subject: Bioinformatics

Total is 14 Results
Separating Fractal and Oscillatory Components in the Power Spectrum of Neurophysiological Signal


Haiguang Wen, Zhongming Liu


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...

Bioinformatics Biomedical Engineering fractal scale-free

Position of MLL1 morphemes in human genomic DNA


Daidong Wang, Elise Novorolsky, Minou Bina, Noorfatin J. Zulkefl, Phillip J. Wyss


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

Localization of potential regulatory signals in the human genome


Minou Bina, Phillip J. Wyss


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...

Bioinformatics Chemistry Codes in Human DNA Gene Regulation Genetic Vocabulary Genomics Human Genome Regulatory Signals Sequence Context Transcription factor binding sites

Occurrences of MLL1 morphemes in human cDNAs retrieved from GenBank


Minou Bina, Phillip J. Wyss


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

Evaluation of Function Predictions for Moonlighting Proteins


Catherine Rayon, Daisuke Kihara, Ishita K. Khan, Meghana Chitale


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...

Biochemistry Bioinformatics Molecular Biosciences proteomics

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP


Daisuke Kihara, Meghana Chitale, Troy Hawkins


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...

Biochemistry Bioinformatics Computational Biology / Methods Genetic Molecular Biosciences Proteins / Metabolism

Threading Without Optimizing Weighting Factor for the Scoring Function Proteins


Daisuke Kihara, David Yifeng


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...

Algorithms Biochemistry Bioinformatics databases Molecular Biosciences Protein Proteins / chemistry

Statistical Potential based Amino Acid Similarity Matrices for Aligning Distantly Related Protein Sequences


Daisuke Kihara, H. Huang, Y.H. Tan


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...

Amino Acids/chemistry Biochemistry Bioinformatics Molecular Biosciences Protein Folding

Comparative genomics of small RNAs in bacterial genomes


Daisuke Kihara, Stan Luban


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...

Bacterial Bacterial/Genetics Biochemistry Bioinformatics Deinococcus/Genetics Escherichiacoli/Metabolism Molecular Biosciences Multigene Family RNA

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