Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

CRISPR/Cas9-mediated knockout of six glycosyltransferase genes in Nicotiana benthamiana for the production of recombinant proteins lacking β-1,2-xylose and core α-1,3-fucose

(2018) Julia Jansing et al.   PLANT BIOTECHNOLOGY JOURNAL

The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons

(2018) Julia Bally et al.   Annual Review of Phytopathology

Recombinant plant-derived human IgE glycoproteomics

(2017) Laura Montero-Morales et al.   Journal of Proteomics

Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses

(2017) Daniel M Lyons et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular engineering and plant expression of an immunoglobulin heavy chain scaffold for delivery of a dengue vaccine candidate

(2017) Mi-Young Kim et al.   PLANT BIOTECHNOLOGY JOURNAL

Immunogenicity of glycans on biotherapeutic drugs produced in plant expression systems—The taliglucerase alfa story

(2017) Bonita Rup et al.   PLoS One

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

Plant-produced anti-dengue virus monoclonal antibodies exhibit reduced antibody-dependent enhancement of infection activity

(2016) Matthew Dent et al.   JOURNAL OF GENERAL VIROLOGY

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data

(2016) Petr Danecek et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Processing of complex N-glycans in IgG Fc-region is affected by core fucosylation

(2015) Alexandra Castilho et al.   mAbs

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

(2015) Michael M. Goodin et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Multiplexed, targeted gene editing inNicotiana benthamianafor glyco-engineering and monoclonal antibody production

(2015) Jin Li et al.   PLANT BIOTECHNOLOGY JOURNAL

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

(2014) Noe Fernandez-Pozo et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Kenlee Nakasugi et al.   PLoS One

Using GBrowse 2.0 to visualize and share next-generation sequence data

(2013) L. D. Stein   BRIEFINGS IN BIOINFORMATICS

N-Glycosylation of Plant-produced Recombinant Proteins

(2013) Dirk Bosch et al.   CURRENT PHARMACEUTICAL DESIGN

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

(2013) Kenlee Nakasugi et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RECONSTRUCTING THE COMPLEX EVOLUTIONARY ORIGIN OF WILD ALLOPOLYPLOID TOBACCOS (NICOTIANASECTIONSUAVEOLENTES)

(2012) Laura J. Kelly et al.   EVOLUTION

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

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 statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Rapid High Yield Production of Different Glycoforms of Ebola Virus Monoclonal Antibody

(2011) Alexandra Castilho et al.   PLoS One

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nicotiana benthamiana as a Production Platform for Artemisinin Precursors

(2010) Teun W. J. M. van Herpen et al.   PLoS One

Molecular characterization of T-DNA integration sites in transgenic birch

(2010) Fan-Suo Zeng et al.   TREES-STRUCTURE AND FUNCTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The effect of individual N-glycans on enzyme activity

(2009) Danielle Skropeta   BIOORGANIC & MEDICINAL CHEMISTRY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Generation of glyco-engineered Nicotiana benthamiana for the production of monoclonal antibodies with a homogeneous human-like N-glycan structure

(2008) Richard Strasser et al.   PLANT BIOTECHNOLOGY JOURNAL

Effect of glycosylation on protein folding: A close look at thermodynamic stabilization

(2008) D. Shental-Bechor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA