Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa.

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Journal of Proteome Research

• Publication date

  2015-10-30

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1021/acs.jproteome.5b00823PMID 26483142
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mammalian skin cell biology: At the interface between laboratory and clinic

  2014cited by this paper
• De novo identification and quantification of single amino-acid variants in human brain.

  2014cited by this paper
• Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

  2014cited by this paper
• Proteogenomics: concepts, applications and computational strategies

  2014cited by this paper
• Proteogenomic database construction driven from large scale RNA-seq data.

  2014cited by this paper
• Integrating Genomic, Transcriptomic, and Interactome Data to Improve Peptide and Protein Identification in Shotgun Proteomics

  2014cited by this paper
• Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

  2014cited by this paper
• Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

  2014cited by this paper
• Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

  2014cited by this paper
• Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing.

  2014cited by this paper
• A draft map of the human proteome

  2014cited by this paper
• Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus.

  2013cited by this paper
• Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation

  2013cited by this paper
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  2013cited by this paper
• Amino acid composition of proteins reduces deleterious impact of mutations

  2013cited by this paper
• customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

  2013cited by this paper
• A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

  2013cited by this paper
• Protein analysis by shotgun/bottom-up proteomics.

  2013cited by this paper
• Predicting the Functional Effect of Amino Acid Substitutions and Indels

  2012cited by this paper
• Population genomic and genome-wide association studies of agroclimatic traits in sorghum

  2012cited by this paper
• De novo derivation of proteomes from transcriptomes for transcript and protein identification

  2012cited by this paper
• Putting the Pieces Together: High-performance LC-MS/MS Provides Network-, Pathway-, and Protein-level Perspectives in Populus*

  2012cited by this paper
• Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.

  2012cited by this paper
• Protein identification using customized protein sequence databases derived from RNA-Seq data.

  2012cited by this paper
• Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.

  2012cited by this paper
• System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap*

  2011cited by this paper
• De Novo Sequencing and Homology Searching‡‡*

  2011cited by this paper
• SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

  2011cited by this paper
• Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

  2011cited by this paper
• TagRecon: high-throughput mutation identification through sequence tagging.

  2010cited by this paper
• IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

  2009cited by this paper
• Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

  2009cited by this paper
• Divalent Metal Ions in Plant Mitochondria and Their Role in Interactions with Proteins and Oxidative Stress-Induced Damage to Respiratory Function1[W][OA]

  2009cited by this paper
• Shotgun proteome profile of Populus developing xylem

  2009cited by this paper
• JBrowse: a next-generation genome browser.

  2009cited by this paper
• RNA-Seq: a revolutionary tool for transcriptomics

  2009cited by this paper
• Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

  2008cited by this paper
• Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms

  2007cited by this paper
• MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.

  2007cited by this paper
• The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

  2006cited by this paper
• PepNovo: de novo peptide sequencing via probabilistic network modeling.

  2005cited by this paper
• Genome-wide association studies for common diseases and complex traits

  2005cited by this paper
• Correlation between Mutation Pressure, Selection Pressure, and Occurrence of Amino Acids

  2003cited by this paper
• The hitch-hiking effect of a favourable gene.

  1974cited by this paper
• Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

  year unknowncited by this paper

• Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

  2024cites this paper
• Elemental profiling and genome-wide association mapping reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

  2024cites this paper
• Seasonal and Water Restriction-Related Changes in Eucalyptus Grandis Leaf Proteins: Shedding Light on the Dark Proteome

  2023cites this paper
• Genome Wide Analysis of Family-1 UDP Glycosyltransferases in Populus trichocarpa Specifies Abiotic Stress Responsive Glycosylation Mechanisms

  2022cites this paper
• Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry.

  2020cites this paper
• Progress in understanding and overcoming biomass recalcitrance: a BioEnergy Science Center (BESC) perspective

  2017influential citation
• Comprehensive and sensitive proteogenomics data analysis strategy based on complementary multi-stage database search

  2017cites this paper
• Polymorphism‐aware protein databases – a prerequisite for an unbiased proteomic analysis of natural populations

  2017cites this paper