Single nucleotide variations: Biological impact and theoretical interpretation

Association of miRNA-related Genetic Polymorphisms and Prognosis in Patients with Esophageal Squamous Cell Carcinoma

(2014) Pei-Wen Yang et al.   ANNALS OF SURGICAL ONCOLOGY

mrSNP: Software to detect SNP effects on microRNA binding

(2014) Mehmet Deveci et al.   BMC BIOINFORMATICS

NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

(2014) Manuel Giollo et al.   BMC GENOMICS

A genetic variant in the LDLRpromoter is responsible for part of the LDL-cholesterol variability in primary hypercholesterolemia

(2014) Isabel De Castro-Orós et al.   BMC Medical Genomics

Silent Mutations Make Some Noise

(2014) Siyuan Zheng et al.   CELL

Functional sequence variants within the SIRT1 gene promoter in indirect inguinal hernia

(2014) Qingluan Han et al.   GENE

Identification of miR-423 and miR-499 Polymorphisms on Affecting the Risk of Hepatocellular Carcinoma in a Large-Scale Population

(2014) Yanyun Ma et al.   Genetic Testing and Molecular Biomarkers

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

95 Identification Of Likely Pathogenic Variants In Patients With Bicuspid Aortic Valve: Correlation Of Complex Genotype With A More Severe Aortic Phenotype

(2014) Catherine Francis et al.   HEART

CDKN2AUnclassified Variants in Familial Malignant Melanoma: Combining Functional and Computational Approaches for Their Assessment

(2014) Maria Chiara Scaini et al.   HUMAN MUTATION

SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features

(2014) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Novel recessive myotilin mutation causes severe myofibrillar myopathy

(2014) Joachim Schessl et al.   NEUROGENETICS

VarMod: modelling the functional effects of non-synonymous variants

(2014) M. Pappalardo et al.   NUCLEIC ACIDS RESEARCH

Effective Automated Feature Construction and Selection for Classification of Biological Sequences

(2014) Uday Kamath et al.   PLoS One

The Hunt for Missing Genes

(2014) J. Kaiser   SCIENCE

Clues from the resilient

(2014) S. H. Friend et al.   SCIENCE

Processed pseudogenes acquired somatically during cancer development

(2014) Susanna L. Cooke et al.   Nature Communications

SDS, a structural disruption score for assessment of missense variant deleteriousness

(2014) Thanawadee Preeprem et al.   Frontiers in Genetics

Effects of the gout-causing Q141K polymorphism and a CFTR ΔF508 mimicking mutation on the processing and stability of the ABCG2 protein

(2013) Hajnalka Sarankó et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

(2013) S. Castellana et al.   BRIEFINGS IN BIOINFORMATICS

A global map for dissecting phenotypic variants in human lincRNAs

(2013) Shangwei Ning et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The silent codon change I507-ATC→ATT contributes to the severity of the ΔF508 CFTR channel dysfunction

(2013) Ahmed Lazrak et al.   FASEB JOURNAL

Trendspotting in the Protein Data Bank

(2013) Helen M. Berman et al.   FEBS LETTERS

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

(2013) S. B. Montgomery et al.   GENOME RESEARCH

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

(2013) Radhakrishnan Sabarinathan et al.   HUMAN MUTATION

Common Polymorphisms in Human Langerin Change Specificity for Glycan Ligands

(2013) Hadar Feinberg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Machine learning in cell biology – teaching computers to recognize phenotypes

(2013) Christoph Sommer et al.   JOURNAL OF CELL SCIENCE

Building a Genome Analysis Pipeline to Predict Disease Risk and Prevent Disease

(2013) Y. Bromberg   JOURNAL OF MOLECULAR BIOLOGY

Protein Kinase A and Phosphodiesterase-4D3 Binding to Coding Polymorphisms of Cardiac Muscle Anchoring Protein (mAKAP)

(2013) Abeer Rababa'h et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effects of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein–Protein Interactions

(2013) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

Impacts of Variation in the Human Genome on Gene Regulation

(2013) Rajini R. Haraksingh et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

De novo mutations in epileptic encephalopathies

(2013) et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

A genomic view of mosaicism and human disease

(2013) Leslie G. Biesecker et al.   NATURE REVIEWS GENETICS

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

NCBI’s Database of Genotypes and Phenotypes: dbGaP

(2013) Kimberly A. Tryka et al.   NUCLEIC ACIDS RESEARCH

Structural and Functional Analysis of Human SOD1 in Amyotrophic Lateral Sclerosis

(2013) Lorenna Giannini Alves Moreira et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Common exonic missense variants in the C2 domain of the human KIBRA protein modify lipid binding and cognitive performance

(2013) K Duning et al.   Translational Psychiatry

Epi4K: Gene discovery in 4,000 genomes

(2012)   EPILEPSIA

Surrogate Genetics and Metabolic Profiling for Characterization of Human Disease Alleles

(2012) J. A. Mayfield et al.   GENETICS

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

The diagnostic utility of exome sequencing in Joubert syndrome and related disorders

(2012) Yoshinori Tsurusaki et al.   JOURNAL OF HUMAN GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

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

Association study of Nogo-related genes with schizophrenia in a Japanese case-control sample

(2011) Daisuke Jitoku et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Improving the prediction of disease-related variants using protein three-dimensional structure

(2011) Emidio Capriotti et al.   BMC BIOINFORMATICS

A novel heterozygous missense mutation G316D of SIX3 gene in a Brazilian patient with holoprosencephaly-like phenotype and Langerhans cell histiocytosis

(2011) Lucilene Arilho Ribeiro et al.   CLINICAL DYSMORPHOLOGY

A novel mutation in TNNT3 associated with Sheldon–Hall syndrome in a Chinese family with vertical talus

(2011) Ning Zhao et al.   European Journal of Medical Genetics

Revisiting Mendelian disorders through exome sequencing

(2011) Chee-Seng Ku et al.   HUMAN GENETICS

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

(2011) Stephanie Hicks et al.   HUMAN MUTATION

Structural and Functional Impact of Cancer-Related Missense Somatic Mutations

(2011) Zhen Shi et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of two novel CAKUT-causing genes by massively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis

(2011) Pawaree Saisawat et al.   KIDNEY INTERNATIONAL

Messing up disorder: how do missense mutations in the tumor suppressor protein APC lead to cancer?

(2011) David P Minde et al.   Molecular Cancer

Mouse library set to be knockout

(2011) Elie Dolgin   NATURE

Predicting phenotypic variation in yeast from individual genome sequences

(2011) Rob Jelier et al.   NATURE GENETICS

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

(2011) G. De Baets et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Point Mutations in Aβ Result in the Formation of Distinct Polymorphic Aggregates in the Presence of Lipid Bilayers

(2011) Phillip M. Pifer et al.   PLoS One

From SNPs to Genes: Disease Association at the Gene Level

(2011) Benjamin Lehne et al.   PLoS One

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites

(2011) Anbu K. Adikesavan et al.   PLoS Genetics

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An Angiotensin II type 1 receptor activation switch patch revealed through Evolutionary Trace analysis

(2010) Marie Mi Bonde et al.   BIOCHEMICAL PHARMACOLOGY

TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing

(2010) Jun Ling Wang et al.   BRAIN

Loss-of-function variants in the genomes of healthy humans

(2010) D. G. MacArthur et al.   HUMAN MOLECULAR GENETICS

Functional analysis of mutations in the ATP loop of the Wilson disease copper transporter, ATP7B

(2010) Leiah M. Luoma et al.   HUMAN MUTATION

MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

(2010) Maxim Barenboim et al.   HUMAN MUTATION

Novel mutations in the long isoform of the USH2A gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa

(2010) T. L. McGee et al.   JOURNAL OF MEDICAL GENETICS

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

A large-scale protein-function database

(2010) Rolf Apweiler et al.   Nature Chemical Biology

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Introduction to machine learning for brain imaging

(2010) Steven Lemm et al.   NEUROIMAGE

Exome Sequencing Reveals VCP Mutations as a Cause of Familial ALS

(2010) Janel O. Johnson et al.   NEURON

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

(2010) James R. Lupski et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors

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

AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements

(2010) M. Masso et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

Epistasis and Its Implications for Personal Genetics

(2009) Jason H. Moore et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Next generation tools for the annotation of human SNPs

(2009) Rachel Karchin   BRIEFINGS IN BIOINFORMATICS

Common vs. rare allele hypotheses for complex diseases

(2009) Nicholas J Schork et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Common Genetic Variation and Human Traits

(2009) David B. Goldstein   NEW ENGLAND JOURNAL OF MEDICINE

A minimal sequence code for switching protein structure and function

(2009) Patrick A. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A three-state prediction of single point mutations on protein stability changes

(2008) Emidio Capriotti et al.   BMC BIOINFORMATICS

The success of the genome-wide association approach: a brief story of a long struggle

(2008) Ku Chee Seng et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The proportion of mutations predicted to have a deleterious effect differs between gain and loss of function genes in neurodegenerative disease

(2008) Paul N. Valdmanis et al.   HUMAN MUTATION

Functional and computational assessment of missense variants in the ataxia-telangiectasia mutated (ATM) gene: mutations with increased cancer risk

(2008) M. Mitui et al.   HUMAN MUTATION

A yeast recombination assay to characterize humanBRCA1missense variants of unknown pathological significance

(2008) Maria Adelaide Caligo et al.   HUMAN MUTATION

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

(2008) Kristi Kerkel et al.   NATURE GENETICS

Sex-specific genetic architecture of human disease

(2008) Carole Ober et al.   NATURE REVIEWS GENETICS

Mutations in the HSP27 (HSPB1) gene cause dominant, recessive, and sporadic distal HMN/CMT type 2

(2008) H. Houlden et al.   NEUROLOGY

Genetic Variation in an Individual Human Exome

(2008) Pauline C. Ng et al.   PLoS Genetics

Correlating observed odds ratios from lung cancer case–control studies to SNP functional scores predicted by bioinformatic tools

(2007) Yong Zhu et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE