| Poster Q01 Investigations on the Systems Biology of Aspergillus niger Andreas Grote (1,2), Alex Dalpiaz (2), Guido Melzer (2), Ursula Rinas (3), Bernd Northemann (2), Petra Dersch (1), Dietmar C. Hempel (2), Dieter Jahn (1) (1) Institute for Microbiology, TU Braunschweig; (2) Institute of Biochemical Engineering, TU Braunschweig; (3) Structural Biology, German Research Center for Biotechnology |
| Abstract: The investigation of the systems biology of the spore forming fungus Aspergillus niger is one of the main objectives of the SFB578. For this purpose the transcriptome, proteome and metabolome are investigated. It is intended to optimize the product synthesis in the cell on different levels by applying bioinformatics algorithms. As a first tool the "Java Codon Adaptation Tool" was developed to offer the possibility to optimize heterologous protein production on a transcriptional level. Contact: andreas.grote@tu-bs.de Keywords: Systems Biology, Aspergillus niger, Codon Usage |
| Poster Q02 The Stability of the Ancestral Eukaryotic Protein Complexome in Extant Eukaryotes and its Implications Hugo Ceulemans, Lijs Beke, Mathieu Bollen Katholieke Universiteit Leuven, Department of Molecular Cell Biology |
| Abstract: We present a study of the ancestral eukaryotic protein complexome, which we defined as the set of protein complexes that extant eukaryotes inherited from their last common ancestor. The ancestral complexome constitutes nearly half of the ancestral proteome and at 90 % conservation of the included 1400 proteins in all studied organisms, proves highly stable. This observation endorses the potential of (sub)complexes as the units of choice for consistent systems modelling across various model eukaryotes. Contact: Hugo.Ceulemans@med.kuleuven.be Keywords: Complexome Orthology |
| Poster Q03 A Computational Framework for Analysis of Dynamic Social Structures Tanya Y. Berger-Wolf (1), Ilya R. Fischhoff (2,3), Daniel I. Rubenstein (2,3), Jared Saia (4), Siva R. Sundaresan (2,3) (1) Department of Computer Science, University of Illinois, Chicago; (2) Department of Ecology & Evolutionary Biology, Princeton University; (3) Mpala Research Centre, Nanyuki, Kenya; (4) Department of Computer Science, University of New Mexico, Albuquerque |
| Abstract: Analysis of many processes in animal populations (disease spread, dominance, reproduction) requires analysis of the network of individual interactions. Until now such analysis was essentially aggregate and static. We show that it may produce incorrect answers and propose a novel conceptual and computational framework for analysis of dynamic interaction networks. Contact: tanyabw@cs.uic.edu Keywords: computational population biology, social networks |
| Poster Q04 Towards Verified Biological Models Avital Sadot (1), Jasmin Fisher (2), Dan Barak (1), Yishai Admanit (1), Michael J. Stern (3), E. Jane Albert Hubbard (4), David Harel (1) (1) Weizmann Institute of Science; (2) Swiss Federal Institute of Technology (EPFL); (3) Yale University School of Medicine; (4) New York University |
| Abstract: Using tools that were originally developed for non-biological system design, we constructed a model of the early lineage of the somatic gonad of C. elegans and focused on an interaction between two cells within this lineage. We tested the model by showing that the simulations were consistent with the set of experimental scenarios. This small-scale modular example demonstrates the potential for using similar approaches for verification by exhaustive testing of models. It also shows the advantages of these approaches for modeling biology. Contact: avitals@weizmann.ac.il Keywords: Modeling, C. elegans, Verification |
| Poster Q05 Evaluating the Design of Biological Cells Using a Computer Workbench Tessa E. Pronk (1,2) , Simon Polstra (2), Andy D. Pimentel (2), Marco Roos (1), Timo M. Breit (1) (1) Integrative BioInformatics Unit, University of Amsterdam; (2) Computer Systems Architecture, University of Amsterdam |
| Abstract: For embedded computer systems as well as for biological cell systems, design is one feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the cell, embedded computer systems in general are well-mapped systems and their behavior can effectively be characterized. Our aim is to construct a framework that focuses on understanding the design options and their consequences within biological cells, based upon ideas from the field of embedded computer systems. Contact: tepronk@science.uva.nl Keywords: Architecture, Design, Computer, Cell Systems |
| Poster Q06 IgTree(c) and MTree(c): Creating and Quantifying Immunoglobulin Variable Region Gene Lineage Trees Ramit Mehr(1), Michal Barak(1), Gitit Shahaf(1), Neta Zuckerman(1), Avital Steiman-Shimony(1), Hanna Edelman(1), Ron Unger(1), Deborah Dunn-Walters(2) (1) The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University Ramat-Gan, Israel; (2) Guy's Hospital, King's College London, UK |
| Abstract: Lineage trees are commonly used to illustrate diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. We developed a novel mathematical algorithm for quantifying the graphical properties of IGV gene lineage trees, allowing the evaluation of the differences between the dynamics of SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. We also created an algorithm that can generate lineage trees from IGV gene sequences. We implemented those algorithms in the programs MTree(c) and IgTree(c) Contact: levanm@mail.biu.ac.il Keywords: Lineage Tree, Immunoglobulin, Hypermutation |
| Poster Q07 NanoSNP: A Computational Platform for High Throughput Quantum Dot Encoded Microsphere SNP Genotyping Colin Clarke, Conrad Bessant Cranfield University |
| Abstract: Quantum dots (QDs) or semiconductor nanocrystals offer advantages over fluorescent dyes for DNA diagnostics. QD-encoded microsphere can be used to create thousands of beads, each with a unique spectral signature. For SNP genotyping, each microsphere is assigned an oligo probe complementary to a sequence around a SNP allele. After DNA amplification and hybridization, the microspheres and thus each SNP are identified rapidly using flow cytometery. We aim to develop computational systems for using QD-encoded microspheres to produce a complete SNP genotyping solution for disease study and forensics. Contact: c.clarke.s03@cranfield.ac.uk Keywords: SNP Genotyping |
| Poster Q08 BioFrame: A Java-based Software Development framework for Bioinformatics Fernando Martinez, Junaid Gamieldien, Darren Otgaar, Dan Jacobson National Bioinformatics Network, South Africa |
| Abstract: Bioframe is an Open Source, Java-based, rapid application development (RAD) framework for Bioinformatics and Computational Biology. Bioframe integrates mature open source tools and frameworks like Biojava, Hibernate, and others, in a robust J2EE environment. The framework is extensible, thread safe, and among other services, provides security, logging, reusable components, templates and wizards to help create and test new web applications, as well as seamless integration between the different layers of an application. Contact: fernando@nbn.ac.za Keywords: Bioinformatics, Java, Software Development |
| Poster Q09 Sequence Dependence of DNA Conformation and Deformation Calculated by Normal Mode Dynamics Michael Levitt (1), Peter S. Stern (2) (1) Stanford University; (2) Weizmann Institute of Science |
| Abstract: In this work, we calculate the stiffness of the DNA double helix using a novel method that depends on the use of normal mode dynamics to calculate the frequencies of the overall bending and twisting motions of a series of DNA sequences. We investigate the dependence of DNA deformability on the base sequence. Small differences in the bending and twisting stiffness are detected by calculating the normal modes of segments of DNA of closely related sequence. The results show that sequences rich in A and T are more easily bent than those rich in G and C. Contact: Peter.Stern@weizmann.ac.il Keywords: DNA bending, Normal Modes |
| Poster Q10 Using DNA Pools for Genotyping Trios Kenneth B. Beckman (1), Kenneth J. Abel (2), Andreas Braun (3), Eran Halperin (4) (1) Children's Hospital Oakland Research Institute; (2) Sequenom, Inc.; (3) Dx. Innovation, Inc.; (4) International Computer Science Institute |
| Abstract: Genotyping of mother-father-child trios is useful in disease association studies, as trios eliminate stratification effects and increase the accuracy of haplotype inference. Unfortunately, it may reduce power, as it uses genotypes of three individuals, with only four independent haplotypes. We describe a method for genotyping a trio using two DNA pools, thus reducing the genotyping cost of trios to that of two individuals. We also exploit linkage disequilibrium to compensate for missing data and genotyping errors. The approach can be applied to any platform that achieves good precision of allele frequency estimates from pools of two individuals. Contact: heran@icsi.berkeley.edu Keywords: Genotyping, DNA Pools, TDT |
| Poster Q11 Building Bioinformatics across Africa Dan Jacobson (1), Nicky Mulder (2), Trushar Shah (3) (1) National Bioinformatics Network (NBN), South Africa; (2) ASBCB & University of Cape Town NBN Node; (3) Biosciences Eastern and Central Africa (BECA) |
| Abstract: "Modern biotechnology is opening up new opportunities to address challenges of increasing food production, stemming environmental degradation, fighting such diseases as malaria, HIV/AIDS and tuberculosis, and enhancing industrialization in Africa." (1) In order for Africa to develop to the point where it can meaningfully participate in the Biosciences it must have the capacity to engage in Bioinformatics. The application of Bioinformatics therefore has great potential to underpin development of solutions to Africa's problems in health and agriculture, and thus to promote economic development. Contact: dan@nbn.ac.za Keywords: NBN, BECA, Africa, NEPAD |
| Poster Q12 A Cooperative Energy Term for Hydrogen Bonds Ami Levy-Moonshine, Tatiana Maximova, Chen Keasar Department of Computer Science, Ben Gurion University of the Negev |
| Abstract: Secondary structure (SS) elements constitute a major part of protein structures. Thus their assembly is an essential step in most of the protein structure prediction processes. In this work, we present a cooperative energy term for hydrogen bonds which takes advantage of the characteristic hydrogen bond patterns of SS. Optimizing under this energy term, results in models that contain native-like SS. The cooperative energy term for hydrogen bonds is implemented within the freely available, molecular modeling package [Bioinformatics 21:3931-3932]. Contact: amilev@cs.bgu.ac.il Keywords: Protein Structure Prediction, Hydrogen Bonds |
| Poster Q13 Combining Inference from Differential Expression and Variability in Microarray Data Analysis Joan Valls (1,2), Monica Grau (1), Xavier Sole (1), Pilar Hernandez (1), David Montaner (3), Joaquin Dopazo (3), Miguel A Peinado (4), Gabriel Capella (1), Miguel Angel Pujana (1), Victor Moreno (1,2) (1) Bioinformatics and Biostatistics Unit, Catalan Institute of Oncology, IDIBELL; (2) Autonomous University of Barcelona; (3) Bioinformatics Department, Centro de Investigacion Principe Felipe; (4) Cancer Research Institute, IDIBELL |
| Abstract: We propose a new procedure for the analysis of microarray data by combining inference from differential expression and variability (CLEAR-test). Analysis of public DNA microarray datasets reveal the performance of the CLEAR-test relative to the t-test and alternative methods for differential expression. Empirical and simulated data analyses demonstrate the greater reproducibility and statistical power of the CLEAR-test with respect to current alternative methods. Contact: mapujana@iconcologia.net |
| Poster Q14 On the Fidelity of Assembly, Binning and Gene Calling of Metagenomes Using Simulated Datasets Konstantinos Mavromatis (1), Natalia Ivanova (1), Kerrie Barry (1), Haris Shapiro (1), Eugene Goltsman (1), Alla Lapidus (1), Alice McHardy (2), Isidore Rigoutsos (2), Asaf Salamov (1), Igor Grigoriev (1) ,Frank Korzeniewski (1), Miriam Land (3), Philip Hugenholtz (1), Nikos C. Kyrpides (1) (1) Joint Genome Institute, Walnut Creek, CA; (2) Thomas J.Watson Research Center, Yorktown Heights, NY; (3) Oak Ridge National Laboratory, Oak Ridge, TN |
| Abstract: To evaluate methods for analysing metagenomes, we constructed three synthetic metagenomic datasets of increasing complexity. Isolate genomes represented real datasets based on genome size, GC content and phylogenetic position. Reads were sampled to match the read depth of corresponding populations in the assemblies. Reads were assembled using three programs (Phrap, Arachne and JAZZ). Contigs were binned using three methods (oligonucleotide frequency, pattern discovery, best blast hit) and genes were predicted using two pipelines (fgenes, Critica/Glimmer). We evaluated the quality of each step and explored the role of the population composition and the algorithms used in the quality of the final dataset. Contact: kmavrommatis@lbl.gov |
| Poster Q15 New Features of The GxxxG Transmembrane Dimerization Motif Eyal Arbely, Zvi Granot, Josef Orly, Isaiah T. Arkin The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem |
| Abstract: In order to understand the differences between the SARS Coronavirus (SCoV) and others of the Coronaviridae, we searched for unique elements in its proteins. We found an insertion of two Glycine residues forming the GxxxG motif in the SCoV spike protein transmembrane domain (TMD); this is surprising, as the GxxxG motif is a dimerization motif, while the SCoV spike protein is trimeric. We show that SCoV spike protein TMD is oligomeric and contributes to the trimerization of the entire protein. We used vibrational spectroscopy to analyze helix-helix interactions formed by the GxxxG motif and found a C-alpha-H...O hydrogen bond between the alpha-helical transmembrane domains of Glycophorin-A with strength 0.88 kcal/mol. Contact: eyalrb@pob.huji.ac.il |
| Poster Q16 Developing a Predictive Tool for Prostate Cancer Metastases using the TRAMP Model Itai Kela (1), Alon Harmelin (2), Judith Chermesh (2), Tami Danon (1), Tova Waks (1), Avi Orr-Urtreger (4), Eytan Domany (3), Zelig Eshhar (1) (1) Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel; (2) Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel; (3) Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel; (4) Genetic Institute, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel |
| Abstract: TRAMP is a genetically engineered mouse model that mimics the pathology of clinical prostate cancer [Greenberg 2003]. We use TRAMP to determine if the ability to determine at diagnosis which patient will develop or already has progressed to disseminated disease will significantly impact the clinical management of cancer. We observed heterogeneity between TRAMP strains and amongst individual mice in time of tumor appearance, cancer progression rate, and time of metastases appearance. These pathological observations are interesting since the oncogenic signal in inbred TRAMP mice initiates cancer at a similar time. Contact: itai.kela@weizmann.ac.il |
| Poster Q17 Gene Expression Profiles of AML Derived Stem Cells; Similarity to Hematopoietic Stem Cells Hilah Gal (1,2), Ninette Amariglio (2), Luba Trakhtenbrot (2), Jasmine Jacob-Hirsh (2), Ofer Margalit (2), Abraham Avigdor (2), Arnon Nagler (2), Sigal Tavor (3), Liat Ein-Dor (1), Tsvee Lapidot (1), Eytan Domany (1), Gideon Rechavi (2), David Givol (1) (1) Weizmann Institute of Science, Israel; (2) Chaim Sheba Medical Center, Tel-Hashomer, Israel; (3) Sourasky Medical Center, Tel-Aviv, Israel |
| Abstract: In our work, we fractionated AML stem cells, CD34+CD38- (LSC), and compared their gene expression profile to the AML differentiated cells (CD34+CD38+). We found 409 modulated genes in LSC, showing under-expression of cell cycle and DNA repair genes, consistent with the quiescent state of stem cells. A large portion of the modulated genes in LSC (34%) were also found to be modulated in normal HSC. We identified the Notch pathway as important in LSC self-renewal. The inhibition of this pathway reduced LSC colony formation. Identification of additional genes that regulate LSC self-renewal may provide new targets for therapy. Contact: hilahg@weizmann.ac.il Keywords: Leukemia, Stem Cells, Microarray, Notch |
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