Department of Cell and Molecular Biology

Department of Cell ... Research Publications

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Dissertations
Upcomming dissertations at Uppsala University

Publications

A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration

Subramanian, Elaiyaraja; Elewa, Ahmed; Brito, Goncalo; Kumar, Anoop et al.

Part of Developmental Cell, p. 450-460, 2023.

DOI for A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration Download full text (pdf) of A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration

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Amino acid substitutions in human growth hormone affect secondary structure and receptor binding

Rajkovic, Andrei; Kanchugal Puttaswamy, Sandesh; Abdurakhmanov, Eldar; Howard, Rebecca et al.

Part of PLOS ONE, 2023.

DOI for Amino acid substitutions in human growth hormone affect secondary structure and receptor binding Download full text (pdf) of Amino acid substitutions in human growth hormone affect secondary structure and receptor binding

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Amino acid substitutions in human growth hormone affect secondary structure and receptor binding

Rajkovic, Andrei; Kanchugal Puttaswamy, Sandesh; Abdurakhmanov, Eldar; Howard, Rebecca et al.

Part of PLOS ONE, 2023.

DOI for Amino acid substitutions in human growth hormone affect secondary structure and receptor binding Download full text (pdf) of Amino acid substitutions in human growth hormone affect secondary structure and receptor binding

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Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia

Maciejowski, William J.; Gile, Gillian H.; Jerlstrom-Hultqvist, Joel; Dacks, Joel B.

Part of International Journal of Parasitology, p. 233-245, 2023.

DOI for Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia
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 Download full text (pdf) of Antibiotic perseverance increases the risk of resistance development

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Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria

Parajuli, Narayan Prasad; Emmerich, Andrew G; Mandava, Chandra Sekhar; Pavlov, Michael Y. et al.

Part of Nature Communications, 2023.

DOI for Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria Download full text (pdf) of Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria

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Autologous hematopoietic stem cell transplantation significantly alters circulating ceramides in peripheral blood of relapsing-remitting multiple sclerosis patients

Vaivade, Aina; Wiberg, Anna; Khoonsari, Payam Emami; Carlsson, Henrik et al.

Part of Lipids in Health and Disease, 2023.

DOI for Autologous hematopoietic stem cell transplantation significantly alters circulating ceramides in peripheral blood of relapsing-remitting multiple sclerosis patients Download full text (pdf) of Autologous hematopoietic stem cell transplantation significantly alters circulating ceramides in peripheral blood of relapsing-remitting multiple sclerosis patients

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Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study

Minh, Nghia Nguyen Thi; Begum, Afshan; Zhang, Jun; Leira, Petter et al.

Part of Journal of Physical Chemistry B, p. 6628-6635, 2023.

DOI for Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study Download full text (pdf) of Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study

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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?
Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture

Wang, Han; Salaipeth, Lakha; Miyazaki, Naoyuki; Suzuki, Nobuhiro et al.

Part of PLoS Pathogens, 2023.

DOI for Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture Download full text (pdf) of Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture

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Cerebrospinal fluid cytokines after autologous haematopoietic stem cell transplantation and intrathecal rituximab treatment for multiple sclerosis

Burman, Joachim; Zhukovskaja, Christina; Svenningsson, Anders; Freyhult, Eva et al.

Part of Brain Communications, 2023.

DOI for Cerebrospinal fluid cytokines after autologous haematopoietic stem cell transplantation and intrathecal rituximab treatment for multiple sclerosis Download full text (pdf) of Cerebrospinal fluid cytokines after autologous haematopoietic stem cell transplantation and intrathecal rituximab treatment for multiple sclerosis

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Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon

Mosquera, Katherine D.; Nilsson, Louise K. J.; de Oliveira, Marta Rodrigues; Rocha, Elerson Matos et al.

Part of Parasites & Vectors, 2023.

DOI for Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon Download full text (pdf) of Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon

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Computational design of the temperature optimum of an enzyme reaction

van der Ent, Florian; Skagseth, Susann; Lund, Bjarte A.; Socan, Jaka et al.

Part of Science Advances, 2023.

DOI for Computational design of the temperature optimum of an enzyme reaction Download full text (pdf) of Computational design of the temperature optimum of an enzyme reaction

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Delineating Plasmodium liver infection across space and time

Hildebrandt, Franziska; Ankarklev, Johan; Matuschewski, Kai

Part of Trends in Parasitology, p. 80-82, 2023.

DOI for Delineating Plasmodium liver infection across space and time
Design Of Drug Efficacy Guided By Free Energy Simulations Of The β2-Adrenoceptor

Panel, Nicolas; Vo, Duc Duy; Kahlous, Nour Aldin; Harald, HuÌbner et al.

Part of Angewandte Chemie International Edition, 2023.

DOI for Design Of Drug Efficacy Guided By Free Energy Simulations Of The β2-Adrenoceptor
Development and Characterization of Novel Selective, Non-Basic Dopamine D-2 Receptor Antagonists for the Treatment of Schizophrenia

Stepnicki, Piotr; Wosko, Sylwia; Bartyzel, Agata; Zieba, Agata et al.

Part of Molecules, 2023.

DOI for Development and Characterization of Novel Selective, Non-Basic Dopamine D-2 Receptor Antagonists for the Treatment of Schizophrenia Download full text (pdf) of Development and Characterization of Novel Selective, Non-Basic Dopamine D-2 Receptor Antagonists for the Treatment of Schizophrenia

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Diarylether-Amino Acid Conjugates as New Class of Anticancer Agents

Thanh Le, Thanh; Huy Vo, Vinh; Thanh Huong Le, Thi; Huy Hoang Vo, Nguyen et al.

Part of CHEMISTRYSELECT, 2023.

DOI for Diarylether-Amino Acid Conjugates as New Class of Anticancer Agents
Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold- Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa

Cotman, Andrej Emanuel; Durcik, Martina; Tiz, Davide Benedetto; Fulgheri, Federica et al.

Part of Journal of Medicinal Chemistry, p. 1380-1425, 2023.

DOI for Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold- Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa Download full text (pdf) of Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold- Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa

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Draft genomes of Blastocystis subtypes from human samples of Colombia

Higuera, Adriana; Salas-Leiva, Dayana E.; Curtis, Bruce; Patino, Luz H. et al.

Part of Parasites & Vectors, 2023.

DOI for Draft genomes of Blastocystis subtypes from human samples of Colombia Download full text (pdf) of Draft genomes of Blastocystis subtypes from human samples of Colombia

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Dynamics of release factor recycling during translation termination in bacteria

Prabhakar, Arjun; Pavlov, Michael Y.; Zhang, Jingji; Indrisiunaite, Gabriele et al.

Part of Nucleic Acids Research, p. 5774-5790, 2023.

DOI for Dynamics of release factor recycling during translation termination in bacteria Download full text (pdf) of Dynamics of release factor recycling during translation termination in bacteria

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Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system

Suades, Albert; Qureshi, Aziz; McComas, Sarah E.; Coincon, Mathieu et al.

Part of Nature Communications, 2023.

DOI for Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system Download full text (pdf) of Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system

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Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Lauterbur, M. Elise; Cavassim, Maria Izabel A.; Gladstein, Ariella L.; Gower, Graham et al.

Part of eLIFE, 2023.

DOI for Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Download full text (pdf) of Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

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Extended cleavage specificities of human granzymes A and K, two closely related enzymes with conserved but still poorly defined functions in T and NK cell-mediated immunity

Aybay, Erdem; Ryu, Jinhye; Fu, Zhirong; Akula, Srinivas et al.

Part of Frontiers in Immunology, 2023.

DOI for Extended cleavage specificities of human granzymes A and K, two closely related enzymes with conserved but still poorly defined functions in T and NK cell-mediated immunity Download full text (pdf) of Extended cleavage specificities of human granzymes A and K, two closely related enzymes with conserved but still poorly defined functions in T and NK cell-mediated immunity

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Gene gain facilitated endosymbiotic evolution of Chlamydiae

Dharamshi, Jennah; Köstlbacher, Stephan; Schön, Max Emil; Collingro, Astrid et al.

Part of Nature Microbiology, p. 40-54, 2023.

DOI for Gene gain facilitated endosymbiotic evolution of Chlamydiae Download full text (pdf) of Gene gain facilitated endosymbiotic evolution of Chlamydiae

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Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222

Chaudhari, Aditya S.; Chatterjee, Aditi; Domingos, Catarina A. O.; Andrikopoulos, Prokopis C. et al.

Part of Protein Science, 2023.

DOI for Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222 Download full text (pdf) of Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222

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Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth

Zhou, Yu; Gunn, Laura; Birch, Rosemary; Andersson, Inger et al.

Part of NATURE PLANTS, p. 978-986, 2023.

DOI for Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth
High cardiomyocyte diversity in human early prenatal heart development

Sylven, Christer; Wärdell, Eva; Månsson-Broberg, Agneta; Cingolani, Eugenio et al.

Part of iScience, 2023.

DOI for High cardiomyocyte diversity in human early prenatal heart development Download full text (pdf) of High cardiomyocyte diversity in human early prenatal heart development

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High prevalence of Escherichia coli co-harboring conjugative plasmids with colistin- and carbapenem resistance genes in a wastewater treatment plant in China

Wang, Di; Zou, Huiyun; Zhao, Ling; Li, Qi et al.

Part of International journal of hygiene and environmental health (Print), 2023.

DOI for High prevalence of Escherichia coli co-harboring conjugative plasmids with colistin- and carbapenem resistance genes in a wastewater treatment plant in China
High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)

Hundsdoerfer, Anna K.; Schell, Tilman; Patzold, Franziska; Wright, Charlotte J. et al.

Part of BMC Genomics, 2023.

DOI for High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae) Download full text (pdf) of High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)

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High-resolution wavefront sensing and aberration analysis of multi-spectral extreme ultraviolet beams

Du, Mengqi; Liu, Xiaomeng; Pelekanidis, Antonios; Zhang, Fengliang et al.

Part of Optica, p. 255-263, 2023.

DOI for High-resolution wavefront sensing and aberration analysis of multi-spectral extreme ultraviolet beams

Open access
House Dust Mite and Cat Dander Extract Induce Asthma-Like Histopathology with an Increase of Mucosal Mast Cells in a Guinea Pig Model

Ramos-Ramirez, Patricia; Liu, Jielu; Mogren, Sofia; Gregory, Joshua et al.

Part of Journal of Immunology Research, 2023.

DOI for House Dust Mite and Cat Dander Extract Induce Asthma-Like Histopathology with an Increase of Mucosal Mast Cells in a Guinea Pig Model Download full text (pdf) of House Dust Mite and Cat Dander Extract Induce Asthma-Like Histopathology with an Increase of Mucosal Mast Cells in a Guinea Pig Model

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Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis

Majumdar, Soneya; Emmerich, Andrew G; Krakovka, Sascha; Mandava, Chandra Sekhar et al.

Part of Nucleic Acids Research, p. 3436-3451, 2023.

DOI for Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis Download full text (pdf) of Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis

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KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes

Crean, Rory M.; Slusky, Joanna S. G.; Kasson, Peter M.; Kamerlin, Shina C. Lynn

Part of Journal of Chemical Physics, 2023.

DOI for KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes Download full text (pdf) of KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes

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Mechanistic dissection of antibody inhibition of influenza entry yields unexpected heterogeneity

Sengar, Anjali; Cervantes, Marcos; Kasson, Peter M.

Part of Biophysical Journal, p. 1996-2006, 2023.

DOI for Mechanistic dissection of antibody inhibition of influenza entry yields unexpected heterogeneity Download full text (pdf) of Mechanistic dissection of antibody inhibition of influenza entry yields unexpected heterogeneity

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Microbial Profiling of Amniotic Fluid, Umbilical Blood and Placenta of the Foaling Mare

Hemberg, Elisabeth; Niazi, Adnan; Guo, Yongzhi; Debnar, Viktoria J. et al.

Part of Animals, 2023.

DOI for Microbial Profiling of Amniotic Fluid, Umbilical Blood and Placenta of the Foaling Mare Download full text (pdf) of Microbial Profiling of Amniotic Fluid, Umbilical Blood and Placenta of the Foaling Mare

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MindReader: Unsupervised Classification of Electroencephalographic Data

Rivas-Carrillo, Salvador Daniel; Akkuratov, Evgeny E.; Valdez Ruvalcaba, Hector; Vargas-Sanchez, Angel et al.

Part of Sensors, 2023.

DOI for MindReader: Unsupervised Classification of Electroencephalographic Data Download full text (pdf) of MindReader: Unsupervised Classification of Electroencephalographic Data

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Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

Seely, Savannah M.; Parajuli, Narayan Prasad; De Tarafder, Arindam; Ge, Xueliang et al.

Part of Nature Communications, 2023.

DOI for Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome Download full text (pdf) of Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

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Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group

Baiao, Guilherme Costa; Schneider, Daniela I.; Miller, Wolfgang J.; Klasson, Lisa

Part of Molecular Phylogenetics and Evolution, 2023.

DOI for Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group Download full text (pdf) of Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group

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N,2,6-Trisubstituted 1H-benzimidazole derivatives as a new scaffold of antimicrobial and anticancer agents: design, synthesis, in vitro evaluation, and in silico studies

Pham, Em Canh; Thi, Tuong Vi Le; Hong, Huong Ha Ly; Thi, Bich Ngoc Vo et al.

Part of RSC Advances, p. 399-420, 2023.

DOI for N,2,6-Trisubstituted 1H-benzimidazole derivatives as a new scaffold of antimicrobial and anticancer agents: design, synthesis, in vitro evaluation, and in silico studies Download full text (pdf) of N,2,6-Trisubstituted 1H-benzimidazole derivatives as a new scaffold of antimicrobial and anticancer agents: design, synthesis, in vitro evaluation, and in silico studies

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New insights into the effect of mutations on affibody-Fc interaction, a molecular dynamics simulation approach

Nosrati, Masoumeh; Housaindokht, Mohammad Reza

Part of Journal of Structural Biology, 2023.

DOI for New insights into the effect of mutations on affibody-Fc interaction, a molecular dynamics simulation approach
Persistent transmission of carbapenem-resistant, hypervirulent Klebsiella pneumoniae between a hospital and urban aquatic environments

Zou, Huiyun; Zhou, Ziyu; Berglund, Björn; Zheng, Beiwen et al.

Part of Water Research, 2023.

DOI for Persistent transmission of carbapenem-resistant, hypervirulent Klebsiella pneumoniae between a hospital and urban aquatic environments
Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

Koenekoop, Lucien; Åqvist, Johan

Part of Molecular biology and evolution, 2023.

DOI for Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction Download full text (pdf) of Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

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Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

Schmidt, Lisa; Van der Spoel, David; Walz, Marie-Madeleine

Part of ACS PHYSICAL CHEMISTRY AU, p. 84-93, 2023.

DOI for Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations Download full text (pdf) of Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

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Proinflammatory allogeneic dendritic cells enhance the therapeutic efficacy of systemic anti-4-1BB treatment

Ali, Arwa; Gao, Menghan; Iskantar, Alexandros; Wang, Hai et al.

Part of Frontiers in Immunology, 2023.

DOI for Proinflammatory allogeneic dendritic cells enhance the therapeutic efficacy of systemic anti-4-1BB treatment Download full text (pdf) of Proinflammatory allogeneic dendritic cells enhance the therapeutic efficacy of systemic anti-4-1BB treatment

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Proteogenomics decodes the evolution of human ipsilateral breast cancer

De Marchi, Tommaso; Pyl, Paul Theodor; Sjöström, Martin; Reinsbach, Susanne Erika et al.

Part of Communications Biology, 2023.

DOI for Proteogenomics decodes the evolution of human ipsilateral breast cancer Download full text (pdf) of Proteogenomics decodes the evolution of human ipsilateral breast cancer

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Rapid adaptations of Legionella pneumophila to the human host

Leenheer, Daniël; Moreno, Anaisa; Paranjape, Kiran; Murray, Susan et al.

Part of Microbial Genomics, 2023.

DOI for Rapid adaptations of Legionella pneumophila to the human host Download full text (pdf) of Rapid adaptations of Legionella pneumophila to the human host

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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 Download full text (pdf) of 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; Brostrom, 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 Download full text (pdf) of Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

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Relationship between iron deficiency and expression of genes involved in iron metabolism in human myocardium and skeletal muscle

Cabrera, C.; Frisk, Christoffer; Lofstrom, U.; Lynga, P. et al.

Part of International Journal of Cardiology, p. 82-88, 2023.

DOI for Relationship between iron deficiency and expression of genes involved in iron metabolism in human myocardium and skeletal muscle Download full text (pdf) of Relationship between iron deficiency and expression of genes involved in iron metabolism in human myocardium and skeletal muscle

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Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"

Åqvist, Johan

Part of ACS Catalysis, p. 10007-10009, 2023.

DOI for Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme" Download full text (pdf) of Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"

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