DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

De novo annotation and characterization of the translatome with ribosome profiling data

(2018) Zhengtao Xiao et al.   NUCLEIC ACIDS RESEARCH

Identifying New Small Proteins in Escherichia coli

(2018) Caitlin E. VanOrsdel et al.   PROTEOMICS

Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database

(2017) Yunxiang Dai et al.   JOURNAL OF PROTEOME RESEARCH

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

(2017) Elvis Ndah et al.   NUCLEIC ACIDS RESEARCH

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence

(2016) Aleksandra A. Miranda-CasoLuengo et al.   BMC GENOMICS

Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling

(2016) Kenji Nakahigashi et al.   DNA RESEARCH

The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)

(2016) Yujin Jeong et al.   Nature Communications

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

The Effect of an Alternate Start Codon on Heterologous Expression of a PhoA Fusion Protein in Mycoplasma gallisepticum

(2015) Indu S. Panicker et al.   PLoS One

The application of terminomics for the identification of protein start sites and proteoforms in bacteria

(2015) Iain J. Berry et al.   PROTEOMICS

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

(2015) Scarlet S. Shell et al.   PLoS Genetics

Identifying (non-)coding RNAs and small peptides: Challenges and opportunities

(2014) Andrea Pauli et al.   BIOESSAYS

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men

(2014) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Sequence selectivity of macrolide-induced translational attenuation

(2014) A. R. Davis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N-terminomics and proteogenomics, getting off to a good start

(2014) Erica M. Hartmann et al.   PROTEOMICS

The Coding and Noncoding Architecture of the Caulobacter crescentus Genome

(2014) Jared M. Schrader et al.   PLoS Genetics

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

(2013) P. B. F. O'Connor et al.   BIOINFORMATICS

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

(2012) Gene-Wei Li et al.   NATURE

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

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

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

(2011) Xiaobin Zheng et al.   BMC GENOMICS

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

(2011) Nicholas T. Ingolia et al.   CELL

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

(2009) N. T. Ingolia et al.   SCIENCE

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

(2008) Albert Pallejà et al.   BMC GENOMICS