COPASI

COPASI's Use In Laboratory Method

2024
Asma U, Bertotti ML, Zamai S, Arnold M, Amorati R, Scampicchio M (2024) A Kinetic Approach to Oxygen Radical Absorbance Capacity (ORAC): Restoring Order to the Antioxidant Activity of Hydroxycinnamic Acids and Fruit Juices. Antioxidants 13:222 Laboratory Method Biochemistry Link
Nashed A, Naidoo KJ (2024) Universal Glycosyltransferase Continuous Assay for Uniform Kinetics and Inhibition Database Development and Mechanistic Studies Illustrated on ST3GAL1, C1GALT1, and FUT1. ACS Omega 9:17518–17532 Enzymology Laboratory Method Link
Nguyen PH, Cui S, Kozarich AM, Rautio A, Roberts AG, Xiong MP (2024) Utilizing surface plasmon resonance as a novel method for monitoring in-vitro P-glycoprotein efflux. Frontiers in Biophysics 2:1367511 Laboratory Method Biochemistry Link

3 publications
2023
Angeli L, Morozova K, Scampicchio M (2023) A kinetic-based stopped-flow DPPH• method. Scientific Reports 13:7621 Laboratory Method Biochemistry Link
Bartosh AV, Sotnikov DV, Zherdev AV, Dzantiev BB (2023) Handling Detection Limits of Multiplex Lateral Flow Immunoassay by Choosing the Order of Binding Zones. Micromachines 14:333 Laboratory Method Immunology Link
Bazylyak LI, Kytsya AR, Lyutyy PY, Korets’ka NI, Pilyuk YaV, Kuntyi OI (2023) Silver nanoparticles produced via a green synthesis using the rhamnolipid as a reducing agent and stabilizer. Applied Nanoscience 13:5251–5263 Laboratory Method Nanotechnology Link
Czarnievicz N, Rubanu MG, Iturralde M, Albarran-Velo J, Diamanti E, Gotor-Fernandez V, Skolimowski M, López-Gallego F (2023) A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors. ChemBioChem 24:e202200614 Laboratory Method Enzymology Link
Dalligos DM, Pilling MJ, Dimitrakis G, Ball LT (2023) Coaxial Dielectric Spectroscopy as an In-Line Process Analytical Technique for Reaction Monitoring. Organic Process Research & Development 27:1094–1103 Laboratory Method Chemistry Link
Eisele N (2023) Electrospray-Ionization Mass Spectrometry for the Analysis and Quantification of Carbanions. Ph.D. Thesis, Georg-August University, Göttingen, Germany Chemistry Laboratory Method Link
Ruiter FAA, King J, Swapnasrita S, Giselbrecht S, Truckenmüller R, LaPointe VLS, Baker MB, Carlier A (2023) Optimization of Media Change Intervals through Hydrogels Using Mathematical Models. Biomacromolecules 24:604–612 Laboratory Method Link
Sotnikov DV, Barshevskaya LV, Zherdev AV, Dzantiev BB (2023) Enhanced Lateral Flow Immunoassay with Double Competition and Two Kinds of Nanoparticles Conjugates for Control of Insecticide Imidacloprid in Honey. Biosensors 13:525 Laboratory Method Link

8 publications
2022
Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F (2022) Protein-Protein Communication Mediated by an Antibody-Responsive DNA Nanodevice. Angewandte Chemie 61:e202115680 Laboratory Method Link
Sotnikov DV, Barshevskaya LV, Bartosh AV, Zherdev AV, Dzantiev BB (2022) Double Competitive Immunodetection of Small Analyte: Realization for Highly Sensitive Lateral Flow Immunoassay of Chloramphenicol. Biosensors 12:343 Laboratory Method Link

2 publications
2021
Angeli L, Imperiale S, Ding Y, Scampicchio M, Morozova K (2021) A Novel Stoichio-Kinetic Model for the DPPH• Assay: The Importance of the Side Reaction and Application to Complex Mixtures. Antioxidants 10:1019 Laboratory Method Link
Berlina AN, Sotnikov DV, Komova NS, Zherdev AV, Dzantiev BB (2021) Limitations for colorimetric aggregation assay of metal ions and ways of their overcoming. Analytical Methods 13:250–257 Laboratory Method Link
Del Giudice D, Spatola E, Valentini M, Bombelli C, Ercolani G, Di Stefano S (2021) Time-programmable pH: decarboxylation of nitroacetic acid allows the time-controlled rising of pH to a definite value. Chemical Science 12:7460–7466 Chemistry Laboratory Method Link

3 publications
2020
Carlson-Stevermer J, Das A, Abdeen AA, Fiflis D, Grindel BI, Saxena S, Akcan T, Alam T, Kletzien H, Kohlenberg L, Goedland M, Dombroe MJ, Saha K (2020) Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases. Nature Communications 11:6277 Laboratory Method Genetics Link
Malig TC, Tan Y, Wisniewski SR, Higman CS, Carrasquillo-Flores R, Ortiz A, Purdum GE, Kolotuchin S, Hein JE (2020) Development of a telescoped synthesis of 4-(1H)-cyanoimidazole core accelerated by orthogonal reaction monitoring. Reaction Chemistry & Engineering 5:1421–1428 Chemistry Laboratory Method Link
Sotnikov DV, Byzova NA, Zvereva EA, Bartosh AV, Zherdev AV, Dzantiev BB (2020) Mathematical modeling of immunochromatographic test systems in a competitive format: Analytical and numerical approaches. Biochemical Engineering Journal 164:107763 Computational Method Laboratory Method Link
Sotnikov DV, Zherdev AV, Dzantiev BB (2020) Lateral Flow Serodiagnosis in the Double-Antigen Sandwich Format: Theoretical Consideration and Confirmation of Advantages. Sensors 21:39 Laboratory Method Link

4 publications
2019
Wade OK, Woehrstein JB, Nickels PC, Strauss S, Stehr F, Stein J, Schueder F, Strauss MT, Ganji M, Schnitzbauer J, Grabmayr H, Yin P, Schwille P, Jungmann R (2019) 124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics. Nano Letters 19:2641–2646 Laboratory Method Link

1 publication
2018
Blumhardt P, Stein J, Mücksch J, Stehr F, Bauer J, Jungmann R, Schwille P (2018) Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy. Molecules 23:3165 Laboratory Method Link
Kaushik AC, Kumar A, Dwivedi VD, Bharadwaj S, Kumar S, Bharti K, Kumar P, Chaudhary RK, Mishra SK (2018) Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. Molecular Neurobiology 55:3224–3236 Biochemistry Pharmacology Laboratory Method Link

2 publications
2017
Chung R, Hein JE (2017) The More, The Better: Simultaneous In Situ Reaction Monitoring Provides Rapid Mechanistic and Kinetic Insight. Topics in Catalysis 60:594–608 Chemistry Laboratory Method Link
Colletto C, Whitaker D, Larrosa I (2017) Determination of 2H KIEs from Competition Experiments: Increased Accuracy via Isotopic Enrichment. Topics in Catalysis 60:589–593 Chemistry Laboratory Method Link
Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT (2017) A proteomic approach to analyse the aspirin-mediated lysine acetylome. Molecular & Cellular Proteomics 16:310–326 Pharmacology Biochemistry Laboratory Method Link
Tolleter D, Chochois V, Poiré R, Price GD, Badger MR (2017) Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach. Journal of Experimental Botany 68:3915–3924 Laboratory Method Physiology Link
Trieu MM, Devine EL, Lamarche LB, Ammerman AE, Greco JA, Birge RR, Theobald DL, Oprian DD (2017) Expression, purification, and spectral tuning of RhoGC, a retinylidene/guanylyl cyclase fusion protein and optogenetics tool from the aquatic fungus Blastocladiella emersonii. Journal of Biological Chemistry 292:10379–10389 Enzymology Laboratory Method Link

5 publications
2016
Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P (2016) Quantitative super-resolution imaging with qPAINT. Nature Methods 13:439–442 Laboratory Method Macromolecular Biochemistry Link

1 publication
2015
Czabany T, Schmölzer K, Luley-Goedl C, Ribitsch D, Nidetzky B (2015) All-in-one assay for beta-D-galactoside sialyltransferases: quantification of productive turnover, error hydrolysis and site selectivity. Analytical Biochemistry 483:47-53 Laboratory Method Enzymology Link
Dromms RA, Styczynski MP (2015) Improved metabolite profile smoothing for flux estimation. Molecular BioSystems 11:2394-2405 Computational Method Laboratory Method Link
Müller JM, Risse JM, Friehs K, Flaschel E (2015) Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Engineering in Life Sciences 15:627-639 Laboratory Method Link
Rezgui A, Madec M, Lallement C, Haiech J (2015) Integration of SBML models for the description of biological system in a lab-on-chip. Proceedings of the 22nd International Conference Mixed Design of Integrated Circuits & Systems 165-70 Computational Method Laboratory Method Link

4 publications
2014
Karonen M, Mattila H, Huang P, Mamedov F, Styring S, Tyystjärvi E (2014) A tandem mass spectrometric method for singlet oxygen measurement. Photochemistry and Photobiology 90:965-971 Laboratory Method Link

1 publication
2013
Skvortsov A, Gray P (2013) A simple model for assessment of anti-toxin antibodies. BioMed Research International 2013:230906 Laboratory Method Link

1 publication
2012

0 publication
2011
Bandaru P, Bansal M, Nemenman I (2011) Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. Journal of Computational Biology 18:147-154 Laboratory Method Computational Method Link

1 publication
2010

0 publication
2009
Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Computational Biology 5:e1000529 Synthetic Biology Computational Method Laboratory Method Link
Gallagher SS, Sable JE, Sheetz MP, Cornish VW (2009) An In Vivo Covalent TMP-Tag Based on Proximity-Induced Reactivity. ACS Chemical Biology 4:547-56 Laboratory Method Link
Menolascina F, Bellomo D, Maiwald T, Bevilacqua V, Ciminelli C, Paradiso A, Tommasi S (2009) Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics 10:S4 Laboratory Method Signaling Link

3 publications
2008

0 publication
2007

0 publication
2006

0 publication
2005

0 publication