Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq (Q56983881)

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18 April 2020

title

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq (English)

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18 April 2020

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1

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18 April 2020

TuKiet T Lam

5

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18 April 2020

Angus C. Nairn

10

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Nenad Sestan

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18 April 2020

9

Mark B Gerstein

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18 April 2020

author name string

Robert R Kitchen

2

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18 April 2020

Jing Zhang

3

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18 April 2020

Rashaun S Wilson

4

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18 April 2020

Joel S Rozowsky

6

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18 April 2020

Kenneth R Williams

7

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18 April 2020

language of work or name

English

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publication date

6 September 2018

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Journal of Proteome Research

18 April 2020

published in

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volume

17

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issue

10

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18 April 2020

page(s)

3431-3444

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describes a project that uses

18 April 2020

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EMBOSS: the European Molecular Biology Open Software Suite

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12 December 2020

A statistical model for identifying proteins by tandem mass spectrometry

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12 December 2020

TANDEM: matching proteins with tandem mass spectra

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12 December 2020

Bioconductor: open software development for computational biology and bioinformatics

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Identification of the UDP-glucuronosyltransferase isoforms involved in mycophenolic acid phase II metabolism.

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Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

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12 December 2020

Decoding protein modifications using top-down mass spectrometry

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Selected reaction monitoring for quantitative proteomics: a tutorial

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Alternative isoform regulation in human tissue transcriptomes

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12 December 2020

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

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12 December 2020

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

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12 December 2020

Analysis and design of RNA sequencing experiments for identifying isoform regulation

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12 December 2020

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

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12 December 2020

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

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Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

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12 December 2020

Transcriptional architecture of the primate neocortex

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The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

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12 December 2020

Total ApoE and ApoE4 isoform assays in an Alzheimer's disease case-control study by targeted mass spectrometry (n=669): a pilot assay for methionine-containing proteotypic peptides

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12 December 2020

Landscape of transcription in human cells

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12 December 2020

GENCODE: the reference human genome annotation for The ENCODE Project

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12 December 2020

Streaming fragment assignment for real-time analysis of sequencing experiments

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Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum

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A proteomics search algorithm specifically designed for high-resolution tandem mass spectra

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The coming age of complete, accurate, and ubiquitous proteomes

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12 December 2020

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

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The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

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12 December 2020

Ribosome profiling: new views of translation, from single codons to genome scale

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12 December 2020

Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP).

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12 December 2020

Translational control of immune responses: from transcripts to translatomes

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12 December 2020

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

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12 December 2020

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

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12 December 2020

Proteome sequencing goes deep.

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12 December 2020

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

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12 December 2020

A strategy for dissecting the architectures of native macromolecular assemblies

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Cell type- and brain region-resolved mouse brain proteome.

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Detecting actively translated open reading frames in ribosome profiling data

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Proteogenomics from a bioinformatics angle: A growing field.

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12 December 2020

Differential Mass Spectrometry Profiles of Tau Protein in the Cerebrospinal Fluid of Patients with Alzheimer's Disease, Progressive Supranuclear Palsy, and Dementia with Lewy Bodies.

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12 December 2020

Genome-wide assessment of differential translations with ribosome profiling data

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12 December 2020

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap

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12 December 2020

Disentangling neural cell diversity using single-cell transcriptomics

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12 December 2020

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

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12 December 2020

Multi-omic data integration enables discovery of hidden biological regularities

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12 December 2020

Targeted proteomics of cannabinoid receptor CB1 and the CB1b isoform.

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12 December 2020

Absolute quantification of myosin heavy chain isoforms by selected reaction monitoring can underscore skeletal muscle changes in a mouse model of amyotrophic lateral sclerosis.

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12 December 2020

Salmon provides fast and bias-aware quantification of transcript expression

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12 December 2020

Molecular and cellular reorganization of neural circuits in the human lineage.

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12 December 2020

A multiregional proteomic survey of the postnatal human brain.

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12 December 2020

10.1021/ACS.JPROTEOME.8B00310

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30125121%20AND%20SRC:MED&resulttype=core&format=json

18 April 2020

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18 April 2020

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