Works matching IS 17520509 AND DT 2013 AND VI 7 AND IP 1

Results: 141

(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-131

By:

Fei He;
Fromion, Vincent;
Westerhoff, Hans V.

Publication type:

Article

RaTrav: a tool for calculating mean first-passage times on biochemical networks.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-130

By:

Torchala, Mieczyslaw;
Chelminiak, Przemyslaw;
Kurzynski, Michal;
Bates, Paul A.

Publication type:

Article

MC<sup>3</sup>: a steady-state model and constraint consistency checker for biochemical networks.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-129

By:

Yousofshahi, Mona;
Ullah, Ehsan;
Stern, Russell;
Hassoun, Soha

Publication type:

Article

Rosen's (M,R) system in process algebra.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-128

By:

Gatherer, Derek;
Galpin, Vashti

Publication type:

Article

Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-122

By:

Kening Li;
Zihui Li;
Ning Zhao;
Yaoqun Xu;
Yongjing Liu;
Yuanshuai Zhou;
Desi Shang;
Fujun Qiu;
Rui Zhang;
Zhiqiang Chang;
Yan Xu

Publication type:

Article

Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-126

By:

Misra, Ashish;
Sriram, Ganesh

Publication type:

Article

sybil - Efficient constraint-based modelling in R.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-125

By:

Gelius-Dietrich, Gabriel;
Desouki, Abdelmoneim Amer;
Fritzemeier, Claus Jonathan;
Lercher, Martin J.

Publication type:

Article

Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-124

By:

Weber, Michael;
Sotoca, Ana M.;
Kupfer, Peter;
Guthke, Reinhard;
van Zoelen, Everardus J.

Publication type:

Article

Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-123

By:

Sen, Partho;
Vial, Henri J.;
Radulescu, Ovidiu

Publication type:

Article

Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-127

By:

Freyre-González, Julio A.;
Manjarrez-Casas, Alejandra M.;
Merino, Enrique;
Martinez-Nuñez, Mario;
Perez-Rueda, Ernesto;
Gutiérrez-Ríos, Rosa-María

Publication type:

Article

Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer’s disease.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-121

By:

Mayburd, Anatoly;
Baranova, Ancha

Publication type:

Article

Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-120

By:

Qinghua Wang;
Venkataramanan, Keerthi Prasad;
Hongzhan Huang;
Papoutsakis, Eleftherios T.;
Wu, Cathy H.

Publication type:

Article

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-119

By:

Williams-DeVane, ClarLynda R.;
Reif, David M.;
Hubal, Elaine Cohen;
Bushel, Pierre R.;
Hudgens, Edward E.;
Gallagher, Jane E.;
Edwards, Stephen W.

Publication type:

Article

Identification of direction in gene networks from expression and methylation.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-118

By:

Simcha, David M.;
Younes, Laurent;
Aryee, Martin J.;
Geman, Donald

Publication type:

Article

Merging concepts - coupling an agent-based model of hematopoietic stem cells with an ODE model of granulopoiesis.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-117

By:

Krinner, Axel;
Roeder, Ingo;
Loeffler, Markus;
Scholz, Markus

Publication type:

Article

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 3, doi. 10.1186/1752-0509-7-116

By:

Büchel, Finja;
Rodriguez, Nicolas;
Swainston, Neil;
Wrzodek, Clemens;
Czauderna, Tobias;
Keller, Roland;
Mittag, Florian;
Schubert, Michael;
Glont, Mihai;
Golebiewski, Martin;
van Iersel, Martijn;
Keating, Sarah;
Rall, Matthias;
Wybrow, Michael;
Hermjakob, Henning;
Hucka, Michael;
Kell, Douglas B.;
Müller, Wolfgang;
Mendes, Pedro;
Zell, Andreas

Publication type:

Article

Translation of SBGN maps: Process Description to Activity Flow.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-115

By:

Vogt, Torsten;
Czauderna, Tobias;
Schreiber, Falk

Publication type:

Article

Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-114

By:

Ponce-de-Léon, Miguel;
Montero, Francisco;
Peretó, Juli

Publication type:

Article

Identification of regulatory structure and kinetic parameters of biochemical networks via mixedinteger dynamic optimization.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-113

By:

Guillén-Gosálbez, Gonzalo;
Miró, Antoni;
Alves, Rui;
Sorribas, Albert;
Jiménez, Laureano

Publication type:

Article

Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-112

By:

Pengping Li;
Xu Hua;
Zhen Zhang;
Jie Li;
Jin Wang

Publication type:

Article

Joint estimation of causal effects from observational and intervention gene expression data.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-111

By:

Rau, Andrea;
Jaffrézic, Florence;
Nuel, Grégory

Publication type:

Article

A combinatorial approach of Proteomics and Systems Biology in unravelling the mechanisms of acute kidney injury (AKI): involvement of NMDA receptor GRIN1 in murine AKI.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-110

By:

Husi, Holger;
Sanchez-Niño, Maria Dolores;
Delles, Christian;
Mullen, William;
Vlahou, Antonia;
Ortiz, Alberto;
Mischak, Harald

Publication type:

Article

Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-103

By:

Massucci, Francesco A.;
Di Nuzzo, Mauro;
Giove, Federico;
Maraviglia, Bruno;
Castillo, Isaac Perez;
Marinari, Enzo;
De Martino, Andrea

Publication type:

Article

Antibacterial mechanisms identified through structural systems pharmacology.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-102

By:

Roger L. Chang;
Lei Xie;
Bourne, Philip E.;
Palsson, Bernhard O.

Publication type:

Article

ENNET: inferring large gene regulatory networks from expression data using gradient boosting.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-106

By:

Sławek, Janusz;
Arodź, Tomasz

Publication type:

Article

Construction of the influenza A virus infectioninduced cell-specific inflammatory regulatory network based on mutual information and optimization.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-105

By:

Suoqin Jin;
Xiufen Zou

Publication type:

Article

Systematic design methodology for robust genetic transistors based on I/O specifications via promoter- RBS libraries.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-109

By:

Yi-Ying Lee;
Chih-Yuan Hsu;
Ling-Jiun Lin;
Chih-Chun Chang;
Hsiao-Chun Cheng;
Tsung-Hsien Yeh;
Rei-Hsing Hu;
Che Lin;
Zhen Xie;
Bor-Sen Chen

Publication type:

Article

A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-107

By:

Kotze, Helen L.;
Armitage, Emily G.;
Sharkey, Kieran J.;
Allwood, James W.;
Dunn, Warwick B.;
Williams, Kaye J.;
Goodacre, Royston

Publication type:

Article

Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-104

By:

Bessho, Kazuhiko;
Shanmukhappa, Kumar;
Sheridan, Rachel;
Shivakumar, Pranavkumar;
Mourya, Reena;
Walters, Stephanie;
Kaimal, Vivek;
Dilbone, Eric;
Jegga, Anil G.;
Bezerra, Jorge A.

Publication type:

Article

Automated design of bacterial genome sequences.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-108

By:

Carrera, Javier;
Jaramillo, Alfonso

Publication type:

Article

Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-101

By:

Hongbo Shi;
Juan Xu;
Guangde Zhang;
Liangde Xu;
Chunquan Li;
Li Wang;
Zheng Zhao;
Wei Jiang;
Zheng Guo;
Xia Li

Publication type:

Article

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-100

By:

Kuperstein, Inna;
Cohen, David P. A.;
Pook, Stuart;
Viara, Eric;
Calzone, Laurence;
Barillot, Emmanuel;
Zinovyev, Andrei

Publication type:

Article

Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-99

By:

Barba, Matthieu;
Dutoit, Raphaël;
Legrain, Christianne;
Labedan, Bernard

Publication type:

Article

Reconstruction of the experimentally supported human protein interactome: what can we learn?

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-96

By:

Klapa, Maria I.;
Tsafou, Kalliopi;
Theodoridis, Evangelos;
Tsakalidis, Athanasios;
Moschonas, Nicholas K.

Publication type:

Article

A comprehensive map of the influenza A virus replication cycle.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-97

By:

Yukiko Matsuoka;
Hiromi Matsumae;
Manami Katoh;
Eisfeld, Amie J.;
Neumann, Gabriele;
Takeshi Hase;
Ghosh, Samik;
Shoemaker, Jason E.;
Lopes, Tiago J. S.;
Tokiko Watanabe;
Shinji Watanabe;
Satoshi Fukuyama;
Hiroaki Kitano;
Yoshihiro Kawaoka

Publication type:

Article

An objective function exploiting suboptimal solutions in metabolic networks.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-98

By:

Wintermute, Edwin H.;
Lieberman, Tami D.;
Silver, Pamela A.

Publication type:

Article

JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-93

By:

Srivastava, Prashant K.;
Hull, Richard P.;
Behmoaras, Jacques;
Petretto, Enrico;
Aitman, Timothy J.

Publication type:

Article

Analysis of L-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-92

By:

Yousuke Nishio;
Soichi Ogishima;
Masao Ichikawa;
Yohei Yamada;
Yoshihiro Usuda;
Tadashi Masuda;
Hiroshi Tanaka

Publication type:

Article

Identification of parameter correlations for parameter estimation in dynamic biological models.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-91

By:

Pu Li;
Quoc Dong Vu

Publication type:

Article

Global insights into energetic and metabolic networks in Rhodobacter sphaeroides.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-89

By:

Saheed Imam;
Noguera, Daniel R.;
Donohue, Timothy J.

Publication type:

Article

An online model composition tool for system biology models.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-88

By:

Coskun, Sarp A.;
Cicek, A. Ercument;
Lai, Nicola;
Dash, Ranjan K.;
Ozsoyoglu, Z. Meral;
Ozsoyoglu, Gultekin

Publication type:

Article

Modularity and evolutionary constraints in a baculovirus gene regulatory network.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-87

By:

Oliveira, Juliana Velasco;
de Brito, Anderson Fernandes;
Braconi, Carla Torres;
Freire, Caio César de Melo;
Iamarino, Atila;
Zanotto, Paolo Marinho de Andrade

Publication type:

Article

Identification of upstream regulators for prognostic expression signature genes in colorectal cancer.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-86

By:

Taejeong Bae;
Kyoohyoung Rho;
Jin Woo Choi;
Katsuhisa Horimoto;
Wankyu Kim;
Sunghoon Kim

Publication type:

Article

Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-85

By:

Asfar S. Azmi;
Aliccia Bollig-Fischer;
Bin Bao;
Bum-Joon Park;
Sun-Hye Lee;
Gyu Yong-Song;
Dyson, Gregory;
Reddy, Chandan K.;
Sarkar, Fazlul H.;
Mohammad, Ramzi M.

Publication type:

Article

Post-translational regulation enables robust p53 regulation.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-83

By:

Yong-Jun Shin;
Kai-Yuan Chen;
Ali H. Sayed;
Brandon Hencey;
Xiling Shen

Publication type:

Article

A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-8

By:

Krengel, Annette;
Hauth, Jan;
Taskinen, Marja-Riitta;
Adiels, Martin;
Jirstrand, Mats

Publication type:

Article

New network topology approaches reveal differential correlation patterns in breast cancer.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-78

By:

Bockmayr, Michael;
Klauschen, Frederick;
Györffy, Balazs;
Denkert, Carsten;
Budczies, Jan

Publication type:

Article

Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-75

By:

Treenut Saithong;
Oratai Rongsirikul;
Saowalak Kalapanulak;
Porntip Chiewchankaset;
Wanatsanan Siriwat;
Supatcharee Netrphan;
Malinee Suksangpanomrung;
Asawin Meechai;
Supapon Cheevadhanarak

Publication type:

Article

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-73

By:

Pinna, Andrea;
Heise, Sandra;
Flassig, Robert J.;
de la Fuente, Alberto;
Klamt, Steffen

Publication type:

Article

The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-95

By:

Palsson, Sirus;
Hickling, Timothy P.;
Bradshaw-Pierce, Erica L.;
Zager, Michael;
Jooss, Karin;
O’Brien, Peter J.;
Spilker, Mary E.;
Palsson, Bernhard O.;
Vicini, Paolo

Publication type:

Article