Publikationer

  • Stratmann, Svea; Yones, Sara A.; Mayrhofer, Markus; Norgren, Nina et al.

    Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

    Ingår i Blood Advances SUPPLEMENTAL INFORMATION FOR: Genomic characterization of adult and pediatric relapsed acute myeloid leukemia reveals novel therapeutic targets, s. 900-912, 2021.

  • Nencetti, Susanna; Cuffaro, Doretta; Nuti, Elisa; Ciccone, Lidia et al.

    Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines

    Ingår i Journal of enzyme inhibition and medicinal chemistry (Print), s. 34-47, 2021.

    Open access
  • Fleetwood, Oliver; Carlsson, Jens; Delemotte, Lucie

    Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

    Ingår i eLIFE, 2021.

    Open access
  • Matricon, Pierre; Suresh, R. Rama; Gao, Zhan-Guo; Panel, Nicolas et al.

    Ligand design by targeting a binding site water

    Ingår i Chemical Science, s. 960-968, 2021.

    Open access
  • Walz, Marie-Madeleine; Van der Spoel, David

    Microscopic origins of conductivity in molten salts unraveled by computer simulations

    Ingår i Communications Chemistry, 2021.

    Open access
  • Wannberg, Johan; Gising, Johan; Lindman, Jens; Salander, Jessica et al.

    N-(Methyloxycarbonyl)thiophene sulfonamides as high affinity AT2 receptor ligands

    Ingår i Bioorganic & Medicinal Chemistry, 2021.

  • Guo, Xiaohu; Söderholm, Annika; Kanchugal Puttaswamy, Sandesh; Isaksen, Geir V et al.

    Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

    Ingår i eLIFE, 2021.

    Open access
  • Cavalli, Marco; Diamanti, Klev; Pan, Gang; Spalinskas, Rapolas et al.

    A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver

    Ingår i Omics, s. 180-194, 2020.

    Open access
  • Raehtz, Kevin D.; Barrenäs, Fredrik; Xu, Cuiling; Busman-Sahay, Kathleen et al.

    African green monkeys avoid SIV disease progression by preventing intestinal dysfunction and maintaining mucosal barrier integrity

    Ingår i PLoS Pathogens, 2020.

    Open access
  • Henschel, Henning; Van der Spoel, David

    An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

    Ingår i Journal of Physical Chemistry Letters, s. 5471-5475, 2020.

    Open access
  • Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A. et al.

    Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

    Ingår i Nature, s. 102-111, 2020.

    Open access
  • Manzetti, Sergio; Trounev, Alexander

    Analytical Solutions for a Supersymmetric Wave‐Equation for Quasiparticles in a Quantum System

    Ingår i Advanced Theory and Simulations, 2020.

  • Carlevaro-Fita, Joana; Lanzos, Andres; Feuerbach, Lars; Hong, Chen et al.

    Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

    Ingår i Communications Biology, 2020.

    Open access
  • Socan, Jaka; Purg, Miha; Åqvist, Johan

    Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

    Ingår i Nature Communications, 2020.

    Open access
  • Machado, Teresa F. G.; Purg, Miha; McMahon, Stephen A.; Read, Benjamin J. et al.

    Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry

    Ingår i ACS Catalysis, s. 15019-15032, 2020.

    Open access
  • Ballante, Flavio; Rudling, Axel; Zeifman, Alexey; Luttens, Andreas et al.

    Docking Finds GPCR Ligands in Dark Chemical Matter

    Ingår i Journal of Medicinal Chemistry, s. 613-620, 2020.

  • Rebollido-Rios, Rocio; Venton, Geoffroy; Sanchez-Redondo, Sara; Iglesias i Felip, Carmela et al.

    Dual disruption of aldehyde dehydrogenases 1 and 3 promotes functional changes in the glutathione redox system and enhances chemosensitivity in nonsmall cell lung cancer

    Ingår i Oncogene, s. 2756-2771, 2020.

    Open access
  • Manzetti, Sergio; Trounev, Alexander

    Electromagnetic Vorticity in a Square-Well Crystal System Described by a Supersymmetric Wave-Equation

    Ingår i Advanced Theory and Simulations, s. 1900186-, 2020.

  • Fleetwood, Oliver; Matricon, Pierre; Carlsson, Jens; Delemotte, Lucie

    Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches

    Ingår i Biochemistry, s. 880-891, 2020.

    Open access
  • Gorini, Giacomo; Fourati, Slim; Vaccari, Monica; Rahman, Mohammad Arif et al.

    Engagement of monocytes, NK cells, and CD4(+) Th1 cells by ALVAC-SIV vaccination results in a decreased risk of SIVmac251 vaginal acquisition

    Ingår i PLoS Pathogens, 2020.

    Open access
  • Vasile, Silvana; Hallberg, Anders; Sallander, Jessica; Hallberg, Mathias et al.

    Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists

    Ingår i Biomolecules, 2020.

    Open access
  • Wang, Xuesong; Jespers, Willem; Bongers, Brandon J.; Jansen, Maria C. C. Habben et al.

    Full length article Characterization of cancer -related somatic mutations in the adenosine A 2B receptor

    Ingår i European Journal of Pharmacology, 2020.

  • Rodriguez-Espigares, Ismael; Torrens-Fontanals, Mariona; Tiemann, Johanna K. S.; Aranda-Garcia, David et al.

    GPCRmd uncovers the dynamics of the 3D-GPCRome

    Ingår i Nature Methods, s. 777-787, 2020.

  • Prah, Alja; Purg, Miha; Stare, Jernej; Vianello, Robert et al.

    How Monoamine Oxidase A Decomposes Serotonin: An Empirical Valence Bond Simulation of the Reactive Step

    Ingår i Journal of Physical Chemistry B, s. 8259-8265, 2020.

    Open access
  • Cabrera, Carin C.; Ekstrom, Mattias; Linde, Cecilia; Persson, Hans et al.

    Increased iron absorption in patients with chronic heart failure and iron deficiency

    Ingår i Journal of Cardiac Failure, s. 440-443, 2020.

    Open access
  • van der Valk, Tom; Vezzi, Francesco; Ormestad, Mattias; Dalen, Love et al.

    Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

    Ingår i Molecular Ecology Resources, s. 1171-1181, 2020.

  • Diamanti, Klev; Visvanathar, Robin; Pereira, Maria J.; Cavalli, Marco et al.

    Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes

    Ingår i Scientific Reports, 2020.

    Open access
  • Barlow, Nicholas; Reddy Vanga, Sudarsana; Sävmarker, Jonas; Sandström, Anja et al.

    Macrocyclic Peptidomimetics as Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

    Ingår i RSC Medicinal chemistry, s. 234-244, 2020.

  • Bortot, Leandro Oliveira; Bashardanesh, Zahedeh; Van der Spoel, David

    Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

    Ingår i Journal of Chemical Information and Modeling, s. 322-331, 2020.

  • Hage, Camilla; Löfgren, Lars; Michopoulos, Filippos; Nilsson, Ralph et al.

    Metabolomic Profile in HFpEF vs HFrEF Patients

    Ingår i Journal of Cardiac Failure, s. 1050-1059, 2020.

  • Mallo-Abreu, Ana; Prieto-Diaz, Ruben; Jespers, Willem; Azuaje, Jhonny et al.

    Nitrogen-Walk Approach to Explore Bioisosteric Replacements in a Series of Potent A(2B) Adenosine Receptor Antagonists

    Ingår i Journal of Medicinal Chemistry, s. 7721-7739, 2020.

  • Campbell, Peter J.; Diamanti, Klev; Komorowski, Jan; Umer, Husen Muhammad et al.

    Pan-cancer analysis of whole genomes

    Ingår i Nature, s. 82-93, 2020.

    Open access
  • Jaiteh, Mariama; Rodríguez-Espigares, Ismael; Selent, Jana; Carlsson, Jens

    Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

    Ingår i PloS Computational Biology, 2020.

    Open access
  • Yildirim, Ahmet; Ghahremanpour, Mohammad Mehdi; Van der Spoel, David

    Propagation of uncertainty in physicochemical data to force field predictions

    Ingår i PHYSICAL REVIEW RESEARCH, 2020.

    Open access
  • Burggraaff, Lindsey; Lenselink, Eelke B.; Jespers, Willem; van Engelen, Jesper et al.

    Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors

    Ingår i Journal of Chemical Information and Modeling, s. 4283-4295, 2020.

    Open access
  • Engen, Karin; Reddy Vanga, Sudarsana; Lundbäck, Thomas; Agalo, Faith et al.

    Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors

    Ingår i ChemistryOpen, s. 325-337, 2020.

    Open access
  • Sommer, Martha E.; Selent, Jana; Carlsson, Jens; De Graaf, Chris et al.

    The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling

    Ingår i ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE, s. 361-370, 2020.

    Open access
  • Henschel, Henning; Andersson, Alfred T.; Jespers, Willem; Ghahremanpour, Mohammad Mehdi et al.

    Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

    Ingår i Journal of Chemical Theory and Computation, s. 3307-3315, 2020.

    Open access
  • Kamerlin, Natasha; Delcey, Mickaël G; Manzetti, Sergio; Van der Spoel, David

    Toward a Computational Ecotoxicity Assay

    Ingår i Journal of Chemical Information and Modeling, s. 3792-3803, 2020.

  • Etemadikhah, Mitra; Niazi, Adnan; Wetterberg, Lennart; Feuk, Lars

    Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes

    Ingår i Scientific Reports, 2020.

    Open access
  • Jespers, Willem; Verdon, Gregory; Azuaje, Jhonny; Majellaro, Maria et al.

    X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A(2A) Adenosine Receptor Antagonists

    Ingår i Angewandte Chemie International Edition, s. 16536-16543, 2020.

    Open access
  • Wright, Shane C.; Kozielewicz, Pawel; Kowalski-Jahn, Maria; Petersen, Julian et al.

    A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection

    Ingår i Nature Communications, 2019.

    Open access
  • Isaksson, Rebecka; Lindman, Jens; Wannberg, Johan; Sallander, Jessica et al.

    A Series of Analogues to the AT2R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode

    Ingår i ChemistryOpen, s. 114-125, 2019.

    Open access
  • Borroto-Escuela, Dasiel O.; Narváez, Manuel; Romero Fernández, Wilber; Pinton, Luca et al.

    Acute Cocaine Enhances Dopamine D2R Recognition and Signaling and Counteracts D2R Internalization in Sigma1R-D2R Heteroreceptor Complexes

    Ingår i Molecular Neurobiology, s. 7045-7055, 2019.

    Open access
  • Cavalli, Marco; Baltzer, Nicholas; Umer, Husen Muhammad; Grau, Jan et al.

    Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases

    Ingår i Scientific Reports, 2019.

    Open access
  • Moghadam, Behrooz Torabi; Etemadikhah, Mitra; Rajkowska, Grazyna; Stocluneier, Craig et al.

    Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods

    Ingår i Journal of Psychiatric Research, s. 41-47, 2019.

  • Rajan, Meenu Rohini; Sotak, Matus; Barrenäs, Fredrik; Shen, Tong et al.

    Comparative analysis of obesity-related cardiometabolic and renal biomarkers in human plasma and serum

    Ingår i Scientific Reports, 2019.

    Open access
  • Walz, Marie-Madeleine; Van der Spoel, David

    Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts

    Ingår i The Journal of Physical Chemistry C, s. 25596-25602, 2019.

  • Lind, Christoffer; Esguerra, Mauricio; Jespers, Willem; Satpati, Priyadarshi et al.

    Free energy calculations of RNA interactions

    Ingår i Methods, s. 85-95, 2019.

  • Jandova, Zuzana; Jespers, Willem; Sotelo, Eddy; Gutiérrez-de-Terán, Hugo et al.

    Free-Energy Calculations for Bioisosteric Modifications of A(3) Adenosine Receptor Antagonists

    Ingår i International Journal of Molecular Sciences, 2019.

    Open access