Johan Elf

Sequence specificity in DNA binding is mainly governed by association

Marklund, Emil; Mao, Guanzhong; Yuan, Jinwen; Zikrin, Spartak et al.

Part of Science, p. 442-445, 2022

• DOI for Sequence specificity in DNA binding is mainly governed by association
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RecA finds homologous DNA by reduced dimensionality search

Wiktor, Jakub; Gynnå, Arvid H.; Leroy, Prune; Larsson, Jimmy et al.

Part of Nature, p. 426-429, 2021

• DOI for RecA finds homologous DNA by reduced dimensionality search
• Download full text (pdf) of RecA finds homologous DNA by reduced dimensionality search

Time-resolved imaging-based CRISPRi screening

Camsund, Daniel; Lawson, Michael J.; Larsson, Jimmy; Jones, Daniel et al.

Part of Nature Methods, p. 86-92, 2020

• DOI for Time-resolved imaging-based CRISPRi screening

DNA surface exploration and operator bypassing during target search

Marklund, Emil; van Oosten, Brad; Mao, Guanzhong; Amselem, Elias et al.

Part of Nature, p. 858-+, 2020

• DOI for DNA surface exploration and operator bypassing during target search
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Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes

Balzarotti, Francisco; Eilers, Yvan; Gwosch, Klaus C.; Gynnå, Arvid H. et al.

Part of Science, p. 606-612, 2017

• DOI for Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes

Kinetics of dCas9 target search in Escherichia coli

Jones, Daniel; Leroy, Prune; Unoson, Cecilia; Fange, David et al.

Part of Science, p. 1420-1423, 2017

• DOI for Kinetics of dCas9 target search in Escherichia coli

The Synchronization of Replication and Division Cycles in Individual E. coli Cells

Walldén, Mats; Fange, David; Lundius, Ebba Gregorsson; Baltekin, Özden et al.

Part of Cell, p. 729-739, 2016

• DOI for The Synchronization of Replication and Division Cycles in Individual E. coli Cells

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

Hammar, Petter; Walldén, Mats; Fange, David; Persson, Fredrik et al.

Part of Nature Genetics, p. 405-+, 2014

• DOI for Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Persson, Fredrik; Linden, Martin; Unoson, Cecilia; Elf, Johan

Part of Nature Methods, p. 265-269, 2013

• DOI for Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Lost in presumption: stochastic reactions in spatial models

Mahmutovic, Anel; Fange, David; Berg, Otto G; Elf, Johan

Part of Nature Methods, 2012

The lac repressor displays facilitated diffusion in living cells

Hammar, Petter; Leroy, Prune; Mahmutovic, Anel; Marklund, Erik G et al.

Part of Science, p. 1595-1598, 2012

• DOI for The lac repressor displays facilitated diffusion in living cells

Stochastic reaction-diffusion kinetics in the microscopic limit

Fange, David; Berg, Otto G; Sjöberg, Paul; Elf, Johan

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19820-19825, 2010

• DOI for Stochastic reaction-diffusion kinetics in the microscopic limit

Effects of macromolecular crowding and DNA looping on gene regulation kinetics.

Li, Gene-Wei; Berg, Otto G.; Elf, Johan

Part of Nature Physics, p. 294-297, 2009

• DOI for Effects of macromolecular crowding and DNA looping on gene regulation kinetics.

Probing transcription factor dynamics at the single-molecule level in a living cell.

Elf, Johan; Li, Gene-Wei; Xie, X Sunney

Part of Science, p. 1191-1194, 2007

• DOI for Probing transcription factor dynamics at the single-molecule level in a living cell.

Selective loss of charging of tRNA isoacceptors during amino acid limitation.

Elf, Johan; Tenson, Tanel; Ehrenberg, Måns

Part of Science, p. 1718-1722, 2003

Culture-free detection of bacteria from blood for rapid sepsis diagnosis

Miguelez, M. Henar Marino; Osaid, Mohammad; Hallström, Erik; Kaya, Kerem et al.

Part of npj Digital Medicine, 2025

• DOI for Culture-free detection of bacteria from blood for rapid sepsis diagnosis
• Download full text (pdf) of Culture-free detection of bacteria from blood for rapid sepsis diagnosis

Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours

Tran, Buu Minh; Larsson, Jimmy; Grip, Anastasia; Karempudi, Praneeth et al.

Part of Nature Communications, 2025

• DOI for Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours
• Download full text (pdf) of Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours

Pooled optical screening in bacteria using chromosomally expressed barcodes

Soares, Ruben R. G.; Garcia-Soriano, Daniela A.; Larsson, Jimmy; Fange, David et al.

Part of Communications Biology, 2025

• DOI for Pooled optical screening in bacteria using chromosomally expressed barcodes
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Anti-correlation of LacI association and dissociation rates observed in living cells

Kandavalli, Vinodh; Zikrin, Spartak; Elf, Johan; Jones, Daniel

Part of Nature Communications, 2025

• DOI for Anti-correlation of LacI association and dissociation rates observed in living cells
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The Escherichia coli chromosome moves to the replisome

Gras, Konrad; Fange, David; Elf, Johan

Part of Nature Communications, 2024

• DOI for The Escherichia coli chromosome moves to the replisome
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Culture-free detection of bacteria from blood for rapid sepsis diagnosis

Miguelez, M. Henar Marino; Osaid, Mohammad; Hallström, Erik; Kaya, Kerem et al.

Part of npj Digital Medicine, 2025

• DOI for Culture-free detection of bacteria from blood for rapid sepsis diagnosis
• Download full text (pdf) of Culture-free detection of bacteria from blood for rapid sepsis diagnosis

Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours

Tran, Buu Minh; Larsson, Jimmy; Grip, Anastasia; Karempudi, Praneeth et al.

Part of Nature Communications, 2025

• DOI for Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours
• Download full text (pdf) of Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours

Pooled optical screening in bacteria using chromosomally expressed barcodes

Soares, Ruben R. G.; Garcia-Soriano, Daniela A.; Larsson, Jimmy; Fange, David et al.

Part of Communications Biology, 2025

• DOI for Pooled optical screening in bacteria using chromosomally expressed barcodes
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Anti-correlation of LacI association and dissociation rates observed in living cells

Kandavalli, Vinodh; Zikrin, Spartak; Elf, Johan; Jones, Daniel

Part of Nature Communications, 2025

• DOI for Anti-correlation of LacI association and dissociation rates observed in living cells
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The Escherichia coli chromosome moves to the replisome

Gras, Konrad; Fange, David; Elf, Johan

Part of Nature Communications, 2024

• DOI for The Escherichia coli chromosome moves to the replisome
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Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle

Karempudi, Praneeth; Gras, Konrad; Amselem, Elias; Zikrin, Spartak et al.

Part of Communications Biology, 2024

• DOI for Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle
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Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

Knöppel, Anna; Broström, Oscar; Gras, Konrad; Elf, Johan et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2023

• DOI for Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle
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Can molecular dynamics be used to simulate biomolecular recognition?

Lüking, Malin; Van der Spoel, David; Elf, Johan; Tribello, Gareth A. A.

Part of Journal of Chemical Physics, 2023

• DOI for Can molecular dynamics be used to simulate biomolecular recognition?

Antibiotic perseverance increases the risk of resistance development

Brandis, Gerrit; Larsson, Jimmy; Elf, Johan

Part of Proceedings of the National Academy of Sciences of the United States of America, 2023

• DOI for Antibiotic perseverance increases the risk of resistance development
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Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

Hallström, Erik; Kandavalli, Vinodh; Ranefall, Petter; Elf, Johan et al.

Part of PloS Computational Biology, 2023

• DOI for Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy
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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization

Amselem, Elias; Broadwater, Bo; Haevermark, Tora; Johansson, Magnus et al.

Part of Nature Communications, 2023

• DOI for Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
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Sequence specificity in DNA binding is mainly governed by association

Marklund, Emil; Mao, Guanzhong; Yuan, Jinwen; Zikrin, Spartak et al.

Part of Science, p. 442-445, 2022

• DOI for Sequence specificity in DNA binding is mainly governed by association
• Download full text (pdf) of Sequence specificity in DNA binding is mainly governed by association

Direct measurements of mRNA translation kinetics in living cells

Metelev, Mikhail; Lundin, Erik; Volkov, Ivan; Gynna, Arvid H. et al.

Part of Nature Communications, 2022

• DOI for Direct measurements of mRNA translation kinetics in living cells
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Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

Lüking, Malin; Elf, Johan; Levy, Yaakov

Part of Journal of Physical Chemistry B, p. 9971-9984, 2022

• DOI for Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study
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Rapid antibiotic susceptibility testing and species identification for mixed samples

Kandavalli, Vinodh; Karempudi, Praneeth; Larsson, Jimmy; Elf, Johan

Part of Nature Communications, 2022

• DOI for Rapid antibiotic susceptibility testing and species identification for mixed samples
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More Than Just Letters and Chemistry: Genomics Goes Mechanics

Deindl, Sebastian; Elf, Johan

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 431-432, 2021

• DOI for More Than Just Letters and Chemistry: Genomics Goes Mechanics

The highly dynamic nature of bacterial heteroresistance impairs its clinical detection

Pereira, Cátia; Larsson, Jimmy; Hjort, Karin; Elf, Johan et al.

Part of Communications Biology, 2021

• DOI for The highly dynamic nature of bacterial heteroresistance impairs its clinical detection
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Imaging-based screens of pool-synthesized cell libraries

Lawson, Michael; Elf, Johan

Part of Nature Methods, p. 358-365, 2021

• DOI for Imaging-based screens of pool-synthesized cell libraries

RecA finds homologous DNA by reduced dimensionality search

Wiktor, Jakub; Gynnå, Arvid H.; Leroy, Prune; Larsson, Jimmy et al.

Part of Nature, p. 426-429, 2021

• DOI for RecA finds homologous DNA by reduced dimensionality search
• Download full text (pdf) of RecA finds homologous DNA by reduced dimensionality search

Time-resolved imaging-based CRISPRi screening

Camsund, Daniel; Lawson, Michael J.; Larsson, Jimmy; Jones, Daniel et al.

Part of Nature Methods, p. 86-92, 2020

• DOI for Time-resolved imaging-based CRISPRi screening

DNA surface exploration and operator bypassing during target search

Marklund, Emil; van Oosten, Brad; Mao, Guanzhong; Amselem, Elias et al.

Part of Nature, p. 858-+, 2020

• DOI for DNA surface exploration and operator bypassing during target search
• Download full text (pdf) of DNA surface exploration and operator bypassing during target search

Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

Liao, Qinghua; Lüking, Malin; Krueger, Dennis M.; Deindl, Sebastian et al.

Part of Journal of Physical Chemistry B, p. 3576-3590, 2019

• DOI for Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition
• Download full text (pdf) of Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

Rotational and Translational Diffusion of Proteins as a Function of Concentration

Bashardanesh, Zahedeh; Elf, Johan; Zhang, Haiyang; Van der Spoel, David

Part of ACS Omega, p. 20654-20664, 2019

• DOI for Rotational and Translational Diffusion of Proteins as a Function of Concentration
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Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories

Lindén, Martin; Elf, Johan

Part of Biophysical Journal, p. 276-282, 2018

• DOI for Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories

Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI

Kipper, Kalle; Eremina, Nadja; Marklund, Emil; Tubasum, Sumera et al.

Part of PLOS ONE, 2018

• DOI for Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI
• Download full text (pdf) of Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI

Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations

Ghosh, Anirban; Baltekin, Özden; Wäneskog, Marcus; Elkhalifa, Dina et al.

Part of EMBO Journal, 2018

• DOI for Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations

tRNA tracking for direct measurements of protein synthesis kinetics in live cells

Volkov, Ivan; Lindén, Martin; Aguirre, Javier; Ieong, Ka-Weng et al.

Part of Nature Chemical Biology, p. 618-626, 2018

• DOI for tRNA tracking for direct measurements of protein synthesis kinetics in live cells

Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli

Kipper, Kalle; Lundius, Ebba G.; Ćurić, Vladimir; Nikic, Ivana et al.

Part of ACS Photonics, p. 233-255, 2017

• DOI for Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli

How Will Kinetics and Thermodynamics Inform Our Future Efforts to Understand and Build Biological Systems?

Doudna, Jennifer; Bar-Ziv, Roy; Elf, Johan; Noireaux, Vincent et al.

Part of CELL SYSTEMS, p. 144-146, 2017

Measuring the Orientation of Single Proteins Interacting with DNA using Fluorescence Polarization Microscopy

Marklund, Emil; Amselem, Elias; Kipper, Kalle; Johansson, Magnus et al.

Part of Biophysical Journal, 2017

Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes

Balzarotti, Francisco; Eilers, Yvan; Gwosch, Klaus C.; Gynnå, Arvid H. et al.

Part of Science, p. 606-612, 2017

• DOI for Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes

In situ genotyping of a pooled strain library after characterizing complex phenotypes

Lawson, Michael J.; Camsund, Daniel; Larsson, Jimmy; Baltekin, Özden et al.

Part of Molecular Systems Biology, 2017

• DOI for In situ genotyping of a pooled strain library after characterizing complex phenotypes
• Download full text (pdf) of In situ genotyping of a pooled strain library after characterizing complex phenotypes

Pointwise error estimates in localization microscopy

Lindén, Martin; Curic, Vladimir; Amselem, Elias; Elf, Johan

Part of Nature Communications, 2017

• DOI for Pointwise error estimates in localization microscopy
• Download full text (pdf) of Pointwise error estimates in localization microscopy

Kinetics of dCas9 target search in Escherichia coli

Jones, Daniel; Leroy, Prune; Unoson, Cecilia; Fange, David et al.

Part of Science, p. 1420-1423, 2017

• DOI for Kinetics of dCas9 target search in Escherichia coli

Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging

Baltekin, Özden; Boucharin, Alexis; Tano, Eva; Andersson, Dan I et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 9170-9175, 2017

• DOI for Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging

Simulated single molecule microscopy with SMeagol

Lindén, Martin; Ćurić, Vladimir; Boucharin, Alexis; Fange, David et al.

Part of Bioinformatics, p. 2394-2395, 2016

• DOI for Simulated single molecule microscopy with SMeagol
• Download full text (pdf) of Simulated single molecule microscopy with SMeagol

The Synchronization of Replication and Division Cycles in Individual E. coli Cells

Walldén, Mats; Fange, David; Lundius, Ebba Gregorsson; Baltekin, Özden et al.

Part of Cell, p. 729-739, 2016

• DOI for The Synchronization of Replication and Division Cycles in Individual E. coli Cells

The helical structure of DNA facilitates binding

Berg, Otto G.; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

Part of Journal of Physics A, 2016

• DOI for The helical structure of DNA facilitates binding

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov et al.

Part of Molecular Microbiology, p. 767-777, 2016

• DOI for Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

Arming the Neighborhood

Koskiniemi, Sanna; Elf, Johan

Part of Developmental Cell, p. 5-6, 2016

• DOI for Arming the Neighborhood

Hypothesis: Homologous Recombination Depends on Parallel Search

Elf, Johan

Part of CELL SYSTEMS, p. 325-327, 2016

• DOI for Hypothesis: Homologous Recombination Depends on Parallel Search

Segmentation and track-analysis in time-lapse imaging of bacteria

Kecheril Sadanandan, Sajith; Baltekin, Özden; Magnusson, Klas E. G.; Boucharin, Alexis et al.

Part of IEEE Journal on Selected Topics in Signal Processing, p. 174-184, 2016

• DOI for Segmentation and track-analysis in time-lapse imaging of bacteria

Staying Clear of the Dragons

Elf, Johan

Part of CELL SYSTEMS, p. 219-220, 2016

• DOI for Staying Clear of the Dragons

What matters for lac repressor searchinvivo ––sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Mahmutovic, Anel; Berg, Otto G; Elf, Johan

Part of Nucleic Acids Research, p. 3454-3464, 2015

• DOI for What matters for lac repressor searchinvivo ––sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Single Molecule Tracking in Living Cells: Multistep Reactions, Simulated Microscopy and New Analysis Methods

Lindén, Martin; Elf, Johan

Part of Biophysical Journal, 2015

Stochastic reaction–diffusion processes with embedded lower-dimensional structures

Wang, Siyang; Elf, Johan; Hellander, Stefan; Lötstedt, Per

Part of Bulletin of Mathematical Biology, p. 819-853, 2014

• DOI for Stochastic reaction–diffusion processes with embedded lower-dimensional structures

Direct Measurements of Transcription Factor Binding and Dissociation at Individual Chromosomal Operators

Elf, Johan

Part of Biophysical Journal, 2014

• DOI for Direct Measurements of Transcription Factor Binding and Dissociation at Individual Chromosomal Operators

Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid

Sanamrad, Arash; Persson, Fredrik; Lundius, Ebba G.; Fange, David et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 11413-11418, 2014

• DOI for Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

Hammar, Petter; Walldén, Mats; Fange, David; Persson, Fredrik et al.

Part of Nature Genetics, p. 405-+, 2014

• DOI for Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking

Ullman, Gustaf; Walldén, Mats; Marklund, Erik G.; Mahmutovic, Anel et al.

Part of Philosophical Transactions of the Royal Society of London. Biological Sciences, 2013

• DOI for High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking

Transcription factor binding kinetics constrain noise suppression via negative feedback

Grönlund, Andreas; Lötstedt, Per; Elf, Johan

Part of Nature Communications, 2013

• DOI for Transcription factor binding kinetics constrain noise suppression via negative feedback

A Bayesian Approach to Single Particle Tracking Analysis

Persson, Fredrik; Linden, Martin; Unoson, Cecilia; Elf, Johan

Part of Biophysical Journal, 2013

• DOI for A Bayesian Approach to Single Particle Tracking Analysis

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

Marklund, Erik G.; Mahmutovic, Anel; Berg, Otto G.; Hammar, Petter et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19796-19801, 2013

• DOI for Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Persson, Fredrik; Linden, Martin; Unoson, Cecilia; Elf, Johan

Part of Nature Methods, p. 265-269, 2013

• DOI for Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Lost in presumption: stochastic reactions in spatial models

Mahmutovic, Anel; Fange, David; Berg, Otto G.; Elf, Johan

Part of Nature Methods, p. 1163-1166, 2012

• DOI for Lost in presumption: stochastic reactions in spatial models

Lost in presumption: stochastic reactions in spatial models

Mahmutovic, Anel; Fange, David; Berg, Otto G; Elf, Johan

Part of Nature Methods, 2012

MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit

Fange, David; Fange, David; Elf, Johan

Part of Bioinformatics, 2012

Positive allosteric feedback regulation of the stringent response enzyme RelA by its product

Shyp, Viktoriya; Tankov, Stoyan; Ermakov, Andrey; Kudrin, Pavel et al.

Part of EMBO Reports, p. 835-839, 2012

• DOI for Positive allosteric feedback regulation of the stringent response enzyme RelA by its product

The lac repressor displays facilitated diffusion in living cells

Hammar, Petter; Leroy, Prune; Mahmutovic, Anel; Marklund, Erik G et al.

Part of Science, p. 1595-1598, 2012

• DOI for The lac repressor displays facilitated diffusion in living cells

MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit

Fange, David; Mahmutovic, Anel; Elf, Johan

Part of Bioinformatics, p. 3155-3157, 2012

• DOI for MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit

Delay-induced anomalous fluctuations in intracellular regulation

Grönlund, Andreas; Lötstedt, Per; Elf, Johan

Part of Nature Communications, 2011

• DOI for Delay-induced anomalous fluctuations in intracellular regulation

Single-molecule investigations of the stringent response machinery in living bacterial cells

English, Brian P.; Hauryliuk, Vasili; Sanamrad, Arash; Tankov, Stoyan et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2011

• DOI for Single-molecule investigations of the stringent response machinery in living bacterial cells

Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40

Kuzmenko, Anton; Tankov, Stoyan; English, Brian P.; Tarassov, Ivan et al.

Part of Scientific reports, p. 195, 2011

• DOI for Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40

Costs and constraints from time-delayed feedback in small gene regulatory motifs

Grönlund, Andreas; Lötstedt, Per; Elf, Johan

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 8171-8176, 2010

• DOI for Costs and constraints from time-delayed feedback in small gene regulatory motifs

Stochastic reaction-diffusion kinetics in the microscopic limit

Fange, David; Berg, Otto G; Sjöberg, Paul; Elf, Johan

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19820-19825, 2010

• DOI for Stochastic reaction-diffusion kinetics in the microscopic limit

RNAs actively cycle on the Sm-like protein Hfq

Fender, Aurelie; Elf, Johan; Hampel, Kornelia; Zimmermann, Bastian et al.

Part of Genes & Development, p. 2621-2626, 2010

• DOI for RNAs actively cycle on the Sm-like protein Hfq

Fokker-Planck approximation of the master equation in molecular biology

Sjöberg, Paul; Lötstedt, Per; Elf, Johan

Part of Computing and Visualization in Science, p. 37-50, 2009

• DOI for Fokker-Planck approximation of the master equation in molecular biology

Effects of macromolecular crowding and DNA looping on gene regulation kinetics.

Li, Gene-Wei; Berg, Otto G.; Elf, Johan

Part of Nature Physics, p. 294-297, 2009

• DOI for Effects of macromolecular crowding and DNA looping on gene regulation kinetics.

Single molecule approaches to transcription factor kinetics in living cells

Li, Gene-Wei; Elf, Johan

Part of FEBS Letters, p. 3979-3983, 2009

• DOI for Single molecule approaches to transcription factor kinetics in living cells

Probing transcription factor dynamics at the single-molecule level in a living cell.

Elf, Johan; Li, Gene-Wei; Xie, X Sunney

Part of Science, p. 1191-1194, 2007

• DOI for Probing transcription factor dynamics at the single-molecule level in a living cell.

Bistable bacterial growth rate in response to antibiotics with low membrane permeability

Elf, Johan; Nilsson, Karin; Tenson, Tanel; Ehrenberg, Måns

Part of Physical Review Letters, 2006

• DOI for Bistable bacterial growth rate in response to antibiotics with low membrane permeability

Noise-induced Min phenotypes in E. coli

Fange, David; Elf, Johan

Part of PloS Computational Biology, p. 637-648, 2006

• DOI for Noise-induced Min phenotypes in E. coli

Stochastic reaction-diffusion simulation with MesoRD.

Hattne, Johan; Fange, David; Elf, Johan

Part of Bioinformatics, p. 2923-4, 2005

What makes ribosome-mediated transcriptional attenuation sensitive to amino

Elf, Johan; Ehrenberg, Måns

Part of PloS Computational Biology, 2005

Over expression of a tRNA(Leu) isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading.

Sörensen, Michael A; Elf, Johan; Bouakaz, Elli; Tenson, Tanel et al.

Part of J Mol Biol, p. 16-24, 2005

Selective charging of tRNA isoacceptors induced by amino-acid starvation.

Dittmar, Kimberly A; Sörensen, Michael A; Elf, Johan; Ehrenberg, Måns et al.

Part of EMBO Rep, p. 151-7, 2005

Ribosome bypassing at serine codons as a test of the model of selective transfer RNA charging.

Lindsley, Dale; Bonthuis, Paul; Gallant, Jonathan; Tofoleanu, Teodora et al.

Part of EMBO Rep, p. 147-50, 2005

Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate-limiting supply of amino acids.

Elf, Johan; Ehrenberg, Måns

Part of Biophys J, p. 132-46, 2005

Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases

Elf, Johan; Ehrenberg, Måns

Part of Systems Biology, p. 230-236, 2004

The bacterial toxin RelE displays codon specific cleavage of mRNAs in the ribosomal A-site

Pedersen, K; Elf, Johan

Part of Cell, p. 131-140, 2003

Near critical phenomena in metabolite pools

Elf, J

Part of Journal, p. 154-170, 2003

Systems biology is taking off.

Ehrenberg, M.; Elf, J; Aurell, E; Sandberg, R et al.

Part of Genome Research, p. 2475-2484, 2003

An efficient algorithm for mesoscopic reaction-diffusion simulation

Elf, J.

Part of Proceedings of the SPIE conference on Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems, 2003

Fast evaluation of fluctuations in biochemical networks with the linear noise approximation.

Elf, J.

Part of Genome Research, p. 2475-2484, 2003

Selective loss of charging of tRNA isoacceptors during amino acid limitation.

Elf, Johan; Tenson, Tanel; Ehrenberg, Måns

Part of Science, p. 1718-1722, 2003

Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons

Elf, J; Berg, OG; Ehrenberg, M

Part of JOURNAL OF MOLECULAR BIOLOGY, p. 941-954, 2001

Single-Molecule Kinetics in Living Cells

Elf, Johan; Barkefors, Irmeli

Part of Annual Review of Biochemistry, p. 635-659, 2019

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Bursting onto the scene?: Exploring stochastic mRNA production in bacteria

Jones, Daniel; Elf, Johan

Part of Current Opinion in Microbiology, p. 124-130, 2018

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Single molecule methods with applications in living cells

Persson, Fredrik; Barkefors, Irmeli; Elf, Johan

Part of Current Opinion in Biotechnology, p. 737-744, 2013

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Studying transcriptional interactions in single cells at sufficient resolution

Walldén, Mats; Elf, Johan

Part of Current Opinion in Biotechnology, p. 81-86, 2011

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Stochastic Modeling of Intracellular Kinetics

Paulsson, Johan; Elf, Johan

Part of System Modeling in Cellular Biology, p. 480, The MIT Press, Cambridge, 2006

Mesoscopic kinetics and its applications in protein synthesis

Elf, Johan; Paulsson, Johan; Berg, Otto; Ehrenberg, Måns

Part of Systems Biology, p. 95-118, Springer-Verlag GmbH, 2005

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Microfluidic chip for large-scale phenotypic characterization of E. coli

Karempudi, Praneeth; Khaji, Zahra; Vallin, Örjan; Tenje, Maria et al.

2019

An Evaluation of the Faster STORM Method for Super-resolution Microscopy

Ishaq, Omer; Elf, Johan; Wählby, Carolina

Part of Proceedings of the 22nd International Conference on Pattern Recognition, p. 4435-4440, 2014

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Problems of high dimension in molecular biology

Elf, Johan; Lötstedt, Per; Sjöberg, Paul

Part of Proc. 19th GAMM Seminar Leipzig on High-dimensional problems, p. 21-30, 2003

LacI follows a helical path while sliding along DNA

Marklund, Erik; Mahmutovic, Anel; Hammar, Petter; van der Spoel, David et al.

Transcription factor dissociation measurements using single molecule chase in living cells

Hammar, Petter; Walldén, Mats; Fange, David; Baltekin, Özden et al.

Fluctuations in replication initiation determine the generation time and size distributions of E. coli cells

Walldén, Mats; Fange, David; Gustaf, Ullman; Marklund, Erik G et al.

RecA mediated homology search finds segregated sister locus in minutes after a double stranded break

Gynnå, Arvid H.; Wiktor, Jakub; Leroy, Prune; Elf, Johan

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Real-time pooled optical screening with single-cell isolation capability

Karempudi, Praneeth; Amselem, Elias; Jones, Daniel; Khaji, Zahra et al.

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Molecular Origins of Kinetics and Selectivity in the lac operon

Lüking, Malin; Yuan, Jinwen; Larsson, Jimmy; Fange, David et al.

Optical pooled screening of a transposon mutant library to identify rare Escherichia coli replication initiation control phenotypes

Broström, Oscar; Karempudi, Praneeth; Amselem, Elias; Tenje, Maria et al.

Helix Propensity in the LacI hinge region mainly balances binding stability against inducibility

Yuan, Jinwen; Lüking, Malin; Zikrin, Spartak; Sen, Beer Chakra et al.

An Optical Pooled Screening Platform for Single-Molecule Measurements in Live Cells: A Pilot Study

Yuan, Jinwen; Kandavalli, Vinodh; Sirman, Dvir; Zikrin, Spartak et al.

Stochastic reaction–diffusion processes with embedded lower dimensional structures

Wang, Siyang; Elf, Johan; Hellander, Stefan; Lötstedt, Per

2012

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Fokker-Planck approximation of the master equation in molecular biology

Sjöberg, Paul; Lötstedt, Per; Elf, Johan

2005

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