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。Widespread non-modular overlapping codes in the coding regions*
Shaked Bergman et al.
PHYSICAL BIOLOGY (2020)
ChimeraUGEM: unsupervised gene expression modeling in any given organism
Alon Diament et al.
BIOINFORMATICS (2019)
Massively Parallel Assays and Quantitative Sequence–Function Relationships
Justin B. Kinney et al.
Annual Review of Genomics and Human Genetics (2019)
Modelling and measuring intracellular competition for finite resources during gene expression
Renana Sabi et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2019)
A feature selection strategy for gene expression time series experiments with hidden Markov models
Roberto A. Cardenas-Ovando et al.
PLOS ONE (2019)
A Composite Approach to Protein Tertiary Structure Prediction: Hidden Markov Model Based on Lattice
Farzad Peyravi et al.
BULLETIN OF MATHEMATICAL BIOLOGY (2019)
Predicting Splicing from Primary Sequence with Deep Learning
Kishore Jaganathan et al.
CELL (2019)
The biochemical basis of microRNA targeting efficacy
Sean E. McGeary et al.
SCIENCE (2019)
MPRAnalyze: statistical framework for massively parallel reporter assays
Tal Ashuach et al.
GENOME BIOLOGY (2019)
T-CNN: Tubelets With Convolutional Neural Networks for Object Detection From Videos
Kai Kang et al.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY (2018)
Codon optimality, bias and usage in translation and mRNA decay
Gavin Hanson et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)
DeepMirTar: a deep-learning approach for predicting human miRNA targets
Ming Wen et al.
BIOINFORMATICS (2018)
Roadblocks and resolutions in eukaryotic translation
Anthony P. Schuller et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)
Accurate design of translational output by a neural network model of ribosome distribution
Robert Tunney et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)
PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants
Izabella Krystkowiak et al.
NUCLEIC ACIDS RESEARCH (2018)
Enhancing heterologous expression in Chlamydomonas reinhardtii by transcript sequence optimization
Iddo Weiner et al.
PLANT JOURNAL (2018)
Translation Elongation and Recoding in Eukaryotes
Thomas E. Dever et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2018)
Accurate design of translational output by a neural network model of ribosome distribution
Robert Tunney et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)
The extent of ribosome queuing in budding yeast
Alon Diament et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
Albert Pla et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation
Khanh Dao Duc et al.
PLOS GENETICS (2018)
Cell-Based Reporter System for High-Throughput Screening of MicroRNA Pathway Inhibitors and Its Limitations
Katerina Brustikova et al.
FRONTIERS IN GENETICS (2018)
Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation
Gilad Shaham et al.
DNA RESEARCH (2018)
Ribonuclease selection for ribosome profiling
Maxim V. Gerashchenko et al.
NUCLEIC ACIDS RESEARCH (2017)
HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons
Roman Prytuliak et al.
NUCLEIC ACIDS RESEARCH (2017)
Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast
Jun Cheng et al.
RNA (2017)
Synonymous Codons: Choose Wisely for Expression
Christina E. Brule et al.
TRENDS IN GENETICS (2017)
Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria
Michael A. Ferrin et al.
ELIFE (2017)
Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning
Sai Zhang et al.
CELL SYSTEMS (2017)
TITER: predicting translation initiation sites by deep learning
Sai Zhang et al.
BIOINFORMATICS (2017)
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Thomas Amort et al.
GENOME BIOLOGY (2017)
Estimation of ribosome profiling performance and reproducibility at various levels of resolution
Alon Diament et al.
BIOLOGY DIRECT (2016)
Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe
Yuriko Harigaya et al.
BMC GENOMICS (2016)
Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination
Estienne Carl Swart et al.
CELL (2016)
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Ariel A. Bazzini et al.
EMBO JOURNAL (2016)
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
David R. Kelley et al.
GENOME RESEARCH (2016)
The Yin and Yang of codon usage
Anton A. Komar
HUMAN MOLECULAR GENETICS (2016)
A model for competition for ribosomes in the cell
Alon Raveh et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2016)
Codon Usage and 30 UTR Length Determine Maternal mRNA Stability in Zebrafish
Yuichiro Mishima et al.
MOLECULAR CELL (2016)
Codon influence on protein expression in E. coli correlates with mRNA levels
Gregory Boel et al.
NATURE (2016)
Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution
Hadas Zur et al.
NUCLEIC ACIDS RESEARCH (2016)
Quantitative assessment of ribosome drop-off in E. coli
Celine Sin et al.
NUCLEIC ACIDS RESEARCH (2016)
Bacteria differently regulate mRNA abundance to specifically respond to various stresses
Alexander Bartholomaeus et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2016)
aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events
Thomas Harrison et al.
PLOS ONE (2016)
The ribosome in action: Tuning of translational efficiency and protein folding
Marina V. Rodnina
PROTEIN SCIENCE (2016)
A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes
Thomas E. Gorochowski et al.
ACS SYNTHETIC BIOLOGY (2016)
Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation
David E. Weinberg et al.
CELL REPORTS (2016)
Roles for Synonymous Codon Usage in Protein Biogenesis
Julie L. Chaney et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 44 (2015)
Codon Optimality Is a Major Determinant of mRNA Stability
Vladimir Presnyak et al.
CELL (2015)
Decoding enhancers using massively parallel reporter assays
Fumitaka Inoue et al.
GENOMICS (2015)
Decoding mechanisms by which silent codon changes influence protein biogenesis and function
Vedrana Bali et al.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2015)
Codon Bias as a Means to Fine-Tune Gene Expression
Tessa E. F. Quax et al.
MOLECULAR CELL (2015)
N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Nian Liu et al.
NATURE (2015)
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
NATURE BIOTECHNOLOGY (2015)
Predicting effects of noncoding variants with deep learning-based sequence model
Jian Zhou et al.
NATURE METHODS (2015)
Ribosome profiling reveals the what, when, where and how of protein synthesis
Gloria A. Brar et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)
Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants
Tuval Ben-Yehezkel et al.
RNA BIOLOGY (2015)
Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats
Andrew S. Wolf et al.
RNA (2015)
Predicting effective microRNA target sites in mammalian mRNAs
Vikram Agarwal et al.
ELIFE (2015)
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge
Hadas Zur et al.
BIOINFORMATICS (2015)
Multiple roles of the coding sequence 5 ' end in gene expression regulation
Tamir Tuller et al.
NUCLEIC ACIDS RESEARCH (2015)
An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation
Arvind R. Subramaniam et al.
CELL (2014)
Most associations between transcript features and gene expression are monotonic
Gilad Shaham et al.
MOLECULAR BIOSYSTEMS (2014)
Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation
Cristina Pop et al.
MOLECULAR SYSTEMS BIOLOGY (2014)
N6-methyladenosine-dependent regulation of messenger RNA stability
Xiao Wang et al.
NATURE (2014)
Translation inhibitors cause abnormalities in ribosome profiling experiments
Maxim V. Gerashchenko et al.
NUCLEIC ACIDS RESEARCH (2014)
The effect of tRNA levels on decoding times of mRNA codons
Alexandra Dana et al.
NUCLEIC ACIDS RESEARCH (2014)
Quantifying the Effect of Ribosomal Density on mRNA Stability
Shlomit Edri et al.
PLOS ONE (2014)
Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function
Alon Diament et al.
NATURE COMMUNICATIONS (2014)
Measurement of average decoding rates of the 61 sense codons in vivo.
Justin Gardin et al.
ELIFE (2014)
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
Arnaud R. Krebs et al.
ELIFE (2014)
A fast weak motif-finding algorithm based on community detection in graphs
Caiyan Jia et al.
BMC BIOINFORMATICS (2013)
Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae
Hadas Zur et al.
BMC BIOINFORMATICS (2013)
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets
Mohsen Khorshid et al.
NATURE METHODS (2013)
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
Sebastian Pechmann et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)
Effect of ribosome shielding on mRNA stability
Carlus Deneke et al.
PHYSICAL BIOLOGY (2013)
Selection on codon bias in yeast: a transcriptional hypothesis
Edoardo Trotta
NUCLEIC ACIDS RESEARCH (2013)
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
Svetlana A. Shabalina et al.
NUCLEIC ACIDS RESEARCH (2013)
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Andrew B. Stergachis et al.
SCIENCE (2013)
Causes and Effects of N-Terminal Codon Bias in Bacterial Genes
Daniel B. Goodman et al.
SCIENCE (2013)
New Universal Rules of Eukaryotic Translation Initiation Fidelity
Hadas Zur et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Kate D. Meyer et al.
CELL (2012)
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
Dan Dominissini et al.
NATURE (2012)
The architecture of eukaryotic translation
Dominique Chu et al.
NUCLEIC ACIDS RESEARCH (2012)
miRmap: Comprehensive prediction of microRNA target repression strength
Charles E. Vejnar et al.
NUCLEIC ACIDS RESEARCH (2012)
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Bradley Zamft et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
A Unified Model of Transcription Elongation: What Have We Learned from Single-Molecule Experiments?
Daibhid O. Maoileidigh et al.
BIOPHYSICAL JOURNAL (2011)
Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments
R. K. P. Zia et al.
JOURNAL OF STATISTICAL PHYSICS (2011)
Identification of genetic elements that autonomously determine DNA methylation states
Florian Lienert et al.
NATURE GENETICS (2011)
Understanding the contribution of synonymous mutations to human disease
Zuben E. Sauna et al.
NATURE REVIEWS GENETICS (2011)
The 3-Base Periodicity and Codon Usage of Coding Sequences Are Correlated with Gene Expression at the Level of Transcription Elongation
Edoardo Trotta
PLOS ONE (2011)
Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model
Shlomi Reuveni et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Composite effects of gene determinants on the translation speed and density of ribosomes
Tamir Tuller et al.
GENOME BIOLOGY (2011)
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences
Thanh Le et al.
BIOINFORMATICS (2010)
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
Christine Vogel et al.
MOLECULAR SYSTEMS BIOLOGY (2010)
BioNumbers-the database of key numbers in molecular and cell biology
Ron Milo et al.
NUCLEIC ACIDS RESEARCH (2010)
RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins
Hilal Kazan et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
A Comprehensive, Quantitative, and Genome-Wide Model of Translation
Marlena Siwiak et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Selection on Codon Bias
Ruth Hershberg et al.
ANNUAL REVIEW OF GENETICS (2008)
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes
So Nakagawa et al.
NUCLEIC ACIDS RESEARCH (2008)
Determinants of protein abundance and translation efficiency in S-cerevisiae
Tamir Tuller et al.
PLOS COMPUTATIONAL BIOLOGY (2007)
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting
O Namy et al.
NATURE (2006)
A novel HMM-based clustering algorithm for the analysis of gene expression time-course data
YJ Zeng et al.
COMPUTATIONAL STATISTICS & DATA ANALYSIS (2006)
Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes
JC Sun et al.
JOURNAL OF MOLECULAR EVOLUTION (2005)
Finding short DNA motifs using permuted Markov models
XY Zhao et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2005)
Markov encoding for detecting signals in genomic sequences
JC Rajapakse et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2005)
A GFP-based reporter system to monitor nonsense-mediated mRNA decay
A Paillusson et al.
NUCLEIC ACIDS RESEARCH (2005)
(log t)(2/3) law of the two dimensional asymmetric simple exclusion process
HT Yau
ANNALS OF MATHEMATICS (2004)
Using hidden Markov models to analyze gene expression time course data
Alexander Schliep et al.
BIOINFORMATICS (2003)
Mining gene expression data using a novel approach based on hidden Markov models
XL Ji et al.
FEBS LETTERS (2003)
A double reporter assay for detecting changes in the ratio of spliced and unspliced mRNA in mammalian cells
MT Nasim et al.
NUCLEIC ACIDS RESEARCH (2002)
Listening to silence and understanding nonsense: Exonic mutations that affect splicing
L Cartegni et al.
NATURE REVIEWS GENETICS (2002)
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
A Krogh et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)