Posts Tagged ‘gpmtg’

Protein folds recognized by an intelligent predictor based-on evolutionary and structural information – Cheung – 2015 – Journal of Computational Chemistry – Wiley Online Library

Sunday, April 17th, 2016

Fold [class] recognized by an…[NN] predictor based-on evolutionary & structural info., w/ particle-swarm training

Ngaam J. Cheung,
Xue-Ming Ding,
Hong-Bin Shen

First published: 27 October 2015
DOI: 10.1002/jcc.24232

PLOS Genetics: A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

Saturday, February 27th, 2016

Model-Based Approach to Inferring…#Cancer Mutation Signatures Assuming independence betw 3 NTs, 11 v 95 parameters

The first contribution of this paper is to suggest a more parsimonious approach to modelling mutation signatures, with the benefit of producing both more stable estimates and more easily interpretable signatures. In brief, we substantially reduce the number of parameters per signature by breaking each mutation pattern into “features”, and assuming independence across mutation features. For example, consider the case where a mutation pattern is defined by the substitution and its two flanking bases. We break this into three features
(substitution, 3′ base, 5′ base), and characterize each mutation signature by a probability distribution for each feature (which, by our independence assumption, are multiplied together to define a distribution on mutation patterns). Since the number of possible values for each feature is 6, 4, and 4 respectively this requires 5 + 3 + 3 = 11 parameters instead of 96 − 1 = 95 parameters. Furthermore, extending this model to account for ±n neighboring bases requires only 5 + 6nparameters instead of 6 × 42n − 1. For example, considering ±2 positions requires 17 parameters instead of 1,535. Finally,
incorporating transcription strand as an additional feature adds just one parameter, instead of doubling the number of parameters. “}}

Identification of neutral tumor evolution across cancer types : Nature Genetics : Nature Publishing Group

Saturday, February 27th, 2016

Neutral tumor #evolution across #cancer types Initial burst of driver events followed by random mutations

Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes: Origins of Affinity and Selectivity: Biophysical Journal

Sunday, November 15th, 2015

#Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes Non-human selectivity studied w. coarse-grained MD

A Multiscale Coarse-Graining Method for Biomolecular Systems – The Journal of Physical Chemistry B (ACS Publications)

Sunday, November 15th, 2015

A Multiscale Coarse-Graining Method for Biomolecul[es] Simplified force field from fitting to all-atom #simulations

Sergei Izvekov and Gregory A. Voth *
J. Phys. Chem. B, 2005, 109 (7), pp 2469–2473
DOI: 10.1021/jp044629q

Syntrophic exchange in synthetic microbial communities

Saturday, March 28th, 2015

Syntrophic exchange in synthetic #microbial communities [& their evolution] Trading metabolically costly amino acids

Genome Biology | Full text | Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation

Friday, February 13th, 2015

WGBS…reveals complementary roles of promoter & gene-body
#methylation in…regulation Has model for gene expression

Realizing the promise of cancer predisposition genes : Nature : Nature Publishing Group

Friday, September 19th, 2014

Mirsynergy: detecting synergistic miRNA regul… Bioinformatics. 2014 – PubMed – NCBI

Saturday, July 19th, 2014

Mirsynergy: detecting synergistic #miRNA regulatory modules by… neighborhood expansion creates overlapping clusters