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Items: 1 to 20 of 273


An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms.

Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A.

Front Immunol. 2019 Jun 25;10:1425. doi: 10.3389/fimmu.2019.01425. eCollection 2019.


BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.

Kolpakov F, Akberdin I, Kashapov T, Kiselev L, Kolmykov S, Kondrakhin Y, Kutumova E, Mandrik N, Pintus S, Ryabova A, Sharipov R, Yevshin I, Kel A.

Nucleic Acids Res. 2019 Jul 2;47(W1):W225-W233. doi: 10.1093/nar/gkz440.


Modeling the Dynamics of Human Liver Failure Post Liver Resection.

Verma BK, Subramaniam P, Vadigepalli R.

Processes (Basel). 2018 Aug;6(8). pii: 115. doi: 10.3390/pr6080115. Epub 2018 Aug 4.


PathMe: merging and exploring mechanistic pathway knowledge.

Domingo-Fernández D, Mubeen S, Marín-Llaó J, Hoyt CT, Hofmann-Apitius M.

BMC Bioinformatics. 2019 May 15;20(1):243. doi: 10.1186/s12859-019-2863-9.


Metabopolis: scalable network layout for biological pathway diagrams in urban map style.

Wu HY, Nöllenburg M, Sousa FL, Viola I.

BMC Bioinformatics. 2019 Apr 15;20(1):187. doi: 10.1186/s12859-019-2779-4.


Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis.

Kühn C, Checa S.

Front Physiol. 2019 Mar 27;10:288. doi: 10.3389/fphys.2019.00288. eCollection 2019.


High-Performance Biocomputing in Synthetic Biology-Integrated Transcriptional and Metabolic Circuits.

Goñi-Moreno A, Nikel PI.

Front Bioeng Biotechnol. 2019 Mar 11;7:40. doi: 10.3389/fbioe.2019.00040. eCollection 2019.


A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae.

Münzner U, Klipp E, Krantz M.

Nat Commun. 2019 Mar 21;10(1):1308. doi: 10.1038/s41467-019-08903-w.


Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli.

Hodgson D, Rowan AD, Falciani F, Proctor CJ.

PLoS Comput Biol. 2019 Jan 24;15(1):e1006685. doi: 10.1371/journal.pcbi.1006685. eCollection 2019 Jan.


Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network.

Cucurull-Sanchez L, Chappell MJ, Chelliah V, Amy Cheung SY, Derks G, Penney M, Phipps A, Malik-Sheriff RS, Timmis J, Tindall MJ, van der Graaf PH, Vicini P, Yates JWT.

CPT Pharmacometrics Syst Pharmacol. 2019 May;8(5):259-272. doi: 10.1002/psp4.12381. Epub 2019 Mar 22.


A computational model to understand mouse iron physiology and disease.

Parmar JH, Mendes P.

PLoS Comput Biol. 2019 Jan 4;15(1):e1006680. doi: 10.1371/journal.pcbi.1006680. eCollection 2019 Jan.


BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.

Hoyt CT, Domingo-Fernández D, Hofmann-Apitius M.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay126.


Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Review.


Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma.

Zhou S, Appleman VA, Rose CM, Jun HJ, Yang J, Zhou Y, Bronson RT, Gygi SP, Charest A.

Life Sci Alliance. 2018 Jun 19;1(3):e201800029. doi: 10.26508/lsa.201800029. eCollection 2018 Jun.


Subunit exchange enhances information retention by CaMKII in dendritic spines.

Singh D, Bhalla US.

Elife. 2018 Nov 12;7. pii: e41412. doi: 10.7554/eLife.41412.


Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform.

Miller RA, Woollard P, Willighagen EL, Digles D, Kutmon M, Loizou A, Waagmeester A, Senger S, Evelo CT.

Version 2. F1000Res. 2018 Jan 17 [revised 2018 Jan 1];7:75. doi: 10.12688/f1000research.13197.2. eCollection 2018.


Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse.

Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11061-E11070. doi: 10.1073/pnas.1809609115. Epub 2018 Nov 6.


Reproducible Research Using Biomodels.

Mendes P.

Bull Math Biol. 2018 Dec;80(12):3081-3087. doi: 10.1007/s11538-018-0498-z. Epub 2018 Sep 6.


In Vitro Tracking of Intracellular Metabolism-Derived Cancer Volatiles via Isotope Labeling.

Lee DK, Na E, Park S, Park JH, Lim J, Kwon SW.

ACS Cent Sci. 2018 Aug 22;4(8):1037-1044. doi: 10.1021/acscentsci.8b00296. Epub 2018 Aug 3.

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