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BMC Systems Biology, Volume 4
Volume 4, 2010
- Tommaso Mazza
, Gennaro Iaccarino
, Corrado Priami:
Snazer: the simulations and networks analyzer. 1 - Antoine Coulon, Olivier Gandrillon, Guillaume Beslon
:
On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter. 2 - Rebecca Hamer, Pao-Yang Chen
, Judith P. Armitage, Gesine Reinert
, Charlotte M. Deane
:
Deciphering chemotaxis pathways using cross species comparisons. 3 - Juuso A. Parkkinen, Samuel Kaski:
Searching for functional gene modules with interaction component models. 4 - Alexey M. Shibeko
, Ekaterina S. Lobanova
, Mikhail A. Panteleev
, Fazoil I. Ataullakhanov:
Blood flow controls coagulation onset via the positive feedback of factor VII activation by factor Xa. 5 - Kieran Smallbone
, Evangelos Simeonidis
, Neil Swainston, Pedro Mendes
:
Towards a genome-scale kinetic model of cellular metabolism. 6 - Stacey D. Finley
, Linda J. Broadbelt, Vassily Hatzimanikatis
:
In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene. 7 - Jianhua Ruan
, Angela K. Dean, Weixiong Zhang
:
A general co-expression network-based approach to gene expression analysis: comparison and applications. 8 - Heinrich J. Huber, Maike A. Laussmann, Jochen H. M. Prehn
, Markus Rehm
:
Diffusion is capable of translating anisotropic apoptosis initiation into a homogeneous execution of cell death. 9 - An-Yuan Guo, Jingchun Sun, Peilin Jia, Zhongming Zhao:
A Novel microRNA and transcription factor mediated regulatory network in schizophrenia. 10 - Eva Balsa-Canto
, Antonio A. Alonso
, Julio R. Banga
:
An iterative identification procedure for dynamic modeling of biochemical networks. 11 - Sarah-Maria Fendt
, Uwe Sauer:
Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates. 12 - Andrei Yu. Zinovyev
, Nadya Morozova, Nora Nonne, Emmanuel Barillot
, Annick Harel-Bellan
, Alexander N. Gorban
:
Dynamical modeling of microRNA action on the protein translation process. 13 - Philippos Peidis, Thomas Giannakouros, Matthew E. Burow, Robert W. Williams
, Robert E. Scott:
Systems genetics analyses predict a transcription role for P2P-R: Molecular confirmation that P2P-R is a transcriptional co-repressor. 14 - Guy Karlebach, Ron Shamir
:
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. 15 - Chung-Ming Chen, Chi Lee, Cheng-Long Chuang, Chia-Chang Wang, Grace S. Shieh:
Inferring genetic interactions via a nonlinear model and an optimization algorithm. 16 - Luke Jostins, Johannes Jaeger
:
Reverse engineering a gene network using an asynchronous parallel evolution strategy. 17 - Núria Domedel-Puig, Iosifina Pournara, Lorenz Wernisch:
Statistical model comparison applied to common network motifs. 18 - Tatiana T. Marquez-Lago, André Leier
, Kevin Burrage
:
Probability distributed time delays: integrating spatial effects into temporal models. 19 - Yu-Chao Wang
, Bor-Sen Chen:
Integrated cellular network of transcription regulations and protein-protein interactions. 20 - Michael Dewar, Visakan Kadirkamanathan
, Manfred Opper, Guido Sanguinetti
:
Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster. 21 - Derek Gatherer
:
So what do we really mean when we say that systems biology is holistic? 22 - Bart S. Hendriks
, Kelly M. Seidl, Jeffrey R. Chabot:
Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro. 23 - Dominic P. Tolle
, Nicolas Le Novère:
Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. 24 - Dominic P. Tolle
, Nicolas Le Novère:
Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. 25 - Zhen Qi, Gary W. Miller, Eberhard O. Voit:
The internal state of medium spiny neurons varies in response to different input signals. 26 - Stefan Streif
, Dieter Oesterhelt, Wolfgang Marwan:
A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis. 27 - Mikael Sunnåker
, Henning Schmidt, Mats Jirstrand
, Gunnar Cedersund:
Zooming of states and parameters using a lumping approach including back-translation. 28 - 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 S. Kohane, James F. Gusella, Marcy E. MacDonald, Vanessa C. Wheeler:
A novel approach to investigate tissue-specific trinucleotide repeat instability. 29 - Areejit Samal
, João F. Matias Rodrigues
, Jürgen Jost, Olivier C. Martin
, Andreas Wagner:
Genotype networks in metabolic reaction spaces. 30 - Seth B. Roberts, Chris M. Gowen, J. Paul Brooks, Stephen S. Fong:
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. 31 - Suresh Swain, Jodie F. Wren, Stephen R. Stürzenbaum, Peter Kille
, A. John Morgan, Tjalling Jager
, Martijs J. Jonker, Peter K. Hankard, Claus Svendsen
, Jenifer Owen, Ann Hedley, Mark L. Blaxter
, David J. Spurgeon:
Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans. 32 - Yuan Xiong, Cathryn Kabacoff, Jonathan Franca-Koh, Peter N. Devreotes, Douglas N. Robinson
, Pablo A. Iglesias
:
Automated characterization of cell shape changes during amoeboid motility by skeletonization. 33 - Jamie Twycross
, Leah R. Band
, Malcolm Bennett
, John R. King
, Natalio Krasnogor:
Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study. 34 - Ayoun Cho, Hongseok Yun, Jin Park, Sang Lee
, Sunwon Park:
Prediction of novel synthetic pathways for the production of desired chemicals. 35 - Amy M. Wiles, Mark Doderer, Jianhua Ruan
, Tingting Gu, Ravi Dashnamoorthy
, Barron Blackman, Alexander J. R. Bishop
:
Building and analyzing protein interactome networks by cross-species comparisons. 36 - Yi Zhang, Kim A. Hatch, Joanna Bacon
, Lorenz Wernisch:
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis. 37 - Bence Mélykúti
, Elias August, Antonis Papachristodoulou
, Hana El-Samad:
Discriminating between rival biochemical network models: three approaches to optimal experiment design. 38 - Chen Li
, Masao Nagasaki
, Ayumu Saito, Satoru Miyano
:
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. 39 - Qiang Zhang, Sudin Bhattacharya
, Douglas Kline, Robert B. Crawford, Rory B. Conolly, Russell S. Thomas
, Norbert E. Kaminski, Melvin E. Andersen
:
Stochastic Modeling of B Lymphocyte Terminal Differentiation and Its Suppression by Dioxin. 40 - Eleonora Piruzian, Sergey Bruskin, Alexander Ishkin, Rustam Abdeev, Sergey Moshkovskii
, Stanislav Melnik, Yuri Nikolsky, Tatiana Nikolskaya:
Integrated network analysis of transcriptomic and proteomic data in psoriasis. 41 - Verena Wolf, Rushil Goel, Maria Mateescu, Thomas A. Henzinger:
Solving the chemical master equation using sliding windows. 42 - Alain Coletta, John W. Pinney, David Y. Weiss Solís, James Marsh, Steve Pettifer
, Teresa K. Attwood
:
Low-complexity regions within protein sequences have position-dependent roles. 43 - Nurul Mohamad, Mikael Bodén
:
The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. 44 - Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha:
OptFlux: an open-source software platform for in silico metabolic engineering. 45 - Juan C. Triviño, Florencio Pazos
:
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. 46 - Jin Gu
, Yang Chen, Shao Li
, Yanda Li:
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. 47 - Guillermo Rodrigo
, Javier Carrera, Santiago F. Elena
, Alfonso Jaramillo
:
Robust dynamical pattern formation from a multifunctional minimal genetic circuit. 48 - Brett A. Boghigian, Hai Shi, Kyongbum Lee, Blaine A. Pfeifer:
Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. 49 - Han Yan, Bo Zhang, Shao Li
, Qianchuan Zhao
:
A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway. 50 - Huiqing Liu, Angela Rose Brannon, Anupama Reddy, Gabriela Alexe, Michael Seiler, Alexandra Arreola, Jay H. Oza
, Ming Yao, David Juan, Louis S. Liou, Shridar Ganesan, Arnold J. Levine, W. Kimryn Rathmell
, Gyan Bhanot:
Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. 51 - Matteo Brilli
, Marco Fondi
, Renato Fani, Alessio Mengoni
, Lorenzo Ferri
, Marco Bazzicalupo, Emanuele G. Biondi:
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. 52 - Joonhoon Kim
, Jennifer L. Reed:
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. 53 - Klaus Maier, Ute Hofmann
, Matthias Reuss, Klaus Mauch:
Dynamics and Control of the Central Carbon Metabolism in Hepatoma Cells. 54 - Hidde de Jong
, Caroline Ranquet, Delphine Ropers
, Corinne Pinel, Johannes Geiselmann
:
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. 55 - Kitiporn Plaimas
, Roland Eils
, Rainer König:
Identifying essential genes in bacterial metabolic networks with machine learning methods. 56 - Ming-yu Hsieh, Shujie Yang
, Mary Raymond-Stinz, Jeremy S. Edwards, Bridget S. Wilson:
Spatio-temporal modeling of signaling protein recruitment to EGFR. 57 - Alexei Vazquez, Jiangxia Liu, Yi Zhou, Zoltán N. Oltvai:
Catabolic efficiency of aerobic glycolysis: The Warburg effect revisited. 58 - Aurélien Mazurie
, Danail Bonchev, Benno Schwikowski
, Gregory A. Buck:
Evolution of metabolic network organization. 59 - Francisco Azuaje, Yvan Devaux, Daniel R. Wagner:
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. 60 - Joachim B. Ritter, Aljoscha Wahl
, Susann Freund, Yvonne Genzel
, Udo Reichl
:
Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profiling. 61 - Elizabeth Allen, Annick Moing
, Timothy M. D. Ebbels
, Mickaël Maucourt, A. Deri Tomos
, Dominique Rolin, Mark A. Hooks:
Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis. 62 - Sobia Raza, Neil McDerment, Paul A. Lacaze
, Kevin A. Robertson, Steven Watterson
, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal
, Tom C. Freeman:
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. 63 - Marc T. Facciotti, Wyming Lee 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:
Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. 64 - Tom C. Freeman, Sobia Raza, Athanasios Theocharidis, Peter Ghazal
:
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. 65 - Andreea Munteanu, Marco Constante
, Mark Isalan
, Ricard V. Solé
:
Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation. 66 - Raj Chari, Bradley P. Coe
, Emily A. Vucic
, William W. Lockwood, Wan L. Lam:
An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. 67 - Subir K. Nandy, Paula Jouhten
, Jens Nielsen
:
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. 68 - Philipp Rumschinski
, Steffen Borchers, Sandro Bosio, Robert Weismantel, Rolf Findeisen
:
Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks. 69 - Hung Ta
, Chang Yoon, Liisa Holm
, Seung Han:
Inferring the physical connectivity of complex networks from their functional dynamics. 70 - Dokyun Na
, Sunjae Lee
, Doheon Lee
:
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. 71 - Xian-Wen Ren, Xiaobo Zhou, Ling-Yun Wu, Xiang-Sun Zhang:
An information-flow-based model with dissipation, saturation and direction for active pathway inference. 72 - Axel Krinner, Martin Hoffmann, Markus Loeffler, Dirk Drasdo, Jörg Galle:
Individual fates of mesenchymal stem cells in vitro. 73 - Zhiao Shi, Catherine K. Derow, Bing Zhang:
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. 74 - Carla J. Davidson, Atul Narang
, Michael G. Surette:
Integration of transcriptional inputs at promoters of the arabinose catabolic pathway. 75 - Ettore Mosca
, Roberta Alfieri
, Ivan Merelli
, Federica Viti
, Andrea Calabria
, Luciano Milanesi
:
A multilevel data integration resource for breast cancer study. 76 - Diana Fusco, Luigi Grassi, Bruno Bassetti, Michele Caselle
, Marco Cosentino Lagomarsino
:
Ordered structure of the transcription network inherited from the yeast whole-genome duplication. 77 - Sreenivas Chavali
, Fredrik Barrenäs, Kartiek Kanduri
, Mikael Benson:
Network properties of human disease genes with pleiotropic effects. 78 - Jonathan Fromentin, Damien Eveillard
, Olivier F. Roux:
Hybrid modeling of biological networks: mixing temporal and qualitative biological properties. 79 - Jonathan E. Dickerson, John W. Pinney, David L. Robertson
:
The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. 80 - Mi Zhang, William R. Schafer
, Rainer Breitling
:
A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. 81 - Chao Wu, Fan Zhang, Xia Li, Shihua Zhang
, Jiang Li, Fei Su, Kongning Li, YuQing Yan:
Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test. 82 - Giovanni Iacono, Claudio Altafini
:
Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks. 83 - Hsiang Ho, Tijana Milenkovic, Vesna Memisevic, Jayavani Aruri, Natasa Przulj
, Anand K. Ganesan:
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. 84 - Nadia Felli
, Luciano Cianetti, Elvira Pelosi
, Alessandra Carè
, Chang Liu, George A. Calin
, Simona Rossi, Cesare Peschle, Giovanna Marziali
, Alessandro Giuliani
:
Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states. 85 - Michal Dabrowski
, Norbert Dojer, Malgorzata Zawadzka
, Jakub Mieczkowski
, Bozena Kaminska
:
Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems. 86 - Nicola Bernabò
, Mauro Mattioli, Barbara Barboni:
The spermatozoa caught in the net: the biological networks to study the male gametes post-ejaculatory life. 87 - Ozgur E. Akman, David A. Rand
, Paul E. Brown, Andrew J. Millar
:
Robustness from flexibility in the fungal circadian clock. 88 - Jason E. Shoemaker
, Kalyan Gayen
, Natàlia Garcia-Reyero, Edward J. Perkins, Daniel L. Villeneuve, Li Liu, Francis J. Doyle:
Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. 89 - Chengxiang Qiu
, Juan Wang, Pengying Yao, Edwin Wang, Qinghua Cui:
microRNA evolution in a human transcription factor and microRNA regulatory network. 90 - Ryo Hashimoto, Kazuko Hirose, Taku Sato, Nobuhiro Fukushima, Nobuaki Miura, Shin-Ichiro Nishimura:
Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank. 91 - 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
:
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. 92 - William J. Bosl, Rong Li:
The role of noise and positive feedback in the onset of autosomal dominant diseases. 93 - Alexander Hunziker, Mogens H. Jensen, Sandeep Krishna:
Stress-specific response of the p53-Mdm2 feedback loop. 94 - Balaji Veeramani, Joel S. Bader
:
Predicting functional associations from metabolism using bi-partite network algorithms. 95 - David van Dijk, Gökhan Ertaylan
, Charles A. B. Boucher, Peter M. A. Sloot:
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. 96 - Hong Yu
, Jialiang Huang, Nan Qiao, Christopher D. Green, Jing-Dong J. Han:
Evaluating diabetes and hypertension disease causality using mouse phenotypes. 97 - Victoria V. Mironova
, Nadezda A. Omelyanchuk, Guy Yosiphon, Stanislav I. Fadeev, Nikolay A. Kolchanov
, Eric Mjolsness, Vitali A. Likhoshvai:
A plausible mechanism for auxin patterning along the developing root. 98 - Yuanfeng Wang, Scott Christley, Eric Mjolsness
, Xiaohui Xie:
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. 99 - Anna C. F. Lewis, Nick S. Jones
, Mason A. Porter, Charlotte M. Deane
:
The function of communities in protein interaction networks at multiple scales. 100 - Simon van Mourik, Aalt D. J. van Dijk, Maarten de Gee, Richard G. H. Immink
, Kerstin Kaufmann
, Gerco C. Angenent, Roeland C. H. J. van Ham, Jaap Molenaar:
Continuous-time modeling of cell fate determination in Arabidopsis flowers. 101 - Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias E. Futschik
, Enrico Capobianco:
Inferring modules from human protein interactome classes. 102 - Thanh-Phuong Nguyen, Ferenc Jordán:
A quantitative approach to study indirect effects among disease proteins in the human protein interaction network. 103 - Andrew E. Teschendorff, Simone Severini:
Increased entropy of signal transduction in the cancer metastasis phenotype. 104 - Abhay K. Singh, Thanura R. Elvitigala, Jeffrey C. Cameron, Bijoy K. Ghosh, Maitrayee Bhattacharyya-Pakrasi, Himadri B. Pakrasi:
Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. 105 - Andrea C. Pfeifer, Daniel Kaschek, Julie Bachmann, Ursula Klingmüller
, Jens Timmer:
Model-based extension of high-throughput to high-content data. 106 - Scott Christley, Briana Lee, Xing Dai
, Qing Nie:
Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. 107 - Steffen Waldherr
, Jingbo Wu, Frank Allgöwer
:
Bridging time scales in cellular decision making with a stochastic bistable switch. 108 - Nail M. Gizzatkulov, Igor Goryanin
, Eugeny A. Metelkin
, Ekaterina A. Mogilevskaya, Kirill Peskov
, Oleg V. Demin:
DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. 109 - Pau Rué
, Jordi Villà-Freixa
, Kevin Burrage
:
Simulation methods with extended stability for stiff biochemical Kinetics. 110 - Mariana Obertello, Gabriel Krouk
, Manpreet S. Katari
, Suzan J. Runko, Gloria M. Coruzzi
:
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. 111 - Tiago J. S. Lopes, Tatyana Luganskaja, Maja Vujic Spasic, Matthias W. Hentze
, Martina U. Muckenthaler
, Klaus Schümann, Jens G. Reich:
Systems analysis of iron metabolism: the network of iron pools and fluxes. 112 - Alexandre Domingues, Susana Vinga
, João Miranda Lemos
:
Optimization strategies for metabolic networks. 113 - Karin Radrich, Yoshimasa Tsuruoka
, Paul D. Dobson, Albert Gevorgyan, Neil Swainston, Gino Baart, Jean-Marc Schwartz
:
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. 114