Parallel Histories of Horizontal Gene Transfer Facilitated Extreme Reduction of Endosymbiont Genomes in Sap-Feeding Insects

Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis

(2013) Calum W. Russell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

(2013) João MP Alves et al.   BMC EVOLUTIONARY BIOLOGY

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

(2013) Filip Husnik et al.   CELL

Defensive Bacteriome Symbiont with a Drastically Reduced Genome

(2013) Atsushi Nakabachi et al.   CURRENT BIOLOGY

The Evolution of Genomic Instability in the Obligate Endosymbionts of Whiteflies

(2013) Daniel B. Sloan et al.   Genome Biology and Evolution

Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

(2013) Gordon M. Bennett et al.   Genome Biology and Evolution

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Metabolic Effectors Secreted by Bacterial Pathogens: Essential Facilitators of Plastid Endosymbiosis?

(2013) Steven G. Ball et al.   PLANT CELL

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

(2012) Xiao-Wei Wang et al.   BMC GENOMICS

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

(2012) Y. D. Kelkar et al.   GENETICS

Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids

(2012) Daniel B. Sloan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

(2012) Bruce A. Curtis et al.   NATURE

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora

(2012) E. C. M. Nowack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont

(2012) S. Shigenobu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The central role of the host cell in symbiotic nitrogen metabolism

(2012) S. J. Macdonald et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs

(2011) John P. McCutcheon et al.   CURRENT BIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Large-Scale Label-Free Quantitative Proteomics of the Pea aphid-BuchneraSymbiosis

(2011) Anton Poliakov et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome Expansion and Differential Expression of Amino Acid Transporters at the Aphid/Buchnera Symbiotic Interface

(2011) D. R. G. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Aphid genome expression reveals host-symbiont cooperation in the production of amino acids

(2011) A. K. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont

(2011) Araceli Lamelas et al.   PLoS Genetics

De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

(2010) Xiao-Wei Wang et al.   BMC GENOMICS

The bacterial essence of tiny symbiont genomes

(2010) John P McCutcheon   CURRENT OPINION IN MICROBIOLOGY

Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola

(2010) A. C. C. Wilson et al.   INSECT MOLECULAR BIOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mosaic origin of the mitochondrial proteome

(2010) Radek Szklarczyk et al.   PROTEOMICS

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY

Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host

(2010) Naruo Nikoh et al.   PLoS Genetics

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Aphids acquired symbiotic genes via lateral gene transfer

(2009) Naruo Nikoh et al.   BMC BIOLOGY

Genome size of Pachypsylla venusta (Hemiptera: Psyllidae) and the ploidy of its bacteriocyte, the symbiotic host cell that harbors intracellular mutualistic bacteria with the smallest cellular genome

(2009) A. Nakabachi et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

Eukaryotic and Eubacterial Contributions to the Establishment of Plastid Proteome Estimated by Large-Scale Phylogenetic Analyses

(2009) K. Suzuki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiotic bacteria enable insect to use a nutritionally inadequate diet

(2009) E Akman Gunduz et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics