Translational efficiency across healthy and tumor tissues is proliferation‐related

Pathways to disease from natural variations in human cytoplasmic tRNAs

(2019) Jeremy T Lant et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues

(2019) Basak Eraslan et al.   Molecular Systems Biology

tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities

(2019) Aristeidis G Telonis et al.   CANCER RESEARCH

Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design

(2019) Aikaterini Alexaki et al.   JOURNAL OF MOLECULAR BIOLOGY

Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

(2019) Adrian Gabriel Torres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level

(2019) Eugenio F. Fornasiero et al.   BMC GENOMICS

tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers

(2019) Zhao Zhang et al.   RNA Biology

Modifications and functional genomics of human transfer RNA

(2018) Tao Pan   CELL RESEARCH

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Codon usage of highly expressed genes affects proteome-wide translation efficiency

(2018) Idan Frumkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repertoires of tRNAs: The Couplers of Genomics and Proteomics

(2018) Roni Rak et al.   Annual Review of Cell and Developmental Biology

The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis

(2017) Paul Schimmel   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Determination of tRNA aminoacylation levels by high-throughput sequencing

(2017) Molly E. Evans et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of noncoding RNA transcription by mammalian RNA polymerase III

(2017) Jong-Lyul Park et al.   Epigenomics

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

(2017) Tasos Gogakos et al.   Cell Reports

Recombination, meiotic expression and human codon usage

(2017) Fanny Pouyet et al.   eLife

LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection

(2017) Sandy Mattijssen et al.   eLife

Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression

(2016) Hani Goodarzi et al.   CELL

A micro-RNA expression signature for human NAFLD progression

(2016) Yan Guo et al.   JOURNAL OF GASTROENTEROLOGY

Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

(2016) Fabricio Loayza-Puch et al.   NATURE

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

(2016) Konrad L. M. Rudolph et al.   PLoS Genetics

Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes

(2015) Yan Guo et al.   BMC GENOMICS

The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

(2015) Fran Supek   JOURNAL OF MOLECULAR EVOLUTION

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Inosine modifications in human tRNAs are incorporated at the precursor tRNA level

(2015) Adrian Gabriel Torres et al.   NUCLEIC ACIDS RESEARCH

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Large-scale profiling of microRNAs for The Cancer Genome Atlas

(2015) Andy Chu et al.   NUCLEIC ACIDS RESEARCH

Expression of CRISPR/Cas single guide RNAs using small tRNA promoters

(2015) Adam L. Mefferd et al.   RNA

Differential and coherent processing patterns from small RNAs

(2015) Sachin Pundhir et al.   Scientific Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Proteomic analysis of colon and rectal carcinoma using standard and customized databases

(2015) Robbert J.C. Slebos et al.   Scientific Data

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

(2014) Hila Gingold et al.   CELL

Differential RISC association of endogenous human microRNAs predicts their inhibitory potential

(2014) Omar Flores et al.   NUCLEIC ACIDS RESEARCH

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

(2012) Hila Gingold et al.   NUCLEIC ACIDS RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages

(2010) Yedael Y. Waldman et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Universal function-specificity of codon usage

(2009) Hamed Shateri Najafabadi et al.   NUCLEIC ACIDS RESEARCH

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

(2009) N. T. Ingolia et al.   SCIENCE

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH