Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics

The Amordad database engine for metagenomics

(2014) Ehsan Behnam et al.   BIOINFORMATICS

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies

(2014) Ying Wang et al.   PLoS One

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses

(2014) B. L. Hurwitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple alignment-free sequence comparison

(2013) Jie Ren et al.   BIOINFORMATICS

Exact Goodness-of-Fit Tests for Markov Chains

(2013) J. Besag et al.   BIOMETRICS

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

(2013) K. Song et al.   BRIEFINGS IN BIOINFORMATICS

A Geometric Interpretation for Local Alignment-Free Sequence Comparison

(2013) Ehsan Behnam 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

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

(2013) Huiguang Yi et al.   NUCLEIC ACIDS RESEARCH

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

One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses

(2012) Leelavati Narlikar et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

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

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

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

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

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

The ‘Expansion-Contraction’ model of Pleistocene biogeography: rocky shores suffer a sea change?

(2009) PETER B. MARKO et al.   MOLECULAR ECOLOGY

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

Modeling ChIP Sequencing In Silico with Applications

(2008) Zhengdong D. Zhang et al.   PLoS Computational Biology