Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs

(2021) Lei Sun et al.   CELL

Deep neural networks for interpreting RNA-binding protein target preferences

(2020) Mahsa Ghanbari et al.   GENOME RESEARCH

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

(2019) Ei-Wen Yang et al.   Nature Communications

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes

(2019) Emad Bahrami-Samani et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites

(2019) Huijuan Feng et al.   MOLECULAR CELL

icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation

(2019) Pan Li et al.   METHODS

Squeeze-and-Excitation Networks

(2019) Jie Hu et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

OUP accepted manuscript

(2018)   BIOINFORMATICS

The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression

(2018) Cindy Meyer et al.   MOLECULAR CELL

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield et al.   NATURE METHODS

Principles for targeting RNA with drug-like small molecules

(2018) Katherine Deigan Warner et al.   NATURE REVIEWS DRUG DISCOVERY

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

POSTAR2: deciphering the post-transcriptional regulatory logics

(2018) Yumin Zhu et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

(2018) Michael J. Gandal et al.   SCIENCE

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

RNA modifications and structures cooperate to guide RNA–protein interactions

(2017) Cole J.T. Lewis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure

(2017) Oz Solomon et al.   Nature Communications

In vitro differentiation of human embryonic stem cells into ovarian follicle-like cells

(2017) Dajung Jung et al.   Nature Communications

RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data

(2016) Yaron Orenstein et al.   BIOINFORMATICS

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency

(2016) Jin Zhang et al.   Cell Stem Cell

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes

(2016) Kristopher W. Brannan et al.   MOLECULAR CELL

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

irCLIP platform for efficient characterization of protein–RNA interactions

(2016) Brian J Zarnegar et al.   NATURE METHODS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

(2016) Ryan A Flynn et al.   Nature Protocols

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

(2016) Boqin Hu et al.   NUCLEIC ACIDS RESEARCH

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival

(2016) Anne E. Conway et al.   Cell Reports

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

SRSF1-Regulated Alternative Splicing in Breast Cancer

(2015) Olga Anczuków et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Specificity and nonspecificity in RNA–protein interactions

(2015) Eckhard Jankowsky et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

(2014) Sean R. Eddy   Annual Review of Biophysics

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

(2014) Ayesha Hasan et al.   PLoS Genetics

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

(2013) Shatakshi Pandit et al.   MOLECULAR CELL

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

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

(2013) M. Hafner et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FMR1 premutation and full mutation molecular mechanisms related to autism

(2011) Randi Hagerman et al.   Journal of Neurodevelopmental Disorders

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

Evidence that Lin28 stimulates translation by recruiting RNA helicase A to polysomes

(2011) J. Jin et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

How RNA Unfolds and Refolds

(2008) Pan T.X. Li et al.   Annual Review of Biochemistry

Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

(2008) A. L. Saltzman et al.   MOLECULAR AND CELLULAR BIOLOGY

EZH1 Mediates Methylation on Histone H3 Lysine 27 and Complements EZH2 in Maintaining Stem Cell Identity and Executing Pluripotency

(2008) Xiaohua Shen et al.   MOLECULAR CELL

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

p100 increases AT1R expression through interaction with AT1R 3'-UTR

(2008) K. Paukku et al.   NUCLEIC ACIDS RESEARCH