| Accepted Posters |
| Category 'J'- Genomics' |
| Poster J01 |
| Alignment of Phylogenetically Unambiguous Indels and Detection of Lateral Gene Transfer in Shewanella |
| John McCrow- University of Southern California |
| Michael Waterman (University of Southern California, Computational Molecular Biology); Kenneth Nealson (University of Southern California, Geobiology); |
| Short Abstract: Indels are valuable for whole genome phylogenetic analysis, yet are often excluded from multiple alignments prior to phylogenetic inference as they are difficult to align unambiguously. We have developed dynamic programming methods to identify phylogenetically unambiguous indels in amino acid sequence, and have analyzed the genomes of sequenced Shewanella. |
| Long Abstract: Click Here |
| Poster J02 |
| Predicting DNA Methylation Status from Sequence Perspective |
| Yudong Cai- Picb, Sibs |
| Lingyi LU (SIBS,CAS, The Key Laboratory of Molecular Systems Biology); Kao Lin (SIBS,CAS, PICB); Xikun Wu (Institute for Animal Health, Institute for Animal Health); Ziliang Qian (SIBS,CAS, The Key Laboratory of Molecular Systems Biology); Zi-Qun Xie (Picb, Sibs, Department Of Combinatorics And Geometry); Yixue Li (SIBS,CAS, The Key Laboratory of Molecular Systems Biology); |
| Short Abstract: We developed a DNA composition based method to analysis the flanking sequence of CpG dinucleotides and thus to predict their methylation status. 5-mer DNA fragments with the most impacts on methylation status were identified by a feature selection method resulted in 77.45% accuracy. |
| Long Abstract: Click Here |
| Poster J03 |
| Frequency Distribution of Complementary Nucleotides and Intra-strand Parity in Chromosomes: a Novel Approach to the Parity Rule II |
| Suvendra Ray- Tezpur University |
| Bhes Raj Powdel (Tezpur University, Mathematical Sciences); Aditya Kumar (Tezpur University, Deaprtment of Molecular Biology and Biotechnology); Pankaj Kumar Jha (Tezpur University, Molecular Biology and Biotechnology); Siddhartha Satapathy (Tezpur University, Computer Science and Engineering); Alak Kumar Buragohain (Tezpur University, Molecular Biology and Biotechnology); Munindra Borah (Tezpur University, Mathematical Sciences); |
| Short Abstract: The parity rule II describes the intra-strand parity in terms of the compositional abundance values of the complementary nucleotides in chromosomes. This work describes the intra-strand parity in terms of the frequency distribution of the compositional abundance values of complementary nucleotides as well as complementary oligonucleotides in chromosomes. |
| Long Abstract: Click Here |
| Poster J04 |
| Noise-reduction filtering for accurate detection of replication-related selection in bacterial genomes |
| Kazuharu Arakawa- Institute for Advanced Biosciences, Keio University |
| Rintaro Saito (Institute for Advanced Biosciences, Keio University, Department of Environment and Information Studies); Masaru Tomita (Institute for Advanced Biosciences, Keio University, Department of Environment and Information Studies); |
| Short Abstract: We report a novel prediction method for replication origin and terminus in bacterial genomes using low-pass filtering through Fast Fourier transform coupled with cumulative skew graphs, and another application of this approach in quantifying the degree of compositional asymmetry in bacterial genomes known as GC skew. |
| Long Abstract: Click Here |
| Poster J05 |
| Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Embryonic Stem Cells |
| Florian Markowetz- Princeton University |
| Eduardo Airoldi (Princeton University, Lewis-Sigler Insitute); Rong Lu (Stanford Univesity, Mol Bio); Ihor Lemischka (Mount Sinai School of Medicine, Stem Cell Institute); Olga G Troyanskaya (Princeton University, Lewis-Sigler Insitute); |
| Short Abstract: We quantify the impact of histone 3 acetylation (H3K9/14) on gene expression in Mouse ES cells over five days of differentiation using a wide array of statistical methods. In a case study we focus on genes central in the regulatory network of Mouse ES cells. |
| Long Abstract: Click Here |
| Poster J06 |
| Data VIsualization Using the Physical Genome |
| Thomas Asbury- Medical University of South Carolina |
| No additional authors |
| Short Abstract: The spatial organization of the genome strongly determines its functionality, yet our current understanding of its architecture is limited. We present a simple multi-resolution model of the physical genome to address significant visualization issues that are likely to arise. |
| Long Abstract: Click Here |
| Poster J07 |
| Apply Bayesian model selection to better query large scale microarray gene expression datasets |
| Ming Hu- University of Michigan, Department of Biostatistics |
| No additional authors |
| Short Abstract: We develop a model-based gene expression query algorithm to query large and heterogeneous microarray gene expression databases. It can identify genes that share correlated gene expression profiles with query gene under a subset of samples. In addition, it can recognize linearly transformed expression patterns and is robust against sporadic outliers. |
| Long Abstract: Click Here |
| Poster J08 |
| Evaluation of Transcriptional Data Reveals Chromosome 8q Amplification and MYC Pathway Activation in High Grade Papillary Renal Cell Carcinoma |
| Kyle Furge- Van Andel Research Institute |
| Jin-Dong Cheng (Van Andel Research Institute, Cancer Genetics); Karl Dykema (Van Andel Research Institute, Quantitative Sciences); Julie Koeman (Van Andel Research Institute, Cytogenetics); Pamela Swiatek (Van Andel Research Institute, Cytogenetics); Ximing Yang (Weill Medical College, Cornell University, Pathology and Laboratory Medicine); Bin Teh (Van Andel Research Institute, Cancer Genetics); Jeff Klomp (Van Andel Research Institute, Quantitative Sciences); |
| Short Abstract: We highlight the utility of using gene expression profiling data to identify both cytogenetic and signal transduction abnormalities in cancer. Transcriptional data was used to generate a molecular genetic model in which amplification of chromosome 8q leads to activation of the c-Myc proto-oncogene in aggressive kidney tumors. |
| Long Abstract: Click Here |
| Poster J09 |
| Metagenomics: A New Frontier for Genomics |
| Geoffrey Siwo- Egerton University |
| Robert Sanaya (Kenya Medical Research Insitute, Centre for Microbiological Research); |
| Short Abstract: Metagenomics- the genomics of uncultured bacterial species- has the potential to enhance our understanding of microbial ecology and broaden our knowledge of life in diverse environments. In this review, we highlight some of the progress made and potential of this new technology. |
| Long Abstract: Click Here |
| Poster J10 |
| OncoGenomics |
| Amit Pande- omics research foundation |
| No additional authors |
| Short Abstract: There are attempts to identify new cancer susceptibility genes by research groups. The novelty of our approach is that by calculating the codon adaptation indices of genes coupled with fuzzy finder algorithm we have been able to identify GAPDH,C19ORF33 and CEBPA in specific tissues,in invasive and non-invasive cancer types. |
| Long Abstract: Click Here |
| Poster J11 |
| A Novel Experimental Design to Tether Whole-Genome Scaffolds to a Genetic Map Using Exon-Enriched Microarrays |
| Thomas Clarke- University of North Carolina |
| Todd Vision (University of North Carolina, Biology); |
| Short Abstract: We model a novel experimental design for tethering WGS scaffolds to a genetic map through shallow sequencing of a mapping population. Using the Mimulus guttatus draft genome assembly, we find that 88.77% of the genome could be mapped by 0.3X sequencing of 60 recombinant inbred lines using exon-enriched capture technology. |
| Long Abstract: Click Here |
| Poster J12 |
| Optimal Spliced Alignments of Short Sequence Reads |
| Ratsch Gunnar- Friedrich Miescher Laboratory of the Max Planck Society |
| Fabio De Bona (Friedrich Miescher Laboratory of the Max Planck Society, Machine Learning in Biology); Korbinian Schneeberger (Max Planck Institute for Developmental Biology, Molecular Biology); Stephan Ossowski (Max Planck Institute for Developmental Biology, Molecular Biology); Gunnar Ratsch (Friedrich Miescher Laboratory of the Max Planck Society, Machine Learning in Biology); |
| Short Abstract: Next generation sequencing technologies produce massive amounts of sequence reads that are short and error prone. We have developed a machine learning based method, called QPALMA, which learns how to combine alignment information with quality scores, splice site predictions and intron length information. We show that the optimal combination leads to considerable improvements in alignment accuracy. |
| Long Abstract: Click Here |
| Poster J13 |
| Characterization of paralogous protein families in rice |
| Haining Lin- Michigan State University |
| Shu Ouyang (J.Craig Venter Institute, Plant Genomics); Amy Egan (University of Maryland, Institute for Genome Sciences & Department of Microbiology & Immunology); Kan Nobuta (University of Delaware, Department of Plant and Soil Sciences & Delaware Biotechnology Institute); Brian Haas (The Broad Institute, Genome Biology Program); Wei Zhu (J.Craig Venter Institute, Plant Genomics); Xun Gu (Iowa State University, Department of Genetics, Development, and Cell Biology); Joana Silva (University of Maryland, Institute for Genome Sciences & Department of Microbiology & Immunology); Blake Meyers (University of Delaware, Department of Plant and Soil Sciences & Delaware Biotechnology Institute ); Robin Buell (Michigan State University, Department of Plant Biology); |
| Short Abstract: We characterized paralogous protein families in rice and compared these with paralogous families in Arabidopsis thaliana. Our data suggest that while co-regulation and conserved function are present in some paralogous protein family members, evolutionary pressures have resulted in functional divergence with differential expression patterns. |
| Long Abstract: Click Here |
| Poster J14 |
| Machine learning approaches to genome-wide prediction of bacterial virulence factors |
| Bing Ma- University of Wisconsin at Madison |
| Bing Ma (University of Wisconsin at Madison, Genome Center of Wisconsin); Jeremy Glasner (University of Wisconsin at Madison, Genome Center of Wisconsin); Nicole Perna (University of Wisconsin at Madison, Genome Center of Wisconsin); |
| Short Abstract: Genome sequences are available for many plant and animal pathogens, but a comprehensive list of virulence-associated genes is not available for any one. We performed genome-wide virulence factor prediction using various supervised machine learning schemes and diverse datasets including phylogenetic profiles, predicted localization, and microarray experiments. |
| Long Abstract: Click Here |
| Poster J15 |
| Assessing the Performance of Short Read Alignment Tools |
| Thomas Keane- Wellcome Trust Sanger Institute |
| Jacqueline McQuillan (Wellcome Trust Sanger Institute, Pathogen Sequencing Unit); Samuel Assefa (Wellcome Trust Sanger Institute, Pathogen Sequencing Unit); |
| Short Abstract: We are now interested in using new sequencing technologies to discover the levels of variation that exist in a population. Consequently, new tools have been developed specifically for the alignment of short reads produced by new sequencing technologies. We have evaluated the performance of these tools under various different conditions. |
| Long Abstract: Click Here |
| Poster J16 |
| Accurate prediction of NAGNAG alternative splicing using Bayesian Networks |
| Rileen Sinha- Leibniz Institute for Age Research - Fritz Lipmann Institute (former IMB Jena), Jena |
| Karol Szafranski (Leibniz Institute for Age Research - Fritz Lipmann Institute (former IMB Jena), Jena, Genome Analysis); Michael Hiller (Albert-Ludwigs-University, Institute of Computer Science, Bioinformatics Group); Klaus Huse (Leibniz Institute for Age Research - Fritz Lipmann Institute (former IMB Jena), Jena, Genome Analysis); Matthias Platzer (Leibniz Institute for Age Research - Fritz Lipmann Institute (former IMB Jena), Jena, Genome Analysis); Rolf Backofen (Albert-Ludwigs-University, Institute of Computer Science, Bioinformatics Group); Swetlana Nikolajewa (Friedrich-Schiller-University, Faculty of Biology and Pharmacy, Department of Bioinformatics); |
| Short Abstract: We used Bayesian Networks (BNs), which are probabilistic graphical models, to accurately predict NAGNAG alternative splicing, involving alternative acceptors separated by 3 nucleotides. The BN achieved a balanced sensitivity and specificity of 92% in-silico, and RT-PCR experiments on 43 putative candidates yielded a validation rate of 79%. |
| Long Abstract: Click Here |
| Poster J17 |
| BioHPC, a parallel HPC software package for sequence and phylogenetic data analysis |
| Qi Sun- Cornell University |
| Jaroslaw Pillardy (Cornell University, CBSU); Robert Bukowski (Cornell University, CBSU); Daniel Ripoll (Cornell University, CBSU); |
| Short Abstract: BioHPC is a software package of some of the commonly used bioinformaticstools implemented on the parallel cluster running Windows CCS. A web based user interface allows users to submit jobs through a web browser. All job, user, data and application administration can also be performed through the web interface. |
| Long Abstract: Click Here |
| Poster J18 |
| Differential coexpression with applications to ageing |
| Jesse Gillis- University of British Columbia |
| No additional authors |
| Short Abstract: Differential coexpression consists of distinguished conditions only by changes in the relationship between genes’ expression levels. A condition might be characterized not by any gene having a particular expression level, but by genes working together differently. We perform a differential coexpression analysis with a focus on ageing. |
| Long Abstract: Click Here |
| Poster J19 |
| systematic non-coding RNA detection in Oxytricha trifallax |
| Seolkyoung Jung- Washington University In St. Louis |
| No additional authors |
| Short Abstract: The unusual genome of the ciliate Oxytricha trifallax permits a simple screen for noncoding RNA genes (ncRNAs). Oxytricha macronuclear chromosomes average just 2.4 kb and generally contain only a single gene. We can enrich for functional ncRNA genes by subtracting chromosomes that encode a protein. |
| Long Abstract: Click Here |
| Poster J20 |
| In Silico design of diagnostic primers for the Identification of Phytopathogen of the genus Xanthomonas. |
| Nelson Gichora- International Institute of Tropical Agriculture |
| No additional authors |
| Short Abstract: We apply a bioinformatics approach to design Phytopathogen diagnostic primers based on the intergenic region of 8 complete Xanthomonas genomes, and test our hypothesis on various Xanthomonas species. Preliminary results show that primers could be designed from this region for the identification of the bacteria at the various taxonomic levels. |
| Long Abstract: Click Here |
| Poster J21 |
| A Bayesian approach to estimate allele-specific copy number |
| Matthew Kowgier- University of Toronto |
| Rafal Kustra (University of Toronto, Department of Public Health Sciences); Michael Escobar (University of Toronto, Department of Public Health Sciences); |
| Short Abstract: SNP arrays can be used for inferring chromosomal intervals distinguished by copy number changes. We present a hierarchical model for estimating allele-specific copy number. By utilizing both between- and within-SNP information across multiple samples we can improve copy number estimates. Our method also provides corresponding uncertainty measures. |
| Long Abstract: Click Here |
| Poster J22 |
| Automation of Family Specific PCR Primer Design |
| Wayne Clarke- University of Saskatchewan |
| No additional authors |
| Short Abstract: Designing family specific PCR primers for conserved intron-spanning regions is a process that presently requires extensive human participation. An automated pipeline was developed that infers intronic regions from a model organism and designs primers in the target organism. We tested the automated pipeline against a manual approach and found a significant reduction in time. |
| Long Abstract: Click Here |
| Poster J23 |
| LTR retrotransposons in the genome of Daphnia pulex |
| Haixu Tang- Indiana University, Bloomington |
| Mina Rho (Indiana University, Computer Science); Sarah Schaack (Indiana University, Biology); xiang Gao (Indiana University, Biology); Sun Kim (Indiana University, Schcool of Informatics); Michael Lynch (Indiana University, Biology); |
| Short Abstract: We identified novel LTR retrotransposons in the Daphnia pulex genome by using a de novo computational approach. For comprehensive analysis of identified elements in the three groups of gypsy, copia, and bel/pao, we conducted phylogenetic analysis on these retroelements with those from four other invertebrate genomes and one plant genome. |
| Long Abstract: Click Here |
| Poster J24 |
| Spontaneous Symmetry Breaking in Genome Evolution |
| Yaroslav Ryabov- NIH |
| Michael Gribskov (Purdue University, Department of Biological Sciences;); |
| Short Abstract: Distribution of exon sizes shows a lognormal pattern typical of a random Kolmogoroff fractioning process. This implies that the process of intron incretion is independent of exon size. All genomes examined have two distinctive classes of exons, which can be derived from a hypothetical ancestral genome by (spontaneous) symmetry breaking. |
| Long Abstract: Click Here |
| Poster J25 |
| Cancer Classification using the 1-D Wavelet Transform and Gaussian Mixture Modeling |
| Adarsh Jose- University of Akron |
| Dale Mugler (University of Akron, Department of Biomedical Engineering); Zhong Hui Duan (University of Akron, Department of Computer Science); |
| Short Abstract: We intend to explore the potential of 1 D Discrete Wavelet transform as a feature extraction tool for classification of gene expression data and later for clustering to develop a class discovery tool. The classification is based on the Gaussian Mixture Model based methods with different combinations evaluated using BIC. |
| Long Abstract: Click Here |
| Poster J26 |
| Space Maps: Knowledge-Supported Visualization of Large High-Throughput Gene Expression Data Sets |
| Nils Gehlenborg- European Bioinformatics Institute |
| Alvis Brazma (European Bioinformatics Institute, Microarray Informatics Group); |
| Short Abstract: We are presenting the Space Map, an interactive visualization method for gene expression profiles from high-throughput gene expression data sets with hundreds to thousands of samples. Biological knowledge is integrated in the form of hierarchies derived from ontologies. The method is designed to make hypothesis generation through visualization more efficient. |
| Long Abstract: Click Here |
| Poster J27 |
| Ab Initio Whole Genome Shotgun Assembly |
| Paul Medvedev- University of Toronto |
| Michael Brudno (University of Toronto, Computer Science); |
| Short Abstract: We present a method for ab initio whole genome shotgun genome assembly with NGS data. We formulate this problem as a minimum cost bidirected flow problem with convex costs, and show that it can be effectively solved with generic flow solvers for the case of bacterial genomes. |
| Long Abstract: Click Here |
| Poster J28 |
| Genome Strategy for recognition sites of restriction enzymes |
| Ken Yamakura- NARA INSTITUTE of SCIENCE and TECHNOLOGY |
| No additional authors |
| Short Abstract: We examined 123 types of cleavage patterns of restriction sites reported by REBASE to estimate whether the recognition sites of their own restriction enzymes are repressed or not. The cleavage sites for their own restriction enzymes are under-abundance in most of the genomespairs of genomes and their own restriction enzymes). |
| Long Abstract: Click Here |
| Poster J29 |
| A clustering method for expression patterns of transcription starting sites |
| Mitsuru Jikeya- Graduate School of Information Science and Technology, Osaka University |
| Shigeto Seno (Graduate School of Information Science and Technology, Osaka University, Bioinformatic Engineering); Yoichi Takenaka (Graduate School of Information Science and Technology, Osaka University, Bioinformatic Engineering); Hideo Matsuda (Graduate School of Information Science and Technology, Osaka University, Bioinformatic Engineering); |
| Short Abstract: Recent works revealed that mammalian genes usually have more than two transcription starting sites (TSSs). The analysis of TSSs is an effective way to elucidate the transcriptional control mechanism. We propose a novel method to cluster TSSs according to their expression patterns in CAGE. |
| Long Abstract: Click Here |
| Poster J30 |
| A method for analysis of tissue-specific alternative transcripts using CAGE tags |
| Shigeto Seno- Osaka University |
| Yoichi Takenaka (Osaka University, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology); Hideo Matsuda (Osaka University, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology); |
| Short Abstract: By the advancement of the genome research, analyses of sequence and microarray data have suggested that alternative splicing plays a major role in gene regulation in higher eukaryotes. Using CAGE tags in addition to ESTs and cDNAs, we have developed a method for exploring tissue-specific alternative transcripts of mouse. |
| Long Abstract: Click Here |
| Poster J31 |
| Automatic Fusion of 3D staining patterns from mouse embryo tomograms |
| Ruben Schilling- Max-Planck Institute for Molecular Genetics |
| Ralf Spörle (Max-Planck Institute for Molecular Genetics, Developmental Genetics); Janis Fehr (University of Freiburg, Chair for pattern recognition and image processing); Bernhard Herrmann (Max-Planck Institute of Molecular Genetics, Developmental Genetics); Martin Vingron (Max-Planck Institute of Molecular Genetics, Computational Molecular Biology); Hans Burkhardt (University of Freiburg, Chair of pattern recognition and image processing); Alexander Schliep (Max-Planck Institute of Molecular Genetics, Computational Molecular Biology); |
| Short Abstract: The spatial distribution of molecular staining patterns, e.g. from gene expression or proteins, is important to understand developmental processes. We show a computational method for the fusion of 3D staining patterns from whole, intact mouse embryo images. The method is non-parametric and does neither require user input nor segmentation. |
| Long Abstract: Click Here |
| Poster J32 |
| Integrative Model of NF-kappa B Action |
| Yu-Hsuan Lin- University of Michigan |
| David States (University of Michigan, Bioinformatics); Jing Gao (University of Michigan, Bioinformatics); Yili Chen (University of Delaware, Delaware Biotechnology Institute); |
| Short Abstract: The NF-kappa B (NF-κB) family of transcription factors plays an essential role for immunity and inflammation. We applied a Bayesian network method using diverse data sources to predict the NF-κB targets. Our analysis suggests that chromatin accessibility and co-factor interaction play important roles in determining the biological active NF-κB binding. |
| Long Abstract: Click Here |
| Poster J33 |
| Galaxy workflows for reproducible analyses of next-generation sequencing data |
| Anton Nekrutenko- Penn State University |
| Wen-Yu Chung (Penn State University, BX); James Taylor (Penn State University, BX); Nate Coraor (Penn State University, BX); Greg Von Kuster (Penn State University, BX); |
| Short Abstract: The next generation of sequencing technologies are still evolving, and there are few tools available for the analysis of short read data. We prsent an integrated system allowing biomedical researchers to upload data, assess data quality, and perform a range of specific analyses including metagenomics and polymorphism detection. |
| Long Abstract: Click Here |
| Poster J34 |
| Structural Polymorphism Discovery Using Optical Mapping |
| Brian Teague- University of Wisconsin - Madison |
| Casey Lamers (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Biology); Steve Goldstein (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Biology); Jeff Kidd (University of Washington, Department of Genome Sciences); Rod Runnheim (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Genomics); Dan Forrest (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Genomics); Gus Potamousis (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Genomics); Chris Churas (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Genomics); Shiguo Zhou (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Genomics); Evan Eichler (University of Washington, Department of Genome Sciences); David Schwartz (University of Wisconsin - Madison, The Laboratory for Molecular and Computational Genomics); |
| Short Abstract: Optical Mapping is a non-traditional platform for the assembly of genome-wide restriction maps by analyzing ensembles of single DNA molecules. We have used Optical Mapping for the discovery of structural genome variations in a small number of normal human genomes, finding thousands of novel structural polymorphisms. |
| Long Abstract: Click Here |
| Poster J35 |
| A mixture model-based analysis for identifying estrogen-induced pol II binding pattern changes in hormone-dependent and antiestrogen-resistant breast cancer cells |
| Weixing Feng- Indiana University School of Medicine |
| Yunlong Liu (Indiana University School of Medicine, Center for Computational Biology and Bioinformatics); Kenneth P. Nephew (Indiana University School of Medicine, Medical Sciences); Tim H.-M. Huang (Ohio State University, Division of Human Cancer Genetics, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center); Lang Li (Indiana University School of Medicine, Center for Computational Biology and Bioinformatics); |
| Short Abstract: We present a Poisson mixture model-based analysis for identifying differences in the distribution of Pol II in transcript regions, measured using ChIP-seq technology. Expectation-maximization (EM) algorithm and particle swarm optimization (PSO) were implemented for the statistical inference. |
| Long Abstract: Click Here |
| Poster J36 |
| Combining multiple microarray studies for improved pathway analysis |
| Kui Shen- University of Pittsburgh |
| George Tseng (University of Pittsburgh, Department of Biostatistics); |
| Short Abstract: Pathway analysis is commonly performed on detected differentially expressed genes in a microarray study. We propose a meta-analysis for combining multiple homogeneous studies in pathway analysis. Simulation and real data analysis show that the proposed meta-analysis increases statistical power and can uncover pathway information that single study can not provide. |
| Long Abstract: Click Here |
| Poster J37 |
| An integrated transcriptome analysis approach to characterise adult neural stem cells and study complex disease. |
| Alistair Chalk- Griffith University |
| Nick Matigian (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Alejandra Vitale (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Stephen Wood (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Jiyuan An (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Greg Sutherland (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Ratneswary Sutharsan (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Rowena Cecil (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Bernadette Ballette (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Matthew Anderson (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Amanda Miotto (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Othmar Korn (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); George Mellick (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Julie Cochrane (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Peter Silburn (University of Queensland, School of Medicine); Jessica Severin (RIKEN Yokohama Institute, Omics Science Center); Mark Robinson (Walter and Eliza Hall Institute of Medical Research, Melbourne); Gordon Smyth (Walter and Eliza Hall Institute of Medical Research, Melbourne); Carsten Daub (RIKEN Yokohama Institute , Omics Science Center); Piero Carninci (RIKEN Yokohama Institute , Omics Science Center); Yoshihide Hayashizaki (RIKEN Yokohama Institute , Omics Science Center); Christine Wells (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); Alan Mackay-Sim (Eskitis Institute for Cell and Molecular Therapies, National Center for Adult Stem Cell Research); |
| Short Abstract: Adult neural stem cells are essential for the functional regeneration of the brain. hOSCs are an important neural stem cell niche easily accessible from patients. We use a combination of high-throughput expression measures to survey the transcriptome of hOSC cell lines and illustrate this approach for studying complex disease. |
| Long Abstract: Click Here |
| Poster J39 |
| Workflow for transcription factor ChIP-Seq data analysis |
| Samuli Eldfors- EMBL-EBI |
| Kairi Tammoja (EMBL, EBI); Mali Salmon-Divon (EMBL, EBI); Liisa Holm (University of Helsinki, Institute of Biotechnology); Paul Bertone (EMBL, EBI); |
| Short Abstract: High-throughput sequencing of chromatin-immunoprecipitated DNA (ChIP-seq) using next-generation sequencing technologies is emerging as the method of choice for genome-wide identification of transcription factor binding sites. We present a data analysis workflow for the genome-wide identification of transcription factor binding sites from ChIP-seq data. |
| Long Abstract: Click Here |
| Poster J40 |
| Characterisation of human lamina associated domains |
| Wouter Meuleman- Netherlands Cancer Institute / Delft University of Technology |
| Ludo Pagie (Netherlands Cancer Institute, ); Marcel Reinders (Delft University of Technology, ); Bas van Steensel (Netherlands Cancer Institute, ); Lodewyk Wessels (Netherlands Cancer Institute / Delft University of Technology, ); |
| Short Abstract: LADs are large segments of the human genome attached to the nuclear lamina, providing insight in how the genome is organised within the nucleus. They are thought to be involved in higher order gene regulation. We study the characteristics of these LADs, to further understand their mechanism and function. |
| Long Abstract: Click Here |
| Poster J41 |
| Discovery of co-occurring copy-number aberrations using a 2d Gaussian kernel convolution approach. |
| Christiaan Klijn- Netherlands Cancer Institute |
| Marcel Reinders (Delt University of Technology, Information and Communications Theory group); Lodewyk Wessels (Netherlands Cancer Institute, Molecular Biology); Jos Jonkers (Netherlands Cancer Institute, Molecular Biology); |
| Short Abstract: Tumorigenesis is a process involving multiple factors of aberration to transform a healthy cell. Here we search for co-occurring DNA copy number changes that might affect co-operating oncogenes and tumor suppressor genes by amplification or deletion. We employ a 2d kernel convolution framework to find significant co-occurring lesions. |
| Long Abstract: Click Here |
| Accepted Posters |
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