Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data
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Title
Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data
Authors
Keywords
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Journal
Frontiers in Pharmacology
Volume 9, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2018-12-04
DOI
10.3389/fphar.2018.01437
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Note: Only part of the references are listed.- Impact of CYP2C19 Genotype on Escitalopram Exposure and Therapeutic Failure: A Retrospective Study Based on 2,087 Patients
- (2018) Marin M. Jukić et al. AMERICAN JOURNAL OF PSYCHIATRY
- Application of Microphysiological Systems to Enhance Safety Assessment in Drug Discovery
- (2018) Lorna Ewart et al. Annual Review of Pharmacology and Toxicology
- Quantification of biases in predictions of protein stability changes upon mutations
- (2018) Fabrizio Pucci et al. BIOINFORMATICS
- Next-Generation Machine Learning for Biological Networks
- (2018) Diogo M. Camacho et al. CELL
- How to Consider Rare Genetic Variants in Personalized Drug Therapy
- (2018) Volker M. Lauschke et al. CLINICAL PHARMACOLOGY & THERAPEUTICS
- Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine
- (2018) Yuan Ji et al. EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
- Comprehensive overview of the pharmacogenetic diversity in Ashkenazi Jews
- (2018) Yitian Zhou et al. JOURNAL OF MEDICAL GENETICS
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- Deep learning in pharmacogenomics: from gene regulation to patient stratification
- (2018) Alexandr A Kalinin et al. PHARMACOGENOMICS
- Prediction and interpretation of deleterious coding variants in terms of protein structural stability
- (2018) François Ancien et al. Scientific Reports
- Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data
- (2018) Vanessa E. Gray et al. Cell Systems
- Human liver spheroids in chemically defined conditions for studies of gene–drug, drug–drug and disease–drug interactions
- (2018) Magnus Ingelman-Sundberg et al. PHARMACOGENOMICS
- An optimized prediction framework to assess the functional impact of pharmacogenetic variants
- (2018) Yitian Zhou et al. PHARMACOGENOMICS JOURNAL
- Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling
- (2017) Jonathan Gallion et al. HUMAN MUTATION
- Genetic effects on gene expression across human tissues
- (2017) François Aguet et al. NATURE
- Mutation effects predicted from sequence co-variation
- (2017) Thomas A Hopf et al. NATURE BIOTECHNOLOGY
- Mechanistic insights into precursor messenger RNA splicing by the spliceosome
- (2017) Yigong Shi NATURE REVIEWS MOLECULAR CELL BIOLOGY
- DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins
- (2017) Daniele Raimondi et al. NUCLEIC ACIDS RESEARCH
- JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
- (2017) Aziz Khan et al. NUCLEIC ACIDS RESEARCH
- SDM: a server for predicting effects of mutations on protein stability
- (2017) Arun Prasad Pandurangan et al. NUCLEIC ACIDS RESEARCH
- Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties
- (2017) Yuliang Pan et al. PLoS One
- Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes
- (2017) Suganthi Balasubramanian et al. Nature Communications
- SNPs in microRNA target sites and their potential role in human disease
- (2017) Adrianna Moszyńska et al. Open Biology
- NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events
- (2017) Min-Kung Hsu et al. PLoS One
- Analysis of population-specific pharmacogenomic variants using next-generation sequencing data
- (2017) Eunyong Ahn et al. Scientific Reports
- A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease
- (2016) Damian Smedley et al. AMERICAN JOURNAL OF HUMAN GENETICS
- REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
- (2016) Nilah M. Ioannidis et al. AMERICAN JOURNAL OF HUMAN GENETICS
- Advancements in Next-Generation Sequencing
- (2016) Shawn E. Levy et al. Annual Review of Genomics and Human Genetics
- ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity
- (2016) Daniel K. Witvliet et al. BIOINFORMATICS
- STRUM: structure-based prediction of protein stability changes upon single-point mutation
- (2016) Lijun Quan et al. BIOINFORMATICS
- ImiRP: a computational approach to microRNA target site mutation
- (2016) Bridget C. Ryan et al. BMC BIOINFORMATICS
- The Genetics of Transcription Factor DNA Binding Variation
- (2016) Bart Deplancke et al. CELL
- Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network
- (2016) WS Bush et al. CLINICAL PHARMACOLOGY & THERAPEUTICS
- Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation
- (2016) Haiming Tang et al. GENETICS
- Rare genetic variants in cellular transporters, metabolic enzymes and nuclear receptors can be important determinants of interindividual differences in drug response
- (2016) Mikael Kozyra et al. GENETICS IN MEDICINE
- microRNA target prediction programs predict many false positives
- (2016) Natalia Pinzón et al. GENOME RESEARCH
- SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach
- (2016) Ivan Getov et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Computational approaches for predicting mutant protein stability
- (2016) Shweta Kulshreshtha et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Predicting RNA secondary structures from sequence and probing data
- (2016) Ronny Lorenz et al. METHODS
- A spectral approach integrating functional genomic annotations for coding and noncoding variants
- (2016) Iuliana Ionita-Laza et al. NATURE GENETICS
- Robust classification of protein variation using structural modelling and large-scale data integration
- (2016) Evan H. Baugh et al. NUCLEIC ACIDS RESEARCH
- ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
- (2016) Haim Ashkenazy et al. NUCLEIC ACIDS RESEARCH
- Requirements for comprehensive pharmacogenetic genotyping platforms
- (2016) Volker M Lauschke et al. PHARMACOGENOMICS
- Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
- (2016) A Chhibber et al. PHARMACOGENOMICS JOURNAL
- Precision Medicine and Rare Genetic Variants
- (2016) Volker M. Lauschke et al. TRENDS IN PHARMACOLOGICAL SCIENCES
- Premature termination codons in modern human genomes
- (2016) Kohei Fujikura Scientific Reports
- Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools
- (2016) Omar Soukarieh et al. PLoS Genetics
- Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation
- (2016) Haiming Tang et al. GENETICS
- Mechanisms and Regulation of Alternative Pre-mRNA Splicing
- (2015) Yeon Lee et al. Annual Review of Biochemistry
- An integrative approach to predicting the functional effects of non-coding and coding sequence variation
- (2015) Hashem A. Shihab et al. BIOINFORMATICS
- DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels
- (2015) Lukas Folkman et al. BIOINFORMATICS
- Better prediction of functional effects for sequence variants
- (2015) Maximilian Hecht et al. BMC GENOMICS
- Non-coding genetic variants in human disease: Figure 1.
- (2015) Feng Zhang et al. HUMAN MOLECULAR GENETICS
- The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity
- (2015) Dominik G. Grimm et al. HUMAN MUTATION
- Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)
- (2015) Christopher Douville et al. HUMAN MUTATION
- Integrative analysis of 111 reference human epigenomes
- (2015) Anshul Kundaje et al. NATURE
- A global reference for human genetic variation
- (2015) Richard A. Gibbs et al. NATURE
- 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
- Predicting effects of noncoding variants with deep learning–based sequence model
- (2015) Jian Zhou et al. NATURE METHODS
- Bioinformatic tools for microRNA dissection
- (2015) Most Mauluda Akhtar et al. NUCLEIC ACIDS RESEARCH
- Genetic variation in the human cytochrome P450 supergene family
- (2015) Kohei Fujikura et al. Pharmacogenetics and Genomics
- Comparison of predicted and actual consequences of missense mutations
- (2015) Lisa A. Miosge et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data
- (2015) Qiongshi Lu et al. Scientific Reports
- Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies
- (2015) C. Dong et al. HUMAN MOLECULAR GENETICS
- DANN: a deep learning approach for annotating the pathogenicity of genetic variants
- (2014) Daniel Quang et al. BIOINFORMATICS
- mrSNP: Software to detect SNP effects on microRNA binding
- (2014) Mehmet Deveci et al. BMC BIOINFORMATICS
- A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
- (2014) Panagiotis Katsonis et al. GENOME RESEARCH
- Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation
- (2014) X. Zhang et al. HUMAN MOLECULAR GENETICS
- SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features
- (2014) Christopher M. Yates et al. JOURNAL OF MOLECULAR BIOLOGY
- Preemptive Genotyping for Personalized Medicine: Design of the Right Drug, Right Dose, Right Time—Using Genomic Data to Individualize Treatment Protocol
- (2014) Suzette J. Bielinski et al. MAYO CLINIC PROCEEDINGS
- Landscape and variation of RNA secondary structure across the human transcriptome
- (2014) Yue Wan et al. NATURE
- Genetic and epigenetic fine mapping of causal autoimmune disease variants
- (2014) Kyle Kai-How Farh et al. NATURE
- A general framework for estimating the relative pathogenicity of human genetic variants
- (2014) Martin Kircher et al. NATURE GENETICS
- Functional annotation of noncoding sequence variants
- (2014) Graham R S Ritchie et al. NATURE METHODS
- MutationTaster2: mutation prediction for the deep-sequencing age
- (2014) Jana Marie Schwarz et al. NATURE METHODS
- In silico prediction of splice-altering single nucleotide variants in the human genome
- (2014) Xueqiu Jian et al. NUCLEIC ACIDS RESEARCH
- 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
- The human splicing code reveals new insights into the genetic determinants of disease
- (2014) H. Y. Xiong et al. SCIENCE
- Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes
- (2014) Antonio Rausell et al. PLoS Computational Biology
- PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
- (2014) Jaroslav Bendl et al. PLoS Computational Biology
- MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing
- (2014) Matthew Mort et al. GENOME BIOLOGY
- mCSM: predicting the effects of mutations in proteins using graph-based signatures
- (2013) Douglas E. V. Pires et al. BIOINFORMATICS
- Identifying Mendelian disease genes with the Variant Effect Scoring Tool
- (2013) Hannah Carter et al. BMC GENOMICS
- In silico tools for splicing defect prediction: a survey from the viewpoint of end users
- (2013) Xueqiu Jian et al. GENETICS IN MEDICINE
- Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants
- (2013) Thomas A. Peterson et al. JOURNAL OF MOLECULAR BIOLOGY
- Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence
- (2013) Ilan Gronau et al. MOLECULAR BIOLOGY AND EVOLUTION
- Genome-wide inference of natural selection on human transcription factor binding sites
- (2013) Leonardo Arbiza et al. NATURE GENETICS
- Rare-disease genetics in the era of next-generation sequencing: discovery to translation
- (2013) Kym M. Boycott et al. NATURE REVIEWS GENETICS
- PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways
- (2013) Anindya Bhattacharya et al. NUCLEIC ACIDS RESEARCH
- MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs
- (2012) Chenxing Liu et al. BMC GENOMICS
- Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models
- (2012) Hashem A. Shihab et al. HUMAN MUTATION
- Regulation of cytoplasmic mRNA decay
- (2012) Daniel R. Schoenberg et al. NATURE REVIEWS GENETICS
- Pharmacogenomics of drug-metabolizing enzymes: a recent update on clinical implications and endogenous effects
- (2012) S C Sim et al. PHARMACOGENOMICS JOURNAL
- Predicting the Functional Effect of Amino Acid Substitutions and Indels
- (2012) Yongwook Choi et al. PLoS One
- A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
- (2012) D. G. MacArthur et al. SCIENCE
- Predicting the effects of frameshifting indels
- (2012) Jing Hu et al. GENOME BIOLOGY
- Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel
- (2011) Abel González-Pérez et al. AMERICAN JOURNAL OF HUMAN GENETICS
- Ranking insertion, deletion and nonsense mutations based on their effect on genetic information
- (2011) Amin Zia et al. BMC BIOINFORMATICS
- TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences
- (2011) Arif O Harmanci et al. BMC BIOINFORMATICS
- Predicting the functional impact of protein mutations: application to cancer genomics
- (2011) Boris Reva et al. NUCLEIC ACIDS RESEARCH
- Using bioinformatics to predict the functional impact of SNVs
- (2010) M. S. Cline et al. BIOINFORMATICS
- Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces
- (2010) Hanka Venselaar et al. BMC BIOINFORMATICS
- Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations
- (2010) Sarah E. Flanagan et al. Genetic Testing and Molecular Biomarkers
- MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets
- (2010) Maxim Barenboim et al. HUMAN MUTATION
- A method and server for predicting damaging missense mutations
- (2010) Ivan A Adzhubei et al. NATURE METHODS
- Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
- (2010) D. Schmidt et al. SCIENCE
- Genome-Wide Association between Branch Point Properties and Alternative Splicing
- (2010) André Corvelo et al. PLoS Computational Biology
- Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
- (2010) Eugene V. Davydov et al. PLoS Computational Biology
- Genomic features defining exonic variants that modulate splicing
- (2010) Adam Woolfe et al. GENOME BIOLOGY
- Identifying novel constrained elements by exploiting biased substitution patterns
- (2009) Manuel Garber et al. BIOINFORMATICS
- Missed threads. The impact of pre-mRNA splicing defects on clinical practice
- (2009) Diana Baralle et al. EMBO REPORTS
- Identification of deleterious mutations within three human genomes
- (2009) S. Chun et al. GENOME RESEARCH
- Detection of nonneutral substitution rates on mammalian phylogenies
- (2009) K. S. Pollard et al. GENOME RESEARCH
- Functional annotations improve the predictive score of human disease-related mutations in proteins
- (2009) Remo Calabrese et al. HUMAN MUTATION
- Construction and functional analyses of a comprehensive σ54 site-directed mutant library using alanine–cysteine mutagenesis
- (2009) Yan Xiao et al. NUCLEIC ACIDS RESEARCH
- CENTROIDFOLD: a web server for RNA secondary structure prediction
- (2009) K. Sato et al. NUCLEIC ACIDS RESEARCH
- HHMD: the human histone modification database
- (2009) Yan Zhang et al. NUCLEIC ACIDS RESEARCH
- Bi-Directional SIFT Predicts a Subset of Activating Mutations
- (2009) William Lee et al. PLoS One
- Role of RNA structure in regulating pre-mRNA splicing
- (2009) M. Bryan Warf et al. TRENDS IN BIOCHEMICAL SCIENCES
- High-Resolution Mapping and Characterization of Open Chromatin across the Genome
- (2008) Alan P. Boyle et al. CELL
- Effectiveness of PTC124 treatment of cystic fibrosis caused by nonsense mutations: a prospective phase II trial
- (2008) Eitan Kerem et al. LANCET
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