Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes
Authors
Keywords
microbiome, genome annotation, microproteins, small open reading frames, machine learning, deep learning
Journal
Cell Host & Microbe
Volume 29, Issue 1, Pages 121-131.e4
Publisher
Elsevier BV
Online
2020-12-07
DOI
10.1016/j.chom.2020.11.002
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search