A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

Activity‐based proteomics reveals nine target proteases for the recombinant protein‐stabilizing inhibitor Sl CYS 8 in Nicotiana benthamiana

(2019) Philippe V. Jutras et al.   PLANT BIOTECHNOLOGY JOURNAL

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tomato subtilase family includes several cell death-related proteinases with caspase specificity

(2018) Sven Reichardt et al.   Scientific Reports

High-throughput sequencing data and the impact of plant gene annotation quality

(2018) Aleksia Vaattovaara et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

Evolutionary History of Subtilases in Land Plants and Their Involvement in Symbiotic Interactions

(2017) Alexander Taylor et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire

(2017) Friederike Grosse-Holz et al.   PLANT BIOTECHNOLOGY JOURNAL

Time-calibrated phylogenetic trees establish a lag between polyploidisation and diversification in Nicotiana (Solanaceae)

(2017) James J. Clarkson et al.   PLANT SYSTEMATICS AND EVOLUTION

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

(2017) Shuqing Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NLR network mediates immunity to diverse plant pathogens

(2017) Chih-Hang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes

(2017) Carlos S. Casimiro-Soriguer et al.   PROTEOMICS

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes

(2015) Xuewen Wang et al.   MOLECULAR GENETICS AND GENOMICS

The SGN VIGS Tool: User-Friendly Software to Design Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics

(2015) Noe Fernandez-Pozo et al.   Molecular Plant

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The EMBL-EBI bioinformatics web and programmatic tools framework

(2015) Weizhong Li et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Plant Molecular Pharming for the Treatment of Chronic and Infectious Diseases

(2014) Eva Stoger et al.   Annual Review of Plant Biology

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

(2014) Hideki Hirakawa et al.   DNA RESEARCH

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

Tobacco rattle virus–based virus-induced gene silencing in Nicotiana benthamiana

(2014) Muthappa Senthil-Kumar et al.   Nature Protocols

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

(2014) Kenlee Nakasugi et al.   PLoS One

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

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

Apoplastic immunity and its suppression by filamentous plant pathogens

(2013) Gunther Doehlemann et al.   NEW PHYTOLOGIST

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

(2012) Fatima Naim et al.   PLoS One

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae)

(2008) I. J. Leitch et al.   ANNALS OF BOTANY

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

(2008) Oliver Keller et al.   BMC BIOINFORMATICS

Enzyme–inhibitor interactions at the plant–pathogen interface

(2008) Johana C Misas-Villamil et al.   CURRENT OPINION IN PLANT BIOLOGY

Nicotiana benthamiana: Its History and Future as a Model for Plant–Pathogen Interactions

(2008) Michael M. Goodin et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY