BMC Systems Biology - oalib

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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

主页: http://www.biomedcentral.com/bmcsystbiol

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Towards a genome-scale kinetic model of cellular metabolism

Kieran Smallbone, Evangelos Simeonidis, Neil Swainston, Pedro Mendes

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

Stacey D Finley, Linda J Broadbelt, Vassily Hatzimanikatis

Searching for functional gene modules with interaction component models

Juuso A Parkkinen, Samuel Kaski

So what do we really mean when we say that systems biology is holistic?

Derek Gatherer

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter

Antoine Coulon, Olivier Gandrillon, Guillaume Beslon

Snazer: the simulations and networks analyzer

Tommaso Mazza, Gennaro Iaccarino, Corrado Priami

Reverse engineering a gene network using an asynchronous parallel evolution strategy

Luke Jostins, Johannes Jaeger

Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates

Sarah-Maria Fendt, Uwe Sauer

Dynamical modeling of microRNA action on the protein translation process

Andrei Zinovyev, Nadya Morozova, Nora Nonne, Emmanuel Barillot, Annick Harel-Bellan, Alexander N Gorban

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia

An-Yuan Guo, Jingchun Sun, Peilin Jia, Zhongming Zhao

An iterative identification procedure for dynamic modeling of biochemical networks

Eva Balsa-Canto, Antonio A Alonso, Julio R Banga

A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis

Stefan Streif, Dieter Oesterhelt, Wolfgang Marwan

Deciphering chemotaxis pathways using cross species comparisons

Rebecca Hamer, Pao-Yang Chen, Judith P Armitage, Gesine Reinert, Charlotte M Deane

Systems genetics analyses predict a transcription role for P2P-R: Molecular confirmation that P2P-R is a transcriptional co-repressor

Philippos Peidis, Thomas Giannakouros, Matthew E Burow, Robert W Williams, Robert E Scott

Diffusion is capable of translating anisotropic apoptosis initiation into a homogeneous execution of cell death

Heinrich J Huber, Maike A Laussmann, Jochen HM Prehn, Markus Rehm

Cloud computing and validation of expandable in silico livers

Glen EP Ropella, C Anthony Hunt

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work

Gregor Warsow, Boris Greber, Steffi SI Falk, Clemens Harder, Marcin Siatkowski, Sandra Schordan, Anup Som, Nicole Endlich, Hans Sch？ler, Dirk Repsilber, Karlhans Endlich, Georg Fuellen

Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation

Andreea Munteanu, Marco Constante, Mark Isalan, Ricard V Solé

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

Tom C Freeman, Sobia Raza, Athanasios Theocharidis, Peter Ghazal

Stress-specific response of the p53-Mdm2 feedback loop

Alexander Hunziker, Mogens H Jensen, Sandeep Krishna

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

Marc T Facciotti, Wyming L Pang, Fang-yin Lo, Kenia Whitehead, Tie Koide, Ken-ichi Masumura, Min Pan, Amardeep Kaur, David J Larsen, David J Reiss, Linh Hoang, Ewa Kalisiak, Trent Northen, Sunia A Trauger, Gary Siuzdak, Nitin S Baliga

Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis

Elizabeth Allen, Annick Moing, Timothy MD Ebbels, Micka？l Maucourt, A Deri Tomos, Dominique Rolin, Mark A Hooks

Individual fates of mesenchymal stem cells in vitro

Axel Krinner, Martin Hoffmann, Markus Loeffler, Dirk Drasdo, Joerg Galle

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks

Philipp Rumschinski, Steffen Borchers, Sandro Bosio, Robert Weismantel, Rolf Findeisen

Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium

Abhay K Singh, Thanura Elvitigala, Jeffrey C Cameron, Bijoy K Ghosh, Maitrayee Bhattacharyya-Pakrasi, Himadri B Pakrasi

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

Raj Chari, Bradley P Coe, Emily A Vucic, William W Lockwood, Wan L Lam

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data

Fei Gu, Hang-Kai Hsu, Pei-Yin Hsu, Jiejun Wu, Yilin Ma, Jeffrey Parvin, Tim H-M Huang, Victor X Jin

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae

Mitra Mirzarezaee, Babak N Araabi, Mehdi Sadeghi

Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network

Gregory M Miller, Babatunde A Ogunnaike, James S Schwaber, Rajanikanth Vadigepalli

Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma

Hua Dong, Li Luo, Shengjun Hong, Hoicheong Siu, Yanghua Xiao, Li Jin, Rui Chen, Momiao Xiong

Solving the chemical master equation using sliding windows

Verena Wolf, Rushil Goel, Maria Mateescu, Thomas A Henzinger

Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system

Ronny Straube, Ernesto M Nicola

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

Nurul Mohamad, Mikael Bodén

microRNA evolution in a human transcription factor and microRNA regulatory network

Chengxiang Qiu, Juan Wang, Pengying Yao, Edwin Wang, Qinghua Cui

Catabolic efficiency of aerobic glycolysis: The Warburg effect revisited

Alexei Vazquez, Jiangxia Liu, Yi Zhou, Zoltán N Oltvai

Evolution of metabolic network organization

Aurélien Mazurie, Danail Bonchev, Benno Schwikowski, Gregory A Buck

Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses

Harin Kanani, Bhaskar Dutta, Maria I Klapa

Constraint-based modeling analysis of the metabolism of two Pelobacter species

Jun Sun, Shelley A Haveman, Olivia Bui, Tom R Fahland, Derek R Lovley

The spermatozoa caught in the net: the biological networks to study the male gametes post-ejaculatory life

Nicola Bernabò, Mauro Mattioli, Barbara Barboni

Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells

J？rg Linde, Duncan Wilson, Bernhard Hube, Reinhard Guthke

Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network

Francisco Azuaje, Yvan Devaux, Daniel R Wagner

Protein complex forming ability is favored over the features of interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks

Sandip Chakraborty, Bratati Kahali, Tapash C Ghosh

Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model

Matthew J Kraeutler, Anthony R Soltis, Jeffrey J Saucerman

Confidence from uncertainty - A multi-target drug screening method from robust control theory

Camilla Luni, Jason E Shoemaker, Kevin R Sanft, Linda R Petzold, Francis J Doyle

In vitro gene regulatory networks predict in vivo function of liver

Youping Deng, David R Johnson, Xin Guan, Choo Y Ang, Junmei Ai, Edward J Perkins

Low-complexity regions within protein sequences have position-dependent roles

Alain Coletta, John W Pinney, David Solís, James Marsh, Steve R Pettifer, Teresa K Attwood

Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis

Jin Gu, Yang Chen, Shao Li, Yanda Li

Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds

Juan C Trivi？o, Florencio Pazos

Defining the antigen receptor-dependent regulatory network that induces arrest of cycling immature B-lymphocytes

Mohammad Jamal, Srikanth Ravichandran, Noor Jailkhani, Samrat Chatterjee, Raina Dua, Kanury VS Rao

A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway

Han Yan, Bo Zhang, Shao Li, Qianchuan Zhao

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