BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

Tiwari DD, Hoffmann N, Didi K, Deshpande S, Ghosh S, Nguyen TVN, Raman K, Hermjakob H, Sheriff R.

2023

doi:10.1101/2023.05.22.540599.

FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast

Ramachandran K, König M, Scharm M, Nguyen TVN, Hermjakob H, Waltemath D, Malik Sheriff RS.

2022

doi:10.20944/preprints202206.0137.v1.

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkac331.

Reproducibility in systems biology modelling.

Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS.

Mol Syst Biol, 2021

doi:10.15252/msb.20209982.

BioModels Parameters: a treasure trove of parameter values from published systems biology models.

Glont M, Arankalle C, Tiwari K, Nguyen TVN, Hermjakob H, Malik-Sheriff RS.

Bioinformatics, 2020

doi:10.1093/bioinformatics/btaa560.

BioModels-15 years of sharing computational models in life science.

Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz1055.

BioModels: expanding horizons to include more modelling approaches and formats.

Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H.

Nucleic Acids Res, 2018

doi:10.1093/nar/gkx1023.

Metabolic network reconstruction and their topological analysis.

Beurton-Aimar M, Nguyen TV, Colombié S.

Methods Mol Biol, 2014

doi:10.1007/978-1-62703-688-7_2.