Michael Hagemann-Jensen

Publications
CV
Public outreach and news

Articles

Article: DEVELOPMENTAL CELL. 2024;:S1534-5807(24)00575-6
Regionalized cell and gene signatures govern esophageal epithelial homeostasis.
Grommisch D; Lund H; Eenjes E; Julien A; Göritz C; Harris RA; Sandberg R; Hagemann-Jensen M; Genander M
Article: NATURE COMMUNICATIONS. 2024;15(1):8634
An atlas of small non-coding RNAs in human preimplantation development.
Russell SJ; Zhao C; Biondic S; Menezes K; Hagemann-Jensen M; Librach CL; Petropoulos S
Article: NATURE CELL BIOLOGY. 2024;26(10):1725-1733
Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts
Ramskold D; Hendriks G-J; Larsson AJM; Mayr JV; Ziegenhain C; Hagemann-Jensen M; Hartmanis L; Sandberg R
Article: NATURE COMMUNICATIONS. 2024;15(1):8373
Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq.
Noble JC; Lentini A; Hagemann-Jensen M; Sandberg R; Reinius B
Article: NATURE IMMUNOLOGY. 2024;25(6):1007-1019
Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells
Carrelha J; Mazzi S; Winroth A; Hagemann-Jensen M; Ziegenhain C; Hogstrand K; Seki M; Brennan MS; Lehander M; Wu B; Meng Y; Markljung E; Norfo R; Ishida H; Stralin KB; Grasso F; Karali CS; Aliouat A; Hillen A; Chari E; Siletti K; Thongjuea S; Mead AJ; Linnarsson S; Nerlov C; Sandberg R; Yoshizato T; Woll PS; Jacobsen SEW
Article: CELL SYSTEMS. 2024;15(2):149-165.e10
Clonally heritable gene expression imparts a layer of diversity within cell types
Mold JE; Weissman MH; Ratz M; Hagemann-Jensen M; Hard J; Eriksson C-J; Toosi H; Berghenstrahle J; Ziegenhain C; von Berlin L; Martin M; Blom K; Lagergren J; Lundeberg J; Sandberg R; Michaeeurolsson J; Frisen J
Article: CANCER RESEARCH. 2024;84(2):211-225
Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts
Moura PL; Mortera-Blanco T; Hofman IJ; Todisco G; Kretzschmar WW; Bjoerklund A-C; Creignou M; Hagemann-Jensen M; Ziegenhain C; Cabrerizo Granados D; Barbosa I; Walldin G; Jansson M; Ashley N; Mead AJ; Lundin V; Dimitriou M; Yoshizato T; Woll PS; Ogawa S; Sandberg R; Jacobsen SEW; Hellstrom-Lindberg E
Article: METHODS IN MOLECULAR BIOLOGY. 2024;2767:189-212
Single-Cell mRNA-sncRNA Co-sequencing of Preimplantation Embryos.
Biondic S; Zhao C; Hagemann-Jensen M; Russell SJ; Vandal K; Canizo J; Librach CL; Petropoulos S
Article: SCIENCE. 2023;382(6675):eadf8486
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics
Engblom C; Thrane K; Lin Q; Andersson A; Toosi H; Chen X; Steiner E; Lu C; Mantovani G; Hagemann-Jensen M; Saarenpaa S; Jangard M; Saez-Rodriguez J; Michaelsson J; Hartman J; Lagergren J; Mold JE; Lundeberg J; Frisen J
Article: MULTIPLE SCLEROSIS AND RELATED DISORDERS. 2023;79:104991
Smoking affects epigenetic ageing of lung bronchoalveolar lavage cells in Multiple Sclerosis
Klose D; Needhamsen M; Ringh MV; Hagemann-Jensen M; Jagodic M; Kular L
Journal article: LEUKEMIA RESEARCH. 2023;128:107135
ACCELERATED RNA SPLICING DYNAMICS DURING ERYTHROID DIFFERENTIATION AMPLIFY MIS-SPLICING IN SF3B1-MUTANT MDS-RS
Moura P; Mortera-Blanco T; Hofman I; Todisco G; Kretzschmar W; Bjorklund A-C; Creignou M; Hagemann-Jensen M; Ziegenhain C; Granados D; Barbosa I; Walldin G; Jansson M; Mead A; Lundin V; Dimitriou M; Yoshizato T; Woll P; Ogawa S; Sandberg R; Jacobsen SE; Hellstrom-Lindberg E
Article: NATURE COMMUNICATIONS. 2023;14(1):982
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics
Jun S-H; Toosi H; Mold J; Engblom C; Chen X; O'Flanagan C; Hagemann-Jensen M; Sandberg R; Aparicio S; Hartman J; Roth A; Lagergren J
Article: NATURE BIOTECHNOLOGY. 2022;40(10):1452-1457
Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
Hagemann-Jensen M; Ziegenhain C; Sandberg R
Article: GENOME RESEARCH. 2022;32(9):1627-1641
Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
Zhao C; Biondic S; Vandal K; Bjoerklund AK; Hagemann-Jensen M; Sommer TM; Canizo J; Clark S; Raymond P; Zenklusen DRR; Rivron N; Reik W; Petropoulos S
Article: AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY. 2022;66(6):638-647
Chronic Obstructive Pulmonary Disease Is Associated with Epigenome-Wide Differential Methylation in BAL Lung Cells
Strom JE; Merid SK; Pourazar J; Blomberg A; Lindberg A; Ringh MV; Hagemann-Jensen M; Ekstrom TJ; Behndig AF; Melen E
Article: NATURE METHODS. 2022;19(5):560-566
Molecular spikes: a gold standard for single-cell RNA counting
Ziegenhain C; Hendriks G-J; Hagemann-Jensen M; Sandberg R
Article: NATURE GENETICS. 2022;54(3):306-317
Transcriptional kinetics and molecular functions of long noncoding RNAs
Johnsson P; Ziegenhain C; Hartmanis L; Hendriks G-J; Hagemann-Jensen M; Reinius B; Sandberg R
Article: FRONTIERS IN GENETICS. 2022;13:1042483
Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis
Needhamsen M; Khoonsari PE; Zheleznyakova GY; Piket E; Hagemann-Jensen M; Han Y; Gierlich J; Ekman D; Jagodic M
Article: MULTIPLE SCLEROSIS JOURNAL. 2021;27(7):1014-1026
Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking
Ringh MV; Hagemann-Jensen M; Needhamsen M; Kullberg S; Wahlstrom J; Grunewald J; Brynedal B; Jagodic M; Ekstrom TJ; Ockinger J; Kular L
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2021;118(17):e2011574118
Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology
Zheleznyakova GY; Piket E; Needhamsen M; Hagemann-Jensen M; Ekman D; Han Y; James T; Khademi M; Al Nimer F; Scicluna P; Huang J; Kockum I; Faridani OR; Olsson T; Piehl F; Jagodic M
Article: PLOS COMPUTATIONAL BIOLOGY. 2021;17(3):e1008772
Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
Larsson AJM; Ziegenhain C; Hagemann-Jensen M; Reinius B; Jacob T; Dalessandri T; Hendriks G-J; Kasper M; Sandberg R
Article: NATURE BIOTECHNOLOGY. 2020;38(6):708-714
Single-cell RNA counting at allele and isoform resolution using Smart-seq3
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramskold D; Hendriks G-J; Larsson AJM; Faridani OR; Sandberg R
Article: EBIOMEDICINE. 2019;46:290-304
Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells
Ringh MV; Hagemann-Jensen M; Needhamsen M; Kular L; Breeze CE; Sjoholm LK; Slavec L; Kullberg S; Wahlstrom J; Grunewald J; Brynedal B; Liu Y; Almgren M; Jagodic M; Ockinger J; Ekstrom TJ
Article: NATURE. 2019;565(7738):251-254
Genomic encoding of transcriptional burst kinetics
Larsson AJM; Johnsson P; Hagemann-Jensen M; Hartmanis L; Faridani OR; Reinius B; Segerstolpe A; Rivera CM; Ren B; Sandberg R
Article: NATURE PROTOCOLS. 2018;13(10):2407-2424
Small-seq for single-cell small-RNA sequencing
Hagemann-Jensen M; Abdullayev I; Sandberg R; Faridani OR
Article: RESPIRATORY RESEARCH. 2018;19(1):68
Expression of MATE1, P-gp, OCTN1 and OCTN2, in epithelial and immune cells in the lung of COPD and healthy individuals
Berg T; Hegelund-Myrback T; Ockinger J; Zhou X-H; Brannstrom M; Hagemann-Jensen M; Werkstrom V; Seidegard J; Grunewald J; Nord M; Gustavsson L
Article: SCIENTIFIC REPORTS. 2017;7(1):5623
Common variants of T-cells contribute differently to phenotypic variation in sarcoidosis
Rivera NV; Hagemann-Jensen M; Ferreira MAR; Kullberg S; Eklund A; Martin NG; Padyukov L; Grunewald J
Article: NATURE BIOTECHNOLOGY. 2016;34(12):1264-1266
Single-cell sequencing of the small-RNA transcriptome
Faridani OR; Abdullayev I; Hagemann-Jensen M; Schell JP; Lanner F; Sandberg R
Article: CLINICAL IMMUNOLOGY. 2016;169:114-120
T-cell activation and HLA-regulated response to smoking in the deep airways of patients with multiple sclerosis
Ockinger J; Hagemann-Jensen M; Kullberg S; Engvall B; Eklund A; Grunewald J; Piehl F; Olsson T; Wahlstrom J
Article: PLOS ONE. 2016;11(8):e0161669
Expression Profile of Six RNA-Binding Proteins in Pulmonary Sarcoidosis
Navratilova Z; Novosadova E; Hagemann-Jensen M; Kullberg S; Kolek V; Grunewald J; Petrek M
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2014;289(45):31576-31590
The Selenium Metabolite Methylselenol Regulates the Expression of Ligands That Trigger Immune Activation through the Lymphocyte Receptor NKG2D
Hagemann-Jensen M; Uhlenbrock F; Kehlet S; Andresen L; Gabel-Jensen C; Ellgaard L; Gammelgaard B; Skov S
Article: JOURNAL OF IMMUNOLOGY. 2014;193(4):1654-1665
The NKG2D Ligand ULBP2 Is Specifically Regulated through an Invariant Chain-Dependent Endosomal Pathway
Uhlenbrock F; Hagemann-Jensen M; Kehlet S; Andresen L; Pastorekova S; Skov S
Article: MOLECULAR IMMUNOLOGY. 2013;53(3):255-264
Regulation of NKG2D-ligand cell surface expression by intracellular calcium after HDAC-inhibitor treatment
Jensen H; Hagemann-Jensen M; Lauridsen F; Skov S
Article: JOURNAL OF IMMUNOLOGY. 2012;188(4):1847-1855
2-Deoxy D-Glucose Prevents Cell Surface Expression of NKG2D Ligands through Inhibition of N-Linked Glycosylation
Andresen L; Skovbakke SL; Persson G; Hagemann-Jensen M; Hansen KA; Jensen H; Skov S
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All other publications

Letter: CELL RESEARCH. 2023;33(11):883-886
Platelet and myeloid lineage biases of transplanted single perinatal mouse hematopoietic stem cells
Stralin KB; Carrelha J; Winroth A; Ziegenhain C; Hagemann-Jensen M; Kettyle LM; Hillen A; Hogstrand K; Markljung E; Grasso F; Seki M; Mazzi S; Meng Y; Wu B; Chari E; Lehander M; Sandberg R; Woll PS; Jacobsen SEW
Preprint: BIORXIV. 2023
Erythroid differentiation intensifies RNA mis-splicing inSF3B1-mutant myelodysplastic syndromes with ring sideroblasts
Moura P; Mortera-Blanco T; Hofman IJF; Todisco G; Kretzschmar W; Björklund A-C; Creignou M; Hagemann-Jensen M; Ziegenhain C; Granados D; Barbosa I; Walldin G; Jansson M; Ashley N; Mead A; Lundin V; Dimitriou M; Yoshizato T; Woll P; Ogawa S; Sandberg R; Jacobsen SE; Hellström-Lindberg E
Preprint: BIORXIV. 2022
Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue
Engblom C; Thrane K; Lin Q; Andersson A; Toosi H; Chen X; Steiner E; Mantovani G; Hagemann-Jensen M; Saarenpää S; Jangard M; Michaëlsson J; Hartman J; Lagergren J; Mold J; Lundeberg J; Frisén J
Preprint: ZAPPYLAB, INC.. 2022
Smart-seq3xpress v2
Hagemann-Jensen M
Preprint: BIORXIV. 2022
Clonally heritable gene expression imparts a layer of diversity within cell types
Mold J; Weissman M; Ratz M; Hagemann-Jensen M; Hård J; Eriksson C-J; Toosi H; Berghenstråhle J; von Berlin L; Martin M; Blom K; Lagergren J; Lundeberg J; Sandberg R; Michaëlsson J; Frisén J
Preprint: ZAPPYLAB, INC.. 2021
Smart-seq3xpress v1
Hagemann-Jensen M
Preprint: ZAPPYLAB, INC.. 2021
Smart-seq3xpress v1
Hagemann-Jensen M
Preprint: BIORXIV. 2021
Scalable full-transcript coverage single cell RNA sequencing with Smart-seq3xpress
Hagemann-Jensen M; Ziegenhain C; Sandberg R
Preprint: BIORXIV. 2021
Molecular spikes: a gold standard for single-cell RNA counting
Ziegenhain C; Hendriks G-J; Hagemann-Jensen M; Sandberg R
Preprint: BIORXIV. 2021
PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data
Jun S-H; Toosi H; Mold J; Engblom C; Chen X; O’Flanagan C; Hagemann-Jensen M; Sandberg R; Aparicio S; Hartman J; Roth A; Lagergren J
Conference publication: SWISS MEDICAL WEEKLY. 2021;151:9S
Extracellular vesicles cause neutrophil dysfunction leading to reduced resistance to secondary bacterial infection during malaria
Babatunde K; Ngara M; Walch M; Subramanian B; Hagemann-Jensen M; Ghiran I; Sandberg R; Irimia D; Mantel PY
Preprint: BIORXIV. 2020
Profiling of small non-coding RNAs across cellular and biofluid compartments: implications for multiple sclerosis immunopathology
Zheleznyakova GY; Piket E; Needhamsen M; Hagemann-Jensen M; Ekman D; Khademi M; Nimer FA; Scicluna P; Faridani O; Olsson T; Piehl F; Jagodic M
Preprint: BIORXIV. 2020
Transcriptional kinetics and molecular functions of long non-coding RNAs
Johnsson P; Ziegenhain C; Hartmanis L; Hendriks G-J; Hagemann-Jensen M; Reinius B; Sandberg R
Preprint: ZAPPYLAB, INC.. 2020
Smart-seq3 Protocol v3
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramsköld D; Hendriks G-J; J.M Larsson A; R. Faridani O; Sandberg R
Preprint: ZAPPYLAB, INC.. 2020
Smart-seq3 Protocol v2
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramsköld D; Hendriks G-J; J.M Larsson A; R. Faridani O; Sandberg R
Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2020;26(3_SUPPL):583
Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking
Ringh M; Hagemann-Jensen M; Needhamsen M; Kullberg S; Wahlstrom J; Grunewald J; Brynedal B; Jagodic M; Ekstrom T; Ockinger J; Kular L
Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2020;26(3_SUPPL):183-184
Profiling of small non-coding rnas across cellular and biofluid compartments in patients with multiple sclerosis
Zheleznyakova G; Piket E; Needhamsen M; Hagemann-Jensen M; Ekman D; Khademi M; Al Nimer F; Scicluna P; Faridani O; Olsson T; Piehl F; Jagodic M
Preprint: BIORXIV. 2019
Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramsköld D; Hendriks G-J; Larsson AJM; Faridani O; Sandberg R
Preprint: ZAPPYLAB, INC.. 2019
Smart-seq3 Protocol v1
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramsköld D; Hendriks G-J; J.M Larsson A; R. Faridani O; Sandberg R
Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2019;25:726
Genome-wide small-noncoding RNA analysis in patients with multiple sclerosis
Zheleznyakova G; Piket E; Needhamsen M; Hagemann-Jensen M; Faridani O; Marabita F; Khademi M; Piehl F; Olsson T; Jagodic M
Thesis / dissertation: 2018
Breathe (in the air) : pulmonary immunology in multiple sclerosis
Hagemann-Jensen, Michael
Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2017;23:499
Epigenetic profiling of bronchoalveolar lavage cells in multiple sclerosis and associations to cigarette smoking
Ringh MV; Hagemann-Jensen M; Sjoholm LK; Grunewald J; Wahlstrom J; Liu Y; Almgren M; Ekstrom TJ; Ockinger J
Conference publication: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2017;86(4):323
Epigenetic profiling of bronchoalveolar lavage cells in multiple sclerosis and associations to cigarette smoking
Ringh MV; Hagemann-Jensen M; Sjoholm LK; Grunewald J; Wahlstrom J; Liu Y; Almgren M; Ekstrom TJ; Ockinger J
Preprint: BIORXIV. 2016
T-cell activation and HLA-regulated response to smoking in the deep airways of patients with multiple sclerosis
Öckinger J; Hagemann-Jensen M; Kullberg S; Engvall B; Eklund A; Grunewald J; Piehl F; Olsson T; Wahlstrom J
Conference publication: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2014;79(6):469
Cell Surface Transport Undercover: The Expression of the Soluble and Surface-Bound NKG2D-Ligand ULBP2 is Dependent on Endosomal Regulation
Uhlenbrock FK; Hagemann-Jensen M; Kehlet SN; Andesen L; Pastorekova S; Skov S
Conference publication: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2014;79(6):458
Characteristics of T Cell Subsets in Smokers and Multiple Sclerosis Patients' Lungs
Hagemann-Jensen M; Ockinger J; Kullberg S; Piehl F; Olsson T; Eklund A; Grunewald J; Wahlstrom J
Conference publication: EUROPEAN RESPIRATORY JOURNAL. 2013;42
Differential regulation of innate immunity in healthy smokers
Ockinger J; Hagemann-Jensen M; Kullberg S; Eklund A; Grunewald J; Wahlstrom J
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Employments

Research Specialist, Department of Cell and Molecular Biology, Karolinska Institutet, 2022-

Degrees and Education

Degree Of Doctor Of Philosophy, Department of Medicine, Solna, Karolinska Institutet, 2018

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