Works matching DE "BIOLOGICAL networks"

Results: 2111

Landscape structure as a driver of eco-evolution in host–parasite systems Open Access.

Published in:

Evolution Letters, 2025, v. 9, n. 3, p. 367, doi. 10.1093/evlett/qraf003

By:

Deshpande, Jhelam N;
Dakos, Vasilis;
Kaltz, Oliver;
Fronhofer, Emanuel A

Publication type:

Article

Design, Synthesis, Anti-Tumor Activity and Molecular Docking Studies of Novel Triphenylphosphine-Containing Formononetin Derivatives.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 11, p. 5280, doi. 10.3390/ijms26115280

By:

Cui, Hongjuan;
Zhao, Yan;
Li, Wei;
Cui, Huanjie;
Han, Jiahong;
Cai, Enbo

Publication type:

Article

SCR-Net: A novel lightweight aquatic biological detection network.

Published in:

PLoS ONE, 2025, v. 20, n. 6, p. 1, doi. 10.1371/journal.pone.0324067

By:

Li, Tao;
Gang, Yijin;
Li, Sumin;
Shang, Yizi

Publication type:

Article

Possible New Candidates Involved to Thalidomide-Related Limbs and Cardiac Defects: A Systems Biology Approach.

Published in:

Biochemical Genetics, 2025, v. 63, n. 3, p. 2140, doi. 10.1007/s10528-024-10790-w

By:

Rengel, Bruna Duarte;
Schuler-Faccini, Lavínia;
Fraga, Lucas Rosa;
Vianna, Fernanda Sales Luiz;
Kowalski, Thayne Woycinck

Publication type:

Article

Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013112

By:

Zhang, Mingfang;
Chitic, Raluca;
Bohté, Sander M.

Publication type:

Article

Stress Centrality of Some Classes of Graphs.

Published in:

Engineering Letters, 2025, v. 33, n. 6, p. 2204

By:

ALAKA, B.;
BHAT, K. ARATHI

Publication type:

Article

Natural products in treating diabetic kidney disease: a visualized bibliometric analysis.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1522074

By:

Liu, Tianlong;
Li, Xiaolin;
Chen, Yidan;
Li, Jinhu;
Wang, Rong;
Ding, Yi;
Liu, Minna

Publication type:

Article

Disulfidptosis in pediatric AML: a multi-omics approach to risk stratification and potential therapeutic strategy.

Published in:

Cancer Cell International, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12935-025-03824-9

By:

Lei, Yichen;
Zhang, Jiasi;
Wang, Yaqin;
Liu, Aiguo

Publication type:

Article

Universal multilayer network embedding reveals a causal link between GABA neurotransmitter and cancer.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06158-5

By:

Pio-Lopez, Léo;
Levin, Michael

Publication type:

Article

Prediction of circRNA–miRNA Interaction Using Graph Attention Network Based on Molecular Attributes and Biological Networks.

Published in:

Processes, 2025, v. 13, n. 5, p. 1318, doi. 10.3390/pr13051318

By:

Almotilag, Abdullah;
Elbashir, Murtada K.;
Mahmood, Mahmood A.;
Mohammed, Mohanad

Publication type:

Article

CoupleMDA: Metapath-Induced Structural-Semantic Coupling Network for miRNA-Disease Association Prediction.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4948, doi. 10.3390/ijms26104948

By:

Li, Zhuojian;
Chen, Guanxing;
Tan, Guang;
Chen, Calvin Yu-Chian

Publication type:

Article

Architecture and stability of tripartite ecological networks with two interaction types.

Published in:

Ecology, 2025, v. 106, n. 5, p. 1, doi. 10.1002/ecy.70098

By:

Zhao, Yangyang;
Zhang, Zhicheng;
Hao, Xiyang;
Zhang, Yongjun;
Si, Xingfeng;
Yan, Chuan

Publication type:

Article

Modeling and understanding locomotion of pneumatic soft robots.

Published in:

Soft Materials, 2018, v. 16, n. 3, p. 151, doi. 10.1080/1539445X.2018.1460379

By:

An, Ning;
Li, Meie;
Zhou, Jinxiong

Publication type:

Article

Forecasting early onset diminished ovarian reserve for young reproductive age women.

Published in:

Journal of Assisted Reproduction & Genetics, 2021, v. 38, n. 7, p. 1853, doi. 10.1007/s10815-021-02155-8

By:

McCallie, Blair R.;
Haywood, Mary;
Denomme, Michelle M.;
Makloski, Rachel;
Parks, Jason C.;
Griffin, Darren K.;
Schoolcraft, William B.;
Katz-Jaffe, Mandy G.

Publication type:

Article

Preface.

Published in:

2020

By:

Formenti, Enrico;
Sené, Sylvain

Publication type:

Editorial

About block-parallel Boolean networks: a position paper.

Published in:

Natural Computing, 2020, v. 19, n. 1, p. 5, doi. 10.1007/s11047-019-09779-x

By:

Demongeot, Jacques;
Sené, Sylvain

Publication type:

Article

Foreword: asynchronous behavior of cellular automata and discrete models.

Published in:

Natural Computing, 2015, v. 14, n. 4, p. 505, doi. 10.1007/s11047-015-9524-3

By:

Dennunzio, Alberto;
Formenti, Enrico;
Mauri, Giancarlo;
Worsch, Thomas

Publication type:

Article

Minimization and equivalence in multi-valued logical models of regulatory networks.

Published in:

Natural Computing, 2015, v. 14, n. 4, p. 555, doi. 10.1007/s11047-015-9525-2

By:

Streck, Adam;
Lorenz, Therese;
Siebert, Heike

Publication type:

Article

An evolutionary procedure for inferring MP systems regulation functions of biological networks.

Published in:

Natural Computing, 2015, v. 14, n. 3, p. 375, doi. 10.1007/s11047-014-9421-1

By:

Castellini, Alberto;
Manca, Vincenzo;
Zucchelli, Mauro

Publication type:

Article

Algorithms and models for complex natural systems.

Published in:

2015

By:

Coello, Carlos;
Franco, Giuditta;
Krasnogor, Natalio;
Pavone, Mario

Publication type:

Editorial

Learning subtree pattern importance for Weisfeiler-Lehman based graph kernels.

Published in:

Machine Learning, 2021, v. 110, n. 7, p. 1585, doi. 10.1007/s10994-021-05991-y

By:

Nguyen, Dai Hai;
Nguyen, Canh Hao;
Mamitsuka, Hiroshi

Publication type:

Article

A revised model of fluid transport optimization in Physarum polycephalum.

Published in:

Journal of Mathematical Biology, 2017, v. 74, n. 3, p. 567, doi. 10.1007/s00285-016-1036-y

By:

Bonifaci, Vincenzo

Publication type:

Article

Computing the structural influence matrix for biological systems.

Published in:

Journal of Mathematical Biology, 2016, v. 72, n. 7, p. 1927, doi. 10.1007/s00285-015-0933-9

By:

Giordano, Giulia;
Cuba Samaniego, Christian;
Franco, Elisa;
Blanchini, Franco

Publication type:

Article

Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.

Published in:

Journal of Mathematical Biology, 2016, v. 72, n. 6, p. 1441, doi. 10.1007/s00285-015-0917-9

By:

Bendahmane, Mostafa;
Ruiz-Baier, Ricardo;
Tian, Canrong

Publication type:

Article

Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations.

Published in:

Journal of Mathematical Biology, 2016, v. 72, n. 3, p. 699, doi. 10.1007/s00285-015-0899-7

By:

Huber, Katharina;
Linz, Simone;
Moulton, Vincent;
Wu, Taoyang

Publication type:

Article

Mean field analysis of a spatial stochastic model of a gene regulatory network.

Published in:

Journal of Mathematical Biology, 2015, v. 71, n. 4, p. 921, doi. 10.1007/s00285-014-0837-0

By:

Sturrock, M.;
Murray, P.;
Matzavinos, A.;
Chaplain, M.

Publication type:

Article

diffuStats: an R package to compute diffusionbased scores on biological networks.

Published in:

Bioinformatics, 2018, v. 34, n. 3, p. 533, doi. 10.1093/bioinformatics/btx632

By:

Picart-Armada, Sergio;
Thompson, Wesley K;
Buil, Alfonso;
Perera-Lluna, Alexandre

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

SANA: simulated annealing far outperforms many other search algorithms for biological network alignment.

Published in:

Bioinformatics, 2017, v. 33, n. 14, p. 2156, doi. 10.1093/bioinformatics/btx090

By:

Mamano, Nil;
Hayes, Wayne B.

Publication type:

Article

Alignment of dynamic networks.

Published in:

Bioinformatics, 2017, v. 33, n. 14, p. i180, doi. 10.1093/bioinformatics/btx246

By:

Vijayan, V.;
Critchlow, D.;
Milenković, T.

Publication type:

Article

NSSRF: global network similarity search with subgraph signatures and its applications.

Published in:

Bioinformatics, 2017, v. 33, n. 11, p. 1696, doi. 10.1093/bioinformatics/btx051

By:

Jiao Zhang;
Sam Kwong;
Yuheng Jia;
Ka-ChunWong

Publication type:

Article

Powerful differential expression analysis incorporating network topology for next-generation sequencing data.

Published in:

Bioinformatics, 2017, v. 33, n. 10, p. 1505, doi. 10.1093/bioinformatics/btw833

By:

Dona, Malathi S. I.;
Prendergast, Luke A.;
Mathivanan, Suresh;
Keerthikumar, Shivakumar;
Salim, Agus

Publication type:

Article

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

Published in:

Bioinformatics, 2017, v. 33, n. 8, p. 1253, doi. 10.1093/bioinformatics/btw812

By:

Bergmann, Frank T.;
Nickerson, David;
Waltemath, Dagmar;
Scharm, Martin

Publication type:

Article

Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods.

Published in:

2017

By:

Yaveroğlu, Ömer Nebil;
Malod-Dognin, Noël;
Milenkovié, Tijana;
Pržulj, Nataša

Publication type:

Letter to the Editor

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1096, doi. 10.1093/bioinformatics/btw731

By:

Balaur, Irina;
Mazein, Alexander;
Saqi, Mansoor;
Lysenko, Artem;
Rawlings, Christopher J.;
Auffray, Charles

Publication type:

Article

Advanced Boolean modeling of biological networks applied to systems pharmacology.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1040, doi. 10.1093/bioinformatics/btw747

By:

Irurzun-Arana, Itziar;
Martín Pastor, José;
Trocóniz, Iñaki F.;
Gómez-Mantilla, José David

Publication type:

Article

RANKS: a flexible tool for node label ranking and classification in biological networks.

Published in:

Bioinformatics, 2016, v. 32, n. 18, p. 2872, doi. 10.1093/bioinformatics/btw235

By:

Valentini, Giorgio;
Frasca, Marco;
Jianyi Lin;
Mesiti, Marco;
Re, Matteo;
Armano, Giuliano

Publication type:

Article

Edge-based sensitivity analysis of signaling networks by using Boolean dynamics.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i763, doi. 10.1093/bioinformatics/btw464

By:

Hung-Cuong Trinh;
Yung-Keun Kwon

Publication type:

Article

LS-GKM: a new gkm-SVM for large-scale datasets.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2196, doi. 10.1093/bioinformatics/btw142

By:

Lee, Dongwon

Publication type:

Article

Inferring gene targets of drugs and chemical compounds from gene expression profiles.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2120, doi. 10.1093/bioinformatics/btw148

By:

Noh, Heeju;
Gunawan, Rudiyanto

Publication type:

Article

CaFE: a tool for binding affinity prediction using end-point free energy methods.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2216, doi. 10.1093/bioinformatics/btw215

By:

Hui Liu;
Tingjun Hou

Publication type:

Article

Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2167, doi. 10.1093/bioinformatics/btw151

By:

Blatti, Charles;
Sinha, Saurabh

Publication type:

Article

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2233, doi. 10.1093/bioinformatics/btw216

By:

Lachmann, Alexander;
Giorgi, Federico M.;
Lopez, Gonzalo;
Califano, Andrea

Publication type:

Article

APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2159, doi. 10.1093/bioinformatics/btw223

By:

Bonnici, Vincenzo;
Busato, Federico;
Micale, Giovanni;
Bombieri, Nicola;
Pulvirenti, Alfredo;
Giugno, Rosalba

Publication type:

Article

Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks.

Published in:

Bioinformatics, 2016, v. 32, n. 12, p. i288, doi. 10.1093/bioinformatics/btw274

By:

Intosalmi, Jukka;
Nousiainen, Kari;
Ahlfors, Helena;
Lähdesmäki, Harri

Publication type:

Article

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.

Published in:

Bioinformatics, 2016, v. 32, n. 4, p. 571, doi. 10.1093/bioinformatics/btv620

By:

Will, Thorsten;
Helms, Volkhard

Publication type:

Article

An algorithm to detect and communicate the differences in computational models describing biological systems.

Published in:

Bioinformatics, 2016, v. 32, n. 4, p. 563, doi. 10.1093/bioinformatics/btv484

By:

Scharm, Martin;
Wolkenhauer, Olaf;
Waltemath, Dagmar

Publication type:

Article

Hyperscape: visualization for complex biological networks.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3390, doi. 10.1093/bioinformatics/btv385

By:

Cromar, Graham L.;
Zhao, Anthony;
Yang, Alex;
Parkinson, John

Publication type:

Article

TiQuant: software for tissue analysis, quantification and surface reconstruction.

Published in:

Bioinformatics, 2015, v. 31, n. 19, p. 3234, doi. 10.1093/bioinformatics/btv346

By:

Friebel, Adrian;
Neitsch, Johannes;
Johann, Tim;
Hammad, Seddik;
Hengstler, Jan G.;
Drasdo, Dirk;
Hoehme, Stefan

Publication type:

Article

MP-GeneticSynth: inferring biological network regulations from time series.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 785, doi. 10.1093/bioinformatics/btu694

By:

Castellini, Alberto;
Paltrinieri, Daniele;
Manca, Vincenzo

Publication type:

Article