GRAND: a database of gene regulatory network models across human conditions.
Ben Guebila M, Lopes-Ramos CM, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush J.
Nucleic Acids Res. 2021 Sep 11. PMID: 34508353
Fellow or Post Doc
Marouen Ben Guebila
Overview
My research is at the interface of genomics, machine learning, and network biology. I often combine tools from these disciplines to address fundamental questions about the functioning of biological systems. I develop open-source, parallel software to leverage high-dimensional biological data to model regulatory genomics, small molecule dynamics, and metabolism in time and space.
I am currently a postdoctoral fellow at the Quackenbush lab at the Biostatistics department.
Bibliography
Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme.
Lopes-Ramos CM, Belova T, Brunner TH, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML.
Cancer Res. 2021 Sep 07. PMID: 34493595
Gene Targeting in Disease Networks.
Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J.
Front Genet. 2021. 12:649942. PMID: 33968133
VFFVA: dynamic load balancing enables large-scale flux variability analysis.
Guebila MB.
BMC Bioinformatics. 2020 Sep 29. 21(1):424. PMID: 32993482
Predicting gastrointestinal drug effects using contextualized metabolic models.
Ben Guebila M, Thiele I.
PLoS Comput Biol. 2019 06. 15(6):e1007100. PMID: 31242176
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.
Nat Protoc. 2019 03. 14(3):639-702. PMID: 30787451