Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae

(2016) Matthew S. Rich et al.   GENETICS

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

(2016) Feng Liu et al.   Scientific Reports

Protein Abundance Control by Non-coding Antisense Transcription

(2016) Florian Huber et al.   Cell Reports

Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae

(2016) Matthew S. Rich et al.   GENETICS

Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

(2016) Yiheng Wang et al.   Scientific Reports

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

Core promoter sequence in yeast is a major determinant of expression level

(2015) Shai Lubliner et al.   GENOME RESEARCH

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

(2015) Ophir Shalem et al.   PLoS Genetics

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

A Random Screen Using a Novel Reporter Assay System Reveals a Set of Sequences That Are Preferred as the TATA or TATA-Like Elements in the CYC1 Promoter of Saccharomyces cerevisiae

(2015) Kiyoshi Watanabe et al.   PLoS One

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements

(2014) Daechan Park et al.   NUCLEIC ACIDS RESEARCH

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts

(2014) Panos Oikonomou et al.   Cell Reports

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

Contemporary, yeast-based approaches to understanding human genetic variation

(2013) Maitreya J Dunham et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Small, synthetic, GC-rich mRNA stem-loop modules 5′ proximal to the AUG start-codon predictably tune gene expression in yeast

(2013) Erwin Lamping et al.   Microbial Cell Factories

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

(2013) S. Dvir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

(2011) Tyler J. Creamer et al.   PLoS Genetics

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An improved yeast transformation method for the generation of very large human antibody libraries

(2010) Lorenzo Benatuil et al.   PROTEIN ENGINEERING DESIGN & SELECTION

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

(2010) John A. Capra et al.   PLoS Computational Biology

Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries

(2009) Thomas C Scanlon et al.   BMC BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH