Volume 1 Supplement 1

BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology

Meeting abstracts

Edited by John Cumbers, Xu Gu, Jong Sze Wong

BioSysBio 2007: Systems Biology, Bioinformatics and Synthetic Biology. Go to conference site.

Manchester, UK11-13 January 2007

Vol 1 Suppl 1 concatenated PDF

Page 1 of 2

rHVDM – a fast and user-friendly R package to predict transcription factor targets from microarray time series data

Authors: Martino Barenco, Sonia Shah, Daniel Brewer, Robin Callard, Jaroslav Stark, Crispin Miller and Michael Hubank

Citation: BMC Systems Biology 2007 1(Suppl 1):S1

Content type: Oral presentation

Published on: 8 May 2007
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A quantitative model for the GCN4 translational control in Saccharomyces cerevisiae

Authors: Tao You, Alistair JP Brown and George M Coghill

Citation: BMC Systems Biology 2007 1(Suppl 1):P1

Content type: Poster presentation

Published on: 8 May 2007
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Elementary flux modes – state-of-the-art implementation and scope of application

Authors: Marco Terzer and Jörg Stelling

Citation: BMC Systems Biology 2007 1(Suppl 1):P2

Content type: Poster presentation

Published on: 8 May 2007
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Effect of microarray data heterogeneity on regulatory gene module discovery

Authors: Alok Mishra and Duncan Gillies

Citation: BMC Systems Biology 2007 1(Suppl 1):S2

Content type: Oral presentation

Published on: 8 May 2007
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Prediction and evolution of transcription factors and their evolutionary families in prokaryotes

Authors: Sarath Chandra Janga

Citation: BMC Systems Biology 2007 1(Suppl 1):P3

Content type: Poster presentation

Published on: 8 May 2007
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Metabolic flux analysis to study the production of a non-ribosomal lipopeptide, CDA, by Streptomyces coelicolor

Authors: Raul Munoz-Hernandez, Ana Katerine de Carvalho Lima Lobato, Hong Bum Kim and Ferda Mavituna

Citation: BMC Systems Biology 2007 1(Suppl 1):S3

Content type: Oral presentation

Published on: 8 May 2007
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Modelling genetic regulatory networks from specified behaviours

Authors: Daniel Mateus, Jean-Paul Comet, Jean-Pierre Gallois and Pascale Le Gall

Citation: BMC Systems Biology 2007 1(Suppl 1):S4

Content type: Oral presentation

Published on: 8 May 2007
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Integration of SABIO-RK in workbenches for kinetic model design

Authors: Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig and Isabel Rojas

Citation: BMC Systems Biology 2007 1(Suppl 1):P4

Content type: Poster presentation

Published on: 8 May 2007
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Visualizing regulatory interactions in metabolic networks

Authors: Stephan Noack, Aljoscha Wahl, Marco Oldiges and Wolfgang Wiechert

Citation: BMC Systems Biology 2007 1(Suppl 1):P5

Content type: Poster presentation

Published on: 8 May 2007
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BacGrid: simulations of bacteria using the grid

Authors: Michael Lees, Brian Logan and John King

Citation: BMC Systems Biology 2007 1(Suppl 1):S5

Content type: Oral presentation

Published on: 8 May 2007
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Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs

Authors: Xu Gu, David Gilbert, Des Higham and Miles Houslay

Citation: BMC Systems Biology 2007 1(Suppl 1):P6

Content type: Poster presentation

Published on: 8 May 2007
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SABIO-RK: a database for biochemical reactions and their kinetics

Authors: Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann and Ulrike Wittig

Citation: BMC Systems Biology 2007 1(Suppl 1):S6

Content type: Oral presentation

Published on: 8 May 2007
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Modelling gradient perception and polarization in chemotaxing Dictyostelium cells

Authors: Jawahar Krishnan

Citation: BMC Systems Biology 2007 1(Suppl 1):P7

Content type: Poster presentation

Published on: 8 May 2007
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Noise characteristics of interlocked repressilators

Authors: Martin Hemberg and Mauricio Barahona

Citation: BMC Systems Biology 2007 1(Suppl 1):S7

Content type: Oral presentation

Published on: 8 May 2007
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Computational identification of tumour suppressor protein p53 target genes

Authors: Siew Chinn Fong, Fiona Paulin and Alastair Thompson

Citation: BMC Systems Biology 2007 1(Suppl 1):P8

Content type: Poster presentation

Published on: 8 May 2007
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Potential role of the glyoxalase pathway as a drug target in Leishmania infantum: an exact steady-state model analysis

Authors: Nuno Filipe Lages, Marta Sousa Silva, António EN Ferreira, Ana Maria Tomás, Carlos Cordeiro and Ana Ponces Freire

Citation: BMC Systems Biology 2007 1(Suppl 1):S8

Content type: Oral presentation

Published on: 8 May 2007
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Integration and analysis of heterogeneous microarray data sources for supporting drug target identification in atherosclerosis

Authors: Anyela Camargo and Francisco Azuaje

Citation: BMC Systems Biology 2007 1(Suppl 1):P9

Content type: Poster presentation

Published on: 8 May 2007
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Engineering a synthetic molecular oscillator based on the Lotka-Volterra dynamic

Authors: Christin Sander, Farah Vohra, John Chattaway, Tom Hinson, John Sy, Jiongjun Bai, Jonathan Wells, Deepti Aswani, Vincent Rouilly, Chueh-Loo Poh, Matthieu Bultelle, Kirsten Jensen, David Mann, Paul Freemont and Richard Kitney

Citation: BMC Systems Biology 2007 1(Suppl 1):S9

Content type: Oral presentation

Published on: 8 May 2007
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A global statistical test for improved detection of gene activity

Authors: David JG Bakewell and Ernst Wit

Citation: BMC Systems Biology 2007 1(Suppl 1):P10

Content type: Poster presentation

Published on: 8 May 2007
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New tools for self-organized pattern formation

Authors: Kaj Bernhardt, Nikhilesh Singh Chand, Elizabeth Carter, Jisun Lee, Yang Xu, Xueni Zhu, Duncan Rowe, JW Ajioka, JM Goncalves, J Haseloff and G Micklem

Citation: BMC Systems Biology 2007 1(Suppl 1):S10

Content type: Oral presentation

Published on: 8 May 2007
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Is the transcript from the overlapping region of two converging genes part of either gene?

Authors: Alastair Spence

Citation: BMC Systems Biology 2007 1(Suppl 1):P11

Content type: Poster presentation

Published on: 8 May 2007
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Arsenic biosenseor: a step further

Authors: Chris French, Judith Nicholson, Farid Bizzari, Jelena Aleksic, Yizhi Cai, Sreemati Lalgudi Seshasayee, Sergii Ivakhno, Bryony Davidson, Jen Wilson, Kim de Mora, Hongwu Ma, Laszlo Kozma-Bognar and Alistair Elfick

Citation: BMC Systems Biology 2007 1(Suppl 1):S11

Content type: Oral presentation

Published on: 8 May 2007
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Progression of oral carcinomas revealed by spectral reordering of a bipartite graph

Authors: Gabriela Kalna, Johanna Thurlow, Keith Vass and Des Higham

Citation: BMC Systems Biology 2007 1(Suppl 1):P12

Content type: Poster presentation

Published on: 8 May 2007
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Linking evolution of protein structures through fragments

Authors: Sanne Abeln and Charlotte M Deane

Citation: BMC Systems Biology 2007 1(Suppl 1):S12

Content type: Oral presentation

Published on: 8 May 2007
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The relationship between domain-domain interaction orientation and sequence similarity

Authors: Emily Jefferson and Geoffrey Barton

Citation: BMC Systems Biology 2007 1(Suppl 1):S13

Content type: Oral presentation

Published on: 8 May 2007
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A systems biology approach to modelling tea (Camellia sinensis)

Authors: Alex Marshall, Sirisha Gollapudi, Jacquie de Silva and Charlie Hodgman

Citation: BMC Systems Biology 2007 1(Suppl 1):P13

Content type: Poster presentation

Published on: 8 May 2007
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Towards quantitative metabolome analysis

Authors: Nadine Stein, Tina Zeller and Marco Oldiges

Citation: BMC Systems Biology 2007 1(Suppl 1):P14

Content type: Poster presentation

Published on: 8 May 2007
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Navigational control of bacteria: the design of a synthetic chemotactic biological system

Authors: James Brown

Citation: BMC Systems Biology 2007 1(Suppl 1):S14

Content type: Oral presentation

Published on: 8 May 2007
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Computational design of proteins with new functions

Authors: Alfonso Jaramillo, Pablo Tortosa, Guillermo Rodrigo, Maria Suarez and Javier Carrera

Citation: BMC Systems Biology 2007 1(Suppl 1):S15

Content type: Oral presentation

Published on: 8 May 2007
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Thermodynamically constrained steady state solution space of the E. coli metabolic network

Authors: Ronan MT Fleming, Aaron Golden and Heinz-Peter Nasheuer

Citation: BMC Systems Biology 2007 1(Suppl 1):P15

Content type: Poster presentation

Published on: 8 May 2007
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Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model

Authors: Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto and Hiroshi Mamitsuka

Citation: BMC Systems Biology 2007 1(Suppl 1):P16

Content type: Poster presentation

Published on: 8 May 2007
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Towards metabolic networks phylogeny using Petri Net-based expansional analysis

Authors: Stefano Lanzeni, Enza Messina and Francesco Archetti

Citation: BMC Systems Biology 2007 1(Suppl 1):P17

Content type: Poster presentation

Published on: 8 May 2007
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Towards a mathematical model of the cAMP pathway in S. cerevisiae

Authors: Thomas Williamson, Frank Bruggemann, Douglas Kell and Lubomira Stateva

Citation: BMC Systems Biology 2007 1(Suppl 1):P18

Content type: Poster presentation

Published on: 8 May 2007
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Bayesian inference of the kinetic parameters of a realistic MAPK/ERK pathway

Authors: Vilda Purutçuoğlu and Ernst Wit

Citation: BMC Systems Biology 2007 1(Suppl 1):P19

Content type: Poster presentation

Published on: 8 May 2007
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Analysis of metabolome data by a maximum likelihood approach

Authors: Claudia Choi, Claudia Hundertmark, Bernhard Thielen, Beatrice Benkert, Richard Münch, Max Schobert, Dietmar Schomburg, Dieter Jahn and Frank Klawonn

Citation: BMC Systems Biology 2007 1(Suppl 1):P20

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The complete denitrification pathway of Geobacillus thermoleovorans

Authors: Duarte Molha, Catherine Hack and Roger Marchant

Citation: BMC Systems Biology 2007 1(Suppl 1):P21

Content type: Poster presentation

Published on: 8 May 2007
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Variance stabilising transformations for NMR metabolomics data

Authors: Helen Parsons and Mark Viant

Citation: BMC Systems Biology 2007 1(Suppl 1):P22

Content type: Poster presentation

Published on: 8 May 2007
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In silico prediction system of CYP450-mediated metabolism profile

Authors: Hyesun Han, Won Seok Oh, Ji Hoon Jung, Doo Nam Kim and Kyoung Tai No

Citation: BMC Systems Biology 2007 1(Suppl 1):P23

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Abstract analysis of pathways using the BN++ software framework

Authors: Jan Küntzer, Benny Kneissl, Oliver Kohlbacher and Hans-Peter Lenhof

Citation: BMC Systems Biology 2007 1(Suppl 1):P24

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A flexible view of metabolic network

Authors: Ko-Yun Lo and Andrew Dalby

Citation: BMC Systems Biology 2007 1(Suppl 1):P25

Content type: Poster presentation

Published on: 8 May 2007
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Designing a chemical program using chemical organization theory

Authors: Naoki Matsumaru, Thorsten Lenser, Thomas Hinze and Peter Dittrich

Citation: BMC Systems Biology 2007 1(Suppl 1):P26

Content type: Poster presentation

Published on: 8 May 2007
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Pride Wizard: generation of standards compliant quantitative proteomics data

Authors: Neil Swainston, Jennifer A Siepen, Andrew R Jones, Sarah R Hart, Henning Hermjakob, Phil Jones and Simon J Hubbard

Citation: BMC Systems Biology 2007 1(Suppl 1):P27

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How to formalise the meaning of a bio-model: a case study

Authors: Christian Knüpfer, Clemens Beckstein and Peter Dittrich

Citation: BMC Systems Biology 2007 1(Suppl 1):P28

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Published on: 8 May 2007
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MicroRNA sequence and expression database

Authors: Koray Dogan Kaya, Gokhan Karakulah, Cengiz Yakicier and Ozlen Konu

Citation: BMC Systems Biology 2007 1(Suppl 1):P29

Content type: Poster presentation

Published on: 8 May 2007
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Visualising the immune repertoire

Authors: Svetlana Mollova, Ida Retter and Werner Müller

Citation: BMC Systems Biology 2007 1(Suppl 1):P30

Content type: Poster presentation

Published on: 8 May 2007
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A bioinformatics approach for the interrogation of molecular events in single cells: transforming fluorescent time-lapse microscopy images into numbers

Authors: Imtiaz Khan, Janet Fisher, Nuria Marquez, Paul Smith and Rachel Errington

Citation: BMC Systems Biology 2007 1(Suppl 1):P31

Content type: Poster presentation

Published on: 8 May 2007
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MaGnET: a software tool for integrated visualisation of functional genomic data relating to the malaria parasite

Authors: Joanna L Sharman and Dietlind L Gerloff

Citation: BMC Systems Biology 2007 1(Suppl 1):P32

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Published on: 8 May 2007
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SHARKview: a tool for the visualization of systems biology data

Authors: John W Pinney, John M Starkovich, Peter Li and David L Robertson

Citation: BMC Systems Biology 2007 1(Suppl 1):P33

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Published on: 8 May 2007
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Set theoretical and algebraic model for redundancies in the genetic code

Authors: Karl Heuer

Citation: BMC Systems Biology 2007 1(Suppl 1):P34

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Chaos game representation of mitochondrial DNA: is it useful in phylogenetic studies?

Authors: Iman Tavassoly, Omid Tavassoly and Mohammad SoltanyRezaee Rad

Citation: BMC Systems Biology 2007 1(Suppl 1):P35

Content type: Poster presentation

Published on: 8 May 2007
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BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology

Meeting abstracts

BMC Systems Biology

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