Human 5′ UTR design and variant effect prediction from a massively parallel translation assay

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

(2019) Nicholas Bogard et al.   CELL

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

(2017) Josh T. Cuperus et al.   GENOME RESEARCH

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

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

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

Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals

(2016) Xi Wang et al.   Molecular Systems Biology

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Translation from the 5' untranslated region shapes the integrated stress response

(2016) S. R. Starck et al.   SCIENCE

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

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

(2016) Feng Liu et al.   Scientific Reports

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

(2016) Kerstin Reuter et al.   PLoS Computational Biology

Tunable protein synthesis by transcript isoforms in human cells

(2016) Stephen N Floor et al.   eLife

Editorial: Yeast synthetic biology: new tools to unlock cellular function

(2015)   FEMS YEAST RESEARCH

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

(2015) Can Cenik 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

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

Quantitative analysis of mammalian translation initiation sites by FACS-seq

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

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek et al.   NUCLEIC ACIDS RESEARCH

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

Tuning gene expression with synthetic upstream open reading frames

(2013) J. P. Ferreira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Before It Gets Started: Regulating Translation at the 5′ UTR

(2012) Patricia R. Araujo et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency

(2012) Sang Woo Seo et al.   METABOLIC ENGINEERING

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ribosomal basis of diamond-blackfan anemia: mutation and database update

(2010) Ilenia Boria et al.   HUMAN MUTATION

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Germline mutations in TMEM127 confer susceptibility to pheochromocytoma

(2010) Yuejuan Qin et al.   NATURE GENETICS

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

(2010) Bart R. Anderson et al.   NUCLEIC ACIDS RESEARCH

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability

(2008) Katalin Karikó et al.   MOLECULAR THERAPY