Bioinformatics in the human interactome project.
Published in Bioinformatics
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.
...Published in Nature Immunology
It is now established that the transcription factors E2A, EBF1 and Foxo1 have critical roles in B cell development. Here we show that E2A and EBF1 bound regulatory elements present in the Foxo1 locus. E2A and EBF1, as well as E2A and Foxo1, in turn, were wired together by a vast spectrum of cis-regulatory sequences. These associations were dynamic ...
Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition.
...Published in Oncotarget
Chemical inhibitors of the checkpoint kinases have shown promise in the treatment of cancer, yet their clinical utility may be limited by a lack of molecular biomarkers to identify specific patients most likely to respond to therapy. To this end, we screened 112 known tumor suppressor genes for synthetic lethal interactions with inhibitors of the C...
Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological ...
Published in Bioinformatics
Siri of the cell: what biology could learn from the iPhone.
Published in Cell
Modern genomics is very efficient at mapping genes and gene networks, but how to transform these maps into predictive models of the cell remains unclear. Recent progress in computer science, embodied by intelligent agents such as Siri, inspires an approach for moving from networks to multiscale models able to predict a range of cellular phenotypes ...
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
Published in Molecular Systems Biology
We present a genome-scale metabolic model for the archaeal methanogen Methanosarcina barkeri. We characterize the metabolic network and compare it to reconstructions from the prokaryotic, eukaryotic and archaeal domains. Using the model in conjunction with constraint-based methods, we simulate the metabolic fluxes and resulting phenotypes induced b...
Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice.
...Published in Otolaryngology - Head and Neck Surgery
