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BMC Systems Biology, Volume 1 - Supplement
Volume 1, Number S-1, May 2007
Poster presentation
- Tao You, Alistair J. P. Brown, George M. Coghill:
A quantitative model for the GCN4 translational control in Saccharomyces cerevisiae. P1 - Marco Terzer, Jörg Stelling:
Elementary flux modes - state-of-the-art implementation and scope of application. P2 - Sarath Chandra Janga:
Prediction and evolution of transcription factors and their evolutionary families in prokaryotes. P3 - Martin Golebiewski
, Saqib Mir, Renate Kania, Olga Krebs
Integration of SABIO-RK in workbenches for kinetic model design. P4 - Stephan Noack, Aljoscha Wahl
Visualizing regulatory interactions in metabolic networks. P5 - Xu Gu, David R. Gilbert, Desmond J. Higham, Miles Houslay:
Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs. P6 - Jawahar Krishnan:
Modelling gradient perception and polarization in chemotaxing Dictyostelium cells. P7 - Siew Fong, Fiona E. M. Paulin, Alastair Thompson:
Computational identification of tumour suppressor protein p53 target genes. P8 - Anyela Camargo, Francisco Azuaje:
Integration and analysis of heterogeneous microarray data sources for supporting drug target identification in atherosclerosis. P9 - David J. Bakewell, Ernst Wit
A global statistical test for improved detection of gene activity. P10 - Alastair Spence:
Is the transcript from the overlapping region of two converging genes part of either gene? P11 - Gabriela Kalna, Johanna Thurlow, J. Keith Vass, Desmond J. Higham:
Progression of oral carcinomas revealed by spectral reordering of a bipartite graph. P12 - Alex Marshall, Sirisha Gollapudi, Jacquie de Silva, Charlie Hodgman:
A systems biology approach to modelling tea (Camellia sinensis). P13 - Nadine Stein, Tina Zeller, Marco Oldiges:
Towards quantitative metabolome analysis. P14 - Ronan M. T. Fleming, Aaron Golden, Heinz-Peter Nasheuer:
Thermodynamically constrained steady state solution space of the E. coli metabolic network. P15 - Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka:
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model. P16 - Stefano Lanzeni, Enza Messina, Francesco Archetti:
Towards metabolic networks phylogeny using Petri Net-based expansional analysis. P17 - Thomas Williamson, Frank Bruggemann, Douglas B. Kell, Lubomira Stateva:
Towards a mathematical model of the cAMP pathway in S. cerevisiae. P18 - Vilda Purutçuoglu, Ernst Wit
Bayesian inference of the kinetic parameters of a realistic MAPK/ERK pathway. P19 - Claudia Choi, Claudia Hundertmark, Bernhard Thielen, Beatrice Benkert, Richard Münch, Max Schobert, Dietmar Schomburg, Dieter Jahn, Frank Klawonn
Analysis of metabolome data by a maximum likelihood approach. P20 - Duarte Molha, Catherine J. Hack, Roger Marchant:
The complete denitrification pathway of Geobacillus thermoleovorans. P21 - Helen M. Parsons, Mark R. Viant:
Variance stabilising transformations for NMR metabolomics data. P22 - Hyesun Han, Wonseok Oh, Jihoon Jung, Doo Nam Kim, Kyoung Tai No:
In silico prediction system of CYP450-mediated metabolism profile. P23 - Jan Küntzer, Benny Kneissl, Oliver Kohlbacher, Hans-Peter Lenhof:
Abstract analysis of pathways using the BN++ software framework. P24 - Ko-Yun Lo, Andrew R. Dalby:
A flexible view of metabolic network. P25 - Naoki Matsumaru, Thorsten Lenser, Thomas Hinze
Designing a chemical program using chemical organization theory. P26 - Neil Swainston, Jennifer A. Siepen, Andrew R. Jones
Pride Wizard: generation of standards compliant quantitative proteomics data. P27 - Christian Knüpfer, Clemens Beckstein, Peter Dittrich:
How to formalise the meaning of a bio-model: a case study. P28 - Koray D. Kaya, Gökhan Karakülah, Cengiz M. Yakicier, Özlen Konu:
MicroRNA sequence and expression database. P29 - Svetlana Mollova, Ida Retter, Werner Müller:
Visualising the immune repertoire. P30 - Imtiaz A. Khan
A bioinformatics approach for the interrogation of molecular events in single cells: transforming fluorescent time-lapse microscopy images into numbers. P31 - Joanna L. Sharman, Dietlind L. Gerloff:
MaGnET: a software tool for integrated visualisation of functional genomic data relating to the malaria parasite. P32 - John W. Pinney, John M. Starkovich, Peter Li, David L. Robertson:
SHARKview: a tool for the visualization of systems biology data. P33 - Karl Heuer:
Set theoretical and algebraic model for redundancies in the genetic code. P34 - Iman Tavassoly, Omid Tavassoly, Mohammad Soltany Rezaee Rad:
Chaos game representation of mitochondrial DNA: is it useful in phylogenetic studies? P35 - Mahbobeh Zarrabi, Hossein Naderi-manesh:
Computational simulations of interactions of the κ-hefutoxin1 with the voltage-gated potassium ion channels. P36 - Natasha Sahgal, Barry Monk, Mohammad Wasil, Naresh Magan:
Fungal volatile fingerprints and machine learning: potential of discriminating and classifying dermatophyte species. P37 - Guillermo Rodrigo, Javier Carrera, Alfonso Jaramillo
ECOLITASTER: cellular biosensor. P38 - Jason Lohmueller, Brendan Hickey, Azeem Kaka, Annie Gao, Jamie Lemon, Victoria Lattanzi, Peter Goldstein, Lick-Kong Tam, Meghan Schmidt, John Cumbers, James Gagnon, Hayato Urabe, Ana Jaklenec, Gary Wessel:
Progress toward the construction of a tri-stable genetic toggle switch in E. coli. P39 - Melanie I. Stefan, Nicolas Le Novère:
Molecules for memory: modelling CaMKII. P40 - Vinayak Doraiswamy, Martin L. Buist, Andrew B. Goryachev:
Computational modelling of chemotaxis in cooperative phenomena in bacterial populations. P41 - Andrew V. Kuznetsov:
DNA interaction with sperm cells: ODE model. P42 - Ana de Carvalho Lima Lobato, Raul Muñoz-Hernandez, Renata Furlan, Gabriel Padilla, Leandro M. Garrido, Gorete Ribeiro de Macedo, Ferda Mavituna:
Metabolic flux analysis for directing metabolism of Streptomyces olindensis from growth to anti-tumor drug (cosmomycin) production. P43 - Chih-Chun Chen, Christopher D. Clack, Sylvia B. Nagl:
Context sensitivity in individual-based modeling. P44 - Eduardo Gonzalez-Couto, Silvia Matteoni
Huntington's disease: from experimental results to interaction networks, patho-pathway construction and disease hypothesis. P45 - Fernando Ortega, Luis Acerenza:
Kinetic constraints on the sensitivity of large metabolic responses. P46 - Khairiah Abd-Karim, Radia Chibani, Ferda Mavituna:
A computational tool for directing Taxus spp. cell culture metabolism from growth to Taxol®, a diterpene alkaloid, production. P47 - Manuel Corpas
PFF - an integrated database of residues and fragments critical for protein folding. P48 - Alper Küçükural
Discrimination of proteins using graph theoretic properties. P49 - Safiyeh Soofian, Hossein Naderi-manesh:
Molecular dynamics simulations studies of aurein 1.2 analogs in water and TFE/water. P50 - Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder:
Visualising protein interaction networks with power graphs. P51 - Dafyd J. Jenkins, Dov J. Stekel
Modelling the evolution of transcriptional control networks using stochastic simulations and evolutionary computational methods. P52 - Derek Gatherer
Less is more: the battle of Moore's law against Bremermann's limit on the field of systems biology. P53 - Evgeny Zatulovskiy
Docking study on mammalian CTR1 copper importer motifs. P54 - Hosil Park, Julie Huxley-Jones, Teresa K. Attwood
A Cys-capping motif unique to small leucine-rich repeat proteins and proteoglycans of the extracellular matrix. P55 - Jamie Allen, Mark Shirley, Steve Rushton, Ajay Kohli, Ehsan Mesbahi:
Predicting gene co-expression from CIS-regulatory regions. P56 - Judit Kumuthini, Conrad Bessant, Paul Wilson, Daniel Crowther:
Gene regulatory network of human adipocyte differentiation. P57 - Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig:
On the correlation between drug-resistant pattern of HIV-1 protease inhibitors and binding free energy and structural changes. P58 - Luke Hakes, Simon C. Lovell, Stephen G. Oliver, David L. Robertson:
Similarity in expression accounts for correlated evolution of interacting proteins. P59 - Frank Notka, Doris Leikam, Asli Bauer, David Raab, Marcus Graf, Ralf Wagner:
Computer aided multi-parameter gene design: impact of synthetic dnas on protein expression enhancement. P60 - Elisa Mori, Sara Brunetti, Sonia Campa, Elena Lodi:
A parallel algorithm for de novo peptide sequencing. P61 - Chris Bridson, Richard J. Morris:
A Bayesian framework for integrating genomic data to aid function prediction. P62 - Le Yu, Stephen Marshall:
Inferring context-sensitive Probabilistic Boolean Networks from gene expression data under multi-biological conditions. P63 - Emmet McIntyre:
Simulating epidermal growth factor receptor interaction with ligand. P64 - Najl V. Valeyev, Nikolai V. Kotov, Ian Postlethwaite, Declan G. Bates:
Mathematical modelling of multi-site protein-ligand interactions. P65 - Michelle S. Scott, Geoffrey J. Barton:
Prediction and ranking of human protein-protein interactions within a Bayesian framework. P66 - Richard D. Pearson:
Microarrays expression measurement. P67 - Mohd Basyaruddin Abdul Rahman, Ahmad Jaafar, Mahiran Basri, Raja Rahman, Abu Salleh, Habibah A. Wahab:
Design of novel semisynethetic metalloenzyme from thermolysin. P68 - Ramazan Saeed, Charlotte M. Deane:
Using the protein interaction network to predict protein folds without homology. P69 - Filippo Menolascina, Stefania Tommasi, Patrizia Chiarappa, Vitoantonio Bevilacqua, Giuseppe Mastronardi, Angelo Paradiso:
Data mining techniques in a CGH-based breast cancer subtype profiling: an immune perspective with comparative study. P70 - Darragh G. McArt, Robert W. Cairns, Gillian Wasson, Kurt Saetzler:
Modelling the comet assay. P71 - Katja Wegner, Johannes F. Knabe, Mark Robinson, Attila Egri-Nagy, Maria J. Schilstra
The NetBuilder' project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks. P72 - Adak Nasiripourdori, Bijan Ranjbar, Hossein Naderi-manesh:
Binding site locations and interaction of the isolated middle loop of snake neurotoxin I with muscle type nicotinic acetylcholine receptor: molecular dynamics and docking simulation study. P73 - Brian Harms, Allen Lee, Ricardo Paxson, Ulrik B. Nielsen, Birgit Schoeberl:
Applications of sensitivity analysis for drug discovery and development in the ErbB receptor network. P74 - J. Keith Vass, Gabriela Kalna, Desmond J. Higham:
Identification of phenotypes in patient microarrays. P75 - Padchanee Sangthong, John M. X. Hughes, John E. G. McCarthy:
Rate control analysis of the translation initiation pathway in S. cerevisiae. P76 - Balázs Papp, Evangelos Simeonidis
Flux balance analysis and its applications. P77 - Witold Dyrka, Jean-Christophe Nebel
A probabilistic context-free grammar for the detection of binding sites from a protein sequence. P78 - Vincent Rouilly, Barry Canton, Poul M. F. Nielsen, Richard Kitney:
Registry of BioBricks models using CellML. P79 - Simon R. Andrews:
ChIPMonk: software for viewing and analysing ChIP-on-chip data. P80 - L. E. Okoror, H. T. Alaiya, P. Aliga:
Function prediction of a newly extracted protein from a newly extracted lassa virus gene. P81 - Allan Orozco:
Estrategic aspects by technology transfer from the academic and business development of the bioinformatics in Costa Rica and the central American region. P82 - Yizhi Cai, Bryony Davidson, Hongwu Ma, Chris French:
Modeling the arsenic biosensor system. P83 - Olga Vasieva, Roland Wolf:
Unraveling functional networks: does gene clustering have a meaning? P84
- Martino Barenco, Sonia H. Shah, Daniel Brewer, Robin Callard, Jaroslav Stark, Crispin J. Miller, Michael Hubank:
rHVDM - a fast and user-friendly R package to predict transcription factor targets from microarray time series data. S1 - Alok Mishra, Duncan Gillies:
Effect of microarray data heterogeneity on regulatory gene module discovery. S2 - Raul Muñoz-Hernandez, Ana de Carvalho Lima Lobato, Hong Kim, Ferda Mavituna:
Metabolic flux analysis to study the production of a non-ribosomal lipopeptide, CDA, by Streptomyces coelicolor. S3 - Daniel Mateus, Jean-Paul Comet, Jean-Pierre Gallois, Pascale Le Gall:
Modelling genetic regulatory networks from specified behaviours. S4 - Michael Lees, Brian S. Logan, John R. King:
BacGrid: simulations of bacteria using the grid. S5 - Isabel Rojas, Martin Golebiewski
SABIO-RK: a database for biochemical reactions and their kinetics. S6 - Martin Hemberg, Mauricio Barahona:
Noise characteristics of interlocked repressilators. S7 - Nuno Lages, Marta Sousa Silva
Potential role of the glyoxalase pathway as a drug target in Leishmania infantum: an exact steady-state model analysis. S8 - 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 S. Freemont, Richard Kitney:
Engineering a synthetic molecular oscillator based on the Lotka-Volterra dynamic. S9 - Kaj Bernhardt, Nikhilesh Chand, Elizabeth Carter, Jisun Lee, Yang Xu, Xueni Zhu, Duncan Rowe, James W. Ajioka, J. M. Gonçalves, Jim Haseloff, Gos Micklem:
New tools for self-organized pattern formation. S10 - Chris French, Judith Nicholson, Farid Bizzari, Jelena Aleksic, Yizhi Cai, Sreemati Seshasayee, Sergii Ivakhno, Bryony Davidson, Jen Wilson, Kim de Mora, Hongwu Ma, Laszlo Kozma-Bognar, Alistair Elfick:
Arsenic biosenseor: a step further. S11 - Sanne Abeln
Linking evolution of protein structures through fragments. S12 - Emily R. Jefferson, Geoffrey J. Barton:
The relationship between domain-domain interaction orientation and sequence similarity. S13 - James Brown:
Navigational control of bacteria: the design of a synthetic chemotactic biological system. S14 - Alfonso Jaramillo
Computational design of proteins with new functions. S15
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