Structure, Function and Diversity of the Healthy Human Microbiome
- C. Huttenhower, D. Gevers, O. White
- Biology, MedicineNature
- 17 May 2012
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals.
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
- R. Overbeek, T. Begley, V. Vonstein
- BiologyNucleic Acids Research
- 7 October 2005
The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.
Flexible structure alignment by chaining aligned fragment pairs allowing twists
The advantages of the FATCAT approach are illustrated by several examples of comparison between proteins known to adopt different conformations, where the FATcAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges.
The Ecoresponsive Genome of Daphnia pulex
- J. Colbourne, M. Pfrender, J. Boore
- Biology, Environmental ScienceScience
- 4 February 2011
The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
FragGeneScan: predicting genes in short and error-prone reads
- Mina Rho, Haixu Tang, Yuzhen Ye
- Biology, EngineeringNucleic Acids Research
- 28 August 2010
A novel gene prediction method FragGeneScan is developed, which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads, which consistently outperformed MetaGene for short reads.
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
- Yongan Zhao, Haixu Tang, Yuzhen Ye
- Computer Science, BiologyBioinform.
- 28 October 2011
RAPSearch2 is presented, a new memory-efficient implementation of the RAPSearch algorithm that uses a collision-free hash table to index a similarity search database and the utilization of an optimized data structure further speeds up the similarity search.
A framework for human microbiome research
Resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times are presented, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far.
FATCAT: a web server for flexible structure comparison and structure similarity searching
FATCAT server implements the recently developed flexible protein structure comparison algorithm FATCAT, which automatically identifies hinges and internal rearrangements in two protein structures.
A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters
- S. Huse, Yuzhen Ye, Yanjiao Zhou, A. Fodor
- BiologyPLoS ONE
- 13 June 2012
It is found that commonalities between samples based on taxonomy could sometimes belie variability at the sub-genus OTU level, and even OTUs present in nearly every subject, or that dominate in some samples, showed orders of magnitude variation in relative abundance emphasizing the highly variable nature across individuals.
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
A parsimony approach, called MinPath (Minimal set of Pathways), is developed for biological pathway reconstructions using protein family predictions, which yields a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.