Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

The CRISPR/Cas9 system for plant genome editing and beyond

(2015) Luisa Bortesi et al.   BIOTECHNOLOGY ADVANCES

Splice variants in the proteome: a promising and challenging field to targeted drug discovery

(2015) Raphael Tavares et al.   DRUG DISCOVERY TODAY

A novel 3′ splice site recognition by the two zinc fingers in the U2AF small subunit

(2015) Hisashi Yoshida et al.   GENES & DEVELOPMENT

The landscape of antisense gene expression in human cancers

(2015) O. Alejandro Balbin et al.   GENOME RESEARCH

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions

(2015) Yaw Sing Tan et al.   Journal of Chemical Theory and Computation

Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation

(2015) Dhirendra Kumar et al.   MOLECULAR & CELLULAR PROTEOMICS

SKIP Confers Osmotic Tolerance during Salt Stress by Controlling Alternative Gene Splicing in Arabidopsis

(2015) Jinlin Feng et al.   Molecular Plant

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts

(2015) John W.S. Brown et al.   PLANT CELL

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

(2015) Shawn R. Thatcher et al.   PLANT PHYSIOLOGY

RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera)

(2015) Mei Yang et al.   PLoS One

Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

(2015) Eleonora de Klerk et al.   TRENDS IN GENETICS

An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses

(2015) Xiangqiang Zhan et al.   Nature Communications

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

(2015) Yasushi Kondo et al.   eLife

Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription

(2014) Sebastian Marquardt et al.   MOLECULAR CELL

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Onco-proteogenomics: cancer proteomics joins forces with genomics

(2014) Javier A Alfaro et al.   NATURE METHODS

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation

(2014) S. R. Thatcher et al.   PLANT CELL

Paired-End Analysis of Transcription Start Sites inArabidopsisReveals Plant-Specific Promoter Signatures

(2014) Taj Morton et al.   PLANT CELL

Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens

(2014) C.-Y. Chang et al.   PLANT PHYSIOLOGY

Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii

(2014) Xi Chen et al.   Proteome Science

NCYM, a Cis-Antisense Gene of MYCN, Encodes a De Novo Evolved Protein That Inhibits GSK3β Resulting in the Stabilization of MYCN in Human Neuroblastomas

(2014) Yusuke Suenaga et al.   PLoS Genetics

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships

(2013) Jan Kosinski et al.   BIOINFORMATICS

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study

(2013) Xiaolei Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Temperature-dependent regulation of flowering by antagonistic FLM variants

(2013) David Posé et al.   NATURE

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

Sorghum Extracellular Leucine-Rich Repeat Protein SbLRR2 Mediates Lead Tolerance in Transgenic Arabidopsis

(2013) Fu-Yuan Zhu et al.   PLANT AND CELL PHYSIOLOGY

The Plant Cell Reviews Alternative Splicing

(2013) N. A. Eckardt   PLANT CELL

Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome

(2013) G. Drechsel et al.   PLANT CELL

Improving your target-template alignment with MODalign

(2012) A. Barbato et al.   BIOINFORMATICS

The Poly(A)-Binding Protein Nuclear 1 Suppresses Alternative Cleavage and Polyadenylation Sites

(2012) Mathias Jenal et al.   CELL

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Pivotal role of the AREB/ABF-SnRK2 pathway in ABRE-mediated transcription in response to osmotic stress in plants

(2012) Yasunari Fujita et al.   PHYSIOLOGIA PLANTARUM

Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

(2012) C. Ruhl et al.   PLANT CELL

Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes

(2012) A. B. James et al.   PLANT CELL

Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana

(2012) Sarah Marie Rosloski et al.   PLANT MOLECULAR BIOLOGY

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)

(2011) Genna L. Andrews et al.   ANALYTICAL CHEMISTRY

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription

(2011) C. Sonmez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors

(2009) Pamela Nicholson et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution

(2009) Daniel A. Pomeranz Krummel et al.   NATURE

To localize or not to localize: mRNA fate is in 3′UTR ends

(2009) Catia Andreassi et al.   TRENDS IN CELL BIOLOGY

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access

(2008) Hideki Goda et al.   PLANT JOURNAL

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA