Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes

Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics

(2020) Patrick Lohmann et al.   Expert Review of Proteomics

MetaRibo-Seq measures translation in microbiomes

(2020) Brayon J. Fremin et al.   Nature Communications

Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes

(2019) Jeremy Weaver et al.   mBio

Unraveling the hidden universe of small proteins in bacterial genomes

(2019) Samuel Miravet‐Verde et al.   Molecular Systems Biology

YshB promotes intracellular replication and is required for Salmonella virulence

(2019) Rajdeep Bomjan et al.   JOURNAL OF BACTERIOLOGY

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

MiPepid: MicroPeptide identification tool using machine learning

(2019) Mengmeng Zhu et al.   BMC BIOINFORMATICS

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

New universe of miniproteins is upending cell biology and genetics

(2019) Mitch Leslie   SCIENCE

MOXI Is a Mitochondrial Micropeptide That Enhances Fatty Acid β-Oxidation

(2018) Catherine A. Makarewich et al.   Cell Reports

Adversarial Controls for Scientific Machine Learning

(2018) Kangway V. Chuang et al.   ACS Chemical Biology

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

CNN-MGP: Convolutional Neural Networks for Metagenomics Gene Prediction

(2018) Amani Al-Ajlan et al.   Interdisciplinary Sciences-Computational Life Sciences

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Dual Toxic-Peptide-Coding Staphylococcus aureus RNA under Antisense Regulation Targets Host Cells and Bacterial Rivals Unequally

(2014) Marie-Laure Pinel-Marie et al.   Cell Reports

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Dual function of the McaS small RNA in controlling biofilm formation

(2013) M. G. Jorgensen et al.   GENES & DEVELOPMENT

Small open reading frames associated with morphogenesis are hidden in plant genomes

(2013) K. Hanada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small proteins: untapped area of potential biological importance

(2013) Mingming Su et al.   Frontiers in Genetics

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Bacterial Transcription Terminators: The RNA 3′-End Chronicles

(2011) Jason M. Peters et al.   JOURNAL OF MOLECULAR BIOLOGY

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey 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

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS