Johan Elf
Professor at Department of Cell and Molecular Biology; Molecular Systems Biology
- Mobile phone:
- +46 70 980 31 35
- E-mail:
- johan.elf@icm.uu.se
- Visiting address:
- Husargatan 3
752 37 UPPSALA - Postal address:
- Box 596
751 24 UPPSALA
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Short presentation
Johan Elf is Professor of Physical Biology at Uppsala University. He is a Wallenberg Academy Scholar and a member of the Uppsala University board and the board of the Royal Academy of Sciences.
His research if is mainly funded by KAW and ERC.
The research in the Elf lab aims to bridge the current gap between quantitative physical models and biological observations in order to identify and resolve inconsistencies in our current understanding of life at the molecular level.
Biography
The Elf group has pioneered single molecule tracking methods by means of fluorescence microscopy in living cells. This is accompanied by development of new microfluidic techniques and corresponding analysis software to control growth conditions and enable automation. The group also designs computational tools for stochastic reaction-diffusion simulation of intracellular kinetics and mathematical modeling of intercellular physiology.
Johan Elf has founded the Uppsala based diagnostics company Astrego. Astrego develops a rapid point of care test for antibiotic susceptibility.
Publications
Selection of publications
- Sequence specificity in DNA binding is mainly governed by association (2022)
- RecA finds homologous DNA by reduced dimensionality search (2021)
- Time-resolved imaging-based CRISPRi screening (2020)
- DNA surface exploration and operator bypassing during target search (2020)
- Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes (2017)
- Kinetics of dCas9 target search in Escherichia coli (2017)
- The Synchronization of Replication and Division Cycles in Individual E. coli Cells (2016)
- Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation (2014)
- Extracting intracellular diffusive states and transition rates from single-molecule tracking data (2013)
- The lac repressor displays facilitated diffusion in living cells (2012)
- Lost in presumption: stochastic reactions in spatial models (2012)
- Stochastic reaction-diffusion kinetics in the microscopic limit (2010)
- Effects of macromolecular crowding and DNA looping on gene regulation kinetics. (2009)
- Probing transcription factor dynamics at the single-molecule level in a living cell. (2007)
- Selective loss of charging of tRNA isoacceptors during amino acid limitation. (2003)
Recent publications
- Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization (2023)
- Antibiotic perseverance increases the risk of resistance development (2023)
- Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy (2023)
- Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle (2023)
- Can molecular dynamics be used to simulate biomolecular recognition? (2023)
All publications
Articles
- Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization (2023)
- Antibiotic perseverance increases the risk of resistance development (2023)
- Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy (2023)
- Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle (2023)
- Can molecular dynamics be used to simulate biomolecular recognition? (2023)
- Rapid antibiotic susceptibility testing and species identification for mixed samples (2022)
- Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study (2022)
- Sequence specificity in DNA binding is mainly governed by association (2022)
- Direct measurements of mRNA translation kinetics in living cells (2022)
- More Than Just Letters and Chemistry (2021)
- Imaging-based screens of pool-synthesized cell libraries (2021)
- The highly dynamic nature of bacterial heteroresistance impairs its clinical detection (2021)
- RecA finds homologous DNA by reduced dimensionality search (2021)
- Time-resolved imaging-based CRISPRi screening (2020)
- DNA surface exploration and operator bypassing during target search (2020)
- Rotational and Translational Diffusion of Proteins as a Function of Concentration (2019)
- Single-Molecule Kinetics in Living Cells (2019)
- Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition (2019)
- Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations (2018)
- Bursting onto the scene? (2018)
- Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI (2018)
- Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories (2018)
- tRNA tracking for direct measurements of protein synthesis kinetics in live cells (2018)
- Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging (2017)
- Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes (2017)
- How Will Kinetics and Thermodynamics Inform Our Future Efforts to Understand and Build Biological Systems? (2017)
- Kinetics of dCas9 target search in Escherichia coli (2017)
- Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli (2017)
- In situ genotyping of a pooled strain library after characterizing complex phenotypes (2017)
- Pointwise error estimates in localization microscopy (2017)
- Measuring the Orientation of Single Proteins Interacting with DNA using Fluorescence Polarization Microscopy (2017)
- The helical structure of DNA facilitates binding (2016)
- Staying Clear of the Dragons (2016)
- Hypothesis (2016)
- Segmentation and track-analysis in time-lapse imaging of bacteria (2016)
- Arming the Neighborhood (2016)
- Simulated single molecule microscopy with SMeagol (2016)
- Oufti (2016)
- The Synchronization of Replication and Division Cycles in Individual E. coli Cells (2016)
- Single Molecule Tracking in Living Cells (2015)
- What matters for lac repressor searchinvivo ––sliding, hopping, intersegment transfer, crowding on DNA or recognition? (2015)
- Direct Measurements of Transcription Factor Binding and Dissociation at Individual Chromosomal Operators (2014)
- Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation (2014)
- Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid (2014)
- Stochastic reaction–diffusion processes with embedded lower-dimensional structures (2014)
- Transcription factor binding kinetics constrain noise suppression via negative feedback (2013)
- Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models (2013)
- Single molecule methods with applications in living cells (2013)
- A Bayesian Approach to Single Particle Tracking Analysis (2013)
- Extracting intracellular diffusive states and transition rates from single-molecule tracking data (2013)
- High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking (2013)
- MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit (2012)
- MesoRD 1.0 (2012)
- The lac repressor displays facilitated diffusion in living cells (2012)
- Lost in presumption: stochastic reactions in spatial models (2012)
- Lost in presumption (2012)
- Positive allosteric feedback regulation of the stringent response enzyme RelA by its product (2012)
- Single-molecule investigations of the stringent response machinery in living bacterial cells (2011)
- Delay-induced anomalous fluctuations in intracellular regulation (2011)
- Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40 (2011)
- Studying transcriptional interactions in single cells at sufficient resolution (2011)
- Stochastic reaction-diffusion kinetics in the microscopic limit (2010)
- RNAs actively cycle on the Sm-like protein Hfq (2010)
- Costs and constraints from time-delayed feedback in small gene regulatory motifs (2010)
- Effects of macromolecular crowding and DNA looping on gene regulation kinetics. (2009)
- Single molecule approaches to transcription factor kinetics in living cells (2009)
- Fokker-Planck approximation of the master equation in molecular biology (2009)
- Probing transcription factor dynamics at the single-molecule level in a living cell. (2007)
- Bistable bacterial growth rate in response to antibiotics with low membrane permeability (2006)
- Noise-induced Min phenotypes in E. coli (2006)
- Selective charging of tRNA isoacceptors induced by amino-acid starvation. (2005)
- Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate-limiting supply of amino acids. (2005)
- What makes ribosome-mediated transcriptional attenuation sensitive to amino (2005)
- Stochastic reaction-diffusion simulation with MesoRD. (2005)
- Ribosome bypassing at serine codons as a test of the model of selective transfer RNA charging. (2005)
- Over expression of a tRNA(Leu) isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading. (2005)
- Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases (2004)
- Systems biology is taking off. (2003)
- An efficient algorithm for mesoscopic reaction-diffusion simulation (2003)
- Near critical phenomena in metabolite pools (2003)
- Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. (2003)
- Selective loss of charging of tRNA isoacceptors during amino acid limitation. (2003)
- The bacterial toxin RelE displays codon specific cleavage of mRNAs in the ribosomal A-site (2003)
- Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons (2001)
- RecA mediated homology search finds segregated sister locus in minutes after a double stranded break
- Transcription factor dissociation measurements using single molecule chase in living cells
- Real-time pooled optical screening with single-cell isolation capability
- Molecular Origins of Kinetics and Selectivity in the lac operon
- LacI follows a helical path while sliding along DNA
- Fluctuations in replication initiation determine the generation time and size distributions of E. coli cells
Chapters
- Stochastic Modeling of Intracellular Kinetics (2006)
- Mesoscopic kinetics and its applications in protein synthesis (2005)
Conferences
- Microfluidic chip for large-scale phenotypic characterization of E. coli (2019)
- An Evaluation of the Faster STORM Method for Super-resolution Microscopy (2014)
- Problems of high dimension in molecular biology (2003)
Reports
