- Home
- Publications
- Publication Search
- Publication Details
Title
Decoding disease: from genomes to networks to phenotypes
Authors
Keywords
-
Journal
NATURE REVIEWS GENETICS
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-08-03
DOI
10.1038/s41576-021-00389-x
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk
- (2021) Christopher Y. Park et al. NATURE GENETICS
- Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
- (2021) Daniel Taliun et al. NATURE
- Base-resolution models of transcription-factor binding reveal soft motif syntax
- (2021) Žiga Avsec et al. NATURE GENETICS
- PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA interaction prediction
- (2020) Qiang Kang et al. BIOINFORMATICS
- Pan-cancer analysis of whole genomes
- (2020) NATURE
- Improved protein structure prediction using potentials from deep learning
- (2020) Andrew W. Senior et al. NATURE
- Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging
- (2020) Ying-Chen Claire Hou et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The mutational constraint spectrum quantified from variation in 141,456 humans
- (2020) Konrad J. Karczewski et al. NATURE
- Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks
- (2020) Vikram Agarwal et al. Cell Reports
- The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting
- (2020) Peter D. Stenson et al. HUMAN GENETICS
- Genomic analyses implicate noncoding de novo variants in congenital heart disease
- (2020) Felix Richter et al. NATURE GENETICS
- Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis
- (2020) Jean-Pierre Roussarie et al. NEURON
- PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities
- (2020) Shilpa Nadimpalli Kobren et al. Cell Systems
- The BioGRID database: A comprehensive biomedical resource of curated protein, genetic and chemical interactions
- (2020) Rose Oughtred et al. PROTEIN SCIENCE
- Identification of pathogenic missense mutations using protein stability predictors
- (2020) Lukas Gerasimavicius et al. Scientific Reports
- Predicting Splicing from Primary Sequence with Deep Learning
- (2019) Kishore Jaganathan et al. CELL
- Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population
- (2019) Haiko Schurz et al. Frontiers in Genetics
- Deep-learning augmented RNA-seq analysis of transcript splicing
- (2019) Zijun Zhang et al. NATURE METHODS
- Selene: a PyTorch-based deep learning library for sequence data
- (2019) Kathleen M. Chen et al. NATURE METHODS
- FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data
- (2019) Daniel Quang et al. METHODS
- Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children
- (2019) Courtney E. French et al. INTENSIVE CARE MEDICINE
- Genomic Medicine–Progress, Pitfalls, and Promise
- (2019) Jay Shendure et al. CELL
- Genomic Analysis in the Age of Human Genome Sequencing
- (2019) Tuuli Lappalainen et al. CELL
- Trans Effects on Gene Expression Can Drive Omnigenic Inheritance
- (2019) Xuanyao Liu et al. CELL
- The Kipoi repository accelerates community exchange and reuse of predictive models for genomics
- (2019) Žiga Avsec et al. NATURE BIOTECHNOLOGY
- Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk
- (2019) Jian Zhou et al. NATURE GENETICS
- Deep learning: new computational modelling techniques for genomics
- (2019) Gökcen Eraslan et al. NATURE REVIEWS GENETICS
- mCSM-PPI2: predicting the effects of mutations on protein–protein interactions
- (2019) Carlos H M Rodrigues et al. NUCLEIC ACIDS RESEARCH
- Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
- (2019) Surag Nair et al. BIOINFORMATICS
- Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning
- (2019) Zakaria Louadi et al. Genes
- Deep learning enables rapid identification of potent DDR1 kinase inhibitors
- (2019) Alex Zhavoronkov et al. NATURE BIOTECHNOLOGY
- A global overview of pleiotropy and genetic architecture in complex traits
- (2019) Kyoko Watanabe et al. NATURE GENETICS
- Assessment of network module identification across complex diseases
- (2019) Sarvenaz Choobdar et al. NATURE METHODS
- The “All of Us” Research Program
- (2019) NEW ENGLAND JOURNAL OF MEDICINE
- Getting the Entire Message: Progress in Isoform Sequencing
- (2019) Simon A. Hardwick et al. Frontiers in Genetics
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives
- (2019) Zishuo Zeng et al. Frontiers in Genetics
- Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation
- (2019) Hannah Gelman et al. Genome Medicine
- DeepMirTar: a deep-learning approach for predicting human miRNA targets
- (2018) Ming Wen et al. BIOINFORMATICS
- SpliceRover: Interpretable Convolutional Neural
- (2018) Jasper Zuallaert et al. BIOINFORMATICS
- Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks
- (2018) Xiaoyong Pan et al. BIOINFORMATICS
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile
- (2018) Uwe Groß et al. BMC GENOMICS
- Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics
- (2018) Corinna Ernst et al. BMC Medical Genomics
- Comprehensive Characterization of Cancer Driver Genes and Mutations
- (2018) Matthew H. Bailey et al. CELL
- Comprehensive annotation of BRCA1 and BRCA2 missense variants by functionally validated sequence-based computational prediction models
- (2018) Steven N. Hart et al. GENETICS IN MEDICINE
- Sequential regulatory activity prediction across chromosomes with convolutional neural networks
- (2018) David R. Kelley et al. GENOME RESEARCH
- Opportunities and obstacles for deep learning in biology and medicine
- (2018) Travers Ching et al. Journal of the Royal Society Interface
- Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
- (2018) Jian Zhou et al. NATURE GENETICS
- From genome-wide associations to candidate causal variants by statistical fine-mapping
- (2018) Daniel J. Schaid et al. NATURE REVIEWS GENETICS
- GIANT 2.0: genome-scale integrated analysis of gene networks in tissues
- (2018) Aaron K Wong et al. NUCLEIC ACIDS RESEARCH
- DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
- (2018) Carlos HM Rodrigues et al. NUCLEIC ACIDS RESEARCH
- Damaging de novo mutations diminish motor skills in children on the autism spectrum
- (2018) Andreas Buja et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Prediction and interpretation of deleterious coding variants in terms of protein structural stability
- (2018) François Ancien et al. Scientific Reports
- Systematic Evaluation of Molecular Networks for Discovery of Disease Genes
- (2018) Justin K. Huang et al. Cell Systems
- Accurate classification of BRCA1 variants with saturation genome editing
- (2018) Gregory M. Findlay et al. NATURE
- A universal SNP and small-indel variant caller using deep neural networks
- (2018) Ryan Poplin et al. NATURE BIOTECHNOLOGY
- A sequence-based, deep learning model accurately predicts RNA splicing branchpoints
- (2018) Joseph M Paggi et al. RNA
- PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP
- (2018) Ritika Ramani et al. BIOINFORMATICS
- Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach
- (2018) Yi Zhang et al. BMC GENOMICS
- Anchor: trans-cell type prediction of transcription factor binding sites
- (2018) Hongyang Li et al. GENOME RESEARCH
- The UK Biobank resource with deep phenotyping and genomic data
- (2018) Clare Bycroft et al. NATURE
- An integrative tissue-network approach to identify and test human disease genes
- (2018) Victoria Yao et al. NATURE BIOTECHNOLOGY
- Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells
- (2018) Ishaan Gupta et al. NATURE BIOTECHNOLOGY
- A map of constrained coding regions in the human genome
- (2018) James M. Havrilla et al. NATURE GENETICS
- Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia
- (2018) Vivek Swarup et al. NATURE MEDICINE
- CADD: predicting the deleteriousness of variants throughout the human genome
- (2018) Philipp Rentzsch et al. NUCLEIC ACIDS RESEARCH
- Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
- (2018) Marina Lizio et al. NUCLEIC ACIDS RESEARCH
- The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019
- (2018) Annalisa Buniello et al. NUCLEIC ACIDS RESEARCH
- beRBP: binding estimation for human RNA-binding proteins
- (2018) Hui Yu et al. NUCLEIC ACIDS RESEARCH
- Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions
- (2018) Shilpa Nadimpalli Kobren et al. NUCLEIC ACIDS RESEARCH
- Integrating co-expression networks with GWAS to prioritize causal genes in maize
- (2018) Robert Schaefer et al. PLANT CELL
- Double-slit photoelectron interference in strong-field ionization of the neon dimer
- (2018) Maksim Kunitski et al. Nature Communications
- Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar
- (2017) Steven M. Harrison et al. GENETICS IN MEDICINE
- ABCA4midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
- (2017) Riccardo Sangermano et al. GENOME RESEARCH
- The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
- (2017) Jochen M. Schwenk et al. JOURNAL OF PROTEOME RESEARCH
- Dermatologist-level classification of skin cancer with deep neural networks
- (2017) Andre Esteva et al. NATURE
- Annotation-free quantification of RNA splicing using LeafCutter
- (2017) Yang I. Li et al. NATURE GENETICS
- High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
- (2017) Julien Lagarde et al. NATURE GENETICS
- Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
- (2017) Yi-Fei Huang et al. NATURE GENETICS
- NetSig: network-based discovery from cancer genomes
- (2017) Heiko Horn et al. NATURE METHODS
- Settling the score: variant prioritization and Mendelian disease
- (2017) Karen Eilbeck et al. NATURE REVIEWS GENETICS
- The Encyclopedia of DNA elements (ENCODE): data portal update
- (2017) Carrie A Davis et al. NUCLEIC ACIDS RESEARCH
- ClinVar: improving access to variant interpretations and supporting evidence
- (2017) Melissa J Landrum et al. NUCLEIC ACIDS RESEARCH
- Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
- (2017) Beryl B. Cummings et al. Science Translational Medicine
- The Human Cell Atlas
- (2017) Aviv Regev et al. eLife
- REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
- (2016) Nilah M. Ioannidis et al. AMERICAN JOURNAL OF HUMAN GENETICS
- Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics
- (2016) Sarah S. Kalia et al. GENETICS IN MEDICINE
- Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
- (2016) David R. Kelley et al. GENOME RESEARCH
- Clinical sequencing: is WGS the better WES?
- (2016) Janine Meienberg et al. HUMAN GENETICS
- Analysis of protein-coding genetic variation in 60,706 humans
- (2016) Monkol Lek et al. NATURE
- A spectral approach integrating functional genomic annotations for coding and noncoding variants
- (2016) Iuliana Ionita-Laza et al. NATURE GENETICS
- Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder
- (2016) Arjun Krishnan et al. NATURE NEUROSCIENCE
- Robust classification of protein variation using structural modelling and large-scale data integration
- (2016) Evan H. Baugh et al. NUCLEIC ACIDS 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
- MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions
- (2016) Minghui Li et al. NUCLEIC ACIDS RESEARCH
- The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
- (2016) Eric W. Deutsch et al. NUCLEIC ACIDS RESEARCH
- HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development
- (2016) Susan J. Lindsay et al. Frontiers in Neuroanatomy
- Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records
- (2016) Riccardo Miotto et al. Scientific Reports
- Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling
- (2015) Pau Creixell et al. CELL
- Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data
- (2015) Caroline F Wright et al. LANCET
- 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
- A method for calculating probabilities of fitness consequences for point mutations across the human genome
- (2015) Brad Gulko et al. NATURE GENETICS
- A method to predict the impact of regulatory variants from DNA sequence
- (2015) Dongwon Lee et al. NATURE GENETICS
- Understanding multicellular function and disease with human tissue-specific networks
- (2015) Casey S Greene et al. NATURE GENETICS
- Pathway and network analysis of cancer genomes
- (2015) NATURE METHODS
- Predicting effects of noncoding variants with deep learning–based sequence model
- (2015) Jian Zhou et al. NATURE METHODS
- SIFT missense predictions for genomes
- (2015) Robert Vaser et al. Nature Protocols
- Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders
- (2015) Neelroop N. Parikshak et al. NATURE REVIEWS GENETICS
- ClinGen — The Clinical Genome Resource
- (2015) Heidi L. Rehm et al. NEW ENGLAND JOURNAL OF MEDICINE
- Gene-Panel Sequencing and the Prediction of Breast-Cancer Risk
- (2015) Douglas F. Easton et al. NEW ENGLAND JOURNAL OF MEDICINE
- FNTM: a server for predicting functional networks of tissues in mouse
- (2015) Jonathan Goya et al. NUCLEIC ACIDS RESEARCH
- Sharing and Specificity of Co-expression Networks across 35 Human Tissues
- (2015) Emma Pierson et al. PLoS Computational Biology
- Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer
- (2015) Matthew Ruffalo et al. PLoS Computational Biology
- Deep learning of the tissue-regulated splicing code
- (2014) Michael K. K. Leung et al. BIOINFORMATICS
- Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
- (2014) Bogdan Pasaniuc et al. BIOINFORMATICS
- DANN: a deep learning approach for annotating the pathogenicity of genetic variants
- (2014) Daniel Quang et al. BIOINFORMATICS
- A general framework for estimating the relative pathogenicity of human genetic variants
- (2014) Martin Kircher et al. NATURE GENETICS
- Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
- (2014) Mark D M Leiserson et al. NATURE GENETICS
- Defining the role of common variation in the genomic and biological architecture of adult human height
- (2014) Andrew R Wood et al. NATURE GENETICS
- DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach
- (2014) D. E. V. Pires et al. NUCLEIC ACIDS RESEARCH
- Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders
- (2014) G. Novarino et al. SCIENCE
- VEGAS2: Software for More Flexible Gene-Based Testing
- (2014) Aniket Mishra et al. Twin Research and Human Genetics
- Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
- (2014) Mahmoud Ghandi et al. PLoS Computational Biology
- Correction: Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes
- (2014) Slavé Petrovski et al. PLoS Genetics
- Unscrambling butterfly oogenesis
- (2013) Jean-Michel Carter et al. BMC GENOMICS
- Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence
- (2013) Ilan Gronau et al. MOLECULAR BIOLOGY AND EVOLUTION
- The Genotype-Tissue Expression (GTEx) project
- (2013) John Lonsdale et al. NATURE GENETICS
- Interaction-based discovery of functionally important genes in cancers
- (2013) Dario Ghersi et al. NUCLEIC ACIDS RESEARCH
- BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations
- (2013) Yves Dehouck et al. NUCLEIC ACIDS RESEARCH
- ClinVar: public archive of relationships among sequence variation and human phenotype
- (2013) Melissa J. Landrum et al. NUCLEIC ACIDS RESEARCH
- Cancer Genome Landscapes
- (2013) B. Vogelstein et al. SCIENCE
- Post-transcriptional control of candidate risk genes for type 1 diabetes by rare genetic variants
- (2012) V M de Jong et al. GENES AND IMMUNITY
- Leveraging models of cell regulation and GWAS data in integrative network-based association studies
- (2012) Andrea Califano et al. NATURE GENETICS
- SIFT web server: predicting effects of amino acid substitutions on proteins
- (2012) Ngak-Leng Sim et al. NUCLEIC ACIDS RESEARCH
- Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
- (2012) M. T. Maurano et al. SCIENCE
- Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks
- (2012) Oded Magger et al. PLoS Computational Biology
- Algorithms for Detecting Significantly Mutated Pathways in Cancer
- (2011) Fabio Vandin et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- A Search for SNCA 3′ UTR Variants Identified SNP rs356165 as a Determinant of Disease Risk and Onset Age in Parkinson’s Disease
- (2011) Lucía F. Cardo et al. JOURNAL OF MOLECULAR NEUROSCIENCE
- Genome partitioning of genetic variation for complex traits using common SNPs
- (2011) Jian Yang et al. NATURE GENETICS
- Accurate Quantification of Functional Analogy among Close Homologs
- (2011) Maria D. Chikina et al. PLoS Computational Biology
- Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
- (2010) C. M. Robbins et al. GENOME RESEARCH
- Deciphering the splicing code
- (2010) Yoseph Barash et al. NATURE
- The NIH Roadmap Epigenomics Mapping Consortium
- (2010) Bradley E Bernstein et al. NATURE BIOTECHNOLOGY
- Common SNPs explain a large proportion of the heritability for human height
- (2010) Jian Yang et al. NATURE GENETICS
- A method and server for predicting damaging missense mutations
- (2010) Ivan A Adzhubei et al. NATURE METHODS
- Network medicine: a network-based approach to human disease
- (2010) Albert-László Barabási et al. NATURE REVIEWS GENETICS
- Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
- (2010) Eugene V. Davydov et al. PLoS Computational Biology
- Associating Genes and Protein Complexes with Disease via Network Propagation
- (2010) Oron Vanunu et al. PLoS Computational Biology
- Exploring the human genome with functional maps
- (2009) C. Huttenhower et al. GENOME RESEARCH
- Detection of nonneutral substitution rates on mammalian phylogenies
- (2009) K. S. Pollard et al. GENOME RESEARCH
- Finding the missing heritability of complex diseases
- (2009) Teri A. Manolio et al. NATURE
- Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
- (2009) Radu Dobrin et al. GENOME BIOLOGY
- Walking the Interactome for Prioritization of Candidate Disease Genes
- (2008) Sebastian Köhler et al. AMERICAN JOURNAL OF HUMAN GENETICS
- A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
- (2008) M. P. Keller et al. GENOME RESEARCH
- ConsensusPathDB—a database for integrating human functional interaction networks
- (2008) Atanas Kamburov et al. NUCLEIC ACIDS RESEARCH
- A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
- (2008) K. Lage et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
- (2008) Sara Mostafavi et al. GENOME BIOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now