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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT. Heirendt L, et al. Among authors: sun y. Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2. Nat Protoc. 2019. PMID: 30787451 Free PMC article.
Do genome-scale models need exact solvers or clearer standards?
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Ebrahim A, et al. Among authors: sun y. Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. Mol Syst Biol. 2015. PMID: 26467284 Free PMC article. No abstract available.
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.
Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson BO. Yang L, et al. Among authors: sun y. Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10810-5. doi: 10.1073/pnas.1501384112. Epub 2015 Aug 10. Proc Natl Acad Sci U S A. 2015. PMID: 26261351 Free PMC article.
Precise Measurement of the e^{+}e^{-}→D_{s}^{+}D_{s}^{-} Cross Section at Center-of-Mass Energies from Threshold to 4.95 GeV.
Ablikim M, Achasov MN, Adlarson P, Afedulidis O, Ai XC, Aliberti R, Amoroso A, An Q, Bai Y, Bakina O, Balossino I, Ban Y, Bao HR, Batozskaya V, Begzsuren K, Berger N, Berlowski M, Bertani M, Bettoni D, Bianchi F, Bianco E, Bortone A, Boyko I, Briere RA, Brueggemann A, Cai H, Cai X, Calcaterra A, Cao GF, Cao N, Cetin SA, Chang JF, Che GR, Chelkov G, Chen C, Chen CH, Chen C, Chen G, Chen HS, Chen HY, Chen ML, Chen SJ, Chen SL, Chen SM, Chen T, Chen XR, Chen XT, Chen YB, Chen YQ, Chen ZJ, Chen ZY, Choi SK, Cibinetto G, Cossio F, Cui JJ, Dai HL, Dai JP, Dbeyssi A, de Boer RE, Dedovich D, Deng CQ, Deng ZY, Denig A, Denysenko I, Destefanis M, De Mori F, Ding B, Ding XX, Ding Y, Ding Y, Dong J, Dong LY, Dong MY, Dong X, Du MC, Du SX, Duan YY, Duan ZH, Egorov P, Fan YH, Fang J, Fang J, Fang SS, Fang WX, Fang Y, Fang YQ, Farinelli R, Fava L, Feldbauer F, Felici G, Feng CQ, Feng JH, Feng YT, Fritsch M, Fu CD, Fu JL, Fu YW, Gao H, Gao XB, Gao YN, Gao Y, Garbolino S, Garzia I, Ge L, Ge PT, Ge ZW, Geng C, Gersabeck EM, Gilman A, Goetzen K, Gong L, Gong WX, Gradl W, Gramigna S, Greco M, Gu MH, Gu YT, Guan CY, Guo AQ, Guo LB, Guo MJ, Guo RP, Guo YP, Guskov A, Gutierrez J, Han KL, Han TT, Hanisch… See abstract for full author list ➔ Ablikim M, et al. Among authors: sun yj, sun yz, sun y. Phys Rev Lett. 2024 Dec 31;133(26):261902. doi: 10.1103/PhysRevLett.133.261902. Phys Rev Lett. 2024. PMID: 39879000
Measurement of Λ_{b}^{0}, Λ_{c}^{+}, and Λ Decay Parameters Using Λ_{b}^{0}→Λ_{c}^{+}h^{-} Decays.
Aaij R, Abdelmotteleb ASW, Abellan Beteta C, Abudinén F, Ackernley T, Adefisoye AA, Adeva B, Adinolfi M, Adlarson P, Agapopoulou C, Aidala CA, Ajaltouni Z, Akar S, Akiba K, Albicocco P, Albrecht J, Alessio F, Alexander M, Aliouche Z, Alvarez Cartelle P, Amalric R, Amato S, Amey JL, Amhis Y, An L, Anderlini L, Andersson M, Andreianov A, Andreola P, Andreotti M, Andreou D, Anelli A, Ao D, Archilli F, Argenton M, Arguedas Cuendis S, Artamonov A, Artuso M, Aslanides E, Ataíde Da Silva R, Atzeni M, Audurier B, Bacher D, Bachiller Perea I, Bachmann S, Bachmayer M, Back JJ, Baladron Rodriguez P, Balagura V, Baldini W, Balzani L, Bao H, Baptista de Souza Leite J, Barbero Pretel C, Barbetti M, Barbosa IR, Barlow RJ, Barnyakov M, Barsuk S, Barter W, Bartolini M, Bartz J, Basels JM, Bashir S, Bassi G, Batsukh B, Battista PB, Bay A, Beck A, Becker M, Bedeschi F, Bediaga IB, Behling NA, Belin S, Bellee V, Belous K, Belov I, Belyaev I, Benane G, Bencivenni G, Ben-Haim E, Berezhnoy A, Bernet R, Bernet Andres S, Bertolin A, Betancourt C, Betti F, Bex J, Bezshyiko I, Bhom J, Bieker MS, Biesuz NV, Billoir P, Biolchini A, Birch M, Bishop FCR, Bitadze A, Bizzeti A, Blake T, Blanc F, Blank JE, Blusk S… See abstract for full author list ➔ Aaij R, et al. Among authors: sun y. Phys Rev Lett. 2024 Dec 31;133(26):261804. doi: 10.1103/PhysRevLett.133.261804. Phys Rev Lett. 2024. PMID: 39878998
Genome sequence of Equine Erythroparvovirus 1, identified in the United States.
Yu YT, Olarte Castillo X, Reboul G, Zehr J, Sun Y, Anderson R, Wang M, Sun Q, Tallmadge R, Sams K, Brown J, Marra N, Stanhope B, Grenier J, Parrish CR, Pusterla N, Divers T, Mittel L, Goodman LB. Yu YT, et al. Among authors: sun y. Microbiol Resour Announc. 2025 Jan 29:e0089724. doi: 10.1128/mra.00897-24. Online ahead of print. Microbiol Resour Announc. 2025. PMID: 39878505
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