ahmedaq
I am a computational biologist with a background in electrical engineering and statistical signal processing.
The Hong Kong University of Science and TechnologyHong Kong
Pinned Repositories
ACE
Fast and flexible code for solving the inverse Ising/Potts inference problem
BrewerMap
[MATLAB] The complete palette of ColorBrewer colormaps. Simple selection by scheme name and map length.
HCV-E2
Software for in silico identification of immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them
Making-elegant-Matlab-figures
A repository comprising multiple functions for making elegant publication-quality figures in MATLAB
MPF-BML
Fast and efficient code to solve the inverse Ising/Potts (aka maximum entropy) problem
MPF-BML-GUI
Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters
Orthogonal-Clustering
A Bayesian method which utilises the rich structure embedded in the sensing matrix for fast sparse signal recovery
PV-vp1
Software for inferring the intrinsic fitness landscape of poliovirus capsid protein (vp1) and comparing it with that of analogous proteins in HIV
RoCA
Software for identifying co-evolutionary sectors in proteins using RoCA
RocaSec
RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins
ahmedaq's Repositories
ahmedaq/Making-elegant-Matlab-figures
A repository comprising multiple functions for making elegant publication-quality figures in MATLAB
ahmedaq/Orthogonal-Clustering
A Bayesian method which utilises the rich structure embedded in the sensing matrix for fast sparse signal recovery
ahmedaq/MPF-BML-GUI
Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters
ahmedaq/RocaSec
RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins
ahmedaq/RoCA
Software for identifying co-evolutionary sectors in proteins using RoCA
ahmedaq/ACE
Fast and flexible code for solving the inverse Ising/Potts inference problem
ahmedaq/BrewerMap
[MATLAB] The complete palette of ColorBrewer colormaps. Simple selection by scheme name and map length.
ahmedaq/HCV-E2
Software for in silico identification of immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them
ahmedaq/MPF-BML
Fast and efficient code to solve the inverse Ising/Potts (aka maximum entropy) problem
ahmedaq/PV-vp1
Software for inferring the intrinsic fitness landscape of poliovirus capsid protein (vp1) and comparing it with that of analogous proteins in HIV
ahmedaq/2019-nCoV-T-Cell-Vaccine-Candidates
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.
ahmedaq/COVIDep
COVIDep: Real-time reporting of vaccine target recommendations for the COVID-19 coronavirus (SARS-CoV-2)
ahmedaq/HCV_E2_1a_1b_evolution
Evolutionary constraints vary across HCV subtypes
ahmedaq/HCV_NS3_Drug_Resistance
Epistasis promotes resistance against HCV NS3 drugs
ahmedaq/HCVE1E2
ahmedaq/HIV-Gag-Immunogens
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.
ahmedaq/Robust-DENV-Vaccine-Candidates
RStudio project for reproducing the results and figures in the paper: "Robust candidates for a universal T cell vaccine against Dengue virus" [submitted]
ahmedaq/SARS2TcellEpitopes
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