相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Ribonuclease selection for ribosome profiling
Maxim V. Gerashchenko et al.
NUCLEIC ACIDS RESEARCH (2017)
A ribosome profiling study of mRNA cleavage by the endonuclease RelE
Jae-Yeon Hwang et al.
NUCLEIC ACIDS RESEARCH (2017)
Identification of Unannotated Small Genes in Salmonella
Jonghwan Baek et al.
G3-GENES GENOMES GENETICS (2017)
Exploring the dark foldable proteome by considering hydrophobic amino acids topology
Tristan Bitard-Feildel et al.
SCIENTIFIC REPORTS (2017)
Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP
Klaus Neuhaus et al.
BMC GENOMICS (2017)
Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation
Sarah Maria Huecker et al.
FEMS MICROBIOLOGY LETTERS (2017)
Detecting actively translated open reading frames in ribosome profiling data
Lorenzo Calviello et al.
NATURE METHODS (2016)
The mysterious orphans of Mycoplasmataceae
Tatiana V. Tatarinova et al.
BIOLOGY DIRECT (2016)
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)
Klaus Neuhaus et al.
BMC GENOMICS (2016)
Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome
Desiree Baumgartner et al.
BMC MICROBIOLOGY (2016)
Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei
Liam Cassidy et al.
JOURNAL OF PROTEOME RESEARCH (2016)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
Enis Afgan et al.
NUCLEIC ACIDS RESEARCH (2016)
Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center
James Marks et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
TMSEG: Novel prediction of transmembrane helices
Michael Bernhofer et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2016)
Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells
Joana Carlevaro-Fita et al.
RNA (2016)
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
Daniel Dar et al.
SCIENCE (2016)
The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)
Yujin Jeong et al.
NATURE COMMUNICATIONS (2016)
Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling
Fuad Mohammad et al.
CELL REPORTS (2016)
Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence
Rafik Neme et al.
ELIFE (2016)
VSEARCH: a versatile open source tool for metagenomics
Torbjorn Rognes et al.
PEERJ (2016)
Unexpected features of the dark proteome
Nelson Perdigao et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Enterohemorrhagic Escherichia coli Colonization of Human Colonic Epithelium In Vitro and Ex Vivo
Steven B. Lewis et al.
INFECTION AND IMMUNITY (2015)
Small Proteins Can No Longer Be Ignored
Gisela Storz et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)
Small membrane proteins - elucidating the function of the needle in the haystack
Grant Kemp et al.
BIOLOGICAL CHEMISTRY (2014)
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states
Byung-Kwan Cho et al.
BMC BIOLOGY (2014)
Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Richard Landstorfer et al.
BMC GENOMICS (2014)
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Ariel A. Bazzini et al.
EMBO JOURNAL (2014)
SearchDOGS Bacteria, Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes
Sean S. OhEigeartaigh et al.
JOURNAL OF BACTERIOLOGY (2014)
Pervasive transcription: illuminating the dark matter of bacterial transcriptomes
Joseph T. Wade et al.
NATURE REVIEWS MICROBIOLOGY (2014)
LocTree3 prediction of localization
Tatyana Goldberg et al.
NUCLEIC ACIDS RESEARCH (2014)
Translation inhibitors cause abnormalities in ribosome profiling experiments
Maxim V. Gerashchenko et al.
NUCLEIC ACIDS RESEARCH (2014)
PredictProtein-an open resource for online prediction of protein structural and functional features
Guy Yachdav et al.
NUCLEIC ACIDS RESEARCH (2014)
Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
Nicholas T. Ingolia et al.
CELL REPORTS (2014)
Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae
Jenna E. Smith et al.
CELL REPORTS (2014)
Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq
Julie L. Aspden et al.
ELIFE (2014)
Long non-coding RNAs as a source of new peptides
Jorge Ruiz-Orera et al.
ELIFE (2014)
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
Patrick B. F. O'Connor et al.
BIOINFORMATICS (2013)
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease
Yu-fei Lin et al.
BMC GENOMICS (2013)
Ribosome heterogeneity: another level of complexity in bacterial translation regulation
Konstantin Byrgazov et al.
CURRENT OPINION IN MICROBIOLOGY (2013)
Transcriptional and functional responses of Escherichia coli O157:H7 growing in the lettuce rhizoplane
Zhe Hou et al.
FOOD MICROBIOLOGY (2013)
On the Immortality of Television Sets: Function in the Human Genome According to the Evolution-Free Gospel of ENCODE
Dan Graur et al.
GENOME BIOLOGY AND EVOLUTION (2013)
Peptidomic discovery of short open reading frame-encoded peptides in human cells
Sarah A. Slavoff et al.
NATURE CHEMICAL BIOLOGY (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
High-resolution view of bacteriophage lambda gene expression by ribosome profiling
Xiaoqiu Liu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Exploring the dark matter of a mammalian proteome by protein structure and function modeling
Michal Brylinski
PROTEOME SCIENCE (2013)
Occurrence of Shiga-toxigenic Escherichia coli in Stomoxys calcitrans (Diptera: Muscidae)
Bruno Gomes de Castro et al.
REVISTA BRASILEIRA DE PARASITOLOGIA VETERINARIA (2013)
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
Evguenia Kopylova et al.
BIOINFORMATICS (2012)
Specialized ribosomes: a new frontier in gene regulation and organismal biology
Shifeng Xue et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2012)
Renal and neurological involvement in typical Shiga toxin-associated HUS
Howard Trachtman et al.
NATURE REVIEWS NEPHROLOGY (2012)
Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes
Xiaobin Zheng et al.
BMC GENOMICS (2011)
Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp strain PCC 7120 to combined-nitrogen deprivation
Britt L. Flaherty et al.
BMC GENOMICS (2011)
Putatively Noncoding Transcripts Show Extensive Association with Ribosomes
Benjamin A. Wilson et al.
GENOME BIOLOGY AND EVOLUTION (2011)
Persistence of Escherichia coli O157:H7 and Its Mutants in Soils
Jincai Ma et al.
PLOS ONE (2011)
Genome-wide antisense transcription drives mRNA processing in bacteria
Inigo Lasa et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Towards the integration of genomics, epidemiological and clinical data
Victor V. Solovyev et al.
GENOME MEDICINE (2011)
Searching in microbial genomes for encoded small proteins
Jos Boekhorst et al.
MICROBIAL BIOTECHNOLOGY (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
BamView: viewing mapped read alignment data in the context of the reference sequence
Tim Carver et al.
BIOINFORMATICS (2010)
Composition bias and the origin of ORFan genes
Inbal Yomtovian et al.
BIOINFORMATICS (2010)
The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell
Thomas Junier et al.
BIOINFORMATICS (2010)
Missing genes in the annotation of prokaryotic genomes
Andrew S. Warren et al.
BMC BIOINFORMATICS (2010)
The primary transcriptome of the major human pathogen Helicobacter pylori
Cynthia M. Sharma et al.
NATURE (2010)
Widespread Antisense Transcription in Escherichia coli
James E. Dornenburg et al.
MBIO (2010)
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
Dapeng Wang et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2010)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Circos: An information aesthetic for comparative genomics
Martin Krzywinski et al.
GENOME RESEARCH (2009)
Nature of the protein universe
Michael Levitt
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Nicholas T. Ingolia et al.
SCIENCE (2009)
A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
Timothy T. Perkins et al.
PLOS GENETICS (2009)
The RAST server: Rapid annotations using subsystems technology
Ramy K. Aziz et al.
BMC GENOMICS (2008)
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
D. Allan Drummond et al.
CELL (2008)
Small membrane proteins found by comparative genomics and ribosome binding site models
Matthew R. Hemm et al.
MOLECULAR MICROBIOLOGY (2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
Translation initiation region sequence preferences in Escherichia coli
Vladimir Vimberg et al.
BMC MOLECULAR BIOLOGY (2007)
Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes
Julie C. Dunning Hotopp et al.
SCIENCE (2007)
Natively unstructured regions in proteins identified from contact predictions
Avner Schlessinger et al.
BIOINFORMATICS (2007)
Identifying bacterial genes and endosymbiont DNA with Glimmer
Arthur L. Delcher et al.
BIOINFORMATICS (2007)
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server
Alessio Ceroni et al.
NUCLEIC ACIDS RESEARCH (2006)
Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
Wei Zhang et al.
GENOME RESEARCH (2006)
The PredictProtein server
B Rost et al.
NUCLEIC ACIDS RESEARCH (2004)
The regulation of bacterial transcription initiation
DF Browning et al.
NATURE REVIEWS MICROBIOLOGY (2004)
Lymphoid follicle-dense mucosa at the terminal rectum is the principal site of colonization of enterohemorrhagic Escherichia coli O157:H7 in the bovine host
SW Naylor et al.
INFECTION AND IMMUNITY (2003)
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures
J Ma et al.
JOURNAL OF BACTERIOLOGY (2002)
Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
T Hayashi et al.
DNA RESEARCH (2001)
Artemis: sequence visualization and annotation
K Rutherford et al.
BIOINFORMATICS (2000)