Name: Ahmed Abdul Quadeer
Type: User
Company: The Hong Kong University of Science and Technology
Bio: I am a computational biologist with a background in electrical engineering and statistical signal processing.
Location: Hong Kong
Blog: http://www.mckayspcb.com/ahmed-abdul-quadeer.html
Ahmed Abdul Quadeer's Projects
R source code and associated data files for reproducing the results of a preliminary study on indentifying potential B cell and T cell targets for a vaccine against 2019-nCoV based on known immunological determinants of SARS-CoV.
Fast and flexible code for solving the inverse Ising/Potts inference problem
[MATLAB] The complete palette of ColorBrewer colormaps. Simple selection by scheme name and map length.
COVIDep: Real-time reporting of vaccine target recommendations for the COVID-19 coronavirus (SARS-CoV-2)
Software for in silico identification of immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them
Evolutionary constraints vary across HCV subtypes
Epistasis promotes resistance against HCV NS3 drugs
This repository includes source code scripts for all the analysis and figures reported in Ahmed et al.’s “Sub-dominant principal components inform new vaccine targets for HIV Gag”. The source code for the analysis is contained in the “Analysis” folder, while the scripts for generating the figures are in the “Figures” folder.
A repository comprising multiple functions for making elegant publication-quality figures in MATLAB
Fast and efficient code to solve the inverse Ising/Potts (aka maximum entropy) problem
Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters
A Bayesian method which utilises the rich structure embedded in the sensing matrix for fast sparse signal recovery
Software for inferring the intrinsic fitness landscape of poliovirus capsid protein (vp1) and comparing it with that of analogous proteins in HIV
RStudio project for reproducing the results and figures in the paper: "Robust candidates for a universal T cell vaccine against Dengue virus" [submitted]
Software for identifying co-evolutionary sectors in proteins using RoCA
RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins
Summary of emerging data about experimentally-identified SARS-CoV-2 T cell epitopes compiled from 1,259 convalescent COVID-19 patients across 8 independent studies