Johan Elf

Sequence specificity in DNA binding is mainly governed by association

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

Ingår i Science, s. 442-445, 2022

• DOI för Sequence specificity in DNA binding is mainly governed by association
• Ladda ner fulltext (pdf) av Sequence specificity in DNA binding is mainly governed by association

RecA finds homologous DNA by reduced dimensionality search

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

Ingår i Nature, s. 426-429, 2021

• DOI för RecA finds homologous DNA by reduced dimensionality search
• Ladda ner fulltext (pdf) av 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.

Ingår i Nature Methods, s. 86-92, 2020

• DOI för 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.

Ingår i Nature, s. 858-+, 2020

• DOI för DNA surface exploration and operator bypassing during target search
• Ladda ner fulltext (pdf) av DNA surface exploration and operator bypassing during target search

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

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

Ingår i Science, s. 606-612, 2017

• DOI för 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.

Ingår i Science, s. 1420-1423, 2017

• DOI för 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.

Ingår i Cell, s. 729-739, 2016

• DOI för 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.

Ingår i Nature Genetics, s. 405-+, 2014

• DOI för 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

Ingår i Nature Methods, s. 265-269, 2013

• DOI för 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

Ingår i Nature Methods, 2012

The lac repressor displays facilitated diffusion in living cells

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

Ingår i Science, s. 1595-1598, 2012

• DOI för 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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 19820-19825, 2010

• DOI för 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

Ingår i Nature Physics, s. 294-297, 2009

• DOI för 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

Ingår i Science, s. 1191-1194, 2007

• DOI för 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

Ingår i Science, s. 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.

Ingår i npj Digital Medicine, 2025

• DOI för Culture-free detection of bacteria from blood for rapid sepsis diagnosis
• Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2025

• DOI för Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours
• Ladda ner fulltext (pdf) av 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.

Ingår i Communications Biology, 2025

• DOI för Pooled optical screening in bacteria using chromosomally expressed barcodes
• Ladda ner fulltext (pdf) av Pooled optical screening in bacteria using chromosomally expressed barcodes

Anti-correlation of LacI association and dissociation rates observed in living cells

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

Ingår i Nature Communications, 2025

• DOI för Anti-correlation of LacI association and dissociation rates observed in living cells
• Ladda ner fulltext (pdf) av Anti-correlation of LacI association and dissociation rates observed in living cells

The Escherichia coli chromosome moves to the replisome

Gras, Konrad; Fange, David; Elf, Johan

Ingår i Nature Communications, 2024

• DOI för The Escherichia coli chromosome moves to the replisome
• Ladda ner fulltext (pdf) av The Escherichia coli chromosome moves to the replisome

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

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

Ingår i npj Digital Medicine, 2025

• DOI för Culture-free detection of bacteria from blood for rapid sepsis diagnosis
• Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2025

• DOI för Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours
• Ladda ner fulltext (pdf) av 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.

Ingår i Communications Biology, 2025

• DOI för Pooled optical screening in bacteria using chromosomally expressed barcodes
• Ladda ner fulltext (pdf) av Pooled optical screening in bacteria using chromosomally expressed barcodes

Anti-correlation of LacI association and dissociation rates observed in living cells

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

Ingår i Nature Communications, 2025

• DOI för Anti-correlation of LacI association and dissociation rates observed in living cells
• Ladda ner fulltext (pdf) av Anti-correlation of LacI association and dissociation rates observed in living cells

The Escherichia coli chromosome moves to the replisome

Gras, Konrad; Fange, David; Elf, Johan

Ingår i Nature Communications, 2024

• DOI för The Escherichia coli chromosome moves to the replisome
• Ladda ner fulltext (pdf) av The Escherichia coli chromosome moves to the replisome

Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle

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

Ingår i Communications Biology, 2024

• DOI för Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle
• Ladda ner fulltext (pdf) av Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle

Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization

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

Ingår i Nature Communications, 2023

• DOI för Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
• Ladda ner fulltext (pdf) av Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization

Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2023

• DOI för Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle
• Ladda ner fulltext (pdf) av Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

Can molecular dynamics be used to simulate biomolecular recognition?

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

Ingår i Journal of Chemical Physics, 2023

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

Antibiotic perseverance increases the risk of resistance development

Brandis, Gerrit; Larsson, Jimmy; Elf, Johan

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2023

• DOI för Antibiotic perseverance increases the risk of resistance development
• Ladda ner fulltext (pdf) av Antibiotic perseverance increases the risk of resistance development

Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

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

Ingår i PloS Computational Biology, 2023

• DOI för Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy
• Ladda ner fulltext (pdf) av Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

Sequence specificity in DNA binding is mainly governed by association

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

Ingår i Science, s. 442-445, 2022

• DOI för Sequence specificity in DNA binding is mainly governed by association
• Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2022

• DOI för Direct measurements of mRNA translation kinetics in living cells
• Ladda ner fulltext (pdf) av Direct measurements of mRNA translation kinetics in living cells

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

Lüking, Malin; Elf, Johan; Levy, Yaakov

Ingår i Journal of Physical Chemistry B, s. 9971-9984, 2022

• DOI för Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study
• Ladda ner fulltext (pdf) av Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

Rapid antibiotic susceptibility testing and species identification for mixed samples

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

Ingår i Nature Communications, 2022

• DOI för Rapid antibiotic susceptibility testing and species identification for mixed samples
• Ladda ner fulltext (pdf) av Rapid antibiotic susceptibility testing and species identification for mixed samples

More Than Just Letters and Chemistry: Genomics Goes Mechanics

Deindl, Sebastian; Elf, Johan

Ingår i TIBS -Trends in Biochemical Sciences. Regular ed., s. 431-432, 2021

• DOI för 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.

Ingår i Communications Biology, 2021

• DOI för The highly dynamic nature of bacterial heteroresistance impairs its clinical detection
• Ladda ner fulltext (pdf) av The highly dynamic nature of bacterial heteroresistance impairs its clinical detection

Imaging-based screens of pool-synthesized cell libraries

Lawson, Michael; Elf, Johan

Ingår i Nature Methods, s. 358-365, 2021

• DOI för 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.

Ingår i Nature, s. 426-429, 2021

• DOI för RecA finds homologous DNA by reduced dimensionality search
• Ladda ner fulltext (pdf) av 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.

Ingår i Nature Methods, s. 86-92, 2020

• DOI för 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.

Ingår i Nature, s. 858-+, 2020

• DOI för DNA surface exploration and operator bypassing during target search
• Ladda ner fulltext (pdf) av 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.

Ingår i Journal of Physical Chemistry B, s. 3576-3590, 2019

• DOI för Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition
• Ladda ner fulltext (pdf) av 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

Ingår i ACS Omega, s. 20654-20664, 2019

• DOI för Rotational and Translational Diffusion of Proteins as a Function of Concentration
• Ladda ner fulltext (pdf) av Rotational and Translational Diffusion of Proteins as a Function of Concentration

Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories

Lindén, Martin; Elf, Johan

Ingår i Biophysical Journal, s. 276-282, 2018

• DOI för 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.

Ingår i PLOS ONE, 2018

• DOI för Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI
• Ladda ner fulltext (pdf) av 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.

Ingår i EMBO Journal, 2018

• DOI för 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.

Ingår i Nature Chemical Biology, s. 618-626, 2018

• DOI för 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.

Ingår i ACS Photonics, s. 233-255, 2017

• DOI för 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.

Ingår i CELL SYSTEMS, s. 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.

Ingår i 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.

Ingår i Science, s. 606-612, 2017

• DOI för 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.

Ingår i Molecular Systems Biology, 2017

• DOI för In situ genotyping of a pooled strain library after characterizing complex phenotypes
• Ladda ner fulltext (pdf) av 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

Ingår i Nature Communications, 2017

• DOI för Pointwise error estimates in localization microscopy
• Ladda ner fulltext (pdf) av Pointwise error estimates in localization microscopy

Kinetics of dCas9 target search in Escherichia coli

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

Ingår i Science, s. 1420-1423, 2017

• DOI för 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 9170-9175, 2017

• DOI för 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.

Ingår i Bioinformatics, s. 2394-2395, 2016

• DOI för Simulated single molecule microscopy with SMeagol
• Ladda ner fulltext (pdf) av 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.

Ingår i Cell, s. 729-739, 2016

• DOI för 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

Ingår i Journal of Physics A, 2016

• DOI för 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.

Ingår i Molecular Microbiology, s. 767-777, 2016

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

Arming the Neighborhood

Koskiniemi, Sanna; Elf, Johan

Ingår i Developmental Cell, s. 5-6, 2016

• DOI för Arming the Neighborhood

Hypothesis: Homologous Recombination Depends on Parallel Search

Elf, Johan

Ingår i CELL SYSTEMS, s. 325-327, 2016

• DOI för 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.

Ingår i IEEE Journal on Selected Topics in Signal Processing, s. 174-184, 2016

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

Staying Clear of the Dragons

Elf, Johan

Ingår i CELL SYSTEMS, s. 219-220, 2016

• DOI för 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

Ingår i Nucleic Acids Research, s. 3454-3464, 2015

• DOI för 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

Ingår i Biophysical Journal, 2015

Stochastic reaction–diffusion processes with embedded lower-dimensional structures

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

Ingår i Bulletin of Mathematical Biology, s. 819-853, 2014

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

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

Elf, Johan

Ingår i Biophysical Journal, 2014

• DOI för 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 11413-11418, 2014

• DOI för 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.

Ingår i Nature Genetics, s. 405-+, 2014

• DOI för 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.

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

• DOI för 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

Ingår i Nature Communications, 2013

• DOI för 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

Ingår i Biophysical Journal, 2013

• DOI för 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 19796-19801, 2013

• DOI för 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

Ingår i Nature Methods, s. 265-269, 2013

• DOI för 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

Ingår i Nature Methods, s. 1163-1166, 2012

• DOI för 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

Ingår i Nature Methods, 2012

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

Fange, David; Fange, David; Elf, Johan

Ingår i 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.

Ingår i EMBO Reports, s. 835-839, 2012

• DOI för 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.

Ingår i Science, s. 1595-1598, 2012

• DOI för 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

Ingår i Bioinformatics, s. 3155-3157, 2012

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

Delay-induced anomalous fluctuations in intracellular regulation

Grönlund, Andreas; Lötstedt, Per; Elf, Johan

Ingår i Nature Communications, 2011

• DOI för 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2011

• DOI för 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.

Ingår i Scientific reports, s. 195, 2011

• DOI för 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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 8171-8176, 2010

• DOI för 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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 19820-19825, 2010

• DOI för 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.

Ingår i Genes & Development, s. 2621-2626, 2010

• DOI för 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

Ingår i Computing and Visualization in Science, s. 37-50, 2009

• DOI för 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

Ingår i Nature Physics, s. 294-297, 2009

• DOI för 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

Ingår i FEBS Letters, s. 3979-3983, 2009

• DOI för 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

Ingår i Science, s. 1191-1194, 2007

• DOI för 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

Ingår i Physical Review Letters, 2006

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

Noise-induced Min phenotypes in E. coli

Fange, David; Elf, Johan

Ingår i PloS Computational Biology, s. 637-648, 2006

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

Stochastic reaction-diffusion simulation with MesoRD.

Hattne, Johan; Fange, David; Elf, Johan

Ingår i Bioinformatics, s. 2923-4, 2005

What makes ribosome-mediated transcriptional attenuation sensitive to amino

Elf, Johan; Ehrenberg, Måns

Ingår i 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.

Ingår i J Mol Biol, s. 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.

Ingår i EMBO Rep, s. 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.

Ingår i EMBO Rep, s. 147-50, 2005

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

Elf, Johan; Ehrenberg, Måns

Ingår i Biophys J, s. 132-46, 2005

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

Elf, Johan; Ehrenberg, Måns

Ingår i Systems Biology, s. 230-236, 2004

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

Pedersen, K; Elf, Johan

Ingår i Cell, s. 131-140, 2003

Near critical phenomena in metabolite pools

Elf, J

Ingår i Journal, s. 154-170, 2003

Systems biology is taking off.

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

Ingår i Genome Research, s. 2475-2484, 2003

An efficient algorithm for mesoscopic reaction-diffusion simulation

Elf, J.

Ingår i 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.

Ingår i Genome Research, s. 2475-2484, 2003

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

Elf, Johan; Tenson, Tanel; Ehrenberg, Måns

Ingår i Science, s. 1718-1722, 2003

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

Elf, J; Berg, OG; Ehrenberg, M

Ingår i JOURNAL OF MOLECULAR BIOLOGY, s. 941-954, 2001

Single-Molecule Kinetics in Living Cells

Elf, Johan; Barkefors, Irmeli

Ingår i Annual Review of Biochemistry, s. 635-659, 2019

• DOI för Single-Molecule Kinetics in Living Cells

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

Jones, Daniel; Elf, Johan

Ingår i Current Opinion in Microbiology, s. 124-130, 2018

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

Single molecule methods with applications in living cells

Persson, Fredrik; Barkefors, Irmeli; Elf, Johan

Ingår i Current Opinion in Biotechnology, s. 737-744, 2013

• DOI för Single molecule methods with applications in living cells

Studying transcriptional interactions in single cells at sufficient resolution

Walldén, Mats; Elf, Johan

Ingår i Current Opinion in Biotechnology, s. 81-86, 2011

• DOI för Studying transcriptional interactions in single cells at sufficient resolution

Stochastic Modeling of Intracellular Kinetics

Paulsson, Johan; Elf, Johan

Ingår i System Modeling in Cellular Biology, s. 480, The MIT Press, Cambridge, 2006

Mesoscopic kinetics and its applications in protein synthesis

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

Ingår i Systems Biology, s. 95-118, Springer-Verlag GmbH, 2005

• DOI för Mesoscopic kinetics and its applications in protein synthesis

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

Ingår i Proceedings of the 22nd International Conference on Pattern Recognition, s. 4435-4440, 2014

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

Problems of high dimension in molecular biology

Elf, Johan; Lötstedt, Per; Sjöberg, Paul

Ingår i Proc. 19th GAMM Seminar Leipzig on High-dimensional problems, s. 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

• DOI för RecA mediated homology search finds segregated sister locus in minutes after a double stranded break
• Ladda ner fulltext (pdf) av RecA mediated homology search finds segregated sister locus in minutes after a double stranded break

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

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

• DOI för Real-time pooled optical screening with single-cell isolation capability

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.

The LacI hinge region balances binding stability against inducibility

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

• DOI för The LacI hinge region balances binding stability against inducibility

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

• Ladda ner fulltext (pdf) av Stochastic reaction–diffusion processes with embedded lower dimensional structures

Fokker-Planck approximation of the master equation in molecular biology

Sjöberg, Paul; Lötstedt, Per; Elf, Johan

2005

• Ladda ner fulltext (pdf) av Fokker-Planck approximation of the master equation in molecular biology