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.
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.
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.
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
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.
ZDOCK: An initial‐stage protein‐docking algorithm
- Rong Chen, Li Li, Z. Weng
- Computer ScienceProteins: Structure, Function, and Bioinformatics
- 1 July 2003
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.
Detection of functional DNA motifs via statistical over-representation.
- M. Frith, Yutao Fu, Liqun Yu, Jiang-fan Chen, U. Hansen, Z. Weng
- BiologyNucleic 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.
Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies
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.