Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length

No abstract is available for this paper.

• Publication year

  2010

• Venue

  J. Comput. Biol.

• Publication date

  2010-01-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1089/cmb.2009.0031PMID 20078394
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

  2008cited by this paper
• Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

  2008influential reference
• Constructions for Clumps Statistics

  2008cited by this paper
• Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes

  2007cited by this paper
• Evaluating GO-based Semantic Similarity Measures

  2007cited by this paper
• Relationship between insertion/deletion (indel) frequency of proteins and essentiality

  2007cited by this paper
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  2007cited by this paper
• Measuring semantic similarity between Gene Ontology terms

  2007cited by this paper
• BMC Bioinformatics BioMed Central Methodology article A new measure for functional similarity of gene products based on Gene Ontology

  2006cited by this paper
• The Universal Protein Resource (UniProt)

  2006cited by this paper
• Large‐scale survey for potentially targetable indels in bacterial and protozoan proteins

  2005cited by this paper
• ProbCons: Probabilistic consistency-based multiple sequence alignment.

  2005cited by this paper
• Correlation between gene expression and GO semantic similarity

  2005cited by this paper
• Parametric Alignment of Drosophila Genomes

  2005cited by this paper
• Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands

  2005cited by this paper
• Applications of Hidden Markov Models for Characterization of Homologous DNA Sequences with a Common Gene

  2005cited by this paper
• SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

  2005cited by this paper
• Selective targeting of indel‐inferred differences in spatial structures of highly homologous proteins

  2005cited by this paper
• An HMM posterior decoder for sequence feature prediction that includes homology information

  2005cited by this paper
• High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome

  2004cited by this paper
• Inching toward reality: An improved likelihood model of sequence evolution

  2004cited by this paper
• The Universal Protein Resource (UniProt)

  2004cited by this paper
• Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.

  2004cited by this paper
• Context of deletions and insertions in human coding sequences

  2004cited by this paper
• Sequence alignments and pair hidden Markov models using evolutionary history.

  2003cited by this paper
• Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation

  2003cited by this paper
• Biological sequence analysis

  2003cited by this paper
• ProClust: improved clustering of protein sequences with an extended graph-based approach

  2002cited by this paper
• Distribution of indel lengths

  2001cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Models of protein sequence evolution and their applications.

  2000cited by this paper
• Can sequence determine function?

  2000cited by this paper
• Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language

  1999influential reference
• Twilight zone of protein sequence alignments.

  1999influential reference
• Horizontal gene transfer among genomes: the complexity hypothesis.

  1999cited by this paper
• An Information-Theoretic Definition of Similarity

  1998cited by this paper
• Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy

  1997cited by this paper
• Local alignment statistics.

  1996cited by this paper
• The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment

  1995cited by this paper
• A simple derivation of exact reliability formulas for linear and circular consecutive-k-of-n: F systems

  1995cited by this paper
• Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria.

  1995cited by this paper
• A Phase Transition for the Score in Matching Random Sequences Allowing Deletions

  1994cited by this paper
• Sequence Comparison Significance and Poisson Approximation

  1994cited by this paper
• Distribution Theory of Runs: A Markov Chain Approach

  1994cited by this paper
• Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

  1993cited by this paper
• Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores

  1992cited by this paper
• An evolutionary model for maximum likelihood alignment of DNA sequences

  1991cited by this paper
• Strong limit theorems of empirical functionals for large exceedances of partial sums of i

  1991cited by this paper
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

  1990cited by this paper
• Development and application of a metric on semantic nets

  1989cited by this paper
• A personal communication

  1989cited by this paper
• Improved tools for biological sequence comparison.

  1988cited by this paper
• An improved algorithm for matching biological sequences.

  1982influential reference
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.

  1970influential reference
• Correlation between Gene Frequency and Population Size

  1963cited by this paper

• Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore

  2016cites this paper
• Predicting the Functional Effects of Human Short Variations Using Hidden Markov Models

  2015cites this paper
• Quantitative prediction of the effect of genetic variation using hidden Markov models

  2014cites this paper
• Bayesian versus data driven model selection for microarray data

  2014cites this paper
• Geometric Approach to Biosequence Analysis

  2014cites this paper
• Computational approaches to species phylogeny inference and gene tree reconciliation.

  2013cites this paper
• The evolution of phenylpropanoid metabolism in the green lineage

  2013cites this paper
• Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress

  2013cites this paper
• The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science

  2012cites this paper
• Speeding up the Consensus Clustering methodology for microarray data analysis

  2011cites this paper
• Data Integration, Metabolic Networks and Systems Biology

  2011cites this paper
• PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA]

  2011cites this paper
• The Three Steps of Clustering in the Post-Genomic Era: A Synopsis

  2010cites this paper
• Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties

  2010cites this paper