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Fusion of a superfamily 1 helicase and an inactivated DNA polymerase is a signature of common evolutionary history of Polintons, polinton-like viruses, Tlr1 transposons and transpovirons

Prevalence of Plasmodium spp. in illegal gold miners in French Guiana in 2015: a hidden but critical malaria reservoir.

© Research

Publication : IEEE transactions on bio-medical engineering

Toward community standards and software for whole-cell modeling

Team: Bioinformatics and Biostatistics HUB

Member: Anna Zhukova

Scientific Fields

Diseases

Organisms

Applications

Technique

Published in IEEE transactions on bio-medical engineering - 10 Jun 2016

Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, Cantarelli M, Chew Y, Costa R, Cursons J, Czauderna T, Goldberg A, Gomez H, Hahn J, Hameri T, Gardiol D, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley J, Moreau B, Naderi-Meshkin H, Palaniappan S, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford N, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai T, Watanabe L, Wendland F, Wolfien M, Yurkovich J, Zhu Y, Zardilis A, Zhukova A, Schreiber F

Link to Pubmed [PMID] – 27305665

IEEE Trans Biomed Eng 2016 Jun;

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells.

METHODS: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML.

RESULTS: Our analysis revealed several challenges to representing WC models using the current standards.

CONCLUSION: We, therefore, propose several new WC modeling standards, software, and databases.

SIGNIFICANCE: We anticipate that these new standards and software will enable more comprehensive models.

Published on: 10 Jun 2016