 277 Gilmer Hall

Laboratory Website

EDUCATION

B.S., Waseda University, Tokyo, Japan, 1979
Ph.D., Sophia University, Tokyo, Japan, 1984

RESEARCH INTERESTS

My research subjects are the weakly electric fishes - unusual electronic animal species that the nature has ever created. Specifically, we focus on the brain mechanisms for electric behaviors of South American and African electric fishes. My research strategy is to combine behavioral experiments for identification of computational algorithms, and neurobiological techniques for identification of underlying neuronal mechanisms. The ultimate goal of my research is to uncover fundamental design principles of the brain using these attractive creatures.

For more information on research interests, visit my lab website.

REPRESENTATIVE PUBLICATIONS

Raymond Keller

RAYMOND KELLER

Alumni Council Thomas Jefferson Professor of Biology
Email: rek3k@virginia.edu
Office: (434) 243-2595
Lab: (434) 243-2596
Office: 308 PLSB

Laboratory Website

REPRESENTATIVE PUBLICATIONS

Keith Kozminski

KEITH KOZMINSKI

Associate Professor of Biology
Email: kkoz@virginia.edu
Office: (434) 243-5336
Lab: (434) 924-3943
Office: 208 PLSB

EDUCATION

B.A. and B.S., State University of New York, Buffalo, 1989
Ph.D., Yale University, 1995
Postdoctoral Research, U. of California, Berkeley, 1995-2001

RESEARCH INTERESTS

Current research in the lab primarily focuses on the role of small G proteins in signal transduction during polarized cell growth. In particular, we are interested in how the Rho-family GTPase Cdc42p promotes protrusion of the cell cortex. In mammalian cells, the protrusions form filopodia and are essential for cell movement during processes such as neuronal migration, wound healing, and immune responses. In some fungi, these protrusions produce a daughter cell or bud. In each of these examples, Cdc42p asymmetrically organizes the actin cytoskeleton and, in turn, the secretory apparatus, prior to polarized growth. Thus, Cdc42p is a key regulator of polarized cell growth. Interestingly, to function properly, Cdc42p itself must acquire an asymmetric distribution on the cell cortex. This observation presents an important question: How does a protein that triggers the development of cellular asymmetry become asymmetrically distributed in the first place and remain asymmetrically distributed? To address this question, the lab has turned to the budding yeast S. cerevisiae (baker's yeast) as an experimental model for Cdc42p-dependent cell polarization. Budding yeast offers many experimental advantages. Among these are the amenability of this organism to classical genetics, molecular genetics, high throughput genomic/proteomic analysis, cell biology, and biochemistry. In addition, and very importantly, polarized cell growth and Cdc42p function in yeast is very similar to that found in mammalian cells. Thus, a less complex eukaryote such as yeast is being used to decipher how more complex eukaryotic cells (i.e., human) function.

REPRESENTATIVE PUBLICATIONS

Yasutis, KM and KG Kozminski. 2013. Cell cycle checkpoint regulators reach a zillion. Cell Cycle 12: 1501-1509. Read Paper

Alfaro, G, J Johansen, SA Dighe, KG Kozminski, and CT Beh. 2011. The sterol-binding protein Kes1/Osh4p is a regulator of polarized exocytosis. Traffic 12: 1521-1536. Read Paper

Yasutis, KM, M Vignali, M Ryder, F Tameire, SA Dighe, S Fields, and KG Kozminski. 2010. Zds2p regulates Swe1p-dependent polarized cell growth in S. cerevisiae via a novel Cdc55p interaction domain. Molecular Biology of the Cell 21: 4373-4386. Read Paper

ARCHIVED PUBLICATIONS

Robert Kretsinger

ROBERT KRETSINGER

Commonwealth Professor of Biology
Email: rhk5i@virginia.edu
Office: (434) 982-5764
Lab: (434) 982-5764
Office: 205 Chemistry Building

EDUCATION

B.A., University of Colorado, 1958
Ph.D., Massachusetts Institute of Technology, 1964
Postdoctoral Research, Medical Research Council Laboratory of Molecular Biology, 1964-65; University of Geneva, 1966-67

RESEARCH INTERESTS

In collaboration with Julie Sando, Anesthesiology U.VA., we have determined the low resolution, three dimensional structure of protein kinase C  from two dimensional crystals grown on phospholipid monolayers by electron microscopy. We are exploring the occurrence and functions of tandemly repeated sequences whose structures are inherently flexible. We are evaluating the placements of amino acid side chains in protein structures, determined by homology modeling. We are analyzing the concerted changes in conformation that accompany the binding of calcium by proteins in the EF-hand homolog family.

REPRESENTATIVE PUBLICATIONS

Sarah Kucenas

SARAH KUCENAS

Assistant Professor of Biology
Email: sk4ub@virginia.edu
Office: (434) 982-5436
Lab: (434) 243-2541
Office: 312 PLSB

Laboratory Website

EDUCATION

B.S., Valparaiso University, 2000
Ph.D., Saint Louis University, 2005
Postdoctoral, Vanderbilt University, 2005-2009

RESEARCH INTERESTS

Formation of a functional nervous system requires the coordinated interactions of several types of cells derived from distinct precursor populations. These cells must often migrate great distances, identify each other, integrate and coordinate their differentiation. This ensures that information can be passed between the central nervous system (CNS) and peripheral nervous system (PNS) targets via peripheral nerves. Investigating the cellular and molecular mechanisms that mediate motor nerve formation will provide important insights into the developmental programs that assemble and maintain functional nervous systems.

The long-term goal of the work in the lab is to understand the development of spinal motor nerve components and how cell-cell interactions result in coordinated differentiation, myelination, maintenance and regeneration of nerves. To begin to address these developmental paradigms, we use zebrafish as a model system because it uniquely provides the opportunity to combine in vivo, time-lapse imaging with genetics.

Current research in the lab is focused on investigating the developmental programs that mediate motor nerve development, maintenance and regeneration. Specifically, we would like to identify the molecular mechsnisms that mediate the interactions between perineurial glia and Schwann cells during spinal motor nerve development. Schwann cells and perineurial glia are derived from distinct precursors but meet at motor nerves and coordinately differentiate as they ensheath. Preliminary data indicate that these coordinate interactions are essential for motor nerve development. Therefore, we hypothesize that sequential and reciprocal interactions are required for differentiation of Schwann cells and perineurial glia along spinal motor nerves. Currently, very little is known about how glial cells communicate in the PNS. This work will begin to address questions like: How are the developmental programs of spinal motor nerve components coordinated? and What are the specific genes and their roles in motor nerve development? From these results we will be able to characterize how perineurial glia and Schwann cells interact during spinal motor nerve formation and how these early interactions result in the development of the PNS and what roles they might play in disease and/or injury.

In the future, we are interested in determining the role of perineurial glia in spinal motor nerve maintenance, disease and regeneration. Considerable growth occurs during juvenile stages after motor nerves have been formed and myelinated. Therefore, motor nerves are constantly remodeled. This remodeling, which occurs during a period still tractable for imaging and genetic manipulations, provides an exceptional model for nervous system maintenance. Using genetic ablation coupled with in vivo imaging, we will investigate the role the perineurium plays in spinal motor nerve maintenance and regeneration in juvenile and adult fish.

REPRESENTATIVE PUBLICATIONS

Lei Li

LEI LI

Assistant Professor of Biology
Email: ll4jn@virginia.edu
Office: (434) 982-5481
Lab: (434) 982-5774
Office: 214 PLSB

Laboratory Website

EDUCATION

B.A., Peking University, 1997
Ph.D., Michigan State University, 2003

RESEARCH INTERESTS

The long-term research interest of my laboratory is to understand how gene expression is regulated in response to internal signals and external stimuli. We use combined high throughput experimental and bioinformatic approaches to address this question at the genome scale in model plant systems. We have been using genomic tiling microarrays and next-generation sequencing technologies to measure a suit of molecular parameters associated with global transcriptional regulation, including profiles of mRNA and non-coding RNAs, epigenetic markings and genome architecture. Results from these experimental approaches entail a hierarchy of information that is processed in living cells through complex regulatory networks. We integrate these experimental data with computational modeling to identify the underlying transcriptional regulatory networks that define biological processes such as endosperm development, hybrid vigor, and phenotypic variation between closely related species. Our results provide insights at the genome level to the u nderstanding of these processes that are important to meet the global challenges of changing climate and ever-increasing demand for food and energy.

For more information about research interests, visit my lab website.

REPRESENTATIVE PUBLICATIONS

Yang X, Li L.(2012) Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. Biology.1:297-310

Yang X, Zhang H, Li L.(2012) Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.Plant J.70(3):421-431

Wu N, Yang X, Li L.(2011) Identification of feed forward loops composed of microRNAs and transcription factors in Arabidopsis.Journal of Biochemistry and Molecular Biology in the Post Genomic Era.1:79-86

Yang X, Li L.(2011) miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics.27(18):2614-2615

Yang X, Zhang H, Li L.(2011) Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data. Genomics.98(1):40-46.

Zhang H, He H, Wang X, Wang X, Yang X, Li L*, Deng XW.(2011) Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J.65(3):346-58. *Co-corresponding authors.

He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW, Li L.(2010) Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics.96(5):308-315

Wang X, Yu Z, Yang X, Deng XW, Li L. (2009) Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. Bioinformatics. 25:1215-1218.

Peng ZY, Zhang H, Liu T, Dzikiewicz KM, Li S, Wang X, Hu G, Zhu Z, Wei X, Zhu QH, Sun Z, Ge S, Ma L, Li L*, Deng XW* (2009)Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Genomics.93:169-178. *Co-corresponding authors.

Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, and Deng XW (2008) A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant. 1,720-731.

Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW (2008) Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol.9,R57.

Deforest Mellon, Jr.

DEFOREST MELLON, JR.

Professor of Biology
Email: dm6d@virginia.edu
Office: (434) 982-5766
Lab: (434) 982-5766
Office: 288 Gilmer Hall

EDUCATION

B.S., Yale University, 1957
Ph.D., The Johns Hopkins University, 1961
Postdoctoral, Stanford University, 1961-1963

RESEARCH INTERESTS

The current focus in our laboratory is to examine the functional competence of chemoreceptor organs based upon their position within an array along the crayfish antennule. Crustaceans exhibit a broad variety of chemoreceptor placement patterns along their antennules. In crayfish, the olfactory receptors, referred to as aesthetascs, are linearly arrayed along the distal half of the antennular lateral flagella. The number of aesthetascs within the array increases with age, but is in a dynamic state of flux: as new aesthetascs are added at the proximal margin of the array at each molt, some older aesthetascs are lost at the distal margin of the array, at the tip of the flagellum. We are interested in the functional consequences resulting from this dynamic regulation of sense organ number. By confining odorant exposure to distinct, well-isolated zones along the array of aesthetascs and measuring the electrical responses of olfactory lobe brain neurons to excitation of olfactory receptor neurons associated with those specific aesthetasc zones, the relative sensitivities of receptors in the different zonal regions can be determined. Our preliminary findings suggest that olfactory receptor neurons within the proximal, nascent zone of the aesthetasc array are significantly more sensitive to standard odorants than those located more distally along the sensor array. Thus, either older olfactory receptor neurons are less sensitive to standard odorants, or older aesthetascs have fewer functionally competent olfactory receptor neurons than younger aesthetascs. These observations indicate possible parallels with the human olfactory mucosa, in which there is a dynamic turnover of olfactory receptor neurons approximately every 30 days.

REPRESENTATIVE PUBLICATIONS

Mellon, DeF., Reidenbach, M.A. (2011) Fluid Mechanical Problems in Crustacean Active Chemoreception. In Barth, F., Humphrey, J.A.C., Srinivasan, M. (eds) Frontiers in Sensing Springer-Verlag, New York.

Micheal Menaker

MICHAEL MENAKER

Commonwealth Professor of Biology
Email: mm7e@virginia.edu
Office: (434) 982-5767
Lab: (434) 982-5768
Office: 408 PLSB

EDUCATION

B.A., Swarthmore College, 1955
Ph.D., Princeton University, 1959
Postdoctoral Research, Harvard University, 1959-1962

RESEARCH INTERESTS

We are working to understand the overall organization of the circadian systems of vertebrates. Currently we have focused our attention on a transgenic rat model in which a circadian clock gene (Per1) has been linked to a luciferase reporter, so that whenever the gene is expressed low levels of light are produced. Using sensitive photomultipliers we are able to track the circadian expression patterns of the Per1 gene in brain slices and in various cultured peripheral tissues. Thus we are able to ask and answer questions that have not previously been approachable such as: Do the clocks in all tissues remain in synchrony following a change in the timing of the light cycle to which the animals are exposed? What are the signals from the brain that influence the clocks in peripheral tissues? How do the temporal relationships among clocks in the brain and those in peripheral structures change during postnatal development? Because circadian rhythmicity is a fundamental property of virtually all living things, understanding of its basic mechanisms is certain to bring practical benefits.

REPRESENTATIVE PUBLICATIONS

Ignacio Provencio

IGNACIO PROVENCIO

Professor of Biology
Email: ip7m@virginia.edu
Office: (434) 924-4412
Lab: (434) 924-4258
Office: 406 PLSB

EDUCATION

B.A., Swarthmore College, 1987
Ph.D., University of Virginia, 1996
Postdoctoral Research, Uniformed Services University, 1996 -1999

RESEARCH INTERESTS

Light is critical for many biological processes. While vision is the most obvious of these, much of our "non-visual" physiology is regulated by light. For example, the internal 24-hour (circadian) clock that controls daily rhythms such as our sleep:wake cycle is reset by light. Responses that are controlled by the sympathetic system such constriction of the eye's pupil, the production of the hormone melatonin, or even heart rate are all regulated by light to some degree. Many of these non-visual responses to light are controlled, at least in part, by a recently discovered class of photoreceptor in the retina.

Melanopsin is the photopigment within these novel photoreceptors that renders them light-sensitive. Our lab is interested in understanding the role that these melanopsin-based photoreceptors play in various non-visual responses to light. In addition, we are trying to elucidate the biochemical details of the signaling cascade that is initiated by melanopsin activation. We hope that these studies will illuminate the broader impact of light on vertebrate physiology.

REPRESENTATIVE PUBLICATIONS

Deborah Roach

DEBORAH ROACH

Associate Professor of Biology
Email: dar2x@virginia.edu
Office: (434) 982-4858
Lab: (434) 982-5273
Office: 266 Gilmer Hall

Laboratory Website

EDUCATION

B.A., Mount Holyoke College, 1978
Ph.D., Duke University, 1984

RESEARCH INTERESTS

The projects in my lab focus on life history evolution and natural selection across different life stages. Graduate student projects range from research into the consequences of selection across different life stages, to plasticity responses across the life cycle, to factors limiting selection at species ranges. I also have a large ongoing project with Plantago lanceloata that was designed to study the demography of aging. Aging can be quantified as either an increase in mortality as individuals in a population get older, or as a decline in physiological functioning. For evolutionary biologists, aging presents a paradox because it is a phenomenon that is clearly disadvantageous to individuals yet natural selection is ineffective at removing it from populations. Two questions arise: First, how universal is aging? In other words is it found in natural populations? Is it found in plants? Secondly, if a species is identified that can escape aging, what unique biological features allow it to do so? For more information on research interests, visit my lab website.

REPRESENTATIVE PUBLICATIONS

Dorothy Schafer

DOROTHY SCHAFER

Associate Professor of Biology, Director of Graduate Studies
Email: das9w@virginia.edu
Office: (434) 243-5297
Lab: (434) 243-5302
Office: 210 PLSB

Laboratory Website

EDUCATION

B.S., SUNY College of Environmental Science & Forestry, 1977
Ph.D., University of Michigan, 1983

RESEARCH INTERESTS

Our research strives to understand how cells maintain their dynamic actin filament cytoskeleton required for many cellular processes, including, cell migration, maintaining shape, and for trafficking. To learn the molecular mechanisms by which dynamic actin filaments provide these diverse cellular functions, we visualize actin dynamics in living cells and complement the in vivo observations with biochemical approaches. The GTPase dynamin2 plays an unexpected role in regulating actin filament dynamics during cell migration and endocytosis. Our recent work implicates dynamin2, together with its interacting partner cortactin, as regulators of actin filament crosslinking that influences the mechanical properties of the cytoskeletal network.

Dynamic actin is also associated with early endosomes and appears to be essential for efficient receptor traffic via endosomal recycling pathways. We aim to understand how of dynamic endosome-associated actin facilitates recycling traffic.

A long-standing interest is to know how cells move. One focus has been on capping protein, a ubiquitous actin-binding protein that regulates filament growth by "capping" the fast-growing end of actin filaments. Proteins of the Ena/VASP family antagonize capping in vitro . We have used TIRF microscopy to determine the mechanisms whereby Ena/VASP proteins regulate cell motility by antagonizing actin filament capping.

REPRESENTATIVE PUBLICATIONS

Sarah Siegrist

SARAH SIEGRIST

Assistant Professor of Biology
Email: ses4gr@virginia.edu
Office: (434) 982-2604
Office: 316 PLSB

EDUCATION

B.S. Miami University, Oxford Ohio, 1990
PhD University of Oregon, Eugene, OR, 2005
Post-doctoral research University of California, Berkeley, CA 2006-2012

RESEARCH INTERESTS

The sheer number and diversity of cell types within the human brain is staggering. Understanding how cellular diversity is generated and organized in such a way that allows organisms to think and behave is of fundamental importance. All neurons within the brain are generated from neural stem cells, which are self-renewing multi-potent progenitors. Neural stem cells play a key role in regulating brain size and cell type diversity, since this population remains actively engaged in the cell cycle throughout development. While much effort is geared towards identifying molecular mechanisms regulating stem cell self-renewal, research in my lab is focused on the converse. What are the molecular mechanisms that terminate neural stem cell divisions once development is complete, which is essential for ensuring proper formation of brain circuitry and to inhibit tissue overgrowth and tumorigenesis. Beyond development, the answer to this fundamental question is of key importance for understanding age-related cognitive declines, mood disorders, and limited regenerative capacity of adult brains. Overall, research in the lab is geared towards gaining a greater understanding of:

(1) Regulation of neural stem cell proliferation by extracellular factors, local and systemic.

(2) Intrinsic signaling programs regulating neural stem cell fate decisions: death versus survival.

(3) Functional and molecular similarities between Drosophila and mammalian neural stem cells

REPRESENTATIVE PUBLICATIONS

Douglas Taylor

DOUGLAS TAYLOR

Commonwealth Professor of Biology
Email: drt3b@virginia.edu
Office: (434) 982-5217
Lab: (434) 982-5218
Office: 059 Gilmer Hall

Laboratory Website

EDUCATION

B.S., Queen's University, 1986
M.S., Queen's University, 1988
Ph.D., Duke University, 1993

RESEARCH INTERESTS

My students, post-docs and I study population genetics and molecular evolution. We are studying invasive species as models for the evolution of geographic range expansion. We also study how evolution is influenced by the fact that populations are distributed in space (population structure). Several projects focus on how selection at one level or organization subsumes, or is subsumed by, selection at higher levels of organization...so-called "levels of selection". This has led us into studies of genetic conflict such as epidemics of selfish genes within natural populations and mitochondrial diseases that result from the accumulation of parasitic organelles within cells. Our work involves a wide variety of methods: phylogenetics & molecular population genetics, field experiments, greenhouse experiments & crossing studies, theory.

For more information on research interests, see my lab webpage.

REPRESENTATIVE PUBLICATIONS

Michael Timko

MICHAEL TIMKO

Professor of Biology
Email: mpt9g@virginia.edu
Office: (434) 982-5817
Lab: (434) 982-5779
Office: 044 Gilmer Hall

Laboratory Website

EDUCATION

B.S., Rutgers, 1975
M.S.., Rutgers University, 1978
Ph.D., Rutgers University, 1980
Postdoctoral Research, Brandeis University, 1980-1982
Postdoctoral Research, Rockefeller University, 1982-1986

RESEARCH INTERESTS

Our research is conducted at the cellular and organismal level using a wide range of biochemical, molecular, and genomic approaches in the laboratory and in silico (computational/ bioinformatic). Our interest can be divided into three main themes. The first focuses on understanding the molecular components and signaling pathways that govern the interaction of the parasitic angiosperms Striga and Alectra with their host species. Through comparative functional genomics we are defining the host defense components and parasite virulence effectors underlying compatible and incompatible host-parasite association. These studies also include an examination of the evolution of parasitism in the Orobanchaceae as a way of determining what makes parasitism in angiosperms an attractive life-history option. A second area of research focuses on the phytohormonal and developmental regulation of nicotine and related alkaloids in tobacco. By targeted manipulation we are attempting to define a cause and effect relationship between the presence of specific plant alkaloid constituents and their derivatives in tobacco smoke, tobacco smoke condensates, or smokeless tobacco extracts and their effects on human cellular function leading to disease using differentiated bronchial and oral (gingivial) cell cultures as models. The final area of work in the lab centers on the development and use of probiotic-based human therapeutics and nutraceuticals for the treatment of intestinal disease, including necrotizing enterocolitis (NEC), a major problem in premature infants.

For more information about research interests, visit my lab webpage

REPRESENTATIVE PUBLICATIONS

Li J, and Timko MP (2009) Gene-for-gene resistance in Striga-cowpea associations. Science 325: 1094.

Westwood JH, Yoder JI, Timko MP, and de Pamphilis CW (2010) The evolution of parasitism in plants. Trends in Plant Science 15: 227-235 doi 10.1016/j.tplants.2010.01.004

Hernandez-Garcia CM, Bouchard RA, Rushton PJ Jones ML, Chen X, Timko MP, and Finer JJ (2010) High level transgenic expression of soybean (Glycine max) GmERF and Gmubi gene promoters isolated by a novel promoter analysis pipeline. BMC Plant Biology 10: 237 doi:10.1186/1471-2229-10-237

Andargie M, Pasquet RS, Gowda BS, Muluvi GM, and Timko MP (2011) Construction of a SSR-based genetic map and identification of QTLs for yield and domestication traits using recombinant inbred lines from a cross between wild X cultivated cowpea (V. unguiculata (L.) Walp.). Molecular Breeding 28: 413-420. DOI 10.1007/s11032-011-9598-2

Zhang H, Bokowiec MT, Rushton PJ, Han S, and Timko MP (2011) Tobacco transcription factors NtMYC2a and NtMYC2b form nuclear complexes with the NtJAZ1 repressor and regulate multiple jasmonate-inducible steps in nicotine biosynthesis. Molecular Plant doi: 10.1093/mp/ssr056

Timko MP, Huang K, and Lis KE (2011) Host resistance and parasite virulence in Striga-host plantinteractions - A shifting balance of power. Weed Science doi: 10.1614/WS-D-11-00039.1 (Posted online June 2011)

Wickett NJ, Honaas LA, Wafula EK, Das M, Huang K, Wu B, Timko MP, Yoder JI, Westwood JH and dePamphilis CW (2011) Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis. Current Biology 21: 20980-2104. doi:10.1016/j.cub.2011.11.011

Michael Wormington

MICHAEL WORMINGTON

Associate Professor and Associate Chair of Biology
Email: ww2t@virginia.edu
Office: (434) 982-5803
Lab: (434) 982-5804
Office: 206 PLSB

EDUCATION

B.A., University of Kansas, 1975
Ph.D., University of Kansas, 1979
Postdoctoral Research, Carnegie Institute, 1979-1982

RESEARCH INTERESTS

MicroRNAs (miRNAs) are small, non-coding RNAs that post-transcriptionally control gene expression by directing either the degradation or translational repression of target mRNAs. miRNAs potentially regulate as many as one-third of all protein-coding genes in vertebrates and have essential roles in controlling diverse aspects of cellular function in numerous physiological contexts. They are particularly important in silencing cell cycle genes that direct cellular proliferation. miRNA biogenesis is a complex process involving distinct multimeric complexes that catalyze sequential RNA processing events. Primary miRNA transcripts are initially processed in the nucleus by the microprocessor complex comprised of Drosha and DGCR8. The resultant pre-miRNAs are exported into the cytoplasm and converted to mature miRNAs by Dicer and bind to the Argonaute (Ago) family of proteins to form the RNA-induced-silencing complex (RISC).

My research uses a combination of molecular, cellular and biochemical approaches to address the develop-mental regulation of miRNA processing and RISC function during Xenopus oogenesis and embryogenesis.

The maternal mRNAs encoding Ago2, DGCR8, Dicer and Drosha are translationally repressed in immature oocytes. Although the processing proteins are present in fully-grown oocytes, miRNA processing is not activated until progesterone-induced meiotic maturation is completed. We are also investigating how the RISC participates in the "egg-to embryo switch" that occurs at the midblastula transition when maternal mRNAs are degraded concomitant with the activation of zygotic transcription. Our goal is to identify the miRNAs and their corresponding mRNA targets that are recruited into the RISC in order to direct the maternal to zygotic transition that enables cellular specialization to ensue after the embryonic cell cycles are attenuated.

REPRESENTATIVE PUBLICATIONS

Martin Wu

MARTIN WU

Assistant Professor of Biology
Email: mw4yv@virginia.edu
Office: (434)-924-4518
Lab: (434) 982-5478
Office: 404 PLSB

Laboratory Website

EDUCATION

B.S., Wuhan University, 1992
Ph.D., The Johns Hopkins University, 2000

RESEARCH INTERESTS

We are interested in studying how microbes evolve, adapt and diversify at the molecular, organismal and community levels. To gain insights into the fundamental mechanisms underlying these processes, we use an interdisciplinary approach that draws upon the fields of genomics, evolutionary biology, computational biology, and ecology. In particular, a large portion of our work will employ phylogenomics -- the synergistic integration of evolutionary and genomic analyses -- to investigate these questions. Research opportunities are available. See my lab homepage for details.

REPRESENTATIVE PUBLICATIONS

2012

✤Ren T, Glatt DU, Nguyen TN, Allen EK, Early SV, Sale M, Winther B, Wu M. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids. Environmental Microbiology (in press)
✤Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology. (in press).
✤Kolling GL, Wu M, Alcantara-Warren C, Durmaz E, Klaenhammer TR, Guerrant RL. Lactic acid production by Streptococcus thermophilus alters Clostridium difficile infection and in vitro Toxin A production. Gut Microbes 2012, 3:6,1-7. doi:10.4161/gutmicrobes.21757.
✤Lu HP, Wang YB, Huang SW, Lin CY, Wu M, Hsieh CH, Yu HT. Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). BMC Genomics. 2012,13:466. doi:10.1186/1471-2164-13-466.
✤Kolling G, Wu M, Guerrant RL. Enteric Pathogens Through Life Stages. Frontiers in Cellular and Infection Microbiology. 2012, 2:114. doi:10.3389/fcimb.2012.00114.
✤Koeppel AF and Wu M. Lineage-dependent ecological coherence in bacteria. FEMS Microbiology Ecology. 2012, doi: 10.1111/j.1574-6941.2012.01387.x. Download 10.1111_j.1574-6941.2012.01387.x.pdf.
✤Sloan DB, Alverson AJ, Wu M, Palmer JD, Taylor DR. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus silene.Genome Biol Evol. 2012, Jan;4(3):294-306. Epub 2012 Jan 12.
✤Wu M and Scott AJ. Phylogenomic Analysis of Bacterial and Archaeal Sequences with AMPHORA2. Bioinformatics 2012, doi: 10.1093/bioinformatics/bts079. Download AMPHORA2.pdf
✤Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 2012 Jan;10(1):e1001241. Epub 2012 Jan 17.
✤Wu M, Chatterji S, Eisen JA. Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 2012, 7(1): e30288. doi:10.1371/journal.pone.0030288

2011

✤Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol 2011 Oct 17;12(10):R100.
✤Wang Z, Kadouri DE and Wu M. Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13. BMC Genomics 2011, 12:453. doi:10.1186/1471-2164-12-453[highly accessed]
✤Wu M and Eisen JA. Towards Automated Phylogenomic Inference in Bruijn, F.J.d., Handbook of molecular microbial ecology I : metagenomics and complementary approaches. 2011, Hoboken, N.J.: Wiley-Blackwell.
✤Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC and Eisen JA. Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS One 2011 6(3): e18011. doi:10.1371/journal.pone.0018011.