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。DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
Chen Chen et al.
BMC BIOINFORMATICS (2021)
Base-resolution models of transcription-factor binding reveal soft motif syntax
Ziga Avsec et al.
NATURE GENETICS (2021)
A survey on deep learning in DNA/RNA motif mining
Ying He et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Improving representations of genomic sequence motifs in convolutional networks with exponential activations
Peter K. Koo et al.
NATURE MACHINE INTELLIGENCE (2021)
Expanding functional protein sequence spaces using generative adversarial networks
Donatas Repecka et al.
NATURE MACHINE INTELLIGENCE (2021)
Designing Eukaryotic Gene Expression Regulation Using Machine Learning
Ronald P. H. de Jongh et al.
TRENDS IN BIOTECHNOLOGY (2020)
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites
Tsu-Pei Chiu et al.
NUCLEIC ACIDS RESEARCH (2020)
RNA Splicing by the Spliceosome
Max E. Wilkinson et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 89 (2020)
Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants
Raphael Leman et al.
BMC GENOMICS (2020)
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
Carl G. de Boer et al.
NATURE BIOTECHNOLOGY (2020)
Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity
Benoit Playe et al.
JOURNAL OF CHEMINFORMATICS (2020)
Deep learning for plant genomics and crop improvement
Hai Wang et al.
CURRENT OPINION IN PLANT BIOLOGY (2020)
A Pretraining-Retraining Strategy of Deep Learning Improves Cell-Specific Enhancer Predictions
Xiaohui Niu et al.
FRONTIERS IN GENETICS (2020)
Model-driven generation of artificial yeast promoters
Benjamin J. Kotopka et al.
NATURE COMMUNICATIONS (2020)
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks
Vikram Agarwal et al.
CELL REPORTS (2020)
Synthetic promoter design in Escherichia coli based on a deep generative network
Ye Wang et al.
NUCLEIC ACIDS RESEARCH (2020)
Fully interpretable deep learning model of transcriptional control
Yi Liu et al.
BIOINFORMATICS (2020)
Automated design of thousands of nonrepetitive parts for engineering stable genetic systems
Ayaan Hossain et al.
NATURE BIOTECHNOLOGY (2020)
Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility
Goro Terai et al.
NUCLEIC ACIDS RESEARCH (2020)
Opening the Black Box: Interpretable Machine Learning for Geneticists
Christina B. Azodi et al.
TRENDS IN GENETICS (2020)
Deep learning for genomics using Janggu
Wolfgang Kopp et al.
NATURE COMMUNICATIONS (2020)
Enhancing the interpretability of transcription factor binding site prediction using attention mechanism
Sungjoon Park et al.
SCIENTIFIC REPORTS (2020)
Epigenome-based splicing prediction using a recurrent neural network
Donghoon Lee et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
Cross-species regulatory sequence activity prediction
David R. Kelley
PLOS COMPUTATIONAL BIOLOGY (2020)
Sources of variation in cell-type RNA-Seq profiles
Johan Gustafsson et al.
PLOS ONE (2020)
Deep learning of immune cell differentiation
Alexandra Maslova et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Codon optimization with deep learning to enhance protein expression
Hongguang Fu et al.
SCIENTIFIC REPORTS (2020)
Fast and Flexible Protein Design Using Deep Graph Neural Networks
Alexey Strokach et al.
CELL SYSTEMS (2020)
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Jan Zrimec et al.
NATURE COMMUNICATIONS (2020)
Predictive design of sigma factor-specific promoters
Maarten Van Brempt et al.
NATURE COMMUNICATIONS (2020)
Permutational analysis of Saccharomyces cerevisiae regulatory elements
Namrita Dhillon et al.
SYNTHETIC BIOLOGY (2020)
Motif grammar: The basis of the language of gene expression
Gergely Nagy et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)
Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model
Li Tang et al.
GENOME RESEARCH (2020)
Learning and interpreting the gene regulatory grammar in a deep learning framework
Ling Chen et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens
Jan Zrimec
MICROBIOLOGYOPEN (2020)
Deep learning for inferring transcription factor binding sites
Peter K. Koo et al.
CURRENT OPINION IN SYSTEMS BIOLOGY (2020)
Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli
Guillaume Urtecho et al.
BIOCHEMISTRY (2019)
The Scope, Functions, and Dynamics of Posttranslational Protein Modifications
A. Harvey Millar et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 70 (2019)
Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues
Basak Eraslan et al.
MOLECULAR SYSTEMS BIOLOGY (2019)
Deep-learning augmented RNA-seq analysis of transcript splicing
Zijun Zhang et al.
NATURE METHODS (2019)
Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence
Jacob D. Washburn et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
MRCNN: a deep learning model for regression of genome-wide DNA methylation
Qi Tian et al.
BMC GENOMICS (2019)
Mechanisms of Bacterial Transcription Termination
Jeffrey W. Roberts
JOURNAL OF MOLECULAR BIOLOGY (2019)
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics
Ziga Avsec et al.
NATURE BIOTECHNOLOGY (2019)
Deep learning: new computational modelling techniques for genomics
Gokcen Eraslan et al.
NATURE REVIEWS GENETICS (2019)
QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants
Vincentius Martin et al.
NUCLEIC ACIDS RESEARCH (2019)
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities
Ameni Trabelsi et al.
BIOINFORMATICS (2019)
A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation
Nicholas Bogard et al.
CELL (2019)
Human 5′ UTR design and variant effect prediction from a massively parallel translation assay
Paul J. Sample et al.
NATURE BIOTECHNOLOGY (2019)
Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays
Rajiv Movva et al.
PLOS ONE (2019)
How the avidity of polymerase binding to the-35/-10 promoter sites affects gene expression
Tal Einav et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Optimizing the dynamics of protein expression
Jan-Hendrik Troesemeier et al.
SCIENTIFIC REPORTS (2019)
CodonWizard - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts
Peter Rehbein et al.
PROTEIN EXPRESSION AND PURIFICATION (2019)
Predicting Splicing from Primary Sequence with Deep Learning
Kishore Jaganathan et al.
CELL (2019)
SpliceFinder: ab initio prediction of splice sites using convolutional neural network
Ruohan Wang et al.
BMC BIOINFORMATICS (2019)
A primer on deep learning in genomics
James Zou et al.
NATURE GENETICS (2019)
Representation learning of genomic sequence motifs with convolutional neural networks
Peter K. Koo et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana
Johan Zicola et al.
NATURE PLANTS (2019)
Accurate prediction of cell type-specific transcription factor binding
Jens Keilwagen et al.
GENOME BIOLOGY (2019)
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks
Shashank Singh et al.
QUANTITATIVE BIOLOGY (2019)
Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead
Cynthia Rudin
NATURE MACHINE INTELLIGENCE (2019)
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
Jingyi Jessica Li et al.
GENOME BIOLOGY (2019)
Tumour heterogeneity and resistance to cancer therapies
Ibiayi Dagogo-Jack et al.
NATURE REVIEWS CLINICAL ONCOLOGY (2018)
Codon optimality, bias and usage in translation and mRNA decay
Gavin Hanson et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)
Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them
Kathrin Leppek et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (vol 46, pg 260, 2017)
Aziz Khan et al.
NUCLEIC ACIDS RESEARCH (2018)
pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks
Stefan Budach et al.
BIOINFORMATICS (2018)
SpliceRover: interpretable convolutional neural networks for improved splice site prediction
Jasper Zuallaert et al.
BIOINFORMATICS (2018)
Patterns of variation in cis-regulatory regions: examining evidence of purifying selection
Thijessen Naidoo et al.
BMC GENOMICS (2018)
70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features
Wenying He et al.
BMC SYSTEMS BIOLOGY (2018)
Methods for interpreting and understanding deep neural networks
Gregoire Montavon et al.
DIGITAL SIGNAL PROCESSING (2018)
Sequential regulatory activity prediction across chromosomes with convolutional neural networks
David R. Kelley et al.
GENOME RESEARCH (2018)
Promoter architecture determines cotranslational regulation of mRNA
Lorena Espinar et al.
GENOME RESEARCH (2018)
Splicing mutations in human genetic disorders: examples, detection, and confirmation
Anna Abramowicz et al.
JOURNAL OF APPLIED GENETICS (2018)
Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
Jian Zhou et al.
NATURE GENETICS (2018)
Using deep learning to model the hierarchical structure and function of a cell
Jianzhu Ma et al.
NATURE METHODS (2018)
Eukaryotic core promoters and the functional basis of transcription initiation
Vanja Haberle 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)
Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort
Raphael Leman et al.
NUCLEIC ACIDS RESEARCH (2018)
DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants
Meng Wang et al.
NUCLEIC ACIDS RESEARCH (2018)
Accurate design of translational output by a neural network model of ribosome distribution
Robert Tunney et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)
DNA structure at the plasmid origin-of-transfer indicates its potential transfer range
Jan Zrimec et al.
SCIENTIFIC REPORTS (2018)
Toward Predictable 5′UTRs in Saccharomyces cerevisiae: Development of a yUTR Calculator
Thomas Decoene et al.
ACS SYNTHETIC BIOLOGY (2018)
Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation
Zhipeng Zhou et al.
eLife (2018)
Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli
Guillaume Cambray et al.
NATURE BIOTECHNOLOGY (2018)
Codon usage influences fitness through RNA toxicity
Pragya Mittal et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
A sequence-based, deep learning model accurately predicts RNA splicing branchpoints
Joseph M. Paggi et al.
RNA (2018)
Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts
Aleksej Zelezniak et al.
CELL SYSTEMS (2018)
Engineering the 5′ UTR-Mediated Regulation of Protein Abundance in Yeast Using Nucleotide Sequence Activity Relationships
Wentao Ding et al.
ACS SYNTHETIC BIOLOGY (2018)
Machine learning annotation of human branchpoints
Bethany Signal et al.
BIOINFORMATICS (2018)
Design of RNA hairpin modules that predictably tune translation in yeast
Tim Weenink et al.
SYNTHETIC BIOLOGY (2018)
Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression
Aditya Kumar et al.
DNA RESEARCH (2017)
Alternative polyadenylation of mRNA precursors
Bin Tian et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Post-transcriptional gene regulation by mRNA modifications
Boxuan Simen Zhao et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
Josh T. Cuperus et al.
GENOME RESEARCH (2017)
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models
Lin Yang et al.
MOLECULAR SYSTEMS BIOLOGY (2017)
Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences
Amin Espah Borujeni et al.
NUCLEIC ACIDS RESEARCH (2017)
Deep learning of the splicing (epi) genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision
Yungang Xu et al.
NUCLEIC ACIDS RESEARCH (2017)
Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them
Jingyi Jessica Li et al.
NUCLEIC ACIDS RESEARCH (2017)
Systematic dissection of genomic features determining transcription factor binding and enhancer function
Sharon R. Grossman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast
Jun Cheng et al.
RNA (2017)
Yeast Terminator Function Can Be Modulated and Designed on the Basis of Predictions of Nucleosome Occupancy
Nicholas J. Morse et al.
ACS SYNTHETIC BIOLOGY (2017)
Regulatory 3' Untranslated Regions of Bacterial mRNAs
Gai-Xian Ren et al.
FRONTIERS IN MICROBIOLOGY (2017)
Nucleotides upstream of the Kozak sequence strongly influence gene expression in the yeast S. cerevisiae
Jing Li et al.
JOURNAL OF BIOLOGICAL ENGINEERING (2017)
Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning
Sai Zhang et al.
CELL SYSTEMS (2017)
Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast
Petri-Jaan Lahtvee et al.
CELL SYSTEMS (2017)
Predicting enhancers with deep convolutional neural networks
Xu Min et al.
BMC BIOINFORMATICS (2017)
BPP: a sequence-based algorithm for branch point prediction
Qing Zhang et al.
BIOINFORMATICS (2017)
A deep auto-encoder model for gene expression prediction
Rui Xie et al.
BMC GENOMICS (2017)
An introduction to deep learning on biological sequence data: examples and solutions
Vanessa Isabell Jurtz et al.
BIOINFORMATICS (2017)
A new method for enhancer prediction based on deep belief network
Hongda Bu et al.
BMC BIOINFORMATICS (2017)
TITER: predicting translation initiation sites by deep learning
Sai Zhang et al.
BIOINFORMATICS (2017)
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning
Christof Angermueller et al.
GENOME BIOLOGY (2017)
Transcription factor-DNA binding: beyond binding site motifs
Sachi Inukai et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2017)
MCAST: scanning for cis-regulatory motif clusters
Charles E. Grant et al.
BIOINFORMATICS (2016)
In the loop: promoter-enhancer interactions and bioinformatics
Antonio Mora et al.
BRIEFINGS IN BIOINFORMATICS (2016)
DeepChrome: deep-learning for predicting gene expression from histone modifications
Ritambhara Singh et al.
BIOINFORMATICS (2016)
Convolutional neural network architectures for predicting DNA-protein binding
Haoyang Zeng et al.
BIOINFORMATICS (2016)
Evaluating tools for transcription factor binding site prediction
Narayan Jayaram et al.
BMC BIOINFORMATICS (2016)
Engineering Cellular Metabolism
Jens Nielsen et al.
CELL (2016)
On the Dependency of Cellular Protein Levels on mRNA Abundance
Yansheng Liu et al.
CELL (2016)
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
David R. Kelley et al.
GENOME RESEARCH (2016)
Deep learning for computational biology
Christof Angermueller et al.
MOLECULAR SYSTEMS BIOLOGY (2016)
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters
Yun Chen et al.
NATURE GENETICS (2016)
Predictable tuning of protein expression in bacteria
Mads T. Bonde et al.
NATURE METHODS (2016)
DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences
Daniel Quang et al.
NUCLEIC ACIDS RESEARCH (2016)
Codon usage is an important determinant of gene expression levels largely through its effects on transcription
Zhipeng Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Translational control by 5′-untranslated regions of eukaryotic mRNAs
Alan G. Hinnebusch et al.
SCIENCE (2016)
Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae
Benjamin Neymotin et al.
G3-GENES GENOMES GENETICS (2016)
DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo
Anthony Mathelier et al.
CELL SYSTEMS (2016)
Distribution and diversity of ribosome binding sites in prokaryotic genomes
Damilola Omotajo et al.
BMC GENOMICS (2015)
Deconvolving the Recognition of DNA Shape from Sequence
Namiko Abe et al.
CELL (2015)
Codon Optimality Is a Major Determinant of mRNA Stability
Vladimir Presnyak et al.
CELL (2015)
Unraveling determinants of transcription factor binding outside the core binding site
Michal Levo et al.
GENOME RESEARCH (2015)
Core promoter sequence in yeast is a major determinant of expression level
Shai Lubliner et al.
GENOME RESEARCH (2015)
Genome-wide discovery of human splicing branchpoints
Tim R. Mercer et al.
GENOME RESEARCH (2015)
Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability
Jan Zrimec et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2015)
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje et al.
NATURE (2015)
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
NATURE BIOTECHNOLOGY (2015)
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
Qiye He et al.
NATURE BIOTECHNOLOGY (2015)
A method to predict the impact of regulatory variants from DNA sequence
Dongwon Lee et al.
NATURE GENETICS (2015)
Predicting effects of noncoding variants with deep learning-based sequence model
Jian Zhou et al.
NATURE METHODS (2015)
Varying levels of complexity in transcription factor binding motifs
Jens Keilwagen et al.
NUCLEIC ACIDS RESEARCH (2015)
Quantitative modeling of transcription factor binding specificities using DNA shape
Tianyin Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
The development and characterization of synthetic minimal yeast promoters
Heidi Redden et al.
NATURE COMMUNICATIONS (2015)
Short Synthetic Terminators for Improved Heterologous Gene Expression in Yeast
Kathleen A. Curran et al.
ACS SYNTHETIC BIOLOGY (2015)
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
Zing Tsung-Yeh Tsai et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast
Gabor Csardi et al.
PLOS GENETICS (2015)
Systematic Dissection of the Sequence Determinants of Gene 3′ End Mediated Expression Control
Ophir Shalem et al.
PLOS GENETICS (2015)
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions
Wei Chen et al.
BIOINFORMATICS (2015)
A primer to frequent itemset mining for bioinformatics
Stefan Naulaerts et al.
BRIEFINGS IN BIOINFORMATICS (2015)
Quantitative profiling of initiating ribosomes in vivo
Xiangwei Gao et al.
NATURE METHODS (2015)
Predicting the human epigenome from DNA motifs
John W. Whitaker et al.
NATURE METHODS (2015)
Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective
Andrey Feklistov et al.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 68 (2014)
Role of DNA sequence based structural features of promoters in transcription initiation and gene expression
Manju Bansal et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
In pursuit of design principles of regulatory sequences
Michal Levo et al.
NATURE REVIEWS GENETICS (2014)
Transcriptional enhancers: from properties to genome-wide predictions
Daria Shlyueva et al.
NATURE REVIEWS GENETICS (2014)
Protein-DNA binding: complexities and multi-protein codes
Trevor Siggers et al.
NUCLEIC ACIDS RESEARCH (2014)
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli
Joao C. Guimaraes et al.
NUCLEIC ACIDS RESEARCH (2014)
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition
Hao Lin et al.
NUCLEIC ACIDS RESEARCH (2014)
Transcription factor binding predicts histone modifications in human cell lines
Dan Benveniste et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Absence of a simple code: how transcription factors read the genome
Matthew Slattery et al.
TRENDS IN BIOCHEMICAL SCIENCES (2014)
Design of synthetic yeast promoters via tuning of nucleosome architecture
Kathleen A. Curran et al.
NATURE COMMUNICATIONS (2014)
Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
Mahmoud Ghandi et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Transcriptional Regulation and Its Misregulation in Disease
Tong Ihn Lee et al.
CELL (2013)
DNA-Binding Specificities of Human Transcription Factors
Arttu Jolma et al.
CELL (2013)
Weak Frustration Regulates Sliding and Binding Kinetics on Rugged Protein-DNA Landscapes
Amir Marcovitz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Evaluation of methods for modeling transcription factor sequence specificity
Matthew T. Weirauch et al.
NATURE BIOTECHNOLOGY (2013)
Genome-wide inference of natural selection on human transcription factor binding sites
Leonardo Arbiza et al.
NATURE GENETICS (2013)
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
Jason D. Buenrostro et al.
NATURE METHODS (2013)
Enhancers: five essential questions
Len A. Pennacchio et al.
NATURE REVIEWS GENETICS (2013)
Determinants of nucleosome positioning
Kevin Struhl et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)
Selection on codon bias in yeast: a transcriptional hypothesis
Edoardo Trotta
NUCLEIC ACIDS RESEARCH (2013)
Measurement and modeling of intrinsic transcription terminators
Guillaume Cambray et al.
NUCLEIC ACIDS RESEARCH (2013)
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets
Christopher Fletez-Brant et al.
NUCLEIC ACIDS RESEARCH (2013)
Species-specific factors mediate extensive heterogeneity of mRNA 3′ ends in yeasts
Zarmik Moqtaderi et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast
Shlomi Dvir et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
EuGene: maximizing synthetic gene design for heterologous expression
Paulo Gaspar et al.
BIOINFORMATICS (2012)
Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements
Lucy W. Barrett et al.
CELLULAR AND MOLECULAR LIFE SCIENCES (2012)
Genomic evidence for elevated mutation rates in highly expressed genes
Chungoo Park et al.
EMBO REPORTS (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
Eilon Sharon et al.
NATURE BIOTECHNOLOGY (2012)
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence
Patricia J. Wittkopp et al.
NATURE REVIEWS GENETICS (2012)
The lac Repressor Displays Facilitated Diffusion in Living Cells
Petter Hammar et al.
SCIENCE (2012)
DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements
Pieter Meysman et al.
BIOINFORMATICS AND BIOLOGY INSIGHTS (2012)
A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA
Eric P. Bishop et al.
ACS CHEMICAL BIOLOGY (2011)
FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
BIOINFORMATICS (2011)
Dancing on DNA: Kinetic Aspects of Search Processes on DNA
Anahita Tafvizi et al.
CHEMPHYSCHEM (2011)
Discriminative prediction of mammalian enhancers from DNA sequence
Dongwon Lee et al.
GENOME RESEARCH (2011)
Global quantification of mammalian gene expression control
Bjoern Schwanhaeusser et al.
NATURE (2011)
Synonymous but not the same: the causes and consequences of codon bias
Joshua B. Plotkin et al.
NATURE REVIEWS GENETICS (2011)
Origins of Specificity in Protein-DNA Recognition
Remo Rohs et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 79 (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)
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
Shane C. Dillon et al.
NATURE REVIEWS MICROBIOLOGY (2010)
Promoter melting triggered by bacterial RNA polymerase occurs in three steps
Jie Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Sequence dependence of DNA bending rigidity
Stephanie Geggier et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Translation efficiency is determined by both codon bias and folding energy
Tamir Tuller et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
The role of DNA shape in protein-DNA recognition
Remo Rohs et al.
NATURE (2009)
ChIP-seq accurately predicts tissue-specific activity of enhancers
Axel Visel et al.
NATURE (2009)
Automated design of synthetic ribosome binding sites to control protein expression
Howard M. Salis et al.
NATURE BIOTECHNOLOGY (2009)
RNA-Seq: a revolutionary tool for transcriptomics
Zhong Wang et al.
NATURE REVIEWS GENETICS (2009)
From DNA sequence to transcriptional behaviour: a quantitative approach
Eran Segal et al.
NATURE REVIEWS GENETICS (2009)
Rho directs widespread termination of intragenic and stable RNA transcription
Jason M. Peters et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation
Itay Tirosh et al.
SCIENCE (2009)
Coding-Sequence Determinants of Gene Expression in Escherichia coli
Grzegorz Kudla et al.
SCIENCE (2009)
General Rules for Optimal Codon Choice
Ruth Hershberg et al.
PLOS GENETICS (2009)
Selection on Codon Bias
Ruth Hershberg et al.
ANNUAL REVIEW OF GENETICS (2008)
Heterologous Protein Expression Is Enhanced by Harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host
Evelina Angov et al.
PLOS ONE (2008)
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes
So Nakagawa et al.
NUCLEIC ACIDS RESEARCH (2008)
OPTIMIZER:: a web server for optimizing the codon usage of DNA sequences
Pere Puigbo et al.
NUCLEIC ACIDS RESEARCH (2007)
Genome-wide mapping of in vivo protein-DNA interactions
David S. Johnson et al.
SCIENCE (2007)
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
Tae Hoon Kim et al.
CELL (2007)
Accurate splice site prediction using support vector machines
Soeren Sonnenburg et al.
BMC BIOINFORMATICS (2007)
Detecting natural selection on cis-regulatory DNA
Matthew W. Hahn
GENETICA (2007)
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
Michael F. Berger et al.
NATURE BIOTECHNOLOGY (2006)
GeneDesign: Rapid, automated design of multikilobase synthetic genes
SM Richardson et al.
GENOME RESEARCH (2006)
cis-Regulatory and protein evolution in orthologous and duplicate genes
CI Castillo-Davis et al.
GENOME RESEARCH (2004)
Evolutionary changes in cis and trans gene regulation
PJ Wittkopp et al.
NATURE (2004)
The regulation of bacterial transcription initiation
DF Browning et al.
NATURE REVIEWS MICROBIOLOGY (2004)
Codon adaptation index as a measure of dominating codon bias
A Carbone et al.
BIOINFORMATICS (2003)
Global analysis of protein expression in yeast
S Ghaemmaghami et al.
NATURE (2003)
DNA binding sites: representation and discovery
GD Stormo
BIOINFORMATICS (2000)