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To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His(6) fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this(More)
Brain-derived neurotrophic factor (BDNF) is a well characterized neurotrophin that mediates a wide variety of activities in the central nervous system, including neuronal differentiation, neuroprotection, and synaptic plasticity. The canonical Wnt signaling pathway is a critical regulator of embryonic development and homeostasis in adult tissues. Our group(More)
Vertebrate circadian rhythms are organized by the hypothalamic suprachiasmatic nucleus (SCN). Despite its physiological importance, SCN development is poorly understood. Here, we show that Lim homeodomain transcription factor 1 (Lhx1) is essential for terminal differentiation and function of the SCN. Deletion of Lhx1 in the developing SCN results in loss of(More)
The landscape of human phosphorylation networks has not been systematically explored, representing vast, unchartered territories within cellular signaling networks. Although a large number of in vivo phosphorylated residues have been identified by mass spectrometry (MS)-based approaches, assigning the upstream kinases to these residues requires biochemical(More)
MOTIVATION The vertebrate retina is a complex neuronal tissue, and its development, normal functioning and response to injury and disease is subject to a variety of genetic factors. To understand better the regulatory and functional relationships between the genes expressed within the retina, we constructed an interactive gene network of the mouse retina by(More)
The identification of cis-regulatory modules (CRMs) can greatly advance our understanding of eukaryotic regulatory mechanism. Current methods to predict CRMs from known motifs either depend on multiple alignments or can only deal with a small number of known motifs provided by users. These methods are problematic when binding sites are not well aligned in(More)
The past decade has witnessed the increasing demands on data-driven business intelligence that led to the proliferation of data-intensive applications. A managed object-oriented programming language such as Java is often the developer's choice for implementing such applications, due to its quick development cycle and rich community resource. While the use(More)
SUMMARY Phosphorylation plays an important role in cellular signal transduction. Current phosphorylation-related databases often focus on the phosphorylation sites, which are mainly determined by mass spectrometry. Here, we present PhosphoNetworks, a phosphorylation database built on a high-resolution map of phosphorylation networks. This high-resolution(More)
The Kaposi sarcoma associated herpesvirus (KSHV) latency associated nuclear antigen (LANA) is expressed in all KSHV associated malignancies and is essential for maintenance of KSHV genomes in infected cells. To identify kinases that are potentially capable of modifying LANA, in vitro phosphorylation assays were performed using an Epstein Barr virus plus(More)
Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme that oxidatively cleaves methyl groups from monomethyl and dimethyl Lys4 of histone H3 (H3K4Me1, H3K4Me2) and can contribute to gene silencing. This study describes the design and synthesis of analogues of a monoamine oxidase antidepressant, phenelzine, and their LSD1 inhibitory properties. A(More)