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imprint1
  • Wed 25 January 2017Imprint
job_old5
  • Fri 21 April 2023Post-doctoral position in phylogenetics and microbial evolution
  • Tue 27 April 2021Computational Biologist/Bioinformatician (50-100%)
  • Wed 06 November 2019Scientific Software Developer/Programmer (50-100%)
  • Tue 22 October 2019Post-Doc position
  • Fri 20 January 2017Post-Doc position in pathogen genomics
nonlab_publication16
  • Fri 09 February 2018Global morphogenetic flow is accurately predicted by the spatial distribution of myosin motors
  • Mon 01 January 2018How pairwise coevolutionary models capture the collective residue variability in proteins
  • Mon 18 December 2017Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana
  • Thu 09 February 2017On the post-glacial spread of human commensal Arabidopsis thaliana
  • Wed 25 January 2017Active tension network model suggests an exotic mechanical state realized in epithelial tissues
  • Wed 25 January 2017Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
  • Wed 25 January 2017Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.
  • Sun 01 January 2017De la variabilit\'e des s\'equences à la pr\'ediction structurale et fonctionnelle : mod\'elisation de familles de prot\'eines homologues
  • Thu 14 July 20161,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana
  • Mon 25 January 2016A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.
  • Mon 25 January 2016Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters.
  • Mon 25 January 2016Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.
  • Fri 01 January 2016Improving landscape inference by integrating heterogeneous data in the inverse Ising problem
  • Fri 01 January 2016Methods for adaptive optimization of enhanced oil recovery performance under uncertainty
  • Sat 25 January 2014The contribution of viral genotype to plasma viral set-point in HIV infection.
  • Fri 25 January 2013Automated analysis of phylogenetic clusters.
notes8
  • Mon 22 January 2018Pipelines with snakemake
  • Wed 27 December 2017Why are spaced seeds more sensitive?
  • Fri 22 December 2017Mutating branching processes in deteriorating environments
  • Fri 22 December 2017Branching processes with time dependent birth and death rates
  • Fri 22 December 2017Neutral site frequency spectra
  • Tue 28 November 2017GTR models
  • Mon 27 November 2017The marginal distribution of the length of a branch
  • Sun 05 November 2017Generating function of critical branching processes
post23
  • Sun 18 June 2023Waves driven by immune evasive variants: How large and how often?
  • Thu 31 October 2019How accurate are branch length estimates in RNA virus phylogenies?
  • Sun 30 December 2018Debating soft vs hard sweeps in RNA viruses is a waste of time
  • Thu 19 April 2018Mugration models and homoplasy analysis in TreeTime
  • Tue 20 March 2018How rapidly does influenza spread?
  • Wed 03 January 2018Does a small transmission bottleneck slow down antigenic evolution?
  • Mon 29 May 2017How hot are Mitochondria?
  • Tue 28 February 2017nextstrain wins the OpenSciencePrize!
  • Thu 01 December 2016Establishment and dynamics of the latent HIV-1 reservoir
  • Mon 17 October 2016Colistin resistance evolution
  • Wed 18 May 2016Does HIV evolve during therapy?
  • Sat 26 March 2016Mutation rates and fitness costs of HIV-1
  • Fri 11 March 2016Prediction of antigenic phenotypes of influenza viruses
  • Mon 14 December 2015Many aspects of intrapatient HIV-1 evolution are predictable
  • Tue 06 October 2015HI.nextflu.org visualizes antigenic evolution of influenza viruses
  • Mon 14 September 2015Recombination in HIV-1 and the "book" of genealogical trees
  • Tue 11 November 2014Now out in eLife: Predicting evolution
  • Thu 05 June 2014Is evolution predictable?
  • Thu 23 January 2014Abundant non-neutral variation in the nematode P. pacificus
  • Tue 05 November 2013Population genetics of rapid adaptation
  • Mon 09 September 2013Deleterious effects of synonymous mutations in HIV
  • Wed 07 August 2013Inferring HIV escape rates
  • Thu 01 August 2013Coalescence in sexual populations under selection
publication113
  • Sat 11 January 2025The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure
  • Sat 11 January 2025Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment
  • Fri 03 January 2025Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes
  • Mon 25 November 2024The consequences of SARS-CoV-2 within-host persistence
  • Fri 18 October 2024Eco-evolutionary dynamics of adapting pathogens and host immunity
  • Thu 11 July 2024Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus Below the Subgroup Level
  • Fri 05 July 2024Lost in the woods: shifting habitats can lead phylogeography astray
  • Mon 18 March 2024How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort
  • Thu 04 January 2024Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions
  • Thu 28 December 2023SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations
  • Wed 20 December 2023Visualizing and quantifying structural diversity around mobile resistance genes
  • Fri 01 December 2023Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant
  • Thu 02 November 2023APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016
  • Sun 15 October 2023SARS-CoV-2 evolution in the Omicron era
  • Mon 11 September 2023Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal
  • Sat 19 August 2023Fitness effects of mutations to SARS-CoV-2 proteins
  • Mon 05 June 2023LAPIS is a fast web API for massive open virus sequencing data
  • Tue 25 April 2023Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses
  • Mon 17 April 2023PanGraph: scalable bacterial pan-genome graph construction
  • Mon 10 April 2023Evolution of the SARS-CoV-2 mutational spectrum
  • Fri 10 February 2023A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
  • Thu 15 December 2022Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates
  • Sat 10 December 2022Contributions of adaptation and purifying selection to SARS-CoV-2 evolution
  • Fri 25 November 2022Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021
  • Tue 08 November 2022Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
  • Thu 01 September 2022Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
  • Tue 23 August 2022Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus
  • Fri 19 August 2022TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
  • Fri 20 May 2022Evolution, geographic spreading, and demographic distribution of Enterovirus D68
  • Fri 04 March 2022CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
  • Tue 25 January 2022Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2
  • Mon 15 November 2021Nextclade: clade assignment, mutation calling and quality control for viral genomes
  • Wed 09 June 2021SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
  • Mon 07 June 2021Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
  • Tue 01 June 2021Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe
  • Tue 25 May 2021Novel SARS-CoV-2 variants: the pandemics within the pandemic
  • Fri 14 May 2021Investigate the origins of COVID-19
  • Fri 07 May 2021Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
  • Thu 25 March 2021SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing
  • Fri 05 March 2021Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses
  • Mon 01 February 2021Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020
  • Thu 07 January 2021Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
  • Wed 11 November 2020Asynchrony between virus diversity and antibody selection limits influenza virus evolution
  • Thu 10 September 2020Cryptic transmission of SARS-CoV-2 in Washington state
  • Wed 02 September 2020Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
  • Wed 26 August 2020Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
  • Thu 20 August 2020Efficient inference, potential, and limitations of site-specific substitution models
  • Wed 06 May 2020Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
  • Thu 26 March 2020Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
  • Thu 19 March 2020COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation
  • Sat 15 February 2020Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
  • Wed 12 February 20202019-novel Coronavirus (2019-nCoV): estimating the case fatality rate – a word of caution
  • Thu 16 January 2020Co-circulation of multiple enterovirus D68 subclades, including a novel B3 cluster, across Europe in a season of expected low prevalence, 2019/20
  • Wed 04 December 2019Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017–2018 influenza season
  • Thu 19 September 2019Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens
  • Fri 28 June 2019A global surveillance system for crop diseases
  • Mon 15 April 2019Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
  • Thu 07 March 2019Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains
  • Sat 19 January 2019Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses
  • Fri 04 January 2019Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform
  • Wed 31 October 2018Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing
  • Wed 24 October 2018Real-Time Analysis and Visualization of Pathogen Sequence Data
  • Tue 04 September 2018Efficient estimation of evolutionary rates by covariance aware regression
  • Tue 28 August 2018Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device
  • Wed 11 July 2018Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales
  • Sat 26 May 2018Nextstrain: real-time tracking of pathogen evolution
  • Sun 18 March 2018Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death
  • Sun 10 December 2017TreeTime: Maximum-likelihood phylodynamic analysis
  • Mon 30 October 2017Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology
  • Wed 25 October 2017panX: pan-genome analysis and exploration
  • Mon 02 October 2017Estimating time of HIV-1 infection from next-generation sequence diversity
  • Mon 19 June 2017Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture
  • Wed 17 May 2017Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering
  • Thu 02 March 2017In vivo mutation rates and the landscape of fitness costs of HIV-1
  • Tue 27 December 2016Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing.
  • Tue 15 November 2016Establishment and stability of the latent HIV-1 DNA reservoir.
  • Sun 19 June 2016Optimizing culture conditions for free-living stages of the nematode parasite Strongyloides ratti
  • Tue 15 March 2016HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell.
  • Mon 07 March 2016Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.
  • Tue 26 January 2016Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus.
  • Tue 15 December 2015Population genomics of intrapatient HIV-1 evolution.
  • Fri 26 June 2015nextflu: real-time tracking of seasonal influenza virus evolution in humans.
  • Sun 15 March 2015Challenges with using primer IDs to improve accuracy of next generation sequencing.
  • Tue 11 November 2014Predicting evolution from the shape of genealogical trees.
  • Tue 01 April 2014Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data.
  • Sat 15 March 2014Genetic diversity in the interference selection limit.
  • Wed 09 October 2013Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation
  • Mon 09 September 2013Inferring HIV Escape Rates from Multi-Locus Genotype Data.
  • Tue 03 September 2013Coalescence and genetic diversity in sexual populations under selection.
  • Wed 28 August 2013Quantifying selection against synonymous mutations in HIV-1 env evolution.
  • Mon 19 August 2013Quantifying the range of a lipid phosphate signal in vivo.
  • Wed 16 January 2013Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses.
  • Wed 16 January 2013Emergence of clones in sexual populations
  • Tue 01 January 2013Genealogies of rapidly adapting populations.
  • Wed 24 October 2012FFPopSim: an efficient forward simulation package for the evolution of large populations.
  • Wed 25 January 2012Dynamic mutation-selection balance as an evolutionary attractor.
  • Wed 25 January 2012Estimating the strength of selective sweeps from deep population diversity data.
  • Thu 17 November 2011Target search on a dynamic DNA molecule.
  • Thu 10 November 2011Statistical genetics and evolution of quantitative traits
  • Mon 01 August 2011Genetic draft and quasi-neutrality in large facultatively sexual populations.
  • Thu 24 February 2011Correlated evolution of nearby residues in Drosophilid proteins.
  • Mon 01 February 2010Rate of adaptation in large sexual populations.
  • Fri 29 January 2010Recombination rate and selection strength in HIV intra-patient evolution.
  • Wed 06 May 2009Blind source separation techniques for the decomposition of multiply labeled fluorescence images.
  • Thu 09 April 2009Competition between recombination and epistasis can cause a transition from allele to genotype selection.
  • Thu 25 January 2007Force-induced DNA slippage.
  • Thu 25 January 2007Optimal flexibility for conformational transitions in macromolecules.
  • Wed 25 January 2006Kinetic accessibility of buried DNA sites in nucleosomes.
  • Wed 25 January 2006Intermediate phase in DNA melting.
  • Tue 25 January 2005DNA as a programmable viscoelastic nanoelement.
  • Tue 01 June 2004Applying spectral fingerprinting to the analysis of FRET images.
  • Sun 25 January 2004Dynamics of force-induced DNA slippage.
  • Thu 01 January 2004Optimizing imaging parameters for the separation of multiple labels in a fluorescence image
research_area4
  • Tue 10 January 2017Evolution of bacteria
  • Tue 10 January 2017HIV evolution
  • Tue 10 January 2017Molecular epidemiology
  • Tue 10 January 2017Theory
software8
  • 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
talk92
  • Tue 24 September 2024"Evolution of SARS-CoV-2, immune escape, and the emergence variants of concern"
  • Thu 23 May 2024"Spread and Immune Escape of Respiratory RNA Viruses"
  • Fri 03 May 2024"Mutation, purifying selection, and adaptive evolution of SARS-CoV-2"
  • Thu 25 April 2024"Mutation, purifying selection, and adaptive evolution of SARS-CoV-2"
  • Mon 08 April 2024"Tracking and predicting the spread and evolution of RNA viruses"
  • Mon 18 March 2024"Co-evolution of RNA viruses and the human immune system"
  • Mon 26 February 2024"Real-time analysis and visualization of pathogen spread with Nextstrain"
  • Fri 10 November 2023"SARS-CoV-2 evolution and interaction with influenza"
  • Thu 31 August 2023"Adaptation and immune escape of SARS-CoV-2"
  • Thu 29 June 2023"Adaptation and immune escape of SARS-CoV-2"
  • Wed 31 May 2023"From pandemic to endemic: the interplay of immunity, viral evolution, and seasonality"
  • Mon 29 May 2023"Evolution of SARS-CoV-2: fitness landscapes, immune escape, and emergence of variants of concern"
  • Thu 27 April 2023
  • Sat 22 April 2023
  • Fri 31 March 2023Visualizing how pathogens spread and change
  • Wed 15 March 2023What can we learn from millions of viral genomes.
  • Tue 14 March 2023Predictability of influenza virus evolution
  • Fri 09 December 2022Determinants of antigenic evolution in SARS-CoV-2 and Influenza Viruses
  • Thu 03 November 2022Contributions of adaptation and purifying selection to SARS-CoV-2 evolution
  • Thu 15 September 2022Moving targets: Genomic epidemiology tools during a pandemic
  • Fri 15 July 2022Transmission, escape, and resistance: how human pathogens adapt and change
  • Tue 10 May 2022Reconstructing, tracking, and predicting viral spread and evolution
  • Mon 09 May 2022Reconstructing, tracking, and predicting viral spread and evolution
  • Fri 01 April 2022Reconstructing, tracking, and predicting viral spread and evolution
  • Wed 23 March 2022Reconstructing, tracking, and predicting viral spread and evolution
  • Tue 28 September 2021Real-time tracking of SARS-CoV-2 using Nextstrain
  • Wed 22 September 2021Real-time tracking of RNA viruses using Nextstrain
  • Fri 17 September 2021Adaptation and convergent evolution of SARS-CoV-2 and other human RNA viruses
  • Mon 13 September 2021Lessons from other viruses: how pandemics start and end
  • Wed 07 July 2021Tracking and predicting SARS-CoV-2 variants with Nextstrain
  • Thu 03 June 2021Real-time tracking of RNA viruses using Nextstrain
  • Thu 08 April 2021Tracking and predicting the evolution of human RNA viruses
  • Wed 10 February 2021Real-time tracking of SARS-CoV-2 using Nextstrain
  • Mon 11 January 2021Population genetics of rapid adaptation and influenza virus evolution
  • Tue 20 October 2020Tracking and predicting the evolution of human RNA viruses
  • Tue 13 October 2020Real-time tracking of SARS-CoV-2 evolution and spread
  • Tue 13 October 2020Modeling and predicting RNA virus evolution
  • Fri 09 October 2020Tracking and predicting viral evolution, from flu to covid-19
  • Wed 23 September 2020Real-time tracking of SARS-CoV-2 spread and evolution
  • Thu 10 September 2020Real-time tracking of SARS-CoV-2 spread and evolution
  • Thu 03 September 2020Real-time tracking of SARS-CoV-2 spread and evolution
  • Thu 03 September 2020Real-time tracking of SARS-CoV-2 spread and evolution
  • Thu 16 July 2020Real-time tracking of SARS-CoV-2 spread and evolution
  • Wed 20 May 2020Evolution and dynamics of SARS-CoV-2
  • Mon 11 May 2020Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
  • Thu 23 April 2020Tracking SARS-CoV-2 using real-time phylogenetics with Nextstrain
  • Tue 21 January 2020Using open data to track and predict infectious disease
  • Thu 10 October 2019Tracking and predicting influenza virus diversity
  • Tue 08 October 2019Using open data to track and predict infectious disease
  • Fri 04 October 2019Within-host evolution of HIV
  • Thu 11 July 2019Real-time tracking of pathogen evolution and spread
  • Wed 03 July 2019Repeatability and predictability in microbial evolution
  • Tue 28 May 2019Population genetics of rapid adaptation and fitness inference from trees
  • Tue 14 May 2019Real-time tracking of RNA virus evolution and spread
  • Thu 07 March 2019RNA virus evolution and the predictability of next year's flu
  • Wed 06 March 2019Tracking and predicting the spread of pathogens and resistance
  • Thu 07 February 2019Tracking infectious disease and drug resistance using whole genome sequencing
  • Mon 21 January 2019Establishment and maintenance of the latent HIV-1 DNA reservoir
  • Mon 05 November 2018Tracking pathogenic bacteria and AMR at the plasmid, genome, and pan-genome level
  • Thu 25 October 2018Real-time phylogenetic analysis of emerging pathogens
  • Fri 19 October 2018Real-time phylogenetic analysis of emerging pathogens
  • Fri 12 October 2018Universality and predictability in RNA virus evolution
  • Wed 26 September 2018The evolution of untreated HIV and maintenance of the latent reservoir
  • Wed 11 July 2018The evolutionary dynamics of untreated HIV and the maintenance of the latent reservoir
  • Tue 12 June 2018Real-time phylodynamics with nextflu and nextstrain
  • Mon 12 March 2018RNA virus evolution and the predictability of next year's flu
  • Thu 08 March 2018Real-time analysis and forecasting of influenza virus evolution
  • Wed 21 February 2018Within-host evolution of HIV and population genetics of rapid adaptation
  • Wed 14 February 2018Real-time tracking, molecular epidemiology, and data sharing
  • Tue 19 December 2017The evolutionary dynamics of untreated HIV and the maintenance of the latent reservoir
  • Thu 09 November 2017Virus evolution and the predictability of next year's flu
  • Sat 21 October 2017Recent progress in understanding evolutionary dynamics
  • Thu 12 October 2017Antigenic evolution of seasonal influenza viruses
  • Mon 09 October 2017Real-time tracking and prediction of RNA virus evolution
  • Fri 06 October 2017Rapid adaptation and the predictability of next year's flu
  • Wed 04 October 2017Virus evolution and the predictability of next year's flu
  • Thu 21 September 2017Virus evolution and the predictability of next year's flu
  • Fri 01 September 2017The evolutionary dynamics of untreated HIV and the maintenance of the latent reservoir
  • Mon 31 July 2017Evolution of HIV, immune escape, and latency
  • Wed 14 June 2017Real-time tracking of seasonal influenza, Ebola, and Zika viruses
  • Fri 09 June 2017Virus evolution and the predictability of next year's flu
  • Thu 25 May 2017Estimating the in-vivo fitness landscape of HIV-1
  • Thu 04 May 2017Virus evolution and the predictability of next year's flu
  • Wed 03 May 2017Within-host evolution of HIV
  • Tue 25 April 2017Tracking and predicting evolution and spread of RNA viruses
  • Mon 03 April 2017Population genetics of rapid adaptation and the predictability of evolution
  • Wed 29 March 2017Virus evolution and the predictability of next year's flu
  • Fri 17 March 2017The evolutionary dynamics of untreated HIV and the maintenance of the latent reservoir
  • Wed 08 March 2017Intra-patient evolution of HIV-1
  • Tue 28 February 2017Tracking and predicting the evolution RNA viruses
  • Tue 10 January 2017Evolution of HIV and influenza viruses
  • Tue 10 January 2017Population genetics of rapid adaptation and the predictability of evolution
talk_hidden1
  • Thu 17 June 2021Patterns of early diversity of SARS-CoV-2
talk_int1
  • Tue 31 July 2018RNA virus evolution and the predictability of next year's flu
talk_internal17
  • Thu 15 November 2018Tracking and predicting the spread of infectious disease
  • Mon 22 October 2018Outlook: Surveillance with Nextstrain
  • Wed 06 June 2018Microbial evolution
  • Wed 06 June 2018Microbial evolution
  • Fri 18 May 2018Learning about evolution from pathogen sequence data
  • Fri 23 March 2018Ist die Evolution von Grippeviren vorhersehbar?
  • Thu 22 February 2018Evolution of RNA viruses
  • Mon 19 February 2018Virus evolution and the predictability of next year's flu
  • Tue 06 February 2018The evolutionary dynamics of untreated HIV and the maintenance of the latent reservoir
  • Fri 24 November 2017Virus evolution and the predictability of next year's flu
  • Mon 02 October 2017In-vitro evolution of colistin resistance
  • Fri 15 September 2017Improving seasonal influenza vaccines by predicting virus evolution
  • Thu 14 September 2017Tracking and predicting evolution and spread of RNA viruses
  • Wed 12 July 2017Recent progress in predictive modeling
  • Tue 20 June 2017Population genetics of rapid adaptation and the predictability of evolution
  • Thu 04 May 2017Virus evolution and the predictability of next year's flu
  • Sun 03 March 2013Technical meeting regarding nextstrain in Switzerland
talk_outreach13
  • Tue 28 March 2023
  • Tue 26 April 2022How pandemics start and end
  • Thu 04 June 2020Evolution and spread of SARS-CoV-2
  • Thu 30 January 2020Ausbruch eines neuartigem Coronavirus in Wuhan
    Hintergründe, Ausbreitung, und Modelierung
    Stand: 2020-01-30
  • Tue 17 September 2019Echtzeit-Analyse, Visualisierung, und Vorhersage der Evolution von Grippe-Viren
  • Wed 27 March 2019Wie gewinnt man gegen Grippe-Viren?
  • Tue 05 February 2019Steckbrief: Das Virom
  • Fri 21 September 2018Using open data to track and predict infectious disease
  • Mon 23 April 2018Ist die Evolution von Grippeviren vorhersehbar?
  • Fri 23 March 2018Ist die Evolution von Grippeviren vorhersehbar?
  • Wed 27 September 2017Virus evolution and the predictability of next year's flu
  • Mon 11 September 2017Data sharing during public health emergencies
  • Wed 12 April 2017Virus evolution and the predictability of next year's flu
talk_outreach_en1
  • Fri 31 January 2020Outbreak of Novel Coronavirus in Wuhan
    Background, Spread, and Modelling
    date: 2020-01-30
talk_outreach_pre1
  • Wed 29 September 2021Using open data to track and predict infectious disease
talk_pre9
  • Sat 05 June 2021Tracking and interpreting novel SARS-CoV-2 variants
  • Wed 12 May 2021Tracking and interpreting novel SARS-CoV-2 variants
  • Tue 27 April 2021Assessing SARS-CoV-2 variants early on
  • Tue 27 April 2021SIB resource candidate: Nextstrain
  • Thu 06 June 2019Real-time tracking and visualization of pathogen sequence data
  • Tue 21 May 2019Incentives and barries to sharing of sequencing data
  • Wed 06 February 2019Real-time tracking and visualization of pathogen sequence data
  • Mon 15 October 2018Data sharing and real-time analysis in Influenza Virus surveillance
  • Sat 02 September 2017Real-time analysis to track and predict pathogen spread
talk_teaching2
  • Wed 23 September 2020Molecular epidemiology and phylogenetic analysis
  • Sun 04 March 2018Real time analysis and visualization of RNA virus evolution
talk_tmp2
  • Wed 01 April 2020Tracking SARS-Cov-2 using viral genomes and projecting its spread
  • Wed 01 April 2020Tracking SARS-Cov-2 using viral genomes and projecting its spread
teaching113
  • Wed 06 November 2024PoL I: Quantitative problems, dimensions, and units
  • Fri 01 November 2024Physics of Life
  • Wed 23 October 2024Virus evolution and the spread of infectious disease
  • Mon 15 January 2024Nextstrain workshop at the Wengen Winter School
  • Wed 15 November 2023Virus evolution and the spread of infectious disease
  • Fri 03 November 2023PoL I: Quantitative problems, dimensions, and units
  • Wed 01 November 2023Physics of Life
  • Thu 14 September 2023SARS-COV-2 workshop
  • Thu 14 September 2023Nextstrain workshop at Bad Honnef
  • Thu 01 December 2022Evolution and spread of Influenza, HIV, and SARS-CoV-2
  • Wed 30 November 2022Virus evolution and the spread of infectious disease
  • Tue 20 September 2022Physics of Life
  • Thu 07 April 2022Virus evolution and population genetics
  • 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
  • Wed 22 December 2021Virus evolution and the spread of infectious disease
  • Sat 04 December 2021Evolution and spread of Influenza, HIV, and SARS-CoV-2
  • Fri 24 September 2021Physics of Life
  • Tue 27 July 2021Nextstrain webinar at Africa CDC
  • Thu 29 April 2021Virus evolution and population genetics
  • Wed 16 December 2020Virus evolution and the spread of infectious disease
  • Fri 04 December 2020Evolution and spread of Influenza, HIV, and SARS-CoV-2
  • Fri 04 December 2020Evolution of human RNA viruses
  • Mon 30 November 2020SARS-CoV-2 und COVID19 -- genomische Epidemilogie in Echtzeit
  • Wed 23 September 2020Introduction to Phylogenetic Analysis
  • Wed 23 September 2020SARS-CoV-2 phylogenetic analysis
  • Wed 23 September 2020SARS-CoV-2 phylogenetic analysis
  • Thu 17 September 2020Physics of Life
  • Tue 15 September 2020PoL I: Quantitative problems, dimensions, and units
  • Thu 23 April 2020Virus evolution and population genetics
  • Wed 11 December 2019Virus evolution and the spread of infectious disease
  • 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 16 September 2019Physics of Life I -- 44702-01
  • 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 25 April 2019Virus evolution and population genetics
  • 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
  • Thu 20 December 2018Information theory and proportional betting
  • Thu 20 December 2018Microbial evolution and the spread of infectious disease
  • Thu 13 December 2018Chromatin organization and structure
  • Wed 12 December 2018Virus evolution and the spread of infectious disease
  • Fri 07 December 2018Virus evolution and the spread of infectious disease
  • Thu 06 December 2018Liquid-liquid phase transitions within cells
  • Thu 06 December 2018Liquid-liquid phase transitions in cell biology
  • Thu 29 November 2018Kinetic proofreading and percolation
  • Thu 22 November 2018Reaction rates and the method of dominant balance
  • Thu 15 November 2018Bistablility, oscillations, and linear stability analysis
  • Wed 07 November 2018Physics of Life
  • Thu 01 November 2018Bifurcations, bistability and oscillations
  • 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
  • Mon 24 September 2018Kinetic Proofreading
  • Thu 20 September 2018The relevant scales of cellular biophysics
  • Thu 12 April 2018Virus evolution and population genetics
  • Tue 10 April 2018Advanced Methods in Computational Sciences
  • Sun 04 March 2018A glimpse into sequence bioinformatics
  • Fri 15 December 2017Evolution of HIV
  • Fri 15 December 2017Applied evolutionary biology: tracking and predicting the spread of disease
  • 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 21 November 2017Liquid-liquid phase transitions in cell biology
  • 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 2017Biological Oscillators, circadian rhythms and temperature compensation
  • Mon 06 November 2017Cytoskeleton -- Solutions to problems
  • Wed 01 November 2017Virus evolution and the spread of infectious disease
  • 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
  • Mon 25 September 2017Kinetic Proofreading
  • 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 24 July 2017Eco-Evolutionary dynamics in Microbial Communities
  • Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities
  • Mon 24 July 2017Eco-Evolutionary dynamics in Microbial Communities -- pan-genomes
  • Tue 04 April 2017Advanced Methods in Computational Sciences
teaching_pre1
  • Fri 25 March 2022Nextstrain workshop at QLife
team27
  • Mon 03 February 2025Greta Brenna
  • Fri 01 November 2024Isabel Joia
  • Fri 12 July 2024Aleksandr Kuznetsov
  • Fri 12 July 2024Benjamin Otter
  • Mon 01 April 2024Georg Angehrn
  • Sun 12 November 2023Luca Sesta
  • Sun 10 July 2022Anna Parker
  • Sun 10 July 2022Laura Urbanska
  • Sat 20 November 2021Cornelius Roemer
  • Sat 20 November 2021János Winkler
  • Sat 20 November 2021Marco Molari
  • Sat 20 November 2021Reto Tschannen
  • Sun 01 March 2020Ivan Aksamentov
  • Sun 01 March 2020Valentin Druelle
  • Tue 01 January 2019Pierre Barrat
  • Wed 01 August 2018Eric Ulrich
  • Sun 14 January 2018Emma Hodcroft
  • Sun 14 January 2018Nicholas Noll
  • Sun 14 January 2018Sanda Dejanic
  • Sat 07 January 2017Bianca Regenbogen
  • Sat 07 January 2017Emmanuel Benard
  • Sat 07 January 2017Fabio Zanini
  • Sat 07 January 2017Pavel Sagulenko
  • Sat 07 January 2017Richard Neher
  • Sat 07 January 2017Taylor Kessinger
  • Sat 07 January 2017Vadim Puller
  • Sat 07 January 2017Wei Ding
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