Tatka L, Smith L, Hellerstein J, Sauro H
J Transl Med. 2023; 21(1):501.
PMID: 37496031
PMC: 10369698.
DOI: 10.1186/s12967-023-04290-5.
Payne D, Renz A, Dunphy L, Lewis T, Drager A, Papin J
NPJ Syst Biol Appl. 2021; 7(1):37.
PMID: 34625561
PMC: 8501023.
DOI: 10.1038/s41540-021-00198-2.
Renz A, Drager A
NPJ Syst Biol Appl. 2021; 7(1):30.
PMID: 34188046
PMC: 8241996.
DOI: 10.1038/s41540-021-00188-4.
Gupta S, Lee R, Faeder J
PLoS Comput Biol. 2020; 16(3):e1007669.
PMID: 32150537
PMC: 7082068.
DOI: 10.1371/journal.pcbi.1007669.
Gilbert J, Pearcy N, Norman R, Millat T, Winzer K, King J
Bioinformatics. 2019; 35(18):3397-3403.
PMID: 30759197
PMC: 6748746.
DOI: 10.1093/bioinformatics/btz088.
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.
Martyushenko N, Almaas E
BMC Bioinformatics. 2019; 20(1):56.
PMID: 30691403
PMC: 6348647.
DOI: 10.1186/s12859-019-2615-x.
Scaling up genetic circuit design for cellular computing: advances and prospects.
Xiang Y, Dalchau N, Wang B
Nat Comput. 2018; 17(4):833-853.
PMID: 30524216
PMC: 6244767.
DOI: 10.1007/s11047-018-9715-9.
RACIPE: a computational tool for modeling gene regulatory circuits using randomization.
Huang B, Jia D, Feng J, Levine H, Onuchic J, Lu M
BMC Syst Biol. 2018; 12(1):74.
PMID: 29914482
PMC: 6006707.
DOI: 10.1186/s12918-018-0594-6.
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification.
Cankorur-Cetinkaya A, Dikicioglu D, Oliver S
Biotechnol Bioeng. 2017; 114(11):2605-2615.
PMID: 28691262
PMC: 5659126.
DOI: 10.1002/bit.26380.
Modeling oxygen requirements in ischemic cardiomyocytes.
McDougal A, Dewey Jr C
J Biol Chem. 2017; 292(28):11760-11776.
PMID: 28487363
PMC: 5512071.
DOI: 10.1074/jbc.M116.751826.
A Liver-Centric Multiscale Modeling Framework for Xenobiotics.
Sluka J, Fu X, Swat M, Belmonte J, Cosmanescu A, Clendenon S
PLoS One. 2016; 11(9):e0162428.
PMID: 27636091
PMC: 5026379.
DOI: 10.1371/journal.pone.0162428.
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.
Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen E, Evelo C
PLoS Comput Biol. 2016; 12(6):e1004989.
PMID: 27336457
PMC: 4918977.
DOI: 10.1371/journal.pcbi.1004989.
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
Granger B, Chang Y, Wang Y, DeLisi C, Segre D, Hu Z
PLoS Comput Biol. 2016; 12(4):e1004875.
PMID: 27081850
PMC: 4833320.
DOI: 10.1371/journal.pcbi.1004875.
Improving collaboration by standardization efforts in systems biology.
Drager A, Palsson B
Front Bioeng Biotechnol. 2014; 2:61.
PMID: 25538939
PMC: 4259112.
DOI: 10.3389/fbioe.2014.00061.
Multi-state modeling of biomolecules.
Stefan M, Bartol T, Sejnowski T, Kennedy M
PLoS Comput Biol. 2014; 10(9):e1003844.
PMID: 25254957
PMC: 4201162.
DOI: 10.1371/journal.pcbi.1003844.
Computer-assisted design for scaling up systems based on DNA reaction networks.
Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y
J R Soc Interface. 2014; 11(93):20131167.
PMID: 24451393
PMC: 3928947.
DOI: 10.1098/rsif.2013.1167.
A system biology approach to identify regulatory pathways underlying the neuroendocrine control of female puberty in rats and nonhuman primates.
Lomniczi A, Wright H, Castellano J, Sonmez K, Ojeda S
Horm Behav. 2013; 64(2):175-86.
PMID: 23998662
PMC: 3933372.
DOI: 10.1016/j.yhbeh.2012.09.013.
A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells.
Helikar T, Kochi N, Kowal B, Dimri M, Naramura M, Raja S
PLoS One. 2013; 8(4):e61757.
PMID: 23637902
PMC: 3630219.
DOI: 10.1371/journal.pone.0061757.
Precise generation of systems biology models from KEGG pathways.
Wrzodek C, Buchel F, Ruff M, Drager A, Zell A
BMC Syst Biol. 2013; 7:15.
PMID: 23433509
PMC: 3623889.
DOI: 10.1186/1752-0509-7-15.
D-Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae.
Stewart B, Navid A, Kulp K, Knaack J, Bench G
Yeast. 2013; 30(2):81-91.
PMID: 23361949
PMC: 3569098.
DOI: 10.1002/yea.2942.