Published in PloS one
High-throughput genetic screens in model microbial organisms are a primary means of interrogating biological systems. In numerous cases, such screens have identified the genes that underlie a particular phenotype or a set of gene-gene, gene-environment or protein-protein interactions, which are then used to construct highly informative network maps...
Published in Biochimie
•Matrin 3 coimmunoprecipitates with GRP78, GRP75 and GSTπ2 in thymoma cells.•We identified MATR3 and its partners by MS/MS analysis and confirmed by immunoblot.•It is suggested that these proteins may assist MATR3 in its functional role in cells.•We propose that TBTO triggers MATR3 degradation via caspase cascade pathway.•The broad-spectrum caspase...
Published in Nature methods
Many forms of cancer have multiple subtypes with different causes and clinical outcomes. Somatic tumor genome sequences provide a rich new source of data for uncovering these subtypes but have proven difficult to compare, as two tumors rarely share the same mutations. Here we introduce network-based stratification (NBS), a method to integrate somat...
Published in Journal of the American Society of Nephrology : JASN
Diabetic kidney disease is the leading cause of ESRD, but few biomarkers of diabetic kidney disease are available. This study used gas chromatography-mass spectrometry to quantify 94 urine metabolites in screening and validation cohorts of patients with diabetes mellitus (DM) and CKD(DM+CKD), in patients with DM without CKD (DM-CKD), and in healthy...
Published in Nature reviews. Genetics
A central goal of systems biology is to elucidate the structural and functional architecture of the cell. To this end, large and complex networks of molecular interactions are being rapidly generated for humans and model organisms. A recent focus of bioinformatics research has been to integrate these networks with each other and with diverse molecu...
Published in Genome research
Several studies have sought systematically to identify protein subcellular locations, but an even larger task is to map which of these proteins conditionally relocates in disease (the mislocalizome). Here, we report an integrative computational framework for mapping conditional location and mislocation of proteins on a proteome-wide scale, called a...
Published in Proceedings of the National Academy of Sciences
The Drosophila defense against pathogens largely relies on the activation of two signaling pathways: immune deficiency (IMD) and Toll. The IMD pathway is triggered mainly by Gram-negative bacteria, whereas the Toll pathway responds predominantly to Gram-positive bacteria and fungi. The activation of these pathways leads to the rapid induction of nu...
Published in Molecular cell
To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 diffe...
Published in Molecular cell
The ability to measure human aging from molecular profiles has practical implications in many fields, including disease prevention and treatment, forensics, and extension of life. Although chronological age has been linked to changes in DNA methylation, the methylome has not yet been used to measure and compare human aging rates. Here, we build a q...
Published in Nature methods
Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set...
