All Tags

• antibiotic resistance1
• antigenic evolution2
• bacteria1
• bioinformatics39
• biophysics42
• branching process5
• chromatin2
• coalescent2
• command line2
• CTL escape1
• cytoskeleton1
• diffusion4
• diffusion theory2
• drug resistance evolution1
• dynamical system2
• ebola1
• enterovirus1
• experimental evolution1
• first-step equation2
• fitness landscape1
• fitness landscapes1
• general time reversible models1
• HIV2
• HIV evolution5
• horizontal transfer1
• image analysis8
• influenza5
• influenza evolution4
• information theory1
• intra-patient evolution1
• Kimura diffusion1
• kinetic proofreading2
• Kingman1
• latent reservoir3
• liquid-liquid phase separation2
• long-read sequencing1
• method of characteristics1
• molecular motors1
• mutation and recombination1
• nanopore1
• nematodes1
• pangenome1
• pangenomes1
• percolation1
• phase transitions in membranes1
• phylogenetics37
• polymers2
• population genetics5
• prediction3
• proportional betting1
• rapid adaptation1
• reaction rates2
• real-time tracking1
• review1
• RNA structure1
• sars-cov-22
• scales4
• site frequency spectra1
• snakemake1
• software1
• solution8
• synonymous mutations1
• target search3
• theory4
• timetree inference1
• zika1

antibiotic resistance

• Mon 17 October 2016Colistin resistance evolution

antigenic evolution

• Tue 10 January 2017Molecular epidemiology
• Fri 11 March 2016Prediction of antigenic phenotypes of influenza viruses

bacteria

• Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities -- pan-genomes

bioinformatics

• Mon 15 January 2024Nextstrain workshop at the Wengen Winter School
• Thu 14 September 2023SARS-COV-2 workshop
• Thu 14 September 2023Nextstrain workshop at Bad Honnef
• Fri 25 March 2022Nextstrain workshop at QLife
• Fri 25 March 2022Installation and data curation
• Fri 25 March 2022Augur and Snakemake
• Fri 25 March 2022SARS-COV-2 workshop
• Fri 25 March 2022SARS-COV-2 workshop solution
• Tue 27 July 2021Nextstrain webinar at Africa CDC
• Wed 23 September 2020Introduction to Phylogenetic Analysis
• Wed 23 September 2020SARS-CoV-2 phylogenetic analysis
• Wed 23 September 2020SARS-CoV-2 phylogenetic analysis
• Tue 08 October 2019Advanced Snakemake
• Tue 08 October 2019Augur and Snakemake
• Tue 08 October 2019Augur and Snakemake for VCF input
• Tue 08 October 2019Colormaps and geographical coordinates
• Tue 08 October 2019Community pages
• Tue 08 October 2019Parsing meta data from fasta files
• Tue 08 October 2019Nextstrain workshop at RIVM
• Tue 08 October 2019Optional parameters of the refine command
• Mon 09 September 2019Augur and Snakemake
• Mon 09 September 2019Augur and Snakemake for VCF input
• Mon 09 September 2019Nextstrain workshop at [BC]2
• Mon 09 September 2019The nextstrain toolchain
• Mon 09 September 2019Installation and data curation
• Mon 09 September 2019Important tips for your own analysis
• Mon 26 August 2019Running nextstrain on GISAID downloads
• Mon 26 August 2019Nextstrain/WHO workshop in Singapore
• Thu 24 January 2019Augur and Snakemake
• Thu 24 January 2019Augur and Snakemake
• Thu 24 January 2019Exploring interactive phylogenies with Auspice
• Thu 24 January 2019Running augur on bacterial data
• Thu 24 January 2019Introduction to Phylogenetic Analysis
• Thu 24 January 2019Nextstrain workshop at KRISP, Durban, South Africa
• Sun 04 March 2018A glimpse into sequence bioinformatics
• Mon 22 January 2018Pipelines with snakemake
• Wed 27 December 2017Why are spaced seeds more sensitive?
• Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities
• Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities

biophysics

• Fri 01 November 2024Physics of Life
• Wed 01 November 2023Physics of Life
• Tue 20 September 2022Physics of Life
• Fri 24 September 2021Physics of Life
• Thu 17 September 2020Physics of Life
• Mon 16 September 2019Physics of Life I -- 44702-01
• Thu 13 December 2018Chromatin organization and structure
• Thu 06 December 2018Liquid-liquid phase transitions within cells
• Thu 29 November 2018Kinetic proofreading and percolation
• Thu 22 November 2018Reaction rates and the method of dominant balance
• Wed 07 November 2018Physics of Life
• Thu 25 October 2018Bacterial gene regulation and signaling
• Thu 18 October 2018Finding binding sites and diffusion limited rates
• Thu 11 October 2018Polymers in biology
• Thu 04 October 2018Brownian motion and Diffusion
• Thu 27 September 2018Solutions: The relevant scales of cellular biophysics
• Thu 27 September 2018Brownian motion, diffusion, and Fick's law
• Thu 20 September 2018The relevant scales of cellular biophysics
• Tue 12 December 2017Kinetic proofreading
• Tue 05 December 2017Chromatin organization and structure
• Tue 28 November 2017Phase transitions in membranes
• Tue 21 November 2017Cytoskeleton -- Solutions to problems
• Tue 21 November 2017Liquid-liquid phase transitions within cells
• Tue 14 November 2017Cytoskeleton -- Solutions to problems
• Tue 14 November 2017Reaction rates and the method of dominant balance
• Tue 07 November 2017Molecular motors
• Mon 06 November 2017Cytoskeleton -- Solutions to problems
• Tue 31 October 2017Cytoskeleton -- Solutions to problems
• Tue 31 October 2017Biophysical properties of the cytoskeleton
• Tue 24 October 2017Diffusion -- Solutions to problems
• Tue 24 October 2017Finding binding sites and diffusion limited rates
• Thu 19 October 2017Polymers in biology
• Tue 17 October 2017Diffusion -- Solutions to problems
• Tue 03 October 2017Diffusion -- Solutions to problems
• Tue 03 October 2017Brownian motion and Diffusion
• Tue 26 September 2017Brownian motion and Diffusion -- Solutions to problems
• Tue 26 September 2017Brownian motion and Diffusion
• Tue 19 September 2017Solutions: The relevant scales of cellular biophysics
• Tue 19 September 2017The relevant scales of cellular biophysics
• Tue 19 September 2017Theoretical Biophysics & mathematical methods
• Tue 19 September 2017Theoretical Biophysics & mathematical methods
• Mon 29 May 2017How hot are Mitochondria?

branching process

• Tue 10 April 2018Advanced Methods in Computational Sciences
• Fri 22 December 2017Mutating branching processes in deteriorating environments
• Fri 22 December 2017Branching processes with time dependent birth and death rates
• Sun 05 November 2017Generating function of critical branching processes
• Tue 04 April 2017Advanced Methods in Computational Sciences

chromatin

• Thu 13 December 2018Chromatin organization and structure
• Tue 05 December 2017Chromatin organization and structure

coalescent

• Tue 10 April 2018Advanced Methods in Computational Sciences
• Tue 04 April 2017Advanced Methods in Computational Sciences

command line

• Sun 04 March 2018A glimpse into sequence bioinformatics
• Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities

CTL escape

• Wed 07 August 2013Inferring HIV escape rates

cytoskeleton

• Tue 31 October 2017Biophysical properties of the cytoskeleton

diffusion

• Thu 04 October 2018Brownian motion and Diffusion
• Thu 27 September 2018Brownian motion, diffusion, and Fick's law
• Tue 03 October 2017Brownian motion and Diffusion
• Tue 26 September 2017Brownian motion and Diffusion

diffusion theory

• Tue 10 April 2018Advanced Methods in Computational Sciences
• Tue 04 April 2017Advanced Methods in Computational Sciences

drug resistance evolution

• Tue 10 January 2017Evolution of bacteria

dynamical system

• Thu 15 November 2018Bistablility, oscillations, and linear stability analysis
• Thu 01 November 2018Bifurcations, bistability and oscillations

ebola

• Tue 28 February 2017nextstrain wins the OpenSciencePrize!

enterovirus

• Tue 10 January 2017Molecular epidemiology

experimental evolution

• Mon 17 October 2016Colistin resistance evolution

first-step equation

• Fri 22 December 2017Mutating branching processes in deteriorating environments
• Sun 05 November 2017Generating function of critical branching processes

fitness landscape

• Sat 26 March 2016Mutation rates and fitness costs of HIV-1

fitness landscapes

• Tue 10 January 2017HIV evolution

general time reversible models

• Tue 28 November 2017GTR models

HIV

• Thu 01 December 2016Establishment and dynamics of the latent HIV-1 reservoir
• Wed 18 May 2016Does HIV evolve during therapy?

HIV evolution

• Sat 26 March 2016Mutation rates and fitness costs of HIV-1
• Mon 14 December 2015Many aspects of intrapatient HIV-1 evolution are predictable
• Mon 14 September 2015Recombination in HIV-1 and the "book" of genealogical trees
• Mon 09 September 2013Deleterious effects of synonymous mutations in HIV
• Wed 07 August 2013Inferring HIV escape rates

horizontal transfer

• Tue 10 January 2017Evolution of bacteria

image analysis

• Thu 19 October 2017PoissonNMF - Example
• Thu 19 October 2017PoissonNTF - Triple stain imaged with Leica SP2
• Thu 19 October 2017ImageJ plug-ins to optimize imaging parameters for fluorescence microscopy
• Thu 19 October 2017PoissonNMF - Documentation
• Thu 19 October 2017PoissonNMF - blind source separation of fluorescence microscopy data
• Thu 19 October 2017PoissonNTF - documentation
• Thu 19 October 2017PoissonNTF - fluorescence microscopy data combining multiple excitations
• Tue 04 April 2017PoissonNMF and multispectral imaging

influenza

• Tue 28 February 2017nextstrain wins the OpenSciencePrize!
• Tue 10 January 2017Molecular epidemiology
• Fri 11 March 2016Prediction of antigenic phenotypes of influenza viruses
• Tue 06 October 2015HI.nextflu.org visualizes antigenic evolution of influenza viruses
• Tue 11 November 2014Now out in eLife: Predicting evolution

influenza evolution

• Thu 31 October 2019How accurate are branch length estimates in RNA virus phylogenies?
• Tue 20 March 2018How rapidly does influenza spread?
• Wed 03 January 2018Does a small transmission bottleneck slow down antigenic evolution?
• Thu 05 June 2014Is evolution predictable?

information theory

• Thu 20 December 2018Information theory and proportional betting

intra-patient evolution

• Tue 10 January 2017HIV evolution

Kimura diffusion

• Fri 22 December 2017Neutral site frequency spectra

kinetic proofreading

• Thu 29 November 2018Kinetic proofreading and percolation
• Tue 12 December 2017Kinetic proofreading

Kingman

• Fri 22 December 2017Neutral site frequency spectra

latent reservoir

• Tue 10 January 2017HIV evolution
• Thu 01 December 2016Establishment and dynamics of the latent HIV-1 reservoir
• Wed 18 May 2016Does HIV evolve during therapy?

liquid-liquid phase separation

• Thu 06 December 2018Liquid-liquid phase transitions within cells
• Tue 21 November 2017Liquid-liquid phase transitions within cells

long-read sequencing

• Tue 10 January 2017Evolution of bacteria

method of characteristics

• Sun 05 November 2017Generating function of critical branching processes

molecular motors

• Tue 07 November 2017Molecular motors

mutation and recombination

• Tue 10 January 2017HIV evolution

nanopore

• Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities

nematodes

• Thu 23 January 2014Abundant non-neutral variation in the nematode P. pacificus

pangenome

• Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities -- pan-genomes

pangenomes

• Tue 10 January 2017Evolution of bacteria

percolation

• Thu 29 November 2018Kinetic proofreading and percolation

phase transitions in membranes

• Tue 28 November 2017Phase transitions in membranes

phylogenetics

• Mon 15 January 2024Nextstrain workshop at the Wengen Winter School
• Thu 14 September 2023SARS-COV-2 workshop
• Thu 14 September 2023Nextstrain workshop at Bad Honnef
• Fri 25 March 2022Nextstrain workshop at QLife
• Fri 25 March 2022Installation and data curation
• Fri 25 March 2022Augur and Snakemake
• Fri 25 March 2022SARS-COV-2 workshop
• Fri 25 March 2022SARS-COV-2 workshop solution
• Tue 27 July 2021Nextstrain webinar at Africa CDC
• Wed 23 September 2020Introduction to Phylogenetic Analysis
• Wed 23 September 2020SARS-CoV-2 phylogenetic analysis
• Wed 23 September 2020SARS-CoV-2 phylogenetic analysis
• Tue 08 October 2019Advanced Snakemake
• Tue 08 October 2019Augur and Snakemake
• Tue 08 October 2019Augur and Snakemake for VCF input
• Tue 08 October 2019Colormaps and geographical coordinates
• Tue 08 October 2019Community pages
• Tue 08 October 2019Parsing meta data from fasta files
• Tue 08 October 2019Nextstrain workshop at RIVM
• Tue 08 October 2019Optional parameters of the refine command
• Mon 09 September 2019Augur and Snakemake
• Mon 09 September 2019Augur and Snakemake for VCF input
• Mon 09 September 2019Nextstrain workshop at [BC]2
• Mon 09 September 2019The nextstrain toolchain
• Mon 09 September 2019Installation and data curation
• Mon 09 September 2019Important tips for your own analysis
• Mon 26 August 2019Running nextstrain on GISAID downloads
• Mon 26 August 2019Nextstrain/WHO workshop in Singapore
• Thu 24 January 2019Augur and Snakemake
• Thu 24 January 2019Augur and Snakemake
• Thu 24 January 2019Exploring interactive phylogenies with Auspice
• Thu 24 January 2019Running augur on bacterial data
• Thu 24 January 2019Introduction to Phylogenetic Analysis
• Thu 24 January 2019Nextstrain workshop at KRISP, Durban, South Africa
• Tue 28 November 2017GTR models
• Mon 27 November 2017The marginal distribution of the length of a branch
• Tue 10 January 2017Theory

polymers

• Thu 11 October 2018Polymers in biology
• Thu 19 October 2017Polymers in biology

population genetics

• Sun 30 December 2018Debating soft vs hard sweeps in RNA viruses is a waste of time
• Tue 10 January 2017Theory
• Mon 14 September 2015Recombination in HIV-1 and the "book" of genealogical trees
• Thu 23 January 2014Abundant non-neutral variation in the nematode P. pacificus
• Tue 05 November 2013Population genetics of rapid adaptation

prediction

• Tue 10 January 2017Molecular epidemiology
• Tue 06 October 2015HI.nextflu.org visualizes antigenic evolution of influenza viruses
• Tue 11 November 2014Now out in eLife: Predicting evolution

proportional betting

• Thu 20 December 2018Information theory and proportional betting

rapid adaptation

• Tue 10 January 2017Theory

reaction rates

• Thu 22 November 2018Reaction rates and the method of dominant balance
• Tue 14 November 2017Reaction rates and the method of dominant balance

real-time tracking

• Tue 10 January 2017Molecular epidemiology

review

• Tue 05 November 2013Population genetics of rapid adaptation

RNA structure

• Mon 09 September 2013Deleterious effects of synonymous mutations in HIV

sars-cov-2

• Sun 18 June 2023Waves driven by immune evasive variants: How large and how often?
• Tue 10 January 2017Molecular epidemiology

scales

• Thu 27 September 2018Solutions: The relevant scales of cellular biophysics
• Thu 20 September 2018The relevant scales of cellular biophysics
• Tue 19 September 2017Solutions: The relevant scales of cellular biophysics
• Tue 19 September 2017The relevant scales of cellular biophysics

site frequency spectra

• Fri 22 December 2017Neutral site frequency spectra

snakemake

• Mon 22 January 2018Pipelines with snakemake

software

• Thu 19 April 2018Mugration models and homoplasy analysis in TreeTime

solution

• Tue 21 November 2017Cytoskeleton -- Solutions to problems
• Tue 14 November 2017Cytoskeleton -- Solutions to problems
• Mon 06 November 2017Cytoskeleton -- Solutions to problems
• Tue 31 October 2017Cytoskeleton -- Solutions to problems
• Tue 24 October 2017Diffusion -- Solutions to problems
• Tue 17 October 2017Diffusion -- Solutions to problems
• Tue 03 October 2017Diffusion -- Solutions to problems
• Tue 26 September 2017Brownian motion and Diffusion -- Solutions to problems

synonymous mutations

• Mon 09 September 2013Deleterious effects of synonymous mutations in HIV

target search

• Thu 25 October 2018Bacterial gene regulation and signaling
• Thu 18 October 2018Finding binding sites and diffusion limited rates
• Tue 24 October 2017Finding binding sites and diffusion limited rates

theory

• Tue 11 November 2014Now out in eLife: Predicting evolution
• Thu 05 June 2014Is evolution predictable?
• Tue 05 November 2013Population genetics of rapid adaptation
• Thu 01 August 2013Coalescence in sexual populations under selection

timetree inference

• Tue 10 January 2017Theory

zika

• Tue 28 February 2017nextstrain wins the OpenSciencePrize!