Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems

(2019) Ying Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs

(2019) Mehmet Tardu et al.   ACS Chemical Biology

Antibody cross-reactivity accounts for widespread appearance of m1A in 5’UTRs

(2019) Anya V. Grozhik et al.   Nature Communications

Limited antibody specificity compromises epitranscriptomic analyses

(2019) Mark Helm et al.   Nature Communications

Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

(2018) Ilya Vainberg Slutskin et al.   Nature Communications

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

A Chemical Signature for Cytidine Acetylation in RNA

(2018) Justin M. Thomas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Landscape of the complete RNA chemical modifications in the human 80S ribosome

(2018) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Random mutagenesis of a hyperthermophilic archaeon identified tRNA modifications associated with cellular hyperthermotolerance

(2018) Izumi Orita et al.   NUCLEIC ACIDS RESEARCH

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

(2017) Donna Matzov et al.   Nature Communications

Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation

(2017) Sunny Sharma et al.   PLoS Genetics

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

(2016) Eric W. Deutsch et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

Direct Identification of Human Cellular MicroRNAs by Nanoflow Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and Database Searching

(2015) Hiroshi Nakayama et al.   ANALYTICAL CHEMISTRY

Mutation of the gene encoding the ribonuclease P RNA in the hyperthermophilic archaeon Thermococcus kodakarensis causes decreased growth rate and impaired processing of tRNA precursors

(2015) Toshifumi Ueda et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

(2015) Goo Jun et al.   GENOME RESEARCH

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

(2015) T. Xu et al.   Journal of Proteomics

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure of the E. coli ribosome–EF-Tu complex at

(2015) Niels Fischer et al.   NATURE

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1

(2015) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells

(2015) Maria Basanta-Sanchez et al.   NUCLEIC ACIDS RESEARCH

‘View From A Bridge’: A New Perspective on Eukaryotic rRNA Base Modification

(2015) Sunny Sharma et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GSK-3 -Regulated N-Acetyltransferase 10 Is Involved in Colorectal Cancer Invasion

(2014) H. Zhang et al.   CLINICAL CANCER RESEARCH

A Single Acetylation of 18 S rRNA Is Essential for Biogenesis of the Small Ribosomal Subunit inSaccharomyces cerevisiae

(2014) Satoshi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible forN4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

(2014) Satoshi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chemical Inhibition of NAT10 Corrects Defects of Laminopathic Cells

(2014) D. Larrieu et al.   SCIENCE

Genetic Techniques for the Archaea

(2013) Joel A. Farkas et al.   Annual Review of Genetics

Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA

(2013) Bajarang V. Kumbhar et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Denaturing reversed phase liquid chromatographic separation of non-coding ribonucleic acids on macro-porous polystyrene-divinylbenzene resins

(2013) Yoshio Yamauchi et al.   JOURNAL OF CHROMATOGRAPHY A

Quantifying the local resolution of cryo-EM density maps

(2013) Alp Kucukelbir et al.   NATURE METHODS

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications

(2012) J. M. Dewe et al.   RNA

Genetics Techniques for Thermococcus kodakarensis

(2012) Travis H. Hileman et al.   Frontiers in Microbiology

Improving Proteomics Mass Accuracy by Dynamic Offline Lock Mass

(2011) Ying Zhang et al.   ANALYTICAL CHEMISTRY

Natural Competence in the Hyperthermophilic ArchaeonPyrococcus furiosusFacilitates Genetic Manipulation: Construction of Markerless Deletions of Genes Encoding the Two Cytoplasmic Hydrogenases

(2011) Gina L. Lipscomb et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain AM4, Capable of Organotrophic Growth and Growth at the Expense of Hydrogenogenic or Sulfidogenic Oxidation of Carbon Monoxide

(2011) P. Oger et al.   JOURNAL OF BACTERIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins

(2010) Ying Zhang et al.   ANALYTICAL CHEMISTRY

Deletion of Switch 3 Results in an Archaeal RNA Polymerase That Is Defective in Transcript Elongation

(2010) Thomas J. Santangelo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation

(2009) Nigel W. Moriarty et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Effect of Dynamic Exclusion Duration on Spectral Count Based Quantitative Proteomics

(2009) Ying Zhang et al.   ANALYTICAL CHEMISTRY

An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes

(2009) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data

(2009) Hiroshi Nakayama et al.   NUCLEIC ACIDS RESEARCH