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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A novel approach to investigate tissue-specific trinucleotide repeat instability

Jong-Min Lee, Jie Zhang, Andrew I Su, John R Walker, Tim Wiltshire, Kihwa Kang, Ella Dragileva, Tammy Gillis, Edith T Lopez, Marie-Josee Boily, Michel Cyr, Isaac Kohane, James F Gusella, Marcy E MacDonald, Vanessa C Wheeler

Gene set analysis exploiting the topology of a pathway

Maria Massa, Monica Chiogna, Chiara Romualdi

Systems analysis of iron metabolism: the network of iron pools and fluxes

Tiago JS Lopes, Tatyana Luganskaja, Maja Vuji？ Spasi？, Matthias W Hentze, Martina U Muckenthaler, Klaus Schümann, Jens G Reich

DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

Nail M Gizzatkulov, Igor I Goryanin, Eugeny A Metelkin, Ekaterina A Mogilevskaya, Kirill V Peskov, Oleg V Demin

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

Eugenio Azpeitia, Mariana Benítez, Iliusi Vega, Carlos Villarreal, Elena R Alvarez-Buylla

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

Martin I Sigurdsson, Neema Jamshidi, Eirikur Steingrimsson, Ines Thiele, Bernhard ？ Palsson

Network properties of human disease genes with pleiotropic effects

Sreenivas Chavali, Fredrik Barrenas, Kartiek Kanduri, Mikael Benson

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

Carola Huthmacher, Andreas Hoppe, Sascha Bulik, Hermann-Georg Holzhütter

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Karin Radrich, Yoshimasa Tsuruoka, Paul Dobson, Albert Gevorgyan, Neil Swainston, Gino Baart, Jean-Marc Schwartz

Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis

Anu Raghunathan, Sookil Shin, Simon Daefler

Statistical inference of the time-varying structure of gene-regulation networks

Sophie Lèbre, Jennifer Becq, Frédéric Devaux, Michael PH Stumpf, Ga？lle Lelandais

Determining and interpreting correlations in lipidomic networks found in glioblastoma cells

Robert G？rke, Anke Meyer-B？se, Dorothea Wagner, Huan He, Mark R Emmett, Charles A Conrad

The protein kinase Mζ network as a bistable switch to store neuronal memory

Hideaki Ogasawara, Mitsuo Kawato

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis

Christoph Kaleta, Anna G？hler, Stefan Schuster, Knut Jahreis, Reinhard Guthke, Swetlana Nikolajewa

Curating the innate immunity interactome

David J Lynn, Calvin Chan, Misbah Naseer, Melissa Yau, Raymond Lo, Anastasia Sribnaia, Giselle Ring, Jaimmie Que, Kathleen Wee, Geoffrey L Winsor, Matthew R Laird, Karin Breuer, Amir K Foroushani, Fiona SL Brinkman, Robert EW Hancock

Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity

Marta Tortajada, Francisco Llaneras, Jesús Picó

Inferring modules from human protein interactome classes

Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias Futschik, Enrico Capobianco

Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis

Mariana Obertello, Gabriel Krouk, Manpreet S Katari, Suzan J Runko, Gloria M Coruzzi

Continuous-time modeling of cell fate determination in Arabidopsis flowers

Simon van Mourik, Aalt DJ van Dijk, Maarten de Gee, Richard GH Immink, Kerstin Kaufmann, Gerco C Angenent, Roeland CHJ van Ham, Jaap Molenaar

Gene expression model (in)validation by Fourier analysis

Tomasz Konopka, Marianne Rooman

Molecular mechanistic associations of human diseases

Philip Stegmaier, Mathias Krull, Nico Voss, Alexander E Kel, Edgar Wingender

A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress

Bin Rui, Tie Shen, Hong Zhou, Jianping Liu, Jiusheng Chen, Xiaosong Pan, Haiyan Liu, Jihui Wu, Haoran Zheng, Yunyu Shi

Dynamics and Control of the Central Carbon Metabolism in Hepatoma Cells

Klaus Maier, Ute Hofmann, Matthias Reuss, Klaus Mauch

Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks

Monika Ray, Weixiong Zhang

Bio-informatics analysis of a gene co-expression module in adipose tissue containing the diet-responsive gene Nnat

Xinzhong Li, Peter A Thomason, Dominic J Withers, James Scott

Bridging time scales in cellular decision making with a stochastic bistable switch

Steffen Waldherr, Jingbo Wu, Frank Allg？wer

Automated characterization of cell shape changes during amoeboid motility by skeletonization

Yuan Xiong, Cathryn Kabacoff, Jonathan Franca-Koh, Peter N Devreotes, Douglas N Robinson, Pablo A Iglesias

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

Joonhoon Kim, Jennifer L Reed

Inferring the conservative causal core of gene regulatory networks

G？kmen Altay, Frank Emmert-Streib

Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment

Andrey Ptitsyn, Amber Schlater, Shane Kanatous

A multilevel data integration resource for breast cancer study

Ettore Mosca, Roberta Alfieri, Ivan Merelli, Federica Viti, Andrea Calabria, Luciano Milanesi

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase

Sonali Patil, Hanna Pincas, Jeremy Seto, German Nudelman, Irina Nudelman, Stuart C Sealfon

Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis

Vitaly A Selivanov, Pedro Vizán, Faustino Mollinedo, Teresa WM Fan, Paul WN Lee, Marta Cascante

Evaluating diabetes and hypertension disease causality using mouse phenotypes

Hong Yu, Jialiang Huang, Nan Qiao, Christopher D Green, Jing-Dong J Han

The function of communities in protein interaction networks at multiple scales

Anna CF Lewis, Nick S Jones, Mason A Porter, Charlotte M Deane

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent

Yuanfeng Wang, Scott Christley, Eric Mjolsness, Xiaohui Xie

Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks

Giovanni Iacono, Claudio Altafini

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test

Chao Wu, Fan Zhang, Xia Li, Shihua Zhang, Jiang Li, Fei Su, Kongning Li, Yuqing Yan

The biological context of HIV-1 host interactions reveals subtle insights into a system hijack

Jonathan E Dickerson, John W Pinney, David L Robertson

Ordered structure of the transcription network inherited from the yeast whole-genome duplication

Diana Fusco, Luigi Grassi, Bruno Bassetti, Michele Caselle, Marco Cosentino Lagomarsino

A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder

Richard C McEachin, Haiming Chen, Maureen A Sartor, Scott F Saccone, Benjamin J Keller, Alan R Prossin, James D Cavalcoli, Melvin G McInnis

Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk

Jason E Shoemaker, Kalyan Gayen, Natàlia Garcia-Reyero, Edward J Perkins, Daniel L Villeneuve, Li Liu, Francis J Doyle

Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states

Nadia Felli, Luciano Cianetti, Elvira Pelosi, Alessandra Carè, Chang Liu, George A Calin, Simona Rossi, Cesare Peschle, Giovanna Marziali, Alessandro Giuliani

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

Hsiang Ho, Tijana Milenkovi？, Vesna Memi？evi？, Jayavani Aruri, Nata？a Pr？ulj, Anand K Ganesan

The role of noise and positive feedback in the onset of autosomal dominant diseases

William J Bosl, Rong Li

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo He, Arnaud Henry, Melanie I Stefan, Jacky L Snoep, Michael Hucka, Nicolas Le Novère, Camille Laibe

Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank

Ryo Hashimoto, Kazuko Hirose, Taku Sato, Nobuhiro Fukushima, Nobuaki Miura, Shin-Ichiro Nishimura

Zooming of states and parameters using a lumping approach including back-translation

Mikael Sunn？ker, Henning Schmidt, Mats Jirstrand, Gunnar Cedersund

Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma

Huiqing Liu, Angela R Brannon, Anupama R Reddy, Gabriela Alexe, Michael W Seiler, Alexandra Arreola, Jay H Oza, Ming Yao, David Juan, Louis S Liou, Shridar Ganesan, Arnold J Levine, WK Rathmell, Gyan V Bhanot

A general co-expression network-based approach to gene expression analysis: comparison and applications

Jianhua Ruan, Angela K Dean, Weixiong Zhang

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