Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

GM Cooper, J Shendure - Nature Reviews Genetics, 2011 - nature.com
Genome and exome sequencing yield extensive catalogues of human genetic variation.
However, pinpointing the few phenotypically causal variants among the many variants …

Predicting the effects of amino acid substitutions on protein function

PC Ng, S Henikoff - Annu. Rev. Genomics Hum. Genet., 2006 - annualreviews.org
Nonsynonymous single nucleotide polymorphisms (nsSNPs) are coding variants that
introduce amino acid changes in their corresponding proteins. Because nsSNPs can affect …

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models

HA Shihab, J Gough, DN Cooper, PD Stenson… - Human …, 2013 - Wiley Online Library
The rate at which nonsynonymous single nucleotide polymorphisms (ns SNP s) are being
identified in the human genome is increasing dramatically owing to advances in whole …

[HTML][HTML] Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel

A González-Pérez, N López-Bigas - The American Journal of Human …, 2011 - cell.com
Several large ongoing initiatives that profit from next-generation sequencing technologies
have driven—and in coming years will continue to drive—the emergence of long catalogs of …

Functional annotations improve the predictive score of human disease‐related mutations in proteins

R Calabrese, E Capriotti, P Fariselli… - Human …, 2009 - Wiley Online Library
Single nucleotide polymorphisms (SNPs) are the simplest and most frequent form of human
DNA variation, also valuable as genetic markers of disease susceptibility. The most …

SNAP: predict effect of non-synonymous polymorphisms on function

Y Bromberg, B Rost - Nucleic acids research, 2007 - academic.oup.com
Many genetic variations are single nucleotide polymorphisms (SNPs). Non-synonymous
SNPs are 'neutral'if the resulting point-mutated protein is not functionally discernible from 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 …

Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 are identified in individuals with congenital hypogonadotropic hypogonadism

H Miraoui, AA Dwyer, GP Sykiotis, L Plummer… - The American Journal of …, 2013 - cell.com
Congenital hypogonadotropic hypogonadism (CHH) and its anosmia-associated form
(Kallmann syndrome [KS]) are genetically heterogeneous. Among the> 15 genes implicated …

Biophysics of protein evolution and evolutionary protein biophysics

T Sikosek, HS Chan - Journal of The Royal Society …, 2014 - royalsocietypublishing.org
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …

Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition

LB Ramsey, GH Bruun, W Yang, LR Treviño… - Genome …, 2012 - genome.cshlp.org
Methotrexate is used to treat autoimmune diseases and malignancies, including acute
lymphoblastic leukemia (ALL). Inter-individual variation in clearance of methotrexate results …