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3rd International Conference and Workshop

Genomic Impact of Eukaryotic Transposable Elements

Organizer: Jerzy Jurka, Genetic Information Research Institute

Friday, February 24, 2012

15:00-18:00 REGISTRATION (Phoebe A. Hearst Social Hall) (hotel) and (Fred Farr Forum) (conference).
18:00-19:00 Dinner (Crocker Dining Hall)
19:30-23:00 Warm-up party/poster previews (Fred Farr Forum) and preparation of audio-visual (Chapel)

The following equipment will be provided in all sessions: an LCD projector, laser pointer and a microphone. Speakers should load their talks at Chapel in the evening preceding the presentations. There will be a limited time for last-minute testing (30 minutes before the morning session and during breaks). Due to time constraints, all 10-minute talks should be limited to communication of your specific results only. Please, leave 2-3 minutes from your allowed time for discussion. The projected discussion time for 15-minute presentations is 3-4 minutes, and for 25-minute presentations it is 4-5 minutes. The opening speaker for each session is the chairman of that session.

Saturday, February 25, 2012

7:30-8:30 Breakfast (Crocker Dining Hall)
8:00-8:50 REGISTRATION (Chapel)
9:00-9:10 Jerzy Jurka Opening remarks
9:10-9:35 David Haussler - Aspects of the evolutionary impact of retrotransposons on vertebrate genomes
9:35-10:00 Norihiro Okada - Mammalian exaptation burst
10:00-10:15 Peter Arndt - A neutral model to explain fat tails in match length distributions
10:15-10:45 Coffee-break (Chapel)/Group photo
10:45-11:10 Nancy Craig - A transposase goes to work
11:10-11:35 Juergen Brosius - BC1 RNA, the significance of a tRNA-derived retrogene for the rodent nervous system
11:35-12:00 Gill Bejerano - Cis regulatory co-option in the human genome
12:00-13:00 Lunch (Crocker Dining Hall)
13:30-13:55 Mark Batzer - The primate mobilome
13:55-14:05 Lucia Carbone - Centromeric activation of a novel lineage-specific composite transposable element in the eastern hoolock gibbon (Hoolock leuconedys)
14:05-14:30 Juergen Schmitz - Traces of the past: what retrotransposons tell us about ancient times
14:30-14:55 Andrew Shedlock - Testing alternative models of TE molecular evolution with amniote phylogenomics
14:55-15:05 Cesar Martins - Transposable elements in fish genomes: a chromosome perspective
15:05-15:20 Ben Koop - Repeat families in the rediploidization and speciation of Salmonids
15:20-15:50 Coffee-break (Chapel)
15:50-16:15 King Jordan - Human MIRs as chromatin organizing elements
16:15-16:40 Matthew Lorincz - Histone H3K9 writers and readers in ERV silencing: a family affair
16:40-16:50 Lucas Gray - The conserved piggyBac transposase fusion protein CSB-PGBD3 collaborates with AP-1 proteins to regulate nearby genes in primates
16:50-17:00 Christoffer Nellaker - The impact of transposable element variants on mouse genomes and genes
17:00-17:10 Nickolai Tchurikov - Genome-wide profiling of fragmentation sites in Drosophila melanogaster chromosomes revealed a strong correlation between fragmentation sites, particular sets of mobile elements and regions of intercalary heterochromatin
17:10-17:20 Yanzhu Ji - Comparative analyses of transposable elements expressed in the transcriptomes of lake sturgeon (Acipenser fulvescens), tiger salamanders (Ambystoma tigrinum), and banner-tailed kangaroo rats (Dipodomys spectabilis)
17:20-17:30 Michael Wilson - Latent regulatory potential of human-specific repetitive elements
17:30-17:40 Heather Murton - Chromatin and the control of LTR retrotransposon silencing and mobilisation in fission yeast
18:00-19:00 Dinner (Woodlands)
19:20-19:45 John Moran - Studies of a human retrotransposon
19:45-19:55 Fabio Macciardi - The genetic signatures of transposable elements (TE) in schizophrenia
19:55-20:05 Natasa Lindic - Trying to pin down the mechanism of APOBEC3s inhibition of retrotransposition
20:05-20:15 Koichi Ishiguro - The genomewide profiling of L1 antisense promoter activity in the human cells
20:15-20:25 Kyle Upton - Technical development of Retrotransposon Capture sequencing (RC-seq)
20:25-23:00 Happy Hours / poster session (Fred Farr Forum)

Sunday, February 26, 2012

7:30-8:30 Breakfast (Crocker Dining Hall)
9:00-9:25 Haig Kazazian - Transcriptome-wide binding of human L1 ORF1 protein reveals its role in Alu retrotransposition and processed pseudogene formation
9:25-9:50 Gerald Schumann - LINE-1 mediated trans-mobilization of human-specific SVA retrotransposons is SVA structure-dependent
9:50-10:00 Annette Damert - Competition for SVAs in gibbons: LAVA and other VNTR containing non-LTR retrotransposons
10:00-10:25 Anthony Furano - Polymer formation and nucleic acid binding properties of the human L1 non-LTR retrotransposon ORF1p protein
10:25-10:45 Coffee-break (Chapel)
10:45-11:10 Holly Wichman - An overview of LINE-1 activity in mammals
11:10-11:35 Cedric Feschotte - Genomes without borders - the misfit origins of genetic novelty
11:35-11:45 Petra Schwalie - Waves of repeat driven CTCF binding expansions have shaped mammalian genomes
11:45-11:55 Ray Malfavon-Borja - Ancient and recurrent evolution of the antiviral gene fusion TRIMCyp in primates
12:00-13:00 Lunch (Crocker Dining Hall)
13:30-13:55 Prescott Deininger - Alu/Alu non-allelic homologous recombination
13:55-14:20 Scott Devine - Studying Alu and L1 mutagenesis in human genomes with DNA sequencing technologies
14:20-14:30 Adam Ewing - Large-scale retroelement detection from the Cancer Genome Atlas
14:30-14:40 Robyn Leary - A novel p53 regulated murine endogenous retrovirus
14:40-14:50 Krassimira Botcheva - Distinct genome-wide p53 binding profile in normal and cancer-derived human cells
14:50-15:00 Elena Helman - RetroSeq: a tool to discover somatic insertion of retrotransposons
15:00-15:25 David Symer - Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
15:25-15:55 Coffee-break (Chapel)
15:55-16:20 Dixie Mager - Complex interactions between endogenous retroviruses and host genes
16:20-16:30 Andrea Schorn - Transposon small RNA expression in the embryonic and trophectoderm lineage
16:30-16:40 Justin Blumenstiel - Dynamics of TE control by the piRNA machinery: The Key Role of Dose
16:40-16:50 Erin Kelleher - Drosophila interspecific hybrids phenocopy piRNA pathway mutants in aberrant piRNA production and TE derepression
16:50-17:00 Fernando Rodriguez - An increase in relative abundance of pi-like RNAs in response to ionizing radiation in the bdelloid rotifer Adineta vaga
17:00-17:10 Mireia Jorda - Epigenetics speaks up for the silent DNA
17:10-17:35 Zsuzsanna Izsvak - Modeling stress signaling and response resulting in transposon activation in human cells
17:35-17:45 Hidetaka Ito - Transgenerational effects and genomic impacts in environmental stress
19:00-22:30 Dinner at Monterey Bay Aquarium: buses depart at 18:45 from (Phoebe A. Hearst Social Hall)

Monday, February 27, 2012

7:30-8:30 Breakfast (Crocker Dining Hall)
9:00-9:25 Damon Lisch - We have met the enemy and he is us: co-regulation of transposons and genes during plant development
9:25-9:40 Marie-Angele Grandbastien - Retroviral-type LTRs as intermediate of the stress response in tobacco
9:40-9:50 Darrell Lizamore - The effect of environmental stress events on the mobility of four LTR retrotransposon families in grapevine (Vitis vinifera) somatic embryo cultures
9:50-10:05 Marie-Anne Van Sluys - Plant LTR-RT study reveals fine-scale individual molecular patterns
10:05-10:30 Susan Wessler - Genome-wide impact of a MITE burst in rice after just 20 generations
10:30-10:50 Coffee-break (Chapel)
10:50-11:15 Irina Arkhipova - Rotifer genomes as a source for discovery of novel types of TEs and TE-related genes
11:15-11:25 Eugene Gladyshev - Biochemical properties of NcRVT protein encoded by a reverse transcriptase-like gene from Neurospora crassa
11:25-11:35 Ken Kraaijeveld - Transposon proliferation in an asexual parasitoid
11:35-11:45 Jens Bast - Comparing the transposable element load in sexual and asexual oribatid mites using whole genome information
11:45-11:55 Sarah Schaack - Transposable Element Copy Number in Sexual and Asexual Daphnia
12:00-13:00 Lunch (Crocker Dining Hall)
13:20-13:45 Dmitri Petrov - Population genetics of transposable elements in Drosophila
13:45-14:10 Cristina Vieira - Drosophila endogenous retrovirus regulation in natural populations
14:10-14:25 Josefa Gonzalez - Adaptive TE insertions in Drosophila
14:25-14:35 Claudia Carareto - Ancestral polymorphism and re-introduction of transposable elements in Drosophila
14:35-14:45 Grace Yuh Chwen Lee - Long-term and short-term evolutionary impacts of transposable elements on Drosophila
14:45-14:55 Anna-Sophie Fiston-Lavier - Screening for transposable element-induced adaptations in Drosophila melanogaster using next-gen sequencing data
14:55-15:05 Rita Daniela Fernandez-Medina - RNAseq reveals abundant transposable element expression in the mosquito Anopheles funestus
15:05-15:35 Coffee-break (Chapel)
15:35-16:00 Eugene Koonin - The multilayer eukaryotic mobilomes: viruses as mobile elements and mobile elements of giant viruses
16:00-16:25 Marcella McClure - The mutualism continuum of retroids
16:25-16:50 Vladimir Kapitonov - "Simple" DNA transposons: scratching the surface
16:50-17:15 Arian Smit - Digging deeper in time; approaches to study ancient transposable elements
17:15-17:25 Sarah Oliveira - Transposable elements: maintenance of centromeric regions and chromosome B origin
17:25-17:35 Erez Levanon - Large scale DNA editing of retrotransposons accelerates mammalian genome evolution
17:35-17:45 Julia Arand - Highthrouput DNA methylation analysis of repetitive elements by hairpin bisulfite sequencing
18:00-19:00 Dinner (Woodlands)
19:30-19:55 Wojciech Makalowski - Repetitive Sequences: Beyond RepBase and RepeatMasker
19:55-20:05 Travis Wheeler - Improved Transposable Element Detection With Profile HMMs In nhmmer
20:05-20:15 David Pollock - Transposable Element Diversification and Evolution
20:15-20:25 Casimir Bamberger - Discovery and Analysis of Transposable Elements with Shotgun Proteomics
20:25-23:00 Happy Hours / poster session (Fred Farr Forum)

Tuesday, February 28, 2012

7:30-8:30 Breakfast (Crocker Dining Hall)
12:00-13:00 Lunch (Crocker Dining Hall)

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