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Conference 2005

June 19-23, 2005

 
Annual Meetings - 2004 SMBE Conference

The 2004 SMBE conference was held Pennsylvania State University, Pennsylvania, June 17-20, 2004. This program has already taken place, but the information provided here may still be helpful if you’re considering attending such a program in the future.

Programs are often repeated on an annual or semi-annual basis...to learn more about future offerings of this program, please go to the contact section of this Web site.


Poster Presentations
Overview
| Speakers | Schedule | Abstracts | Posters

Name of Presenter Poster Title
Guillaume Achaz Slow turnover of HIV-1 populations in chronically infected individuals.
Stephane Aris-Brosou Parameterization of codon models, bias and implications for translational selection
Gregory Baillie Evolution and retrotransposition of betaretroviruses in mice, rats, and other mammals.
John Baines Analysis of candidates for positive selection identified by a microsatellite screen of natural populations of the house mouse
Mamta Bajaj Predicting amphipathic helices through statistical analysis
Marta Barluenga Sympatric speciation in a crater lake cichlid in the Neotropics: the Midas Cichlid species complex
Norman Barr Molecular systematics of the genus Ceratitis (Diptera: Tephritidae)using mitochondrial and nuclear genes
Fabia Ursula Battistuzzi A genomic timescale of prokaryote evolution and early Earth history
Marc Bauchet Underdominant selection in cow growth hormone genes
Kevin Beckmann Identification of Single Copy Genes for Phylogenetic and Functional Analysis
Ulfar Bergthorsson Transcription and RNA editing of horizontally transferred mitochondrial genes in flowering plants
Jim Biedler Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity
Jaime Blair Phylogenetic Sequence Analysis of Eukaryotic Genomes
Barbara Bliss Whole genome evidence for multiple transfers among plant organelles
Ingo Braasch Genome evolution of cichlid fishes - insights from receptor tyrosine kinases
Stephan Brunner Comparative Sequencing of Maize: Structure and Origin of Allelic Non-Colinearities
Kira Bulazel Expanded centromere composition of the sex chromosomes of the marsupial Macropus rufogriseus (red-necked wallaby)
Carlos D. Bustamante Optimal Tests for Inferring Natural Selection from Comparative Population Genomic Data
Andrea Carboni Preliminary study of Phaseolus vulgaris L. evolution through non-TIR NBS LRR Resistance Gene Homologues analysis.
David Carlini Context-dependent codon bias and mRNA stability in the yeast transcriptome
Susan L. Carney Expression and molecular population genetic analysis of hemoglobin subunits in the deep-sea hydrothermal vent tubeworm, Ridgeia piscesae
Andre Cavalcanti Life without non-coding DNA: Analysis of a pilot genome of Oxytricha trifallax's macronucleus
Raphaëlle Chaix Lineages, clans, tribes: mythological or genetic entities?
Dimitra Chalkia Evolution of Formins in Eukaryotes
Sara Chambers Phylogeny of ATP Synthase Subunits in Chordate Mitochondrial Genomes
Soochin Cho Frequent Loss of Introns During Nematode Evolution
Wen-Yu Chung A Perl Module for Molecular Evolution
Richard Cordaux Amplification dynamics of Alu elements in the human genome
Andrew J. Crawford Phylogeny, Cenozoic biogeography, and multiple independent mitochondrial gene order rearrangements in Central American frogs of the genus Eleutherodactylus.
Jo Anne Crouch Phylogenetic estimation of adaptation and speciation in populations of the phytopathogenic fungus Colletotrichum graminicola
Liying Cui Rapid Evolution of Yabby Family Transcription Factors in Angiosperms
Brian Cusack Alternative splicing and evolution of duplicated genes
Tal Dagan Unitary Pseudogenes in Bacterial Genomes: Lifestyle and Gene Loss
Jayatri Das Structural Conservation of the Nuclear-Encoded Subunits of Cytochrome C Oxidase Underlies Evolving Functional Sites
Jed Dean Expanding the role of Reciprocal Hemizygosity Scanning (RHS)
Paramvir Dehal Insights into the Evolution of Gene Structure using Whole Genome Sequence
Theresa Delaney Investigating the Influence of Genetic Code Evolution over Different Genetic Distances
Masatsugu Denawa Intron evolution in the P-type ATPase superfamily: A new property of conserved introns in the conserved domains
Claude dePamphilis The Floral Genome Project: Origin and Diversification of Floral Regulatory Genes
Mary Doherty Molecular Markers for Assessing Community Diverstiy of Coastal Ciliates
Irina S. Druzhinina Resolving the molecular evolution of recently diverged fungal taxa using Bayesian phylogenetic inferences: application to the "harzianum/tomentosum" clade in Trichoderma
Ronald Ellis Females, Hermaphrodites and Developmental Bias
Brian Erickson Genomic Analysis of Transporter Proteins in the Malaria Parasite Plasmodium falciparum
Kiyoshi Ezawa Statistical analysis of gene conversion in mouse and rat genomes
Michael Ferdig Biological processes underlying complex multiple-drug resistance in the malaria parasite, Plasmodium falciparum
Gianni Ferreri The Paradoxical Conservation of an Active Marsupial Retroelement
Cedric Feschotte Merlin: a new superfamily of DNA transposons present in diverse animal genomes and related to bacterial IS1016 insertion sequences
Pilar Francino Applying the comparative method to bacterial genome evolution.
Richard Frankham Comparative rates of loss of quantitative and molecular genetic variation in finite populations
Hunter Fraser Detecting selection using a single genome sequence
Skanth Ganesan Comparative Analysis of Gene Prediction Methods and Development of a Fungal Genome Database System
Audrey Gasch Coevolution of cis-regulatory elements and their DNA binding proteins
in fungi
Fan Ge Estimation of Extent of Horizontal Gene Trasfer in Microbial Genomes
Armando Geraldes Contrasting patterns of introgression at X-linked loci across the European rabbit hybrid zone
Cynthia Gibas An Interactive Web Resource for Comparative Analysis of Chloroplast Genomes
Cynthia Gibas GenoMosaic: On-Demand Multiple Genome Comparison and Comparative Annotation
Andrew Gibson Mutational Patterns in Mammalian Mitochondrial DNA and Phylogenetic Inferences
Leslie Goertzen Multiple copies of atp8 in the mitochondrial genome of Amborella trichopoda support a horizontal gene transfer hypothesis.
Paula Goetting-Minesky Male mutation bias in Perissodactyla and Cetacea
Mary Katherine Gonder Demographic History of Khoisan Speakers of Tanzania Inferred from mtDNA Control Region Sequences
Yi Gong Estimation of Deleterious Genomic Mutation Rate of Drosophila melanogaster by the Binscy Assay
Josefa Gonzalez A BAC-based physical map of the Drosophila buzzatii genome
Jeffrey Good Molecular evolution and genomic location of genes expressed during spermatogenesis in the mouse
Michael Goodisman Genomic analysis of social insect development: A microarray-based study of gene expression in larval and adult ants
Hiroki Goto Comparative study of the regulation and catalytic efficiency of alpha-amylase in Drosophila melanogaster
Autumn Griffin Understanding the Phylogeography of Ciliates Using Molecular Markers: Halteria grandinella and Meseres corlissi
Wendy Grus Lineage-specific expansions of vomeronasal pheromone receptor gene families in mice and rats
Jianying Gu Are isochores vanishing in mammals?
Xun Gu Genome Phylogenetic Analysis Based on Extended Gene Contents, and Tree of Life
Sheng Gu Simulation studies on the role of premeiotic clusters of mutations in single-gene speciation using Genetic Simulation Library
Jeremiah Hackett Migration of a Plastid Genome to the Nucleus in a Peridinin Dinoflagellate
Penelope Haddrill Inferring the selective and demographic history of Drosophila melanogaster populations using multi-locus data
Mehrdad Hajibabaei DNA barcoding: identification of animals using a molecular evolutionary approach
Indrani Halder Estimation of BioGeographical Ancestry in Admixed Populations
Weilong Hao Patterns of bacterial gene movement
Li Hao Genomic Organization and Evolutionary Analysis of Ly49 Genes Encoding Rodent Natural Killer Cell Receptors: Rapid Evolution by Repeated Gene Duplication
Toshiyuki Hayakawa Gene conversion of Sialic binding domains by Pseudogenes in the CD33-related Siglec Gene Cluster
Einat Hazkani-Covo Rarity of conservation in highly regulated operons
Blair Hedges A molecular timescale for eukaryote evolution and the rise of complex life
Ryan Hernandez Selecting Forward: A Simulation Approach to Modeling Evolution
Bradley Hersh Cis-regulatory evolution of the Ultrabithorax-target gene knot in the Drosophila haltere
Emma Hill Characterizing Ancient Protein Evolutionary Relationships via Structure.
Jinling Huang Phylogenomic evidence of organelle loss and gene transfer in Cryptosporidium parvum
Melanie Huntley Comparative Proteomics: Repetitive Simple Sequences and Neurological Proteins
Gavin Huttley Modeling the impact of DNA methylation on the evolution of BRCA1
Hiroko Ishiyama Nucleotide polymorphism and divergence in the PgiC gene between four closely related Shorea species (Dipterocarpaceae)
Takeshi Itoh Intensity of Natural Selection after Horizontal Gene Transfer in Bacteria
Mineyo Iwase Ectopic gene conversion between sex chromosomal KAL-1 and KALY in primates
Jeffrey Jensen The Effects of Demography on Tests of Neutrality: A goodness-of-fit test to distinguish rejections due to demography from selection
Michael Jensen-Seaman Genetic Structure of the Laboratory Rat (Rattus norvegicus)
Hanna Johannesson Evolution of surface antigens of the human pathogenic fungi Coccidioides immitis and C. posadasii
King Jordan Sequence evolution and the human gene expression network
Frank G. Jørgensen Comparative analysis of protein coding sequences from Human, Mouse and the domesticated Pig
Gila Kahila Bar-Gal Genetic and morphometric differences between two populations of gray wolves in Israel: hybrids or not?
Esther Kamau Linkage disequilibrium and diversity around the self-incompatibility locus.
Satoko Kaneko Processed pseudogenes for regulating functional Makorin genes in mammals
Takao Kasuga Comparative genomics within the genus Neurospora
Yumiko Kato Recent independent origins of annual Zostera marina from the perennial
Kelly Ketcham MC1R variation is not linked to small-scale melanic plumage patterns in two passerine birds.
Junhyong Kim CIPRes: Building the compuational infrastructure for estimating Tree of Life and benchmarking phylogeny algorithms
Takashi Kitano Genome Sequence Analyses of Human, Chimpanzee, and Gorilla HOXA Clusters
Wen-Ya Ko Lineage-specific molecular evolution in the Drosophila melanogaster species subgroup
Hongzhi Kong Rapid Birth-and-Death Evolution in the SKP1 Gene Family
Carolin Kosiol Protein Sequence Evolution: Markov or non-Markov?
Natalia Kouprina The SPANX gene family of cancer-testis specific antigens: rapid evolution and amplification in African great apes and hominids
Sudhir Kumar MEGA3: An Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment
Christian Landry Genetic variation for phenotypic plasticity in budding yeast: effects on the regulatory network
Laura Landweber Patterns and Process of Gene Scrambling and Unscrambling in Ciliates
Pascal Lapierre Whole genome analyses on the class levels: is there a consensus phylogeny?
Betty R. Lawton The Search for Genetic Footprints of Intergenomic Conflict: Imprinting and Rapid Evolution of IGF2 in the Poeciliid Fishes
Brian Lazzaro Evolutionary and Quantitative Genetics of D. melanogaster innate immunity.
Zhenguo Lin Plant Homologs of Yeast DNA Repair Genes
Chiao-Feng Lin Phylogenetic Analysis of U12-Dependent Introns in Arabidopsis thaliana and Rice Genomes
Yi Lu The Error Minimization of Escherichia coli Protein-coding Genes
Guoqing Lu Mining Mitochondrial Single Nucleotide Polymorphisms (SNPs) associated with human population evolution and genetics diseases
Olivier Lucas Evolution of a protein-protein interaction in vertebrates
Jing Luo Evolution of Hox gene clusters in young polyploidy fishes
Jennifer Mack Centromeric Drive in Mixed Karyotypes of P. Maniculatus and P. Polionotus F1, N1 AND F2 Hybrids
An Mannaert Posterior Hox gene variation in amphibians
Xianyun Mao Identifying loci under positive natural selection indicated by high branch link in population comparison
Meghan Marzelli The Role of Segmental Duplications in Genome Evolution in Marsupials
Jens Mayer Characterization of human endogenous retrovirus families HERV-K11, HERV-K14 and HERV-K22
Casey McGrath Molecular appropraches to studying genome evolution in ciliates
Lisa McGraw Genes regulated by mating, sperm or seminal proteins in mated female Drosophila melanogaster
Joel McNeal Mitochondrial DNA suggests 12 origins of parasitism in angiosperms and implicates parasitic plants as vectors of horizontal gene transfer.
Richard Meisel Conserved motifs are found at D. pseudoobscura rearrangement breakpoints.
José Melo-Ferreira Fine-scale analysis of ancient mtDNA introgression of Lepus timidus into L. granatensis and L. europaeus from the Iberian Peninsula
Jorge Mena-Ali S-allele diversity and sequence divergence in natural populations of Solanum carolinense
Thomas Merritt The structure and population genetics of the breakpoints associated with
cosmopolitan inversion In(3R)Payne in Drosophila melanogaster
Christiane I. Meyer Different genes cause similar melanophore patterns in two Xiphophorus species
Paras Kuamr Mishra Study of Causes of Hybrid Sterility in the Drosophila Bipectinata Complex and Its Impact on Testis and Seminal Vesicle Morphology
Adriana Maria Montano Convergent and Parallel Evolution of Peptidoglycan Recognition Proteins in Mammalian Innate Immune System
Kristi Montooth Modeling metabolic performance in Drosophila
Richard Moore The signature of selective sweeps in Arabidopsis thaliana
Geoffrey Morris Transcription factor binding divergence of duplicate genes
Alan Moses Maximum likelihood estimation and hypothesis testing for phylogenetic analysis of transcription factor binding sites
Jeffrey Mower The Genus Plantago Provides a Unique Opportunity to Identify Horizontal Gene Transfer in Plant Mitochondria
Jongmin Nam Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms.
Bárbara Negre Rearrangement of the Drosophila Hox gene complex: Genomic characterization of the labial-proboscipedia split in Drosophila buzzatii
Bárbara Negre Rearrangement of the Drosophila Hox gene complex: Expression of labial, proboscipedia and abdominal-A in species with different gene arrangements
Anton Nekrutenko Reconciling the Numbers: ESTs vs. Protein-Coding Genes
Nikolas Nikolaidis Origins and evolution of immunoglobulin (Ig-like) domain containing receptors of the innate immune system
Heather Norton Pigmentation candiate gene variation and possible evidence for natural selection in human populations
Masafumi Nozawa Origin of sirene: a paradigm of exon shuffling and gene duplication in Drosophila
Ryosuke Ohniwa Molecular evolution of the SNARE families: Q-SNARE preceded R-SNARE.
Hideyuki Okamura Kingdom specific subfamilies of the P-type ATPase evolved from methanogens and suggest the possibility of
polyphyletic eukaryogenesis
Han Chuan Ong Repeated independent transfer of a mitochondrial gene to the nucleus in grasses
Juan C. Opazo Evolution of insulin gene in caviomorph rodents
Stephen Opiyo Usage of multivariate methods in protein family classification
Marta Pascual Selection and speciation of colour morphs in Pseudodistoma crucigaster (Ascidiacea: Polyclinidae)
Bret Payseur Testing Genotype-Phenotype Association in Natural Populations
Jill Pecon-Slattery Evolution of genes located on the Y-chromosome in the cat family Felidae
Concepcion Perez Independent and Repeat Coat Color Mutations Found Amongst Australian Populations of Domestic Norway Rats
Stephen Peterson EF-1 alpha intron position and number changes among Penicillium species
Jaros Phinchongsakuldit Genomic analysis of promoter: Long-PCR and Pseudo-recombination
Katarzyna Pirog Cryptic diversity in the tide-pool ciliate Strombidium oculatum.
K.J. Pittman The Concept of Subspecies in Evolutionary Biology
Ondrej Podlaha Non-neutral evolution of the transcribed pseudogene Makorin1-p1 in mice
Loic Ponger Evolution of the DNA methylation in the eukaryotes
Matthew Portnoy Multi-Species Comparative Sequence Analysis of the GDF6 Growth Differentiation Gene
Anuphap Prachumwat Higher Gene Duplicabilities for Metabolic Proteins than for Non-Metabolic Proteins in Yeast and E. coli
Ellen Pritham Unexpected diversity and differential amplification of transposable elements in four species of Entamoeba protozoans
Antoni Rafalski Comparative Sequencing of Maize: Structure and Origin of Allelic Non-Colinearities
Frances Raftis Patterns of Replacements at Changing Protein Interfaces
Narayanan Raghupathy The role of duplication in the evolution of vertebrate insulin
signalling
Uma Ramakrishnan Precision and Accuracy of Divergence Time Estimates from STR and SNPSTR Variation
Edward Ramos Identification of Functional Cis-Regulatory Modules by Comparative Analysis of Drosophila melanogaster and Drosophila pseudoobscura.
Tavares Raquel Comparative analysis of nuclear receptors expression patterns
Denise Raterman Phylogenetic relationships of the cuscuses and brushtail possums (Marsupialia: Phalangeridae)
Noah Reynolds Evolutionary history of antifreeze glycoproteins in Gadidae inferred from molecular phylogenetic analysis.
Aaron O. Richardson Horizontal transfer of a cis-spliced group II intron from a eudicot to a monocot, Hedychium coronatum
Igor Rogozin Evolution of splice signals and protosplice sites
Alejandro P. Rooney Amino Acid-Rich Selection on Protein-Coding Genes
Michael Rosenberg Fidelity of Sequence Alignment Procedure in Establishing Site Homology in Comparative Genomics
Wayne Rossiter PLA2 venom loci show evidence for positive selection in Sistrurus rattlesnakes with different diets
Stefan Rothenburg Identification of a new Z-DNA binding protein (PKZ) from zebrafish - new insights into the evolution of Z-DNA binding proteins
Scott Roy Complex Ancient Genomes
Tovah Salcedo Nucleotide variation on the X chromosome in a natural population of house mice, Mus domesticus
Maribel Sanchez Identification of Cell Cycle Control Proteins in the Genome of Malaria Parasite Plasmodium falciparum
Hiromi Sawai The tempo and mode of HLA evolution mediated through the dual function
Mark Scally Phylogenetic comparison of mammalian BRCA1 sequences and the relevance to human disease.
Deena Schmidt Adaptive evolution drives the diversification of zinc-finger binding domains.
Erin Schuenzel Identification of shifts in natural selection and indications of host adaptation in the plant pathogen Xylella fastidiosa
Dietmar Schwarz Ecologically mediated hybrid speciation in a diploid, bisexual animal
Andrew M. Shedlock Reptile genome structure inferred from BAC-end sequence analysis of the American Alligator and Painted Turtle.
Dawn Simon Divergent Histories of Group I Introns in Lichen Fungi
Kevin Simonelic Fitness consequences of intraspecific hybridization in Caenorhabditis elegans
Colleen Sinclair Molecular analysis of the telomere regions in scleractinian coral, Acropora surculosa
Anu Sirviö Mapping the genome of ant species Acromyrmex echinatior
Oona Snoeyenbos-West Molecular Phylogeny of Phyllopharyngean Ciliates and their Group I Introns
Nan Song Accurate classification of multidomain protein families
Sasa Stefanovic Transcompartmental gene duplication in action - the cox2 case in legumes (Phaseoleae, Fabaceae)
Daniel Stoebel Two ways linkage affects the rate of neutral substitution
Sankar Subramanian Gene Expression Intensity Shapes Evolutionary Rates of the Vertebrate Proteins
Zuzana Swigonova Structure and evolution of the chromosomal region containing the r/b gene of rice, maize, and sorghum
Aya Takahashi A high frequency null mutant of an odorant-binding protein, Obp57e
Hiroshi Tanaka Analysis of Within-patient Drug Resistance Evolution by Reconstructing Longitudinal Phylogenetic Tree of HIV-1 pol Gene under HAART
Tsuyoshi Tanaka Evolution of vitamin B6 (Pyridoxine) metabolism by gain and loss of genes
James Taylor Are transitions at CpG dinucleotides replication dependent?
Emma Teeling Conservation of the X chromosome across Eutheria; 105 million years of conservation revealed through comparative radiation hybrid maps.
Philip Terry Evolution of 3-isopropylmalate dehydrogenase.
Karin Tetzlaff Dynamics of rDNA in 400 generations of Drosophila melanogaster
Bart Thornburg Transposable Elements as a Source of Mammalian Transcription Factors
Tatiana Uinuk-ool Genomic organization of lamprey CD45 gene
Araxi Urrutia Codon usage in human genes under: Beyond GC content and context mutations
Louie van de Lagemaat The human and chimpanzee genomes differ by over 8500 retroelement insertions
Chendhore Veerappan Molecular evolutionary analysis of the SET domain protein families in fungal genomes
Benjamin Vernot Notung 2.0: A Program for Evaluating and Optimizing Gene Duplications and Losses in Gene Trees.
Kerr Wall PlantTribes: A global classification for Arabidopsis and Rice Proteins
Guanfang Wang Genome-wide analysis of Arabidopsis cyclins and comparative phylogenetic analysis of plant cyclin-like proteins
Teruaki Watabe V3 loop conformations of HIV-1 and structural features associated with viral tropism
Daniel Weinreich Rapid evolutionary escape from a local fitness peak in large populations
Andrew Whitehead Evolutionary analysis of variation in global gene expression among Killifish populations
Alex Wilson How divergent are they? Investigating the potential for cross-species application of pea aphid microarrays in the green peach aphid.
Gabriela Wlasiuk The agouti locus and coat color variation in the rock pocket mouse, Chaetodipus intermedius
Alex Wong Evidence for positive selection on genes expressed in the reproductive tract of female Drosophila melanogaster
Gang Wu Synthetic Gene Designer: Bioinformatics tools to improve heterologous gene expression.
Jinchuan Xing Molecular Phylogeny of Cercopithecidae (Old World Monkeys) as inferred by Alu insertions
Laura Zahn Evolution of MADS-box genes in the Angiosperms
Xian Zhang Evidence for R2 element activity in Drosophila simulans population
Zhongming Zhao Neighboring-nucleotide effects on single nucleotide polymorphisms (SNPs) in the mouse genome
Olga Zhaxybayeva Cladogenesis, Coalescence and the Evolution of the Three Domains of Life
Lan Zhu A Composite Likelihood Ratio Test for Detecting Natural Selection from Site Frequency Data
Rebecca Zufall Developmental Genome Processing and Protein Evolution in the Ciliate Chilodonella uncinata
The Walter
M. Fitch Prize honors the best presentation in this symposium.

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