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Sat 21 January 2017Imprint

Wed 01 November 2017Group meeting and journal club

Wed 06 November 2019Scientific Software Developer/Programmer (50-100%)
Tue 22 October 2019Post-Doc position
Fri 20 January 2017Post-Doc position in pathogen genomics

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_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
Sat 21 January 2017Active tension network model suggests an exotic mechanical state realized in epithelial tissues
Sat 21 January 2017Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Sat 21 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
Thu 21 January 2016A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.
Thu 21 January 2016Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters.
Thu 21 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
Tue 21 January 2014The contribution of viral genotype to plasma viral set-point in HIV infection.
Mon 21 January 2013Automated analysis of phylogenetic clusters.

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

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

Sun 19 January 2020Efficient inference, potential, and limitations of site-specific substitution models
Sat 18 January 2020Evolution, geographic spreading, and demographic distribution of Enterovirus D68
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.
Sat 21 January 2012Dynamic mutation-selection balance as an evolutionary attractor.
Sat 21 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.
Sun 21 January 2007Force-induced DNA slippage.
Sun 21 January 2007Optimal flexibility for conformational transitions in macromolecules.
Sat 21 January 2006Kinetic accessibility of buried DNA sites in nucleosomes.
Sat 21 January 2006Intermediate phase in DNA melting.
Fri 21 January 2005DNA as a programmable viscoelastic nanoelement.
Tue 01 June 2004Applying spectral fingerprinting to the analysis of FRET images.
Wed 21 January 2004Dynamics of force-induced DNA slippage.
Thu 01 January 2004Optimizing imaging parameters for the separation of multiple labels in a fluorescence image

Sat 21 January 2012Fluctuations of fitness distributions and the rate of Muller's ratchet.

Tue 10 January 2017Evolution of bacteria
Tue 10 January 2017HIV evolution
Tue 10 January 2017Molecular epidemiology
Tue 10 January 2017Theory

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

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

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

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

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

Sun 04 March 2018Real time analysis and visualization of RNA virus evolution

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 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

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