THE BIOLOGY OF GENOMES

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Abstracts are listed alphabetically by presenting author.

Presenting Author

Abstract title

Talk/Poster

Abras, D.A.

Effect of nematic fields on DNA elongation

poster

Absher, D.

Genome-wide characterization of 51 human populations from the human genome diversity project

poster

Ahsan, B.

High throughput 5' end mRNA data analysis pipeline

poster

Akagi, K.

Extensive variation between inbreed mouse strains due to endogenous L1 retrotransposition

poster

Albert, T.J.

Development of an optimized oligonucleotide microarray for capturing the entire human exome for high throughput sequencing

poster

Albrechtsen, A.

Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

poster

Andersson, B.

Meta-genomic screening for new viruses—Exploration of the human virome

poster

Andersson, L.B.

A Cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse

talk

Andreasen, C.H.

ROC curves of bootstrap samples used to predict type 2 diabetes status using validated SNPs

poster

Andres, A.M.

Balancing selection in the human genome—From genomic signals to evolution of individual genes

poster

Antonacci, F.

Discovery and characterization of human/great-ape inversion polymorphisms

poster

Apodaca, J.

Evolution of the transcriptional response to oxygen limitation in the enterobacteria

poster

Arndt, P.F.

Mutagenic processes associated with transcription

talk

Avraham, S.

The Plant Ontology database—A community resource for plant structure and developmental stages controlled vocabulary and annotations

poster

Bachtrog, D.

Pervasive adaptive evolution on a newly formed X chromosome

poster

Bainbridge, M.

Genome-wide exon-specific variation discovery in a HapMap trio with array capture and high-throughput sequencing

poster

Barnes, C.

Association testing with common copy number variants

poster

Barnett, D.

Whole-genome, complete mutational profiling using next-generation short-read sequencing

poster

Batzer, M.A.

L1 recombination-mediated deletions generate human genetic variation

talk

Bell, G.W.

Towards a complete planarian gene catalog

poster

Bellott, D.W.

Convergent evolution of the human and chicken sex chromosomes

poster

Benovoy, D.M.

Effect of polymorphisms within probe target sequences on olignonucleotide microarray experiments

poster

Bentley, D.R.

Sequencing and analysis of an African human genome

talk

Berlin, A.

Sequencing and defining diversity of rare HCV genotypes using 454

poster

Bird, C.

Spatial gene expression of human paralogs

poster

Boffelli, D.

Phyloepigenomic comparison of human and chimpanzee

poster

Borel, C.

The genetic control of microRNA expression variation in humans

poster

Boycheva, S.S.

Construction of a pilA gene knockout mutant of A. temperans

poster

Boyle, A.

F-Seq—A feature density estimator for high-throughput sequence tags

poster

Bradley, R.K.

Ancestral reconstruction of proteins and ncRNAs

poster

Bradley, R.K.

Genome-wide survey for mRNA localization signals in Drosophila

poster

Brejova, B.

A probabilistic model of gene structure evolution

poster

Bruhn, L.

Genome-wide oligonucleotide array-based measurements of copy number variations

poster

Bujold, D.

GenoByte—A high performance storage engine for high-throughput genotyping

poster

Busby, M.A.

An informatics pipeline for miRNA profiling using next-generation sequencing platforms

poster

Bustamante, C.D.

Sign, sign, everywhere a sign—High density hapoltype maps of the dog, human, and cow genomes reveal extensive human reorganization of domesticated genomes

talk

Cain, S.

A complete system for community genome annotation

poster

Carbone, L.

The Gibbon—A genomic puzzle

poster

Carlborg, O.

Multi-locus epitasis leads to hybrid inferiority in domestic fowl

poster

Carninci, P.

Cap-analysis gene expression (CAGE) analysis of transcriptional complexity and regulation

poster

Carninci, P.

Repetitive elements are globally expressed in mammalian cells

poster

Carter, D.M.

Whole genome sequence variation in 70 Saccharomyces strains

poster

Carvalho Silva, D.

Merging gene sets to validate vertebrate genomes

poster

Caspi, A.

Noncoding genome variation contributes to measures of selection in plasmodium genes

poster

Celniker, S.E.

The modENCODE (model organism Encylopedia of DNA Elements) Project

talk

Charlier, C.

Highly effective SNP-based association mapping and management of recessive defects in livestock

talk

Chen, K.

Detection of indels and novel splice variants using Illumina reads from cDNA libraries

poster

Cherukuri, P.F.

Predicting intolerance of amino acid alterations in conserved domains

poster

Cheung, V.G.

Ataxia telangiectasia—A complex disorder?

poster

Chuang, J.H.

Universality in regional mutation rates and silent site selective pressures

poster

Church, D.M.

The Genome Reference Consortium

poster

Clark, A.G.

Inference from short-reads to tandem gene arrays

poster

Coller, H.A.

A search for conserved sequences in coding regions reveals that microRNAs target coding regions and suggests a mechanistic difference in coding regions versus 3'UTRs

poster

Conrad, D.

A comprehensive map of common copy number variation

poster

Cooper, G.M.

Systematic assessment of copy-number variant detection via genome-wide SNP genotyping

poster

Cooper, S.J.

Profiling of small molecule metabolites in S. cerevisiae

poster

Cotsapas, C.J.

Towards a 'functional HapMap' with genetic dissection of drug metabolism in vivo and in vitro

poster

Cox, A.J.

Informatics of whole human genome sequencing

poster

Cuomo, C.A.

Comparative analysis of 8 pathogenic and non-pathogenic Candida species

poster

Dagan, T.

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

talk

Davuluri, R.

A high-resolution map of alternative promoters that are active in different mouse tissues

poster

De La Vega, F.M.

SNP identification and genotyping by short-read next generation sequencing

poster

Dean, M.

Genome wide association studies of breast cancer

talk

Degenhardt, J.D.

Increased CCL3L copy number is protective against simian AIDS in rhesus macaque

poster

Dermitzakis, E.

Population genetics and genomics of human gene expression

talk

Devine, S.

1.7 million structural variants in the genomes of diverse humans

poster

Di Palma, F.

All creatures great and small—Vertebrate genome sequencing at the Broad Institute

poster

Diehl, A.

A new method for identifying regulatory sequences under lineage-specific selection

poster

Dimas, A.

Exploring epistatic effects between regulatory and protein-coding variation

poster

DiRienzo, A.

Adaptations to climate in candidate genes for common metabolic disorders

talk

Djebali, S.

Efficient targeted transcript discovery via array-based normalization of race libraries

poster

Dolan, M.E.

Describing biological regulation in the gene ontology

poster

Dolan, M.E.

MouseCyc—A curated biochemical pathways database for the laboratory mouse

poster

Donato, L.J.

Binding site specificity in genomes—The role of allosteric DNA modulation in protein-DNA assembly

poster

Donnelly, P.J.

A Bayesian multipoint allele sharing method for genome-wide association studies

poster

Durbin, R.M.

The 100 Genomes Project—Obtaining a deep catalog of human genetic variation with new sequencing technology

poster

Edwards, J.R.

Novel approach to whole genome methylation profiling applied to epigenetic alterations in breast cancer

talk

Eichler, E.E.

Ancient introgression and evolutionary recurrence of human genome structural variation

talk

Eisen, M.B.

Transcription factors bind promiscuously, but are they doing anything?

poster

Elnitski, L.L.

Detection and characterization of silencers and enhancer-blockers in the greater CFTR region

poster

Erlich, Y.

Machine-learning approach to improving the accuracy of next-generation sequencing

poster

Estivill, X.

Spectrum of genomic structural variation in human populations

poster

Fernandez-Banet, J.

Improvements in Ensembl human genome annotation

poster

Feuk, L.

The database of genomic variants (DGV)—Annotating structural genomic variation

poster

Flicek, P.

Extending ENCODE annotation to the entire genome

poster

Forman, J.J.

A method for mining arbitrarily large multiple alignments finds evidence for DNA sequence motifs under recent positive selection

poster

Fredman, D.

Reconstructing the evolutionary history of genomic regulatory blocks

poster

Friedli, M.

An in vivo unbiased screen for enhancer activity using lentivector-mediated transgenesis

poster

Fu, Y.

SOLiD™ sequencing and 2-Base encoding

poster

Fujiyama, A.

Joint Porphyra genome project to reveal early development of plant systems

poster

Furey, T.

High-resolution mapping and characterization of open chromatin across the genome

poster

Futreal, A.

Identification of somatic mutations in human cancer—Whole genome shotgun sequencing of a small cell lung cancer and matching constitutional genome

talk

Gabriel, S.B.

Variant discovery in WGAS follow-up—Towards complete characterization of rare and common variation

talk

Gaffney, D.

Quantifying the evolution of alternative splicing in mammals using exon arrays

poster

Galagan, J.

Integrated genomics for tuberculosis drug resistance and metabolism

poster

Gao, H.

Identifying the optimal number of clusters via the Deviance Information Criterion

poster

Garber, M.

A new statistical framework for detecting functional constraint using comparative genomics

poster

Georges, M.A.

Searching for rare Crohn's Disease susceptibility variants

talk

Gibbs, R.A.

Genome biology at the Baylor College of Medicine Human Genome Sequence Center

poster

Gonzales-Garay, M.

Genboree Discovery System and its application in The Cancer Genome Atlas (TCGA) project

poster

Goode, D.

A consistent effect of constraint on sequence variation in the human genome

poster

goodson, m.r.

Identifying functional biases within QTL datasets

poster

Goodstadt, L.

Extensive changes to the mouse gene repertoire

poster

Gordon, D.

Using Consed and Cross_match in resequencing projects

poster

Goto, H.

Evolution of X-degenerate Y chromosome genes in greater apes—Conservation of gene content in human and gorilla, but not chimpanzee

poster

Grabherr, M.

Finding signatures of adaptive evolution in populations of three-spine sticklebacks

poster

Green, R.E.

Transcriptional profiles of male and female D. melanogaster as revealed by deep sequencing

talk

Grundberg, E.

Population variation in cis-regulation of gene expression in human primary cells

poster

Gundem, G.

Intogen—Integrating different types of oncogenomic data

poster

Guttman, M.

Chromatin structure reveals thousands of highly conserved, large non-coding RNAs in mammals

poster

Haas, B.J.

Genome dynamics in the potato blight organism may define aspects of pathogenesis

poster

Haghighi, F.

DNA methylation profiling of major depression

poster

Han, K.

Genome-wide target site triplication of Alu elements in the human genome

poster

Hansoul, S.C.

Phenotype prediction using animal breeding methodology—Application to Crohn's Disease

poster

Hardison, R.C.

Determinants of DNA occupancy by mammalian transcription factors—History and current events

poster

Harris, R.A.

Design of a primate comparative methylation array

poster

Harris, T.

Towards integrative customizable displays for a model organism database

poster

Hashimoto, S.

High-resolution analysis of the 5'-end transcriptome in a colon cancer cell line treated with epigenetic drugs

poster

Hattori, M.

Comparative metagenomics revealed commonly enriched gene sets in human intestine

poster

Haussler, D.H.

Reconstructing ancestral genomes using the infinite sites model of genome evolution

poster

Haynes, B.C.

Reverse engineering transcriptional networks from static and dynamic data

poster

Hazkani-Covo, E.

Can numts be used to identify unstable genomic regions?

poster

Hellmann, I.

CpG dinuleotides in primate evolution

poster

Herrero, J.

ENREDO, PECAN and ORTHEUS, accurate and realistic genome wide alignment and ancestor reconstruction

talk

Higasa, K.

Impact of definitive haplotypes for detecting recent positive selection

poster

Himmelbauer, H.

BeetSeq—A reference genome sequence for sugar beet

poster

Hodges, E.C.

Refined platforms for selective re-sequencing of genomic regions associated with breast cancer

talk

Hoffman, M.M.

The properties of natural selection in mammalian promoters

poster

Hoffmann, K.

Region capture for next generation sequencing

poster

Hong, L.

Genetics and genomics of mammalian pigment patterns—Tortoiseshell, calico, and Ohno's law

poster

Huang, W.

A benchmarking platform for next-generation sequence read assembly and polymorphism discovery tools

poster

Hubner, N.

Identification and mapping of single nucleotide polymorphisms for genetic analysis in the rat

poster

Hurle, B.

Comparative genomic studies of the kallikrein and WFDC loci provide insights about primate genome evolution

poster

Hurles, M.E.

The contribution of common and rare copy number variants to disease risk in seven common diseases

talk

Hussin, J.

Haplotype allelic classes in the lactase persistence locus

poster

Hyland, F.

Whole genome sequencing of a Yoruba sample—54,000 small indels in a Yoruba sample are highly underrepresented in coding regions and are overrepresented in certain genes

poster

Imamura, H.

Is the local mutation rate different in orthologous mammalian locations?

poster

Irie, T.

The correlation analysis between primary DNA sequences and transcriptional activities in HEK293 cells

poster

Ishikawa, S.

CNV detection by microfluidic digital array

poster

Iskow, R.

A novel assay to detect recent transposon insertions in the human genome

poster

Jeffares, D.

Selective constraint in the small and compact genomes of malaria parasites (Plasmodium sp.)

poster

Johansson, H.

Selector and extractor probes for multiplex targeted copy-number and sequence analyses

poster

Johnson, P.

Estimating recombination rate in microbial populations

poster

Johnston, H.R.

Population demographic history can cause the appearance of recombination hotspots

poster

Joseph, J.M.

The actinome of D. discoideum in comparison to actins and actin-related proteins from other organisms

poster

Kapranov, P.

New classes of RNAs associated with 5' ends of non-coding transcripts

talk

Katzman, S.

UCSC Genome Browser display of 1000 genomes

poster

Kellis, M.

Comparative genomics of Drosophila and mammalian species

talk

Kelso, J.F.

A complete Neanderthal mitochondrial genome sequence

poster

Kemkemer, C.

An ancient addition to the ancestral part of the mammalian X chromosome was already enriched for brain specific genes

poster

Kidd, J.M.

"New" human genome sequences that are variable among individuals

talk

Kim, T.

Association mapping study for circadian clock variation of N. crassa natural population

poster

Kirkness, E.F.

Evaluation of paired-end tags for detection of variation between human genome sequences

poster

Kitts, P.

NCBI resources for genome assemblies defined in AGP format

poster

Kokocinski, F.

Enhanced UTR definition using additional evidence

poster

Kordis, D.

Synapsid paleogenomics—The enormous impact of the end-Permian ecological catastrophe on the genome structure and evolution of mammals

poster

Kozyavkin, S.A.

Triplex DNA in T. thermophilus siphoviruses and genome fragility

talk

Kramer, M.

wikiLIMS—Developing a laboratory information management system for next generation sequencing data

poster

Kukita, Y.

Detection of human copy number variations using a collection of complete hydatidiform moles—A strategy of CNV-detection using human haploid genomes

poster

Kulevich, S.E.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for top-down proteomics

poster

Kuroki, Y.

Comprehensive analyses of Y chromosomes toward understanding of the male-specific genome functions

poster

Kuroshu, R.M.

Short read multiclone assembly accelerates sequencing full-length cDNA clones

poster

Kuruvilla, F.G.

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms, and rare CNVs

poster

Kuttykrishnan, S.

A dynamic model of the glucose transport network in S. cerevisiae

poster

Kvikstad, E.M.

Ride the wavelet—Scale-specific dynamic of genomic contexts flanking small insertions and deletions

poster

Kwan, T.

Genome-wide analysis of tissue-specific genetic variation in transcript isoform processing

poster

Landry, C.R.

An in vivo map of the yeast protein interactome

poster

Lappalainen, T.

Signatures of genetic drift, admixture and natural selection in the genomic landscape of North European populations

poster

Larkin, D.M.

Evidence for adaptive and negatively selected chromosome rearrangements in amniote evolution

poster

Lawson, H.A.

Connecting genotype to phenotype—The molecular evolution of craniofacial growth and development

poster

Lee, A.P.

Comparison of elephant shark, human and teleost fish genomes reveals evolutionary changes in the regulatory regions of teleost fishes

poster

Lee, C.

The fine-scale and complex architecture of 1086 human copy number variant (CNV) regions as defined by custom high-density oligonucleotide microarrays

poster

Lefebvre, J.

InfRec—A heuristic tool to analyze recombination rate at the sequence level

poster

Lenhard, B.

Type 2 diabetes susceptibility variants fall within anciently conserved chromosomal domains of transcriptional regulator genes

poster

Levin, J.

Identifying somatic mutations in cancer and expression level changes with Illumina cDNA sequencing

poster

Li, H.

Inference of human population history from whole genome sequence of a single individual

talk

Li, H.

MAQ—Mapping and assembling short read sequences using quality scores

poster

Li, L.

Bayesian mixture models for case-control genome-wide association studies

poster

Li, L.

GADEM—A Genetic Algorithm guided formation of spaced Dyads coupled with an Em algorithm for Motif discovery

poster

Li, S.

Association studies involving over 90,000 samples demonstrate that common variants near to MC4R influence fat mass, weight and risk of obesity

poster

Liang, C.

Evidence-based gene builds in plant genomes

poster

Lieberman, E.

Transposons are a major force spreading insulators across the mammalian genome

poster

Limborska, S.A.

Analysis of PARK2 and LRRK2 defects in sporadic Parkinson's patients from Russia

poster

Lin, J.

Exploring legumen genome evolution by sequence analysis of homeologous regions of soybean and legume species

poster

Lister, R.

Highly integrated single base resolution maps of the epigenome in Arabidopsis

poster

Liu, B.

Antibiotic resistance genes database (ARDB)

poster

Liu, G.

Analysis of cattle copy number variation reveals insights into the evolution of ruminants

poster

Liu, M.

CpG island methylation on mammalian X chromosomes

poster

Logsdon, B.

A statistical framework for inferring pathway structure from gene expression data

poster

Lopez-Bigas, N.

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation

poster

Lowe, C.B.

Select extant species harbor ancient mobile elements exapted by humans

poster

Lu, D.V.

Cross-species cDNA-to-genome alignment—Program accuracy depends on evolutionary distance

poster

Lunter, G.

10% of the human genome is evolutionarily conserved

poster

MacArthur, D.G.

Recent positive selection on a common human null allele associated with athletic performance

poster

Maguire, J.

Improved and applied quality scores for new DNA sequencing technologies

poster

Maia, A.

Studying susceptibility to breast cancer using allelic variation of gene expression

poster

Maier, E.J.

Optimizing phylogenetic substitution models for N-SCAN gene prediction

poster

Malcolm, T.L.

Identifying functional CNEs using enhancer trap-containing BACs as transgenes in zebrafish

poster

Margulies, E.H.

De novo genome sequencing and assembly using short sequence reads and reduced representation libraries

talk

Marques, A.

Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes

poster

Marques, A.

Functional diversification of duplicate genes through subcellular adaptation of encoded proteins

poster

Marques-Bonet, T.

Characterization of great ape and human specific duplications reveals a burst of activity in the common ancestor

talk

Marth, G.T.

Informatics tools for human genome resequencing

poster

Matsumoto, T.

Construction and end-sequence of full-length cDNA clones from a malting barley—Towards understanding of barley transcriptome

poster

McCarroll, S.A.

Genome-wide analysis of SNP and copy number variation in 1,170 individuals from multiple populations

talk

McEwen, G.K.

The effect of sequence quality on comparative genomics analyses

poster

McGuire, A.

Cross-kingdom patterns of alternative splicing and splice recognition

poster

McKay, S.J.

The Genetic Genome Browser—New features

poster

McLaughlin, S.F.

Large-scale SNP detection in a human genome achieved by sequencing of fragment and paired-end libraries

poster

McVean, G.A.

Identification of a DNA sequence motif associated with hotspots for genome instability

talk

McVicker, G.P.

Background selection explains patterns of neutral diversity in primate genomes

talk

Meader, S.J.

Applying the neutral indel model to real and simulated genomes for diverse metazoans

poster

Mersha, T.

A candidate gene discovery procedure for obesity-related linkage studies

poster

Meyer, K.B.

Allele-specific upregulation of FGFR2 increases susceptibility to breast cancer

poster

Meyer, M.

High-throughput targeted sequencing of ancient and forensic DNA

poster

Meynert, A.M.

An explanatory model for vertebrate enhancers

poster

Mezey, J.G.

Genome-wide association analysis of genotype by cigarette smoking interactions affecting small airway epithelium gene expression

poster

Milosavljevic, A.

Comprehensive basepair-level map of chromosomal aberrations in the MCF-7 breast cancer cell line yields insights into the clonal evolution of a cancer genome

poster

Montgomery, S.

Implications of trans-acting regulatory interactions in lymphoblast cells on the functional and structural organization of the human genome

poster

Morgante, M.

Genome proteome and transcriptome of the grapevine (V. vinifera) improved using new sequencing technologies

poster

Morgante, M.

Resequencing of a second grapevine genome reveals frequent SNP and structural variation

poster

Mori, H.

Extreme sequence conservation of 16S rRNA gene copies

poster

Mueller, J.L.

The mouse X chromosome is enriched for multi-copy testis genes exhibiting post-meiotic expression

poster

Muralidhara, C.

Singular value decomposition analysis of 16S rRNA sequence alignments reveals phylogenetic subgroups and corresponding characteristic sites

poster

Muzny, D.M.

Multi-platform mammalian assemblies using next generation technology

poster

Nadeau, P.

Testing haplotype allelic classes by coalescence simulations

poster

Nagarajan, N.

Framework for cost-effective, hybrid assembly of genomes using Sanger and 454 sequencing

poster

Nakatani, Y.

Clear chromosome-wide synteny conservation between chicken (G. gallus) microchromosomes and silkworm (B. mori) chromosomes

poster

Navarro, A.

Copy number variation in the great apes

poster

Navarro, A.

The role of genetic heterogeneity in inter-population replication trials of disease risk variants

poster

Navratilova, P.

Cis-regulatory activity of conserved non-coding elements residing in megabase and multigene regions around transcription factor genes

poster

Nayak, R.R.

Identifying gene expression regulatory networks in lymphoblastoid cells

poster

Neafsey, D.E.

Widespread selection and frequent recombination in the genome of P. falciparium malaria

talk

Negrete, O.D.

DNA nanotechnology via DNA microarrays

poster

Nekrutenko, A.

Short-read analysis with Galaxy—Windshield genomics and beyond

poster

Nica, A.

Using gene expression to investigate the genetic basis of complex disorders

talk

Noonan, J.P.

Human-specific gain of function in a developmental enhancer

talk

Nowick, K.

Rapid divergence of KRAB-ZNF expression between human and chimpanzee B-lymphoblasts

poster

Nusbaum, C.

Biological applications and process development for massively parallel sequencing technologies

talk

Oleksyk, T.K.

Evolution and worldwide distribution of APOL1, APOL2, APOL3, APOL4 and MYH9 In human populations

poster

O'Malley, R.C.

Sequencing the genome, transcriptome, methylome and smRNAome of the Arabidopsis ecotype, Cape Verde Island

talk

Omberg, L.

Integrative analysis of genome-scale expression data from yeast cell cycle time courses under different oxidative stress conditions

poster

Ong, I.

Approaches to combining and analyzing time-series expression data

poster

Ophoff, R.A.

Genomic survey of DNA methylation in twin pairs reveals large degree of genetic control and independent strong effects of age and gender

poster

Paabo, S.

The Neanderthal genome project

talk

Pang, A.

Identification of structural variation using clone-end sequence mapping

poster

Parker, H.G.

No dog is an island—Mapping fixed traits in purebred domestic dogs

poster

Parla, J.

High-throughput genetic resequencing of target genomic regions

poster

Parnell, L.D.

Identifying genetic variants underlying differential response to the diet

poster

Pastinen, T.

Common cis variants alter expression of complex disease genes

poster

Peckham, H.

A high-resolution structural variation map of a human genome by next-generation, high-throughput paired-end sequencing

poster

Pe'er, I.

A genomic survey of preferential allelic amplification in lung and breast cancer

poster

Peltonen, L.

The genome-wide patterns of variation exposes significant substructure in a founder population

poster

Pertea, M.

OperonDB—A comprehensive database of predicted operons in microbial genomes

poster

Petri, V.

Pathway data at the Rat Genome Database

poster

Phanstiel, D.

Quantitation of protein expression in human IPS cells using iTRAQ, ETD, and beam-type CAD on an Orbitrap mass spectrometer

poster

Plagnol, V.