Classification of PTEN missense VUS through exascale simulations

Integration of Deep Learning with Ramachandran Plot Molecular Dynamics Simulation for Genetic Variant Classification

(2023) Benjamin Tam et al.   iScience

FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery

(2023) Chirag Parsania et al.   BRIEFINGS IN BIOINFORMATICS

Human BRCA pathogenic variants were originated during recent human history

(2022) Jiaheng Li et al.   Life Science Alliance

Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations

(2022) Siddharth Sinha et al.   Briefings in Functional Genomics

Genome interpretation using in silico predictors of variant impact

(2022) Panagiotis Katsonis et al.   HUMAN GENETICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN

(2021) Shawn Fayer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers

(2021) Kenneth A. Matreyek et al.   Genome Medicine

PTEN as a Guardian of the Genome: Pathways and Targets

(2020) Xinyi Fan et al.   Cold Spring Harbor Perspectives in Medicine

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

(2019) Juan J Galano-Frutos et al.   BRIEFINGS IN BIOINFORMATICS

A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships

(2018) Taylor L. Mighell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multiplex assessment of protein variant abundance by massively parallel sequencing

(2018) Kenneth A. Matreyek et al.   NATURE GENETICS

The functions and regulation of the PTEN tumour suppressor: new modes and prospects

(2018) Yu-Ru Lee et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Clinical implications of PTEN loss in prostate cancer

(2018) Tamara Jamaspishvili et al.   Nature Reviews Urology

Multiplexed assays of variant effects contribute to a growing genotype–phenotype atlas

(2018) Jochen Weile et al.   HUMAN GENETICS

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum 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

ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units

(2015) Johann Biedermann et al.   BIOPHYSICAL JOURNAL

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Design and application of implicit solvent models in biomolecular simulations

(2014) Jens Kleinjung et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

(2014) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

(2012) Fangzhou Yao et al.   BMC BIOINFORMATICS

Lifetime Cancer Risks in Individuals with Germline PTEN Mutations

(2012) M.-H. Tan et al.   CLINICAL CANCER RESEARCH

Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system

(2012) Sereina Riniker et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

A comprehensive functional analysis of PTEN mutations: implications in tumor- and autism-related syndromes

(2011) Isabel Rodríguez-Escudero et al.   HUMAN MOLECULAR GENETICS

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

(2011) Zheng Yang et al.   JOURNAL OF STRUCTURAL BIOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

A temperature predictor for parallel tempering simulations

(2008) Alexandra Patriksson et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS