Related references
Note: Only part of the references are listed.Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana
Ping Wang et al.
PLANT CELL (2022)
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
Bo Wang et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2022)
Integration of multi-omics data reveals interplay between brassinosteroid and Target of Rapamycin Complex signaling in Arabidopsis
Christian Montes et al.
NEW PHYTOLOGIST (2022)
Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology
Jinfeng Chen et al.
NUCLEIC ACIDS RESEARCH (2022)
Multiomic Data Integration in the Analysis of Drought-Responsive Mechanisms in Quercus ilex Seedlings
Victor M. Guerrero-Sanchez et al.
PLANTS-BASEL (2022)
Integrative analysis in Pinus revealed long-term heat stress splicing memory
Victor Roces et al.
PLANT JOURNAL (2022)
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
Runxuan Zhang et al.
GENOME BIOLOGY (2022)
An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
Laura Fancello et al.
GENOME BIOLOGY (2022)
Enhanced protein isoform characterization through long-read proteogenomics
Rachel M. Miller et al.
GENOME BIOLOGY (2022)
Proteoforms and their expanding role in laboratory medicine
Lauren M. Forgrave et al.
PRACTICAL LABORATORY MEDICINE (2022)
An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development
Chun-Kai Huang et al.
GENOME BIOLOGY (2022)
Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene
Klara Kosova et al.
FRONTIERS IN PLANT SCIENCE (2021)
Integrative analysis of the nuclear proteome in Pinus radiata reveals thermopriming coupled to epigenetic regulation
Laura Lamelas et al.
JOURNAL OF EXPERIMENTAL BOTANY (2020)
Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation(1)
Mo-Xian Chen et al.
PLANT PHYSIOLOGY (2020)
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Matthew T. Parker et al.
ELIFE (2020)
Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
Alison D. Tang et al.
NATURE COMMUNICATIONS (2020)
Mass-spectrometry-based draft of the Arabidopsis proteome
Julia Mergner et al.
NATURE (2020)
Proteomic and interactomic insights into the molecular basis of cell functional diversity
Isabell Bludau et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)
New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs
Shoudong Zhang et al.
NUCLEIC ACIDS RESEARCH (2020)
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome
Jiawen Cui et al.
PLANT METHODS (2020)
A complex metabolic rearrangement towards the accumulation of glycerol and sugars consequence of a proteome remodeling is required for the survival of Chlamydomonas reinhardtii growing under osmotic stress
Francisco J. Colina et al.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY (2020)
Pinus Susceptibility to Pitch Canker Triggers Specific Physiological Responses in Symptomatic Plants: An Integrated Approach
Joana Amaral et al.
FRONTIERS IN PLANT SCIENCE (2019)
Multiomics resolution of molecular events during a day in the life of Chlamydomonas
Daniela Strenkert et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Stress-induced senescence and plant tolerance to abiotic stress
Nir Sade et al.
JOURNAL OF EXPERIMENTAL BOTANY (2018)
Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain et al.
NATURE BIOTECHNOLOGY (2018)
System-wide analysis of short-term response to high temperature in Pinus radiata
Monica Escandon et al.
JOURNAL OF EXPERIMENTAL BOTANY (2017)
Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata
Jesus Pascual et al.
MOLECULAR & CELLULAR PROTEOMICS (2017)
Methods, Tools and Current Perspectives in Proteogenomics
Kelly V. Ruggles et al.
MOLECULAR & CELLULAR PROTEOMICS (2017)
Salmon provides fast and bias-aware quantification of transcript expression
Rob Patro et al.
NATURE METHODS (2017)
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Andy T. Kong et al.
NATURE METHODS (2017)
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
Runxuan Zhang et al.
NUCLEIC ACIDS RESEARCH (2017)
Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings
Fu-Yuan Zhu et al.
PLANT JOURNAL (2017)
Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification
Honglan Li et al.
BMC GENOMICS (2016)
The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata
Jesus Pascual et al.
JOURNAL OF PROTEOMICS (2016)
Long-read sequence assembly of the gorilla genome
David Gordon et al.
SCIENCE (2016)
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Wei Shen et al.
PLOS ONE (2016)
AtRTD - a comprehensive reference transcript dataset resource foraccurate quantification of transcript-specific expression in Arabidopsis thaliana
Runxuan Zhang et al.
NEW PHYTOLOGIST (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Improving the quality of protein identification in non-model species. Characterization of Quercus ilex seed and Pinus radiata needle proteomes by using SEQUEST and custom databases
M. Cristina Romero-Rodriguez et al.
JOURNAL OF PROTEOMICS (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome
Gabriele Drechsel et al.
PLANT CELL (2013)
The different proteomes of Chlamydomonas reinhardtii
Luis Valledor et al.
JOURNAL OF PROTEOMICS (2012)
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
Maria Kalyna et al.
NUCLEIC ACIDS RESEARCH (2012)
The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis
Giselle M. Knudsen et al.
PLOS ONE (2011)
Analysis and validation of proteomic data generated by tandem mass spectrometry
Alexey I. Nesvizhskii et al.
NATURE METHODS (2007)
Interpretation of shotgun proteomic data - The protein inference problem
AI Nesvizhskii et al.
MOLECULAR & CELLULAR PROTEOMICS (2005)
Dark-inducible genes from Arabidopsis thaliana are associated with leaf senescence and repressed by sugars
Y Fujiki et al.
PHYSIOLOGIA PLANTARUM (2001)
Share Paper
