Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives

J Xu, P Yang, S Xue, B Sharma, M Sanchez-Martin… - Human genetics, 2019 - Springer
In the field of cancer genomics, the broad availability of genetic information offered by next-
generation sequencing technologies and rapid growth in biomedical publication has led to …

Statistical analysis of rare sequence variants: an overview of collapsing methods

C Dering, C Hemmelmann, E Pugh… - Genetic …, 2011 - Wiley Online Library
With the advent of novel sequencing technologies, interest in the identification of rare
variants that influence common traits has increased rapidly. Standard statistical methods …

Mutation effects predicted from sequence co-variation

TA Hopf, JB Ingraham, FJ Poelwijk, CPI Schärfe… - Nature …, 2017 - nature.com
Many high-throughput experimental technologies have been developed to assess the
effects of large numbers of mutations (variation) on phenotypes. However, designing …

A method and server for predicting damaging missense mutations

IA Adzhubei, S Schmidt, L Peshkin, VE Ramensky… - Nature …, 2010 - nature.com
2). For instance, in this setting with m= 10 and q= 10, IDA found 4, 4, 5, 1 and 2 true positives
for the five different networks, whereas Lasso found 1, 1, 0, 1 and 2 true positives and Elastic …

Dysfunction of lipid sensor GPR120 leads to obesity in both mouse and human

A Ichimura, A Hirasawa, O Poulain-Godefroy… - Nature, 2012 - nature.com
Free fatty acids provide an important energy source as nutrients, and act as signalling
molecules in various cellular processes,,,. Several G-protein-coupled receptors have been …

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

V López-Ferrando, A Gazzo, X De La Cruz… - Nucleic acids …, 2017 - academic.oup.com
We present here a full update of the PMut predictor, active since 2005 and with a large
acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine …

Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity

S Teng, A Sobitan, R Rhoades, D Liu… - Briefings in …, 2021 - academic.oup.com
The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-
2) is responsible for the binding to the permissive cells. The receptor-binding domain (RBD) …

Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension

ED Austin, L Ma, C LeDuc… - Circulation …, 2012 - Am Heart Assoc
Background—Heritable and idiopathic pulmonary arterial hypertension (PAH) are
phenotypically identical and associated with mutations in several genes related to …

Comparison of predicted and actual consequences of missense mutations

LA Miosge, MA Field, Y Sontani… - Proceedings of the …, 2015 - National Acad Sciences
Each person's genome sequence has thousands of missense variants. Practical
interpretation of their functional significance must rely on computational inferences in the …

The role of balanced training and testing data sets for binary classifiers in bioinformatics

Q Wei, RL Dunbrack Jr - PloS one, 2013 - journals.plos.org
Training and testing of conventional machine learning models on binary classification
problems depend on the proportions of the two outcomes in the relevant data sets. This may …