PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants

The patterns of deleterious mutations during the domestication of soybean

(2021) Myung-Shin Kim et al.   Nature Communications

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

(2021) Matthew B. Hufford et al.   SCIENCE

Hydrogen peroxide sensor HPCA1 is an LRR receptor kinase in Arabidopsis

(2020) Feihua Wu et al.   NATURE

MISTIC: A prediction tool to reveal disease-relevant deleterious missense variants

(2020) Kirsley Chennen et al.   PLoS One

SSR1 is involved in maintaining the function of mitochondria electron transport chain and iron homeostasis upon proline treatment in Arabidopsis

(2020) Hui Ling Han et al.   JOURNAL OF PLANT PHYSIOLOGY

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

(2020) Vikas Pejaver et al.   Nature Communications

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

(2019) Shane Horsefield et al.   SCIENCE

Control of Grain Size and Weight by the OsMKKK10-OsMKK4-OsMAPK6 Signaling Pathway in Rice

(2018) Ran Xu et al.   Molecular Plant

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants

(2018) Najmeh Alirezaie et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Crop SNP db: a database of SNP array data for Brassica crops and hexaploid bread wheat

(2018) Armin Scheben et al.   PLANT JOURNAL

A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants

(2018) Maxim S. Kovalev et al.   Frontiers in Plant Science

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

(2017) Peter D. Stenson et al.   HUMAN GENETICS

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Uncovering hidden variation in polyploid wheat

(2017) Ksenia V. Krasileva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contributions of Zea mays subspecies mexicana haplotypes to modern maize

(2017) Ning Yang et al.   Nature Communications

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation

(2016) Haiming Tang et al.   BIOINFORMATICS

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

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

(2016) Monkol Lek et al.   NATURE

AtKC1 and CIPK23 Synergistically Modulate AKT1-Mediated Low-Potassium Stress Responses in Arabidopsis

(2016) Xue-Ping Wang et al.   PLANT PHYSIOLOGY

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

VariSNP, A Benchmark Database for Variations From dbSNP

(2015) Gerard C.P. Schaafsma et al.   HUMAN MUTATION

A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis

(2015) Min Zhang et al.   PLANT JOURNAL

Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis

(2015) Mu Gao et al.   STRUCTURE

Point Mutations in Centromeric Histone Induce Post-zygotic Incompatibility and Uniparental Inheritance

(2015) Sundaram Kuppu et al.   PLoS Genetics

PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants

(2015) Abhishek Niroula et al.   PLoS One

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

The mitochondrial proteins AtHscB and AtIsu1 involved in Fe–S cluster assembly interact with the Hsp70-type chaperon AtHscA2 and modulate its catalytic activity

(2014) Laura Leaden et al.   MITOCHONDRION

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

Iron/sulfur proteins biogenesis in prokaryotes: Formation, regulation and diversity

(2013) Béatrice Roche et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology

(2013) Catharina Steentoft et al.   EMBO JOURNAL

MISTIC: mutual information server to infer coevolution

(2013) Franco L. Simonetti et al.   NUCLEIC ACIDS RESEARCH

The Pattern and Distribution of Deleterious Mutations in Maize

(2013) Sofiane Mezmouk et al.   G3-Genes Genomes Genetics

SNPdbe: constructing an nsSNP functional impacts database

(2012) C. Schaefer et al.   BIOINFORMATICS

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

(2012) Narendra Kumar et al.   BIOINFORMATICS

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

Purification and Characterization of ZmRIP1, a Novel Reductant-Inhibited Protein Tyrosine Phosphatase from Maize

(2012) B. Li et al.   PLANT PHYSIOLOGY

Development and Characterization of a New TILLING Population of Common Bread Wheat (Triticum aestivum L.)

(2012) Liang Chen et al.   PLoS One

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

(2012) Mingjun Wang et al.   PLoS One

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice

(2010) Torsten Günther et al.   THEORETICAL AND APPLIED GENETICS

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

(2010) Timothy Nugent et al.   PLoS Computational Biology

SOLpro: accurate sequence-based prediction of protein solubility

(2009) Christophe N. Magnan et al.   BIOINFORMATICS

In Planta Mutagenesis Determines the Functional Regions of the Wheat Puroindoline Proteins

(2009) L. Feiz et al.   GENETICS

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Identification, analysis, and prediction of protein ubiquitination sites

(2009) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HSEpred: predict half-sphere exposure from protein sequences

(2008) Jiangning Song et al.   BIOINFORMATICS

Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase

(2008) Yum L. Yip et al.   HUMAN MUTATION