New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

Large Local Analysis of the Unaligned Genome and Its Application

(2013) Lianping Yang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

(2013) Kai Song et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

(2012) Jonathan Göke et al.   BIOINFORMATICS

Comparison of metagenomic samples using sequence signatures

(2012) Bai Jiang et al.   BMC GENOMICS

Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads

(2012) Zhiyuan Zhai et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

(2012) Jiemeng Liu et al.   NUCLEIC ACIDS RESEARCH

Variable length local decoding and alignment-free sequence comparison

(2012) Gilles Didier et al.   THEORETICAL COMPUTER SCIENCE

New powerful statistics for alignment-free sequence comparison under a pattern transfer model

(2011) Xuemei Liu et al.   JOURNAL OF THEORETICAL BIOLOGY

A new distribution vector and its application in genome clustering

(2011) Bo Zhao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

The Power of Detecting Enriched Patterns: An HMM Approach

(2010) Zhiyuan Zhai et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics

(2010) Lin Wan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Assembly free comparative genomics of short-read sequence data discovers the needles in the haystack

(2010) CHARLES H. CANNON et al.   MOLECULAR ECOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

On finding minimal absent words

(2009) Armando J Pinho et al.   BMC BIOINFORMATICS

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Composition vector approach to whole-genome-based prokaryotic phylogeny: Success and foundations

(2009) Qiang Li et al.   JOURNAL OF BIOTECHNOLOGY

Alignment-Free Sequence Comparison (I): Statistics and Power

(2009) Gesine Reinert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

(2009) Z. Xu et al.   NUCLEIC ACIDS RESEARCH

Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method

(2009) G. A. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

(2009) S.-R. Jun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Approximate word matches between two random sequences

(2008) Conrad J. Burden et al.   ANNALS OF APPLIED PROBABILITY

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

(2008) Qi Dai et al.   BIOINFORMATICS

Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'

(2008) Qi Dai et al.   BMC BIOINFORMATICS

Empirical distribution of k-word matches in biological sequences

(2008) Sylvain Forêt et al.   PATTERN RECOGNITION