Computational identification of promoters and first exons in the human genome

By Ramana V. Davuluri, Ivo Grosse, Michael Ruogu Zhang. Nature Genetics, 2001

430 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/87b98f8c11092d40650c96487c432c327d701f22

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In Molecular Biology

Citations in the corpus

Current Protocols in Bioinformatics (2002, methodology): “For example, one could run CorePromoter (Zhang, 1998b), CpG_Promoter (Ioshikhes and Zhang, 2000), FirstEF (a first exon finder; Davuluri et al., 2001), JTEF (a last exon finder; Tabaska et al., 2001), and Polyadq (a polyA site finder; Tabaska and Zhang, 1999).”
Current methods of gene prediction, their strengths and weaknesses. (2002, neutral): “Already, a program especially dedicated to predicting 3¢-terminal exons (107) and another for identifying 5¢-terminal exons (108) have been made available from M.”
The UCSC Genome Browser Database: update 2006 (2005, background): “FirstEF shows exon, promoter and CpG window predictions from the FirstEF program (45).”
The Ensembl gene annotation system (2016, methodology): “The ab initio algorithms include Genscan (64), for predicting gene models; Eponine (65), for finding transcription start sites; CpG (Gos Micklem, unpublished software), for finding CpG islands; tRNAscan-SE (66), for finding potential tRNA genes and FirstEF (67), for identifying the first exons of tr”
DWE: Discriminating Word Enumerator (2005, methodology): “Increasingly accurate methods for detecting transcription start sites (TSSs), such as Davuluri et al. (2001) and Scherf et al. (2000), enable localization of promoter regions.”
Control of developmental regulators by Polycomb in human embryonic stem cells. (2006, neutral): “, 2000), FirstEF (Davuluri et al., 2001), ACEview (www.”
DeePromoter: Robust Promoter Predictor Using Deep Learning (2019, methodology): “Finally, GpG-based predictors utilized the location of GpG islands as the promoter region or the first exon region in the human genes usually contains GpG islands (Ioshikhes and Zhang, 2000; Davuluri et al., 2001; Lander et al., 2001; Ponger and Mouchiroud, 2002).”
Computational analysis of core promoters in the Drosophila genome (2002, background): “Prediction and analysis of core promoters have been active areas of research in computational biology [6], with several recent publications on prediction of human promoters [7-10].”
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome (2007, methodology): “For this, we retrieved the following annotations from the University of California Santa Cruz (UCSC) genome browser: (i) we matched promoters with the First Exon Finder (FirstEF) prediction”
The State of the Art of Mammalian Promoter Recognition (2003, methodology): “The FirstExonFinder utilises various discriminatory functions including recognition of the first splice site (intron 1) to predict transcription start sites and has been applied to the 15 kb sequences upstream of known genes on chromosomes 21 and 22, using the approximate position of the gene start ”
TRED: a transcriptional regulatory element database, new entries and other development (2007, methodology): “We used our promoter prediction program FirstEF (4) to predict promoters in the genomes of human, mouse and rat.”
Computational definition of sequence motifs governing constitutive exon splicing. (2004, background): “That the overlap is not 100% may be related to the fact that the CpG content of these ESEs is unusually high in every case cited above; the average is more than 10% of all dinucleotides.”