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
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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.

Ingår i npj Digital Medicine, 2025

• DOI för Culture-free detection of bacteria from blood for rapid sepsis diagnosis
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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
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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
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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
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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.

Ingår i Communications Biology, 2024

• DOI för Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle
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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
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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.

Ingår i Journal of Chemical Physics, 2023

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

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
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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
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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.

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
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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

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
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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
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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
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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
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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

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

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
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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
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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
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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

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
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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
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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

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
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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

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

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

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

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
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Kinetics of dCas9 Target Search in Escherichia Coli

Jones, Daniel; Unoson, Cecilia; Leroy, Prune; Curic, Vladimir et al.

Ingår i Biophysical Journal, 2017

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

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

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
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Real- Time Single Protein Tracking with Polarization Readout using a Confocal Microscope

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

Ingår i Biophysical Journal, 2017

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

In Vivo Measurements of Protein Synthesis Kinetics using Single-Molecule Tracking of E.Coli tRNAS

Volkov, Ivan; Aguirre, Javier; Lindén, Martin; Elf, Johan et al.

Ingår i Biophysical Journal, 2016

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

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

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
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Staying Clear of the Dragons

Elf, Johan

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

• DOI för Staying Clear of the Dragons

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

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

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

Lindén, Martin; Elf, Johan

Ingår i Biophysical Journal, 2015

What matters for lac repressor search in vivo-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 search in vivo-sliding, hopping, intersegment transfer, crowding on DNA or recognition?
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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?

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