Neurophysiological field-potential signals con- sist of both arrhythmic and rhythmic patterns indicative of the fractal and oscillatory dynamics arising from likely distinct mechanisms. Here, we present a new method, namely the irregular-resampling auto-sp...
Mixed Lineage Leukemia 1 (MLL or MLL1) may play a central role in the recruitment of transcription factors to chromatin to regulate the expression of genes associated with !CpG islands. We have previously shown that MLL1 binds specific DNA sequence ele...
Binding Sites Bioinformatics Cell division Chemistry Chromatin structure Cis-elements Codes in DNA CpG islands Gene bookmarking Gene Regulation Mammalian genomes Mitosis MLL MLL binding sites Mouse genome Regulatory codes TREs Trithorax response elements
Supplementary materials for the publication entitled: "Discovering sequences with potential regulatory characteristics." Bina M, Wyss P, Lazarus SA, Shah SR, Ren W, Szpankowski W, Crawford GE, Park SP, Song XC. Access dataset in genome browser. In the huma...
The human genome may include overlapping codes to accommodate a wide-range of selective pressures imposed by various cellular requirements. In this context, we have examined whether occurrences of MLL1 morphemes in exons of human genes may impose constrai...
Biochemistry Bioinformatics Chemistry Coding sequences Codon bias Codon selection Codon utilization CpG islands Exon Exons Genomics Human Genome MLL1 morphemes in CDSs MLL1 morphemes in exons Morphemes MLL1 Overlapping codes Regulatory codes in DNA Trithorax response elements
In the human genome, regulatory signals are dispersed in DNA sequences and segments that control gene expression. We have developed a computational model to localize the position of potential regulatory signals in human genomic DNA. In this publication...
Binding-site Biochemistry Bioinformatics Codes in Human DNA DNASE-I hypersensitive sites Gene Regulation Genetic Vocabulary Human Genome Hypersensitive Sites Molecular Biosciences Promoter Regions Regulatory Signals Sequence Context Transcription factor binding sites Transcription Factors
The performances of PFP, ESG, and PSI-BLAST in predicting the functional diversity of moonlighting proteins were analyzed. PFP shows overall better performance in predicting diverse moonlighting functions as compared with PSI-BLAST and ESG. Recall by PSI-B...
BACKGROUND: A new paradigm of biological investigation takes advantage of technologies that produce large high throughput datasets, including genome sequences, interactions of proteins, and gene expression. The ability of biologists to analyze and interpre...
Optimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the...
Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more exp...
In recent years, various families of small non-coding RNAs (sRNAs) have been discovered by experimental and computational approaches, both in bacterial and eukaryotic genomes. Although most of them await elucidation of their function, it has been reported...
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