Works matching DE "SYSTEMS biology"

Results: 3901

The plk1 Gene Regulatory Network Modeling Identifies Three Circuits for plk1 -mediated Genomic Instability Leading to Neoplastic Transformation.

Published in:

Life (2075-1729), 2025, v. 15, n. 5, p. 799, doi. 10.3390/life15050799

By:

Suescum-Holguín, Jeison F.;
Clavijo-Buriticá, Diana Carolina;
Carrillo-Borda, Edward Fabian;
Quimbaya, Mauricio Alberto

Publication type:

Article

Synthesizing Time-Series Gene Expression Data to Enhance Network Inference Performance Using Autoencoder.

Published in:

Applied Sciences (2076-3417), 2025, v. 15, n. 10, p. 5768, doi. 10.3390/app15105768

By:

Anh, Cao-Tuan;
Kwon, Yung-Keun

Publication type:

Article

Leveraging genome-scale metabolic models to understand aerobic methanotrophs.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrae102

By:

Wutkowska, Magdalena;
Tláskal, Vojtěch;
Bordel, Sergio;
Stein, Lisa Y;
Nweze, Justus Amuche;
Daebeler, Anne

Publication type:

Article

Bacterial development: Racing to decide.

Published in:

Nature Reviews Microbiology, 2012, v. 10, n. 2, p. 84, doi. 10.1038/nrmicro2735

By:

Muers, Mary

Publication type:

Article

Using movies to analyse gene circuit dynamics in single cells.

Published in:

Nature Reviews Microbiology, 2009, v. 7, n. 5, p. 383, doi. 10.1038/nrmicro2056

By:

Locke, James C. W.;
Elowitz, Michael B.

Publication type:

Article

Systems Biology: Functional analysis of natural microbial consortia using community proteomics.

Published in:

Nature Reviews Microbiology, 2009, v. 7, n. 3, p. 196, doi. 10.1038/nrmicro2080

By:

VerBerkmoes, Nathan C.;
Denef, Vincent J.;
Hettich, Robert L.;
Banfield, Jillian F.

Publication type:

Article

What Should We Call 'Systems Biology'?

Published in:

2011

By:

Smith, Desmond

Publication type:

Opinion

The Era of Big Data Analytics.

Published in:

Bio-IT World, 2011, v. 10, n. 1, p. 61

By:

RUSSELL, JOHN

Publication type:

Article

A model of chlorophyll a fluorescence induction kinetics with explicit description of structural constraints of individual photosystem II units.

Published in:

Photosynthesis Research, 2013, v. 117, n. 1-3, p. 339, doi. 10.1007/s11120-013-9894-2

By:

Xin, Chang-Peng;
Yang, Jin;
Zhu, Xin-Guang

Publication type:

Article

Identification of components in biochemical pathways: extensive application to SBML models.

Published in:

Natural Computing, 2014, v. 13, n. 3, p. 351, doi. 10.1007/s11047-014-9433-x

By:

Pardini, Giovanni;
Milazzo, Paolo;
Maggiolo-Schettini, Andrea

Publication type:

Article

Petri net models for the semi-automatic construction of large scale biological networks.

Published in:

Natural Computing, 2011, v. 10, n. 3, p. 1077, doi. 10.1007/s11047-009-9151-y

By:

Ming Chen;
Hariharaputran, Sridhar;
Hofestädt, Ralf;
Kormeier, Benjamin;
Spangardt, Sarah

Publication type:

Article

Hybrid Petri net based modeling for biological pathway simulation.

Published in:

Natural Computing, 2011, v. 10, n. 3, p. 1099, doi. 10.1007/s11047-009-9164-6

By:

Matsuno, Hiroshi;
Nagasaki, Masao;
Miyano, Satoru

Publication type:

Article

Preface: Petri nets for Systems and Synthetic Biology.

Published in:

Natural Computing, 2011, v. 10, n. 3, p. 987, doi. 10.1007/s11047-011-9263-z

By:

Heiner, Monika

Publication type:

Article

P systems with active membranes: trading time for space.

Published in:

Natural Computing, 2011, v. 10, n. 1, p. 167, doi. 10.1007/s11047-010-9189-x

By:

Porreca, Antonio E.;
Leporati, Alberto;
Mauri, Giancarlo;
Zandron, Claudio

Publication type:

Article

A review of the nondeterministic waiting time algorithm.

Published in:

Natural Computing, 2011, v. 10, n. 1, p. 139, doi. 10.1007/s11047-010-9195-z

By:

Jack, John;
Păun, Andrei;
Rodríguez-Patón, Alfonso

Publication type:

Article

On discrete models and immunological algorithms for protein structure prediction.

Published in:

Natural Computing, 2011, v. 10, n. 1, p. 91, doi. 10.1007/s11047-010-9196-y

By:

Cutello, Vincenzo;
Morelli, Giuseppe;
Nicosia, Giuseppe;
Pavone, Mario;
Scollo, Giuseppe

Publication type:

Article

Hybrid Functional Petri Nets as MP systems.

Published in:

Natural Computing, 2010, v. 9, n. 1, p. 61, doi. 10.1007/s11047-009-9121-4

By:

Castellini, Alberto;
Franco, Giuditta;
Manca, Vincenzo

Publication type:

Article

Deterministic and stochastic P systems for modelling cellular processes.

Published in:

Natural Computing, 2010, v. 9, n. 2, p. 457, doi. 10.1007/s11047-009-9158-4

By:

Gheorghe, Marian;
Manca, Vincenzo;
Romero-Campero, Francisco J.

Publication type:

Article

Information networks for disease: commonalities in human management networks and within-host signalling networks.

Published in:

European Journal of Plant Pathology, 2012, v. 133, n. 1, p. 75, doi. 10.1007/s10658-012-9963-y

By:

Garrett, K.

Publication type:

Article

Systems biology approach to Wilson's disease.

Published in:

BioMetals, 2011, v. 24, n. 3, p. 455, doi. 10.1007/s10534-011-9430-9

By:

Burkhead, Jason L.;
Gray, Lawrence W.;
Lutsenko, Svetlana

Publication type:

Article

Optimal resource allocation enables mathematical exploration of microbial metabolic configurations.

Published in:

Journal of Mathematical Biology, 2017, v. 75, n. 6/7, p. 1349, doi. 10.1007/s00285-017-1118-5

By:

Tournier, Laurent;
Goelzer, Anne;
Fromion, Vincent

Publication type:

Article

Inverse problems from biomedicine.

Published in:

Journal of Mathematical Biology, 2013, v. 67, n. 1, p. 143, doi. 10.1007/s00285-012-0523-z

By:

Lu, James;
August, Elias;
Koeppl, Heinz

Publication type:

Article

The interaction graph structure of mass-action reaction networks.

Published in:

Journal of Mathematical Biology, 2012, v. 65, n. 2, p. 375, doi. 10.1007/s00285-011-0462-0

By:

Domijan, Mirela;
Pécou, Elisabeth

Publication type:

Article

Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast.

Published in:

Journal of Mathematical Biology, 2011, v. 62, n. 5, p. 685, doi. 10.1007/s00285-010-0350-z

By:

Marucci, Lucia;
Santini, Stefania;
Bernardo, Mario;
di Bernardo, Diego

Publication type:

Article

Identification of feedback loops embedded in cellular circuits by investigating non-causal impulse response components.

Published in:

Journal of Mathematical Biology, 2010, v. 60, n. 2, p. 285, doi. 10.1007/s00285-009-0263-x

By:

Dong, Chao-Yi;
Yoon, Tae-Woong;
Bates, Declan;
Cho, Kwang-Hyun

Publication type:

Article

Statistical model checking for biological applications.

Published in:

International Journal on Software Tools for Technology Transfer, 2015, v. 17, n. 4, p. 527, doi. 10.1007/s10009-014-0343-0

By:

Zuliani, Paolo

Publication type:

Article

Erratum to: Pressure cycling technology (PCT) reduces effects of inhibitors of the PCR.

Published in:

2014

By:

Marshall, Pamela;
King, Jonathan;
Lawrence, Nathan;
Lazarev, Alexander;
Gross, Vera;
Budowle, Bruce

Publication type:

Erratum

High-altitude pulmonary hypertension: a comprehensive review of mechanisms and management.

Published in:

2025

By:

Yang, Xitong;
Liu, Hong;
Wu, Xinhua

Publication type:

Literature Review

Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms.

Published in:

Applied Microbiology & Biotechnology, 2011, v. 90, n. 2, p. 407, doi. 10.1007/s00253-011-3172-z

By:

Porteus, Bianca;
Kocharunchitt, Chawalit;
Nilsson, Rolf E.;
Ross, Tom;
Bowman, John P.

Publication type:

Article

Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism.

Published in:

Applied Microbiology & Biotechnology, 2010, v. 88, n. 5, p. 1065, doi. 10.1007/s00253-010-2854-2

By:

Kohlstedt, Michael;
Becker, Judith;
Wittmann, Christoph

Publication type:

Article

The metabolomics of carotenoids in engineered cell factory.

Published in:

Applied Microbiology & Biotechnology, 2009, v. 83, n. 6, p. 989, doi. 10.1007/s00253-009-2069-6

By:

Guan-Nan Liu;
Yue-Hui Zhu;
Jian-Guo Jiang

Publication type:

Article

Advances in phosphopeptide enrichment techniques for phosphoproteomics.

Published in:

Amino Acids, 2012, v. 43, n. 3, p. 1009, doi. 10.1007/s00726-012-1288-9

By:

Beltran, Luisa;
Cutillas, Pedro

Publication type:

Article

A combined model of hepatic polyamine and sulfur amino acid metabolism to analyze S-adenosyl methionine availability.

Published in:

Amino Acids, 2012, v. 42, n. 2/3, p. 597, doi. 10.1007/s00726-011-1035-7

By:

Reyes-Palomares, Armando;
Montañez, Raúl;
Sánchez-Jiménez, Francisca;
Medina, Miguel

Publication type:

Article

Systems bioenergetics of creatine kinase networks: physiological roles of creatine and phosphocreatine in regulation of cardiac cell function.

Published in:

Amino Acids, 2011, v. 40, n. 5, p. 1333, doi. 10.1007/s00726-011-0854-x

By:

Guzun, R.;
Timohhina, N.;
Tepp, K.;
Gonzalez-Granillo, M.;
Shevchuk, I.;
Chekulayev, V.;
Kuznetsov, A.;
Kaambre, T.;
Saks, V.

Publication type:

Article

Novel Holistic Approaches for Overcoming Therapy Resistance in Pancreatic and Colon Cancers.

Published in:

Medical Principles & Practice, 2016, v. 25, p. 3, doi. 10.1159/000435814

By:

Sarkar, Fazlul H.

Publication type:

Article

Comparative analysis of waterlogging and drought stress regulatory networks in barley (Hordeum vulgare).

Published in:

Functional Plant Biology, 2025, v. 52, n. 3, p. 1, doi. 10.1071/FP24051

By:

Panahi, Bahman

Publication type:

Article

Characteristic features of measurements and modeling for biosystems in phase spaces of states.

Published in:

Measurement Techniques, 2011, v. 53, n. 12, p. 1404, doi. 10.1007/s11018-011-9673-4

By:

Eskov, V. M.;
Eskov, V. V.;
Filatova, O. E.

Publication type:

Article

Structural features of sensory two component systems: a synthetic biology perspective.

Published in:

Biochemical Journal, 2023, v. 480, n. 2, p. 127, doi. 10.1042/BCJ20210798

By:

Nieves, Marcos;
Buschiazzo, Alejandro;
Trajtenberg, Felipe

Publication type:

Article

A structural approach to understanding enzymatic regulation of chemical reaction networks.

Published in:

Biochemical Journal, 2022, v. 479, n. 11, p. 1265, doi. 10.1042/BCJ20210545

By:

Atsushi Mochizuki

Publication type:

Article

Systems approaches to investigate the role of NF-κB signaling in aging.

Published in:

Biochemical Journal, 2022, v. 479, n. 2, p. 161, doi. 10.1042/BCJ20210547

By:

Masatoshi Haga;
Mariko Okada

Publication type:

Article

Acclimation, adaptation, traits and trade-offs in plankton functional type models: reconciling terminology for biology and modelling.

Published in:

Journal of Plankton Research, 2015, v. 37, n. 4, p. 683, doi. 10.1093/plankt/fbv036

By:

FLYNN, KEVIN J.;
ST JOHN, MICHAEL;
RAVEN, JOHN A.;
SKIBINSKI, DAVID O. F.;
ALLEN, J. ICARUS;
MITRA, ADITEE;
HOFMANN, EILEEN E.

Publication type:

Article

PySCeSToolbox: a collection of metabolic pathway analysis tools.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 124, doi. 10.1093/bioinformatics/btx567

By:

Christensen, Carl D;
Hofmeyr, Jan-Hendrik S;
Rohwer, Johann M

Publication type:

Article

Interactive network visualization in Jupyter notebooks: visJS2jupyter.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 126, doi. 10.1093/bioinformatics/btx581

By:

Rosenthal, Sara Brin;
Len, Julia;
Webster, Mikayla;
Gary, Aaron;
Birmingham, Amanda;
Fisch, Kathleen M

Publication type:

Article

Orthologue chemical space and its influence on target prediction.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 72, doi. 10.1093/bioinformatics/btx525

By:

Mervin, Lewis H;
Bulusu, Krishna C;
Kalash, Leen;
Afzal, Avid M;
Svensson, Fredrik;
Firth, Mike A;
Barrett, Ian;
Engkvist, Ola;
Bender, Andreas

Publication type:

Article

A nonparametric significance test for sampled networks.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 64, doi. 10.1093/bioinformatics/btx419

By:

Elliott, Andrew;
Leicht, Elizabeth;
Whitmore, Alan;
Reinert, Gesine;
Reed-Tsochas, Felix

Publication type:

Article

PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data.

Published in:

Bioinformatics, 2017, v. 33, n. 24, p. 4007, doi. 10.1093/bioinformatics/btx499

By:

Gloaguen, Yoann;
Morton, Fraser;
Daly, Rónán;
Gurden, Ross;
Rogers, Simon;
Wandy, Joe;
Wilson, David;
Barrett, Michael;
Burgess, Karl

Publication type:

Article

Efficient inference for sparse latent variable models of transcriptional regulation.

Published in:

Bioinformatics, 2017, v. 33, n. 23, p. 3776, doi. 10.1093/bioinformatics/btx508

By:

Zhenwen Dai;
Iqbal, Mudassar;
Lawrence, Neil D.;
Rattray, Magnus

Publication type:

Article

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

Published in:

Bioinformatics, 2017, v. 33, n. 23, p. 3822, doi. 10.1093/bioinformatics/btx492

By:

Radom, Marcin;
Rybarczyk, Agnieszka;
Szawulak, Bartłomiej;
Andrzejewski, Hubert;
Chabelski, Piotr;
Kozak, Adam;
Formanowicz, Piotr

Publication type:

Article

Inferring transcriptional logic from multiple dynamic experiments.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3437, doi. 10.1093/bioinformatics/btx407

By:

Minas, Giorgos;
Jenkins, Dafyd J.;
Rand, David A.;
Finkenstädt, Bärbel

Publication type:

Article

FALCON: a toolbox for the fast contextualization of logical networks.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3431, doi. 10.1093/bioinformatics/btx380

By:

De Landtsheer, Sébastien;
Trairatphisan, Panuwat;
Lucarelli, Philippe;
Sauter, Thomas

Publication type:

Article