Posts by Tag Phylogenetics 12 Infectious disease modelling 7 Statistics 6 Coalescent theory 6 Molecular evolution 5 Web development 4 Bioinformatics 4 Programming 3 Virus evolution 2 LLM tools 2 Academic writing 1 Productivity 1 Phylogenetics May 22: Course notes: Molecular Evolution workshop in Marine Biological Laboratory, US January 12: Paper digest: More structured coalescent papers: on Erik M. Volz’s work January 10: Paper digest: Genomic Inference of Transmission History (Non structured coalescent methods) January 04: Paper digest: More structured coalescent papers: on Nicola F. Muller and Nicola De Maio January 03: Paper digest: Efficient Bayesian inference under the structured coalescent (Timothy G. Vaughan et al., 2014) December 28: Course notes: coalescent theory and structured coalescent basics December 26: Book notes: Analysis of Phylogenetics and Evolution with R December 18: Book notes: Bayesian Evolutionary Analysis with BEAST (theory) December 16: Course notes: Bayesian phylogenetics basics March 09: Book notes: Coalescent theory: An introduction February 25: Paper digest: Global spread and invasion dynamics of SARS-CoV-2 September 20: Paper digest: UShER - placing new genomes onto a existing phylogenetic tree (Nat Genet, 2021) Back to Top ↑ Infectious disease modelling March 01: Paper digest: Modelling pathogens with many strains August 11: Paper digest: Informing policy via dynamic models: cholera in Haiti (Jesse Wheeler) July 04: Paper digest: Simulation-based Inference for Partially Observed Markov Process Models with Spatial Coupling (Kidus Asfaw) May 25: Course notes: Simulation-based Inference for Epidemiological Dynamics (Aaron A. King) May 12: Course notes: Computational Statistics and Machine Learning (Fall 2020 by Nicholas Zabaras via YouTube) April 30: Book notes: Epidemics, Models and Data using R (Ottar N. Bjørnstad, 2018) April 11: Course notes: Infectious Disease Modelling (Imperial College London via Coursera) Back to Top ↑ Statistics January 18: Book notes: Molecular Evolution: A Statistical Approach by Ziheng Yang October 22: Course notes: Essence of linear algebra (3b1b) May 12: Course notes: Computational Statistics and Machine Learning (Fall 2020 by Nicholas Zabaras via YouTube) December 17: Course notes: Machine Learning (Lee Hung-yi, 2016) October 17: Paper digest: Antibody cross-reactome against flu surface glycoproteins (Nat Immunol, 2017) September 21: Book notes: Introduction to Probability (Dimitri P. Bertsekas and John N. Tsitsiklis, 2008) Back to Top ↑ Coalescent theory January 15: Paper digest: Coalescent with reassortment January 12: Paper digest: More structured coalescent papers: on Erik M. Volz’s work January 04: Paper digest: More structured coalescent papers: on Nicola F. Muller and Nicola De Maio January 03: Paper digest: Efficient Bayesian inference under the structured coalescent (Timothy G. Vaughan et al., 2014) December 28: Course notes: coalescent theory and structured coalescent basics March 09: Book notes: Coalescent theory: An introduction Back to Top ↑ Molecular evolution May 22: Course notes: Molecular Evolution workshop in Marine Biological Laboratory, US March 06: Paper digest: Selection on synonymous sites: the unwanted transcript hypothesis (Nat Rev Genet, 2024) January 18: Book notes: Molecular Evolution: A Statistical Approach by Ziheng Yang April 15: Workshop Notes: Models and Inference in Population Genetics IV: Fragmentation-coalescence and related models September 10: epitope_diversity: Estimating the mutation diversity within a genomic region (e.g. epitope) Back to Top ↑ Web development September 02: View count is available September 01: Comments are now functional in blog posts August 31: How to embed PDF in html August 30: First blog: A new start Back to Top ↑ Bioinformatics June 12: Rosalind notes: Bioinformatics stronghold October 30: Paper digest: Adaptation and Selection in SARS-CoV-2 evolution (Preprint, 2022) October 17: Paper digest: Antibody cross-reactome against flu surface glycoproteins (Nat Immunol, 2017) September 20: Paper digest: UShER - placing new genomes onto a existing phylogenetic tree (Nat Genet, 2021) Back to Top ↑ Programming November 14: Deploying web-based code editor and Github Copilot on my local machine September 10: epitope_diversity: Estimating the mutation diversity within a genomic region (e.g. epitope) September 09: Cross-compiling Rust programs (for Linux and Windows) on Mac OS Back to Top ↑ Virus evolution October 18: Paper digest: Detecting and quantifying sgRNA using periscope (Parker et al.) October 30: Paper digest: Adaptation and Selection in SARS-CoV-2 evolution (Preprint, 2022) Back to Top ↑ LLM tools November 14: Deploying web-based code editor and Github Copilot on my local machine November 09: Deploying a large language model (LLM) on my local machine Back to Top ↑ Academic writing February 01: Book notes: The Scientist’s Guide to Writing Back to Top ↑ Productivity January 07: Time Zone Converter for Meeting Scheduling Back to Top ↑ Total words: 4520
January 10: Paper digest: Genomic Inference of Transmission History (Non structured coalescent methods)
January 03: Paper digest: Efficient Bayesian inference under the structured coalescent (Timothy G. Vaughan et al., 2014)
September 20: Paper digest: UShER - placing new genomes onto a existing phylogenetic tree (Nat Genet, 2021)
July 04: Paper digest: Simulation-based Inference for Partially Observed Markov Process Models with Spatial Coupling (Kidus Asfaw)
May 12: Course notes: Computational Statistics and Machine Learning (Fall 2020 by Nicholas Zabaras via YouTube)
May 12: Course notes: Computational Statistics and Machine Learning (Fall 2020 by Nicholas Zabaras via YouTube)
October 17: Paper digest: Antibody cross-reactome against flu surface glycoproteins (Nat Immunol, 2017)
September 21: Book notes: Introduction to Probability (Dimitri P. Bertsekas and John N. Tsitsiklis, 2008)
January 03: Paper digest: Efficient Bayesian inference under the structured coalescent (Timothy G. Vaughan et al., 2014)
March 06: Paper digest: Selection on synonymous sites: the unwanted transcript hypothesis (Nat Rev Genet, 2024)
April 15: Workshop Notes: Models and Inference in Population Genetics IV: Fragmentation-coalescence and related models
September 10: epitope_diversity: Estimating the mutation diversity within a genomic region (e.g. epitope)
October 17: Paper digest: Antibody cross-reactome against flu surface glycoproteins (Nat Immunol, 2017)
September 20: Paper digest: UShER - placing new genomes onto a existing phylogenetic tree (Nat Genet, 2021)
September 10: epitope_diversity: Estimating the mutation diversity within a genomic region (e.g. epitope)
