Deepak Kolippakkam

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Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86%(More)
UNLABELLED We report a comprehensive and quantitative analysis of the mouse liver and plasma proteomes. The method used is based on extensive fractionation of intact proteins, further separation of proteins based on their abundance and size, and high-accuracy mass spectrometry. This analysis reached a depth in proteomic profiling not reported to date for a(More)
Key pathological processes in Alzheimer's disease (AD) include the accumulation of amyloid beta peptide (Abeta) which, in excess, triggers pathological cascades including widespread inflammation, partly reflected by chronic microglial activation. It has previously been suggested that CD40/CD40L interaction promotes AD like pathology in transgenic mice.(More)
The mammalian target of rapamycin (mTOR) pathway, a major regulator of translation, is frequently activated in hepatocellular carcinomas. We investigated the effects of mTOR activation in the human HepaRG cells, which possess potent hepatocytic differentiation capability. Differentiation of HepaRG cells into functional and polarized hepatocyte-like cells(More)
Due to the digitization of data and advances in technology, it has become extremely easy to obtain and store large quantities of data, particularly Multimedia data. Fields ranging from Commercial to Military need to analyze these data in an efficient and fast manner. Presently, tools for mining images are few and require human intervention. Feature(More)
UNLABELLED Physico-chemical properties of amino acids can be used to study protein sequence profiles, folding and function. We collated 242 properties for the 20 naturally occurring amino acids and created a dataset. The dataset is available as a database named APDbase( Amino acid Physico-chemical properties Data base). The database can be queried using(More)
Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ± 500 Da. In a(More)
We have employed a genomic approach in homogenous cell culture to investigate the fundamental transcriptional responses which occur in neurons over time as a consequence of a single 30-min exposure to cocaine. Data from 24 Affymetrix microarrays, representing eight treatment groups, were analyzed by GeneChip Operating Software and then further mined by(More)
In the version of this article initially published, the first three bars in the histogram in Figure 1a should have read “No vehicle,” “No Dz” and “Dz13” instead of “No Dz,” “Dz13” and “Dz13scr.” The legend of Figure 1a should have included the sentences: “‘No vehicle’ represents the normoxia control without vehicle (transfection agent) or DNAzyme or siRNA.(More)
Keyword searching is the most common form of document search on the Web. Many Web publishers manually annotate the META tags and titles of their pages with frequently queried phrases in order to improve their placement and ranking. A “hidden phrase” is defined as a phrase that occurs in the META tag of a Web page but not in its body. In this paper we(More)