Molecular mechanisms of disease-causing missense mutations

S Stefl, H Nishi, M Petukh, AR Panchenko… - Journal of molecular …, 2013 - Elsevier
Genetic variations resulting in a change of amino acid sequence can have a dramatic effect
on stability, hydrogen bond network, conformational dynamics, activity and many other …

Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure

L Gerasimavicius, BJ Livesey, JA Marsh - Nature communications, 2022 - nature.com
Most known pathogenic mutations occur in protein-coding regions of DNA and change the
way proteins are made. Taking protein structure into account has therefore provided great …

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

F Cheng, J Zhao, Z Zhao - Briefings in bioinformatics, 2016 - academic.oup.com
Cancer is often driven by the accumulation of genetic alterations, including single nucleotide
variants, small insertions or deletions, gene fusions, copy-number variations, and large …

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

D Tamborero, A Gonzalez-Perez… - Bioinformatics, 2013 - academic.oup.com
Motivation: Gain-of-function mutations often cluster in specific protein regions, a signal that
those mutations provide an adaptive advantage to cancer cells and consequently are …

Comprehensive assessment of cancer missense mutation clustering in protein structures

A Kamburov, MS Lawrence, P Polak… - Proceedings of the …, 2015 - National Acad Sciences
Large-scale tumor sequencing projects enabled the identification of many new cancer gene
candidates through computational approaches. Here, we describe a general method to …

The 3D mutational constraint on amino acid sites in the human proteome

B Li, DM Roden, JA Capra - Nature communications, 2022 - nature.com
Quantification of the tolerance of protein sites to genetic variation has become a cornerstone
of variant interpretation. We hypothesize that the constraint on missense variation at …

[HTML][HTML] Spatial clustering of de novo missense mutations identifies candidate neurodevelopmental disorder-associated genes

SH Lelieveld, L Wiel, H Venselaar, R Pfundt… - The American Journal of …, 2017 - cell.com
Haploinsufficiency (HI) is the best characterized mechanism through which dominant
mutations exert their effect and cause disease. Non-haploinsufficiency (NHI) mechanisms …

Finding driver mutations in cancer: Elucidating the role of background mutational processes

AL Brown, M Li, A Goncearenco… - PLoS computational …, 2019 - journals.plos.org
Identifying driver mutations in cancer is notoriously difficult. To date, recurrence of a mutation
in patients remains one of the most reliable markers of mutation driver status. However …

[HTML][HTML] The emerging potential for network analysis to inform precision cancer medicine

K Ozturk, M Dow, DE Carlin, R Bejar… - Journal of molecular …, 2018 - Elsevier
Precision cancer medicine promises to tailor clinical decisions to patients using genomic
information. Indeed, successes of drugs targeting genetic alterations in tumors, such as …

Towards precision medicine: advances in computational approaches for the analysis of human variants

TA Peterson, E Doughty, MG Kann - Journal of molecular biology, 2013 - Elsevier
Variations and similarities in our individual genomes are part of our history, our heritage,
and our identity. Some human genomic variants are associated with common traits such as …