When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants

KA Pagel, V Pejaver, GN Lin, HJ Nam, M Mort… - …, 2017 - academic.oup.com
Motivation Loss-of-function genetic variants are frequently associated with severe clinical
phenotypes, yet many are present in the genomes of healthy individuals. The available …

Protein classification using modified n-grams and skip-grams

SMA Islam, BJ Heil, CM Kearney, EJ Baker - Bioinformatics, 2018 - academic.oup.com
Motivation Classification by supervised machine learning greatly facilitates the annotation of
protein characteristics from their primary sequence. However, the feature generation step in …

In silico prediction of in vitro protein liquid–liquid phase separation experiments outcomes with multi-head neural attention

D Raimondi, G Orlando, E Michiels, D Pakravan… - …, 2021 - academic.oup.com
Motivation Proteins able to undergo liquid–liquid phase separation (LLPS) in vivo and in
vitro are drawing a lot of interest, due to their functional relevance for cell life. Nevertheless …

Ultra-fast global homology detection with discrete cosine transform and dynamic time war**

D Raimondi, G Orlando, Y Moreau, WF Vranken - Bioinformatics, 2018 - academic.oup.com
Motivation Evolutionary information is crucial for the annotation of proteins in bioinformatics.
The amount of retrieved homologs often correlates with the quality of predicted protein …

Kernel-based logistic regression model for protein sequence without vectorialization

Y Fong, S Datta, IS Georgiev, PD Kwong… - Biostatistics, 2015 - academic.oup.com
Protein sequence data arise more and more often in vaccine and infectious disease
research. These types of data are discrete, high-dimensional, and complex. We propose to …

Understanding protein function through statistical inference and evolutionary analysis

WT Clark - 2013 - search.proquest.com
The ability to characterize the functional behavior of an individual protein in a variety of
different contexts is one of the cornerstones of carrying out biological investigations. Its …

[書籍][B] Protein Function Prediction and Its Application to Prioritizing Disease-Associated Mutations

Y Jiang - 2020 - search.proquest.com
Protein is one of the fundamental elements in living organisms and understanding its
function is a key to understand life at a molecular level. With impressive advances in …

Machine Learning-assisted Prediction of Structure and Function of Cystine-stabilized Peptides and Optimization of Expression in an E. coli System

SMA Islam - 2018 - search.proquest.com
Cystine-stabilized peptides are promising prospects for the pharmaceutical industry as
biologics. These peptides carry out a variety of useful functions which could be exploited to …

Computational Assessment of the Molecular Mechanisms Impacted by Genetic Variation

KA Pagel - 2018 - search.proquest.com
The abundance of genetic variation brought about by high-throughput sequencing
technologies has led to increased necessity for computational methods to characterize the …