Controversies in modern evolutionary biology: the imperative for error detection and quality control

GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns

(2011) Xinan Yang et al.   BIOINFORMATICS

The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics

(2011) Anthony Levasseur et al.   Biology Direct

Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

(2011) John W Stiller   BMC EVOLUTIONARY BIOLOGY

Genome builders face the competition

(2011) Erika Check Hayden   NATURE

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Error and Error Mitigation in Low-Coverage Genome Assemblies

(2011) Melissa J. Hubisz et al.   PLoS One

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection

(2011) Omer Gokcumen et al.   GENOME BIOLOGY

Phylogenomics with incomplete taxon coverage: the limits to inference

(2010) Michael J Sanderson et al.   BMC EVOLUTIONARY BIOLOGY

Assessment of orthologous splicing isoforms in human and mouse orthologous genes

(2010) Federico Zambelli et al.   BMC GENOMICS

Alternative splicing: global insights

(2010) Martina Hallegger et al.   FEBS Journal

Genome assembly quality: Assessment and improvement using the neutral indel model

(2010) S. Meader et al.   GENOME RESEARCH

Different Phylogenomic Approaches to Resolve the Evolutionary Relationships among Model Fish Species

(2010) E. Negrisolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes

(2010) Elie Desmond et al.   RESEARCH IN MICROBIOLOGY

Identification of mammalian orthologs using local synteny

(2009) Jin Jun et al.   BMC GENOMICS

The effect of sequencing errors on metagenomic gene prediction

(2009) Katharina J Hoff   BMC GENOMICS

Dealing with missing values in large-scale studies: microarray data imputation and beyond

(2009) T. Aittokallio   BRIEFINGS IN BIOINFORMATICS

Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease

(2009) A.J. de Smith et al.   CYTOGENETIC AND GENOME RESEARCH

Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates

(2009) K. S. Kassahn et al.   GENOME RESEARCH

Adaptive evolution of young gene duplicates in mammals

(2009) M. V. Han et al.   GENOME RESEARCH

The difficulty of avoiding false positives in genome scans for natural selection

(2009) S. Mallick et al.   GENOME RESEARCH

Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates

(2009) Jin Jun et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora

(2009) Ingi Agnarsson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

Identifying protein-coding genes in genomic sequences

(2009) Jennifer Harrow et al.   GENOME BIOLOGY

Syntenator: Multiple gene order alignments with a gene-specific scoring function

(2008) Christian Rödelsperger et al.   Algorithms for Molecular Biology

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

(2008) Alinda Nagy et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Estimation of Phylogenetic Inconsistencies in the Three Domains of Life

(2008) V. Soria-Carrasco et al.   MOLECULAR BIOLOGY AND EVOLUTION

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Designating eukaryotic orthology via processed transcription units

(2008) Meng-Ru Ho et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

(2007) Michael R. Brent   NATURE REVIEWS GENETICS