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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Insight is given into the connections between chromatin modifications and transcriptional regulatory activity and a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2) is uncovered, providing a new tool for the functional annotation of the human genome. Expand
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts. Expand
Assessing computational tools for the discovery of transcription factor binding sites
The purpose of the current assessment is to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools. Expand
ZDOCK: An initial‐stage protein‐docking algorithm
A new scoring function for the initial stage of unbound docking is presented that combines the recently developed pairwise shape complementarity with desolvation and electrostatics and shows superior performance, especially for the antibody‐antigen category of test cases. Expand
Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies
Strong loss-of-function mutations in ago3 are described and it is found that Ago3 acts to amplify piRNA pools and to enforce on them an antisense bias, increasing the number of piRNAs that can act to silence transposons. Expand
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
- B. Pierce, K. Wiehe, Howook Hwang, Bong-Hyun Kim, T. Vreven, Z. Weng
- Medicine, Computer Science
- 15 June 2014
This paper presents a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers, and provides options for users to guide the scoring and the selection of output models. Expand
Detection of functional DNA motifs via statistical over-representation.
- M. Frith, Yutao Fu, Liqun Yu, Jiang-fan Chen, U. Hansen, Z. Weng
- Biology, Medicine
- Nucleic acids research
- 15 March 2004
Clover has the potential to greatly accelerate characterization of signals that regulate transcription, and compares favorably with an ab initio motif discovery algorithm based on sequence alignment, when the motif library includes only a homolog of the factor that actually regulates the sequences. Expand
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
An integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. Expand
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
The TREM2-APOE pathway is identified as a major regulator of microglial functional phenotype in neurodegenerative diseases and serves as a novel target that could aid in the restoration of homeostatic microglia. Expand
The ENCODE (ENCyclopedia Of DNA Elements) Project
The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. Expand