Works matching IS 17520509 AND DT 2018 AND VI 12 AND IP 1

Results: 57

Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0668-5

By:

Song, Min;
Finley, Stacey D.

Publication type:

Article

Parameter estimation of qualitative biological regulatory networks on high performance computing hardware.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0670-y

By:

Saeed, Muhammad Tariq;
Ahmad, Jamil;
Baumbach, Jan;
Pauling, Josch;
Shafi, Aamir;
Paracha, Rehan Zafar;
Hayat, Asad;
Ali, Amjad

Publication type:

Article

Qualitative modelling of the interplay of inflammatory status and butyrate in the human gut: a hypotheses about robust bi-stability.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0667-6

By:

Neumann, Gunter;
Wall, Rebecca;
Rangel, Ignacio;
Marques, Tatiana M.;
Repsilber, Dirk

Publication type:

Article

Reframing gene essentiality in terms of adaptive flexibility.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0653-z

By:

Guzmán, Gabriela I.;
Olson, Connor A.;
Hefner, Ying;
Phaneuf, Patrick V.;
Catoiu, Edward;
Crepaldi, Lais B.;
Micas, Lucas Goldschmidt;
Palsson, Bernhard O.;
Feist, Adam M.

Publication type:

Article

The anticancer mechanism investigation of Tanshinone II<sub>A</sub> by pharmacological clustering in protein network.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0606-6

By:

Cao, Yan-feng;
Wang, Shi-feng;
Li, Xi;
Zhang, Yan-ling;
Qiao, Yan-jiang

Publication type:

Article

Retraction Note: detangling PPI networks to uncover functionally meaningful clusters.

Published in:

2018

By:

Hall-Swan, Sarah;
Crawford, Jake;
Newman, Rebecca;
Cowen, Lenore J.

Publication type:

Correction Notice

Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0632-4

By:

Martínez, Juan A.;
Rodriguez, Alberto;
Moreno, Fabian;
Flores, Noemí;
Lara, Alvaro R.;
Ramírez, Octavio T.;
Gosset, Guillermo;
Bolivar, Francisco

Publication type:

Article

Multi-component gene network design as a survival strategy in diverse environments.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0609-3

By:

Luo, Xinyue;
Song, Ruijie;
Acar, Murat

Publication type:

Article

A method for efficient Bayesian optimization of self-assembly systems from scattering data.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0592-8

By:

Thomas, Marcus;
Schwartz, Russell

Publication type:

Article

Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0610-x

By:

Sagar, Adithya;
LeCover, Rachel;
Varner, Jeffrey;
Shoemaker, Christine

Publication type:

Article

Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0605-7

By:

Cook, Daniel;
Achanta, Sirisha;
Hoek, Jan B.;
Ogunnaike, Babatunde A.;
Vadigepalli, Rajanikanth

Publication type:

Article

Escher-FBA: a web application for interactive flux balance analysis.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0607-5

By:

Rowe, Elliot;
Palsson, Bernhard O.;
King, Zachary A.

Publication type:

Article

Sex differences in hepatic one-carbon metabolism.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0621-7

By:

Sadre-Marandi, Farrah;
Dahdoul, Thabat;
Reed, Michael C.;
Nijhout, H. Frederik

Publication type:

Article

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0620-8

By:

Conrad, T.;
Kniemeyer, O.;
Henkel, S. G.;
Krüger, T.;
Mattern, D. J.;
Valiante, V.;
Guthke, R.;
Jacobsen, I. D.;
Brakhage, A. A.;
Vlaic, S.;
Linde, J.

Publication type:

Article

The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0608-4

By:

Olney, Kimberly C.;
Nyer, David B.;
Vargas, Daniel A.;
Wilson Sayres, Melissa A.;
Haynes, Karmella A.

Publication type:

Article

Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0601-y

By:

Rowland, Michael A.;
Wear, Hannah;
Watanabe, Karen H.;
Gust, Kurt A.;
Mayo, Michael L.

Publication type:

Article

A systematic survey of centrality measures for protein-protein interaction networks.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0598-2

By:

Ashtiani, Minoo;
Salehzadeh-Yazdi, Ali;
Razaghi-Moghadam, Zahra;
Hennig, Holger;
Wolkenhauer, Olaf;
Mirzaie, Mehdi;
Jafari, Mohieddin

Publication type:

Article

Evaluating model reduction under parameter uncertainty.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0602-x

By:

Frøysa, Håvard G.;
Fallahi, Shirin;
Blaser, Nello

Publication type:

Article

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0584-8

By:

Smith, Robert W.;
van Rosmalen, Rik P.;
Martins dos Santos, Vitor A. P.;
Fleck, Christian

Publication type:

Article

An ensemble of mathematical models showing diauxic growth behaviour.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0604-8

By:

Kremling, Andreas;
Geiselmann, Johannes;
Ropers, Delphine;
de Jong, Hidde

Publication type:

Article

Extracting proteins involved in disease progression using temporally connected networks.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0600-z

By:

Anand, Rajat;
Sarmah, Dipanka Tanu;
Chatterjee, Samrat

Publication type:

Article

Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0597-3

By:

Strome, Bob;
Hsu, Ian Shenyen;
Li Cheong Man, Mitchell;
Zarin, Taraneh;
Nguyen Ba, Alex;
Moses, Alan M.

Publication type:

Article

RACIPE: a computational tool for modeling gene regulatory circuits using randomization.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0594-6

By:

Huang, Bin;
Jia, Dongya;
Feng, Jingchen;
Levine, Herbert;
Onuchic, José N.;
Lu, Mingyang

Publication type:

Article

How accurate is automated gap filling of metabolic models?

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0593-7

By:

Karp, Peter D.;
Weaver, Daniel;
Latendresse, Mario

Publication type:

Article

A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0603-9

By:

Liu, Guan-Sheng;
Ballweg, Richard;
Ashbaugh, Alan;
Zhang, Yin;
Facciolo, Joseph;
Cushion, Melanie T.;
Zhang, Tongli

Publication type:

Article

High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0599-1

By:

Sedghamiz, Hooman;
Morris, Matthew;
Craddock, Travis J. A.;
Whitley, Darrell;
Broderick, Gordon

Publication type:

Article

Single molecules can operate as primitive biological sensors, switches and oscillators.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0596-4

By:

Hernansaiz-Ballesteros, Rosa D.;
Cardelli, Luca;
Csikász-Nagy, Attila

Publication type:

Article

SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0581-y

By:

Woodhouse, Steven;
Piterman, Nir;
Wintersteiger, Christoph M.;
Göttgens, Berthold;
Fisher, Jasmin

Publication type:

Article

Dynamic elementary mode modelling of non-steady state flux data.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0589-3

By:

Folch-Fortuny, Abel;
Teusink, Bas;
Hoefsloot, Huub C.J.;
Smilde, Age K.;
Ferrer, Alberto

Publication type:

Article

Landscape reveals critical network structures for sharpening gene expression boundaries.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0595-5

By:

Li, Chunhe;
Zhang, Lei;
Nie, Qing

Publication type:

Article

<italic>Escherichia coli</italic> B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0587-5

By:

Fang, Xin;
Monk, Jonathan M.;
Mih, Nathan;
Du, Bin;
Sastry, Anand V.;
Kavvas, Erol;
Seif, Yara;
Smarr, Larry;
Palsson, Bernhard O.

Publication type:

Article

NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. 1, doi. 10.1186/s12918-018-0590-x

By:

Preston, Claudia C.;
Wyles, Saranya P.;
Reyes, Santiago;
Storm, Emily C.;
Eckloff, Bruce W.;
Faustino, Randolph S.

Publication type:

Article

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0588-4

By:

McNally, Colin P.;
Borenstein, Elhanan

Publication type:

Article

Principal process analysis of biological models.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0586-6

By:

Casagranda, Stefano;
Touzeau, Suzanne;
Ropers, Delphine;
Gouzé, Jean-Luc

Publication type:

Article

Identification of reaction organization patterns that naturally cluster enzymatic transformations.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. 1, doi. 10.1186/s12918-018-0583-9

By:

Vazquez-Hernandez, Carlos;
Loza, Antonio;
Peguero-Sanchez, Esteban;
Segovia, Lorenzo;
Gutierrez-Rios, Rosa-Maria

Publication type:

Article

Reconstruction of a genome-scale metabolic model for <italic>Actinobacillus succinogenes</italic> 130Z.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0585-7

By:

Pereira, Bruno;
Miguel, Joana;
Vilaça, Paulo;
Soares, Simão;
Rocha, Isabel;
Carneiro, Sónia

Publication type:

Article

A computational framework for complex disease stratification from multiple large-scale datasets.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0556-z

By:

De Meulder, Bertrand;
Lefaudeux, Diane;
Bansal, Aruna T.;
Mazein, Alexander;
Chaiboonchoe, Amphun;
Ahmed, Hassan;
Balaur, Irina;
Saqi, Mansoor;
Pellet, Johann;
Ballereau, Stéphane;
Lemonnier, Nathanaël;
Sun, Kai;
Pandis, Ioannis;
Yang, Xian;
Batuwitage, Manohara;
Kretsos, Kosmas;
van Eyll, Jonathan;
Bedding, Alun;
Davison, Timothy;
Dodson, Paul

Publication type:

Article

Simulating heterogeneous populations using Boolean models.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0591-9

By:

Ross, Brian C.;
Boguslav, Mayla;
Weeks, Holly;
Costello, James C.

Publication type:

Article

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0582-x

By:

Zhang, Qingyang

Publication type:

Article

New perspectives: systems medicine in cardiovascular disease.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0579-5

By:

Kramer, Frank;
Just, Steffen;
Zeller, Tanja

Publication type:

Article

Evolution of computational models in BioModels Database and the Physiome Model Repository.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0553-2

By:

Scharm, Martin;
Gebhardt, Tom;
Touré, Vasundra;
Bagnacani, Andrea;
Salehzadeh-Yazdi, Ali;
Wolkenhauer, Olaf;
Waltemath, Dagmar

Publication type:

Article

KDiamend: a package for detecting key drivers in a molecular ecological network of disease.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0531-8

By:

Lyu, Mengxuan;
Chen, Jiaxing;
Jiang, Yiqi;
Dong, Wei;
Fang, Zhou;
Li, Shuaicheng

Publication type:

Article

Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0535-4

By:

Yim, Soorin;
Yu, Hasun;
Jang, Dongjin;
Lee, Doheon

Publication type:

Article

Regulation of dual specificity phosphatases in breast cancer during initial treatment with Herceptin: a Boolean model analysis.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0534-5

By:

Buiga, Petronela;
Elson, Ari;
Tabernero, Lydia;
Schwartz, Jean-Marc

Publication type:

Article

Counting motifs in dynamic networks.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0533-6

By:

Mukherjee, Kingshuk;
Hasan, Md Mahmudul;
Boucher, Christina;
Kahveci, Tamer

Publication type:

Article

Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0532-7

By:

Yu, Hui;
Mao, Kui-Tao;
Shi, Jian-Yu;
Huang, Hua;
Chen, Zhi;
Dong, Kai;
Yiu, Siu-Ming

Publication type:

Article

Putative human sperm Interactome: a networks study.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0578-6

By:

Ordinelli, Alessandra;
Bernabò, Nicola;
Orsini, Massimiliano;
Mattioli, Mauro;
Barboni, Barbara

Publication type:

Article

Comparisons of gene coexpression network modules in breast cancer and ovarian cancer.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0530-9

By:

Zhang, Shuqin

Publication type:

Article

Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0529-2

By:

Ranjan, Bobby;
Chong, Ket Hing;
Zheng, Jie

Publication type:

Article

Discovery of Boolean metabolic networks: integer linear programming based approach.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0528-3

By:

Qiu, Yushan;
Jiang, Hao;
Ching, Wai-Ki;
Cheng, Xiaoqing

Publication type:

Article