Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

Molecular Profiling of Neurons Based on Connectivity

(2014) Mats I. Ekstrand et al.   CELL

Neurogenesis in the Striatum of the Adult Human Brain

(2014) Aurélie Ernst et al.   CELL

Proteomic screening of glutamatergic mouse brain synaptosomes isolated by fluorescence activated sorting

(2014) Christoph Biesemann et al.   EMBO JOURNAL

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

(2014) M. Sakurai et al.   GENOME RESEARCH

Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors

(2014) C. Gonzalez et al.   JOURNAL OF NEUROSCIENCE

Space–time wiring specificity supports direction selectivity in the retina

(2014) Jinseop S. Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Whole-genome analyses of whole-brain data: working within an expanded search space

(2014) Sarah E Medland et al.   NATURE NEUROSCIENCE

Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)

(2014) Ranen Aviner et al.   Nature Protocols

Proteomics reveal energy metabolism and mitogen-activated protein kinase signal transduction perturbation in human Borna disease virus Hu-H1-infected oligodendroglial cells

(2014) X. Liu et al.   NEUROSCIENCE

Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing

(2014) Barbara Treutlein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular neuroanatomy: a generation of progress

(2014) Jonathan D. Pollock et al.   TRENDS IN NEUROSCIENCES

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

(2014) Roser Corominas et al.   Nature Communications

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

(2014) Jingyi Jessica Li et al.   PeerJ

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

Dynamics of Hippocampal Neurogenesis in Adult Humans

(2013) Kirsty L. Spalding et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Phosphorylation of neuronal Lysine-Specific Demethylase 1LSD1/KDM1A impairs transcriptional repression by regulating interaction with CoREST and histone deacetylases HDAC1/2

(2013) Emanuela Toffolo et al.   JOURNAL OF NEUROCHEMISTRY

Zebrafish brain proteomics reveals central proteins involved in neurodegeneration

(2013) Mohammed Gebriel et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Neuron Enriched Nuclear Proteome Isolated from Human Brain

(2013) Eric B. Dammer et al.   JOURNAL OF PROTEOME RESEARCH

Spatial and Temporal Effects in Protein Post-translational Modification Distributions in the Developing Mouse Brain

(2013) Alistair V. G. Edwards et al.   JOURNAL OF PROTEOME RESEARCH

Recent advances in quantitative neuroproteomics

(2013) George E. Craft et al.   METHODS

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

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Deciphering the functions and regulation of brain-enriched A-to-I RNA editing

(2013) Jin Billy Li et al.   NATURE NEUROSCIENCE

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

Visualizing presynaptic function

(2013) Ege T Kavalali et al.   NATURE NEUROSCIENCE

Proteomic Analysis of Primary Cultured Rat Cortical Neurons in Chemical Ischemia

(2013) Jung-Woo Seo et al.   NEUROCHEMICAL RESEARCH

The Central Dogma Decentralized: New Perspectives on RNA Function and Local Translation in Neurons

(2013) Christine E. Holt et al.   NEURON

Small-Volume Analysis of Cell–Cell Signaling Molecules in the Brain

(2013) Elena V Romanova et al.   NEUROPSYCHOPHARMACOLOGY

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

(2013) Hamid Mirzaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential effects of cocaine on histone posttranslational modifications in identified populations of striatal neurons

(2013) Emmanuelle Jordi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A perspective on proteomics in cell biology

(2013) Yasmeen Ahmad et al.   TRENDS IN CELL BIOLOGY

Global Proteome Analysis of the NCI-60 Cell Line Panel

(2013) Amin Moghaddas Gholami et al.   Cell Reports

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

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

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Quantitative Trait Loci Mapping of the Mouse Plasma Proteome (pQTL)

(2012) L. M. Holdt et al.   GENETICS

Quantitative Analysis of the Detergent-Insoluble Brain Proteome in Frontotemporal Lobar Degeneration Using SILAC Internal Standards

(2012) Nicholas T. Seyfried et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS

(2012) Zia Khan et al.   Molecular Systems Biology

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Translational control in cellular and developmental processes

(2012) Jian Kong et al.   NATURE REVIEWS GENETICS

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

The future of the human connectome

(2012) D.C. Van Essen et al.   NEUROIMAGE

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case

(2012) Gloria Lopez-Casado et al.   PROTEOMICS

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants

(2012) Fanggeng Zou et al.   PLoS Genetics

Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding

(2012) Falk Butter et al.   PLoS Genetics

DISC1: Structure, Function, and Therapeutic Potential for Major Mental Illness

(2011) Dinesh C. Soares et al.   ACS Chemical Neuroscience

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

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

(2011) Nicholas T. Ingolia et al.   CELL

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

(2011) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

Transcriptomic and Quantitative Proteomic Analysis of Transporters and Drug Metabolizing Enzymes in Freshly Isolated Human Brain Microvessels

(2011) Ramzi Shawahna et al.   MOLECULAR PHARMACEUTICS

Mapping intact protein isoforms in discovery mode using top-down proteomics

(2011) John C. Tran et al.   NATURE

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Rapid empirical discovery of optimal peptides for targeted proteomics

(2011) Andrew B Stergachis et al.   NATURE METHODS

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies

(2010) Kristen M. Naegle et al.   MOLECULAR & CELLULAR PROTEOMICS

Whole-genome association mapping of gene expression in the human prefrontal cortex

(2010) C Liu et al.   MOLECULAR PSYCHIATRY

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Post-translational modifications in signal integration

(2010) Yonathan Lissanu Deribe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Acetylation of Tau Inhibits Its Degradation and Contributes to Tauopathy

(2010) Sang-Won Min et al.   NEURON

A regulatory toolbox of MiniPromoters to drive selective expression in the brain

(2010) E. Portales-Casamar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

Knockout mice in understanding the mechanism of action of lithium: Table 1

(2009) Galila Agam et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Neuroproteomics Approaches to Decipher Neuronal Regeneration and Degeneration

(2009) Faneng Sun et al.   MOLECULAR & CELLULAR PROTEOMICS

Large-scale Proteomics Analysis of the Human Kinome

(2009) Felix S. Oppermann et al.   MOLECULAR & CELLULAR PROTEOMICS

A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage

(2009) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

(2009) Esperanza Fernández et al.   Molecular Systems Biology

Molecular genetics and imaging technologies for circuit-based neuroanatomy

(2009) Benjamin R. Arenkiel et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

(2009) Alexander W Bell et al.   NATURE METHODS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Neuroproteomics: understanding the molecular organization and complexity of the brain

(2009) Alex Bayés et al.   NATURE REVIEWS NEUROSCIENCE

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

(2009) Matthew B. Johnson et al.   NEURON

DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms

(2009) K. Nakata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Proteomic Studies of a Single CNS Synapse Type: The Parallel Fiber/Purkinje Cell Synapse

(2009) Fekrije Selimi et al.   PLOS BIOLOGY

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

Dysregulated Editing of Serotonin 2C Receptor mRNAs Results in Energy Dissipation and Loss of Fat Mass

(2008) Y. Kawahara et al.   JOURNAL OF NEUROSCIENCE

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Cell type–specific regulation of DARPP-32 phosphorylation by psychostimulant and antipsychotic drugs

(2008) Helen S Bateup et al.   NATURE NEUROSCIENCE

A technicolour approach to the connectome

(2008) Jeff W. Lichtman et al.   NATURE REVIEWS NEUROSCIENCE

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH