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imprint1
  • Tue 07 February 2017Imprint
internal1
  • Wed 01 November 2017Group meeting and journal club
job_old1
  • Fri 20 January 2017Post-Doc position in pathogen genomics
master_thesis2
  • Sat 04 February 2017Master thesis: Reconstructing influenza spread and evolution jointly from all eight genome segments
  • Fri 03 February 2017Master thesis: Real-time tracking of animal influenza viruses
nonlab_publication9
  • Fri 09 February 2018Global morphogenetic flow is accurately predicted by the spatial distribution of myosin motors
  • Tue 07 February 2017Active tension network model suggests an exotic mechanical state realized in epithelial tissues
  • Tue 07 February 2017Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
  • Tue 07 February 2017Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.
  • Sun 07 February 2016A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.
  • Sun 07 February 2016Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters.
  • Sun 07 February 2016Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.
  • Fri 07 February 2014The contribution of viral genotype to plasma viral set-point in HIV infection.
  • Thu 07 February 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
post21
  • 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
publication55
  • Wed 31 October 2018Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing
  • Tue 30 October 2018Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen
  • Wed 24 October 2018Real-Time Analysis and Visualization of Pathogen Sequence Data
  • Tue 18 September 2018Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing
  • 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.
  • Tue 07 February 2012Dynamic mutation-selection balance as an evolutionary attractor.
  • Tue 07 February 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.
  • Wed 07 February 2007Force-induced DNA slippage.
  • Wed 07 February 2007Optimal flexibility for conformational transitions in macromolecules.
  • Tue 07 February 2006Kinetic accessibility of buried DNA sites in nucleosomes.
  • Tue 07 February 2006Intermediate phase in DNA melting.
  • Mon 07 February 2005DNA as a programmable viscoelastic nanoelement.
  • Tue 01 June 2004Applying spectral fingerprinting to the analysis of FRET images.
  • Sat 07 February 2004Dynamics of force-induced DNA slippage.
  • Thu 01 January 2004Optimizing imaging parameters for the separation of multiple labels in a fluorescence image
publications2
  • Tue 28 August 2018Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device
  • Tue 07 February 2012Fluctuations of fitness distributions and the rate of Muller's ratchet.
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
talk36
  • 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_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_outreach7
  • 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_pre3
  • 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_teaching1
  • Sun 04 March 2018Real time analysis and visualization of RNA virus evolution
teaching60
  • 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
  • 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
team13
  • 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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