NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks

NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks. Suhas V Vasaikar, Aditya K Padhi, Bhyravabhotla Jayaram and James Gomes. BMC Neuroscience 2013, 14:3 doi:10.1186/1471-2202-14-3, Published: 3 January 2013

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It is in this light that we have created a database, NeuroDNet, that includes information about twelve neurodegenerative diseases - adrenomyeloneuropathy, Alzheimer disease, amyotrophic lateral sclerosis, ataxia-telangiectasia, dentatorubral-pallidoluysian atrophy, Friedreich ataxia, frontotemporal dementia, Huntington disease, Lewy body dementia, Parkinson disease, prion disease, progressive supranuclear palsy. It accounts for the interactions and regulation between signaling molecules, genes and proteins. This database is also the first of its kind, which enables the construction and analysis of NDDs through PPI, regulatory and Boolean networks. We also present the results of three case studies, which demonstrate the power of the analytical tools featured in NeuroDNet.

In Epigenomics, Location Is Everything: Researchers Exploit Gene Position to Test 'Histone Code'

In Epigenomics, Location Is Everything: Researchers Exploit Gene Position to Test 'Histone Code'. Menzies Chen, Katherine Licon, Rei Otsuka, Lorraine Pillussend, Trey Idekersend. Cell Reports, 03 January 2013

Also: Science News, Jan. 3, 2013,
Jan. 3, 2013 — In a novel use of gene knockout technology, researchers at the University of California, San Diego School of Medicine tested the same gene inserted into 90 different locations in a yeast chromosome -- and discovered that while the inserted gene never altered its surrounding chromatin landscape, differences in that immediate landscape measurably affected gene activity.