Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies

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

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

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data

(2013) Feng Zeng et al.   NUCLEIC ACIDS RESEARCH

Comparison of metagenomic samples using sequence signatures

(2012) Bai Jiang et al.   BMC GENOMICS

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing

(2012) Xuejian Xiong et al.   PLoS One

HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences

(2011) Tarini Ghosh et al.   BMC BIOINFORMATICS

Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton

(2011) Xiaozhen Mou et al.   Environmental Microbiology Reports

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim

(2010) S. Balzer et al.   BIOINFORMATICS

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume

(2010) Gregory J. Dick et al.   ENVIRONMENTAL MICROBIOLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

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

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

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel

(2010) Jack A. Gilbert et al.   Standards in Genomic Sciences

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

(2009) Rachel S. Poretsky et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume

(2009) Gregory J. Dick et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

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

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

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

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