Clinical Genomics Lund

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SciLifeLab Infrastructure Unit Since 2016.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2016

Ended: Current

Year 2022

PubMed DOI Crossref
UROSCAN and UROSCANSEQ: a large-scale multicenter effort towards translation of molecular bladder cancer subtypes into clinical practice - from biobank to RNA-sequencing in real time.
Liedberg F, Abrahamsson J, Bernardo C, ..., Sjödahl G, Eriksson P
Scand J Urol - (-) 1-8 [2022-12-20; online 2022-12-20]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.
Mañas A, Aaltonen K, Andersson N, ..., Gisselsson D, Bexell D
Sci Adv 8 (43) eabq4617 [2022-10-28; online 2022-10-28]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia, and solid tumor metastasis.
Grigoryan A, Zacharaki D, Balhuizen A, ..., Bexell D, Bourgine PE
Sci Transl Med 14 (666) eabm6391 [2022-10-12; online 2022-10-12]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia.
Pilheden M, Ahlgren L, Hyrenius-Wittsten A, ..., Gawad C, Hagström-Andersson AK
Hemasphere 6 (10) e785 [2022-10-00; online 2022-09-30]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Distinct subcellular autophagy impairments in induced neurons from patients with Huntington's disease.
Pircs K, Drouin-Ouellet J, Horváth V, ..., Barker RA, Jakobsson J
Brain 145 (9) 3035-3057 [2022-09-14; online 2021-12-23]
Clinical Genomics Lund [Service]
DOI Crossref
Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction
Safi F, Dhapola P, Warsi S, ..., Thakur RK, Karlsson G
Cell Rep 39 (6) 110798 [2022-05-00; online 2022-05-00]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells.
Rosa FF, Pires CF, Kurochkin I, ..., Scheding S, Pereira CF
Sci Immunol 7 (69) eabg5539 [2022-03-04; online 2022-03-04]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.
Johansson PA, Brattås PL, Douse CH, ..., Eichler EE, Jakobsson J
Cell Stem Cell 29 (1) 52-69.e8 [2022-01-06; online 2021-10-07]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Amplification of ERBB2 (HER2) in embryonal rhabdomyosarcoma: A potential treatment target in rare cases?
Mitra S, Sydow S, Magnusson L, ..., Gisselsson D, Mertens F
Genes Chromosomes Cancer 61 (1) 5-9 [2022-01-00; online 2021-09-01]
Clinical Genomics Lund [Service]

Year 2021

PubMed DOI Crossref
CD105+CD90+CD13+ identifies a clonogenic subset of adventitial lung fibroblasts.
Kadefors M, Rolandsson Enes S, Åhrman E, ..., Scheding S, Westergren-Thorsson G
Sci Rep 11 (1) 24417 [2021-12-24; online 2021-12-24]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation.
Engström K, Mandakh Y, Garmire L, ..., Erlandsson L, Hansson SR
Toxics 9 (12) 338 [2021-12-06; online 2021-12-06]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Different Responses to Neoadjuvant Chemotherapy in Urothelial Carcinoma Molecular Subtypes.
Sjödahl G, Abrahamsson J, Holmsten K, ..., Ullén A, Liedberg F
Eur. Urol. - (-) - [2021-11-12; online 2021-11-12]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification.
Eriksson P, Marzouka NA, Sjödahl G, ..., Liedberg F, Höglund M
Bioinformatics - (-) - [2021-11-12; online 2021-11-12]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
cGMP-PKG dependent transcriptome in normal and degenerating retinas: Novel insights into the retinitis pigmentosa pathology.
Zhou J, Rasmussen M, Ekström P
Exp. Eye Res. 212 (-) 108752 [2021-11-00; online 2021-08-31]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Targeted genomic investigations in a population-based cohort of mantle cell lymphoma reveal novel clinically relevant targets.
Rodrigues JM, Porwit A, Hassan M, Ek S, Jerkeman M
Leuk. Lymphoma 62 (11) 2637-2647 [2021-11-00; online 2021-06-03]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia.
Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T
Semin. Cancer Biol. - (-) - [2021-10-01; online 2021-10-01]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Genomic and transcriptomic characterization of desmoplastic small round cell tumors.
Sydow S, Versleijen-Jonkers YMH, Hansson M, ..., Flucke UE, Mertens F
Genes Chromosomes Cancer 60 (9) 595-603 [2021-09-00; online 2021-05-17]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Anti-tumor effects of rigosertib in high-risk neuroblastoma.
Radke K, Hansson K, Sjölund J, ..., Gisselsson D, Bexell D
Transl Oncol 14 (8) 101149 [2021-08-00; online 2021-06-09]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Single-cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs.
Pfisterer U, Bräunig J, Brattås P, ..., Karlsson G, Fioretos T
Genes Chromosomes Cancer 60 (7) 504-524 [2021-07-00; online 2021-03-15]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease.
Wijk SC, Prabhala P, Michaliková B, ..., Westergren-Thorsson G, Magnusson M
Am J Respir Cell Mol Biol 65 (1) 103-113 [2021-07-00; online 2021-04-01]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis.
Khademi SMH, Gabrielaite M, Paulsson M, ..., Marvig RL, Påhlman LI
mSystems - (-) e0052321 [2021-06-29; online 2021-06-29]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Trailblazing precision medicine in Europe: A joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany.
Stenzinger A, Edsjö A, Ploeger C, ..., Rosenquist R, GMS working groups and ZPM working groups
Semin. Cancer Biol. - (-) - [2021-05-24; online 2021-05-24]
Clinical Genomics Lund [Service] Clinical Genomics Stockholm [Collaborative] Clinical Genomics Uppsala [Collaborative]
PubMed
[Precision diagnostics and therapy in hematological malignancies].
Hellström Lindberg E, Cavelier L, Cammenga J, ..., Fioretos T, Rosenquist R
Lakartidningen 118 (-) - [2021-05-10; online 2021-05-10]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Activation of endogenous retroviruses during brain development causes an inflammatory response.
Jönsson ME, Garza R, Sharma Y, ..., Jern P, Jakobsson J
EMBO J. 40 (9) e106423 [2021-05-03; online 2021-03-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer.
Ku A, Fredsøe J, Sørensen KD, ..., Lilja H, Ceder Y
Front Oncol 11 (-) 631021 [2021-03-25; online 2021-03-25]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Prevalence of germline pathogenic variants in 22 cancer susceptibility genes in Swedish pediatric cancer patients.
von Stedingk K, Stjernfelt KJ, Kvist A, ..., Olsson H, Øra I
Sci Rep 11 (1) 5307 [2021-03-05; online 2021-03-05]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer.
Kaminska K, Akrap N, Staaf J, ..., Bosch A, Honeth G
Breast Cancer Res. 23 (1) 26 [2021-02-18; online 2021-02-18]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
multiclassPairs: An R package to train multiclass pairbased classifier.
Marzouka NA, Eriksson P
Bioinformatics - (-) - [2021-02-05; online 2021-02-05]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts.
Stegmayr J, Alsafadi HN, Langwiński W, ..., Leigh ND, Wagner DE
Am J Physiol Lung Cell Mol Physiol 320 (2) L232-L240 [2021-02-01; online 2020-10-28]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
MAP3K6 Mutations in a Neurovascular Disease Causing Stroke, Cognitive Impairment, and Tremor.
Ilinca A, Englund E, Samuelsson S, ..., Lindgren AG, Puschmann A
Neurol Genet 7 (1) e548 [2021-02-00; online 2021-01-21]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells.
Niklasson CU, Fredlund E, Monni E, ..., Bronner ME, Mohlin S
Dev. Dyn. 250 (2) 191-236 [2021-02-00; online 2020-09-26]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Lund [Service]
PubMed DOI Crossref
BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features.
Tolomeo D, Agostini A, Macchia G, ..., Mertens F, Storlazzi CT
Hum Cell 34 (1) 238-245 [2021-01-00; online 2020-08-27]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Year 2020

PubMed DOI Crossref
Associations between serum concentrations of perfluoroalkyl substances and DNA methylation in women exposed through drinking water: A pilot study in Ronneby, Sweden.
Xu Y, Jurkovic-Mlakar S, Lindh CH, ..., Jakobsson K, Engström K
Environ Int 145 (-) 106148 [2020-12-00; online 2020-09-30]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship.
Marzouka NA, Lindgren D, Eriksson P, ..., Axelson H, Höglund M
Sci Rep 10 (1) 19539 [2020-11-11; online 2020-11-11]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction.
Daoud F, Holmberg J, Alajbegovic A, ..., Swärd K, Albinsson S
Cellular and Molecular Gastroenterology and Hepatology 11 (2) 623-637 [2020-09-28; online 2020-09-28]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma.
Hansson K, Radke K, Aaltonen K, ..., Gisselsson D, Bexell D
Sci Transl Med 12 (562) - [2020-09-23; online 2020-09-25]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
A dynamic mutational landscape associated with an inter-regionally diverse immune response in malignant rhabdoid tumour.
Yasui H, Valind A, Karlsson J, ..., Backman T, Gisselsson D
J. Pathol. 252 (1) 22-28 [2020-09-00; online 2020-07-22]
Clinical Genomics Lund
PubMed DOI Crossref
13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking.
Yang M, Safavi S, Woodward EL, ..., Nord KH, Paulsson K
Blood 136 (8) 946-956 [2020-08-20; online 2020-05-10]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing.
Brofelth M, Ekstrand AI, Gour S, ..., Axelsson U, Borrebaeck CAK
Commun Biol 3 (1) 339 [2020-07-03; online 2020-07-03]
Clinical Genomics Lund
PubMed DOI Crossref
PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells.
Hofvander J, Jo VY, Fletcher CDM, ..., Magnusson L, Mertens F
Mod. Pathol. 33 (7) 1331-1340 [2020-07-00; online 2020-01-13]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Molecular changes during progression from nonmuscle invasive to advanced urothelial carcinoma.
Sjödahl G, Eriksson P, Patschan O, ..., Liedberg F, Höglund M
Int. J. Cancer 146 (9) 2636-2647 [2020-05-01; online 2019-11-14]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma.
Puls F, Agaimy A, Flucke U, ..., Arbajian E, Mertens F
Am. J. Surg. Pathol. 44 (5) 594-606 [2020-05-00; online 2020-01-09]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells.
Li H, Lim HC, Zacharaki D, ..., Hansson J, Scheding S
Haematologica 105 (5) 1206-1215 [2020-05-00; online 2019-08-01]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Deep sequencing of myxoinflammatory fibroblastic sarcoma.
Arbajian E, Hofvander J, Magnusson L, Mertens F
Genes Chromosomes Cancer 59 (5) 309-317 [2020-05-00; online 2020-01-31]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Clonal competition within complex evolutionary hierarchies shapes AML over time.
Sandén C, Lilljebjörn H, Orsmark Pietras C, ..., Ågerstam H, Fioretos T
Nat Commun 11 (1) 579 [2020-02-05; online 2020-02-05]
Clinical Genomics Lund
PubMed DOI Crossref
Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development.
Köster J, Arbajian E, Viklund B, ..., Mandahl N, Mertens F
Cancer Genet 241 (-) 34-41 [2020-02-00; online 2019-12-10]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund

Year 2019

PubMed DOI Crossref
Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile.
Hofvander J, Puls F, Pillay N, ..., Nilsson J, Mertens F
J. Pathol. 249 (4) 425-434 [2019-12-00; online 2019-08-27]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Molecular pathology of the luminal class of urothelial tumors.
Bernardo C, Eriksson P, Marzouka NA, ..., Sjödahl G, Höglund M
J. Pathol. 249 (3) 308-318 [2019-11-00; online 2019-08-27]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Molecular subtypes applied to a population-based modern cystectomy series do not predict cancer-specific survival.
Kollberg P, Chebil G, Eriksson P, Sjödahl G, Liedberg F
Urol Oncol 37 (10) 791-799 [2019-10-00; online 2019-05-02]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
FLT3N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis.
Hyrenius-Wittsten A, Pilheden M, Falqués-Costa A, ..., Järås M, Hagström-Andersson AK
Leukemia 33 (9) 2310-2314 [2019-09-00; online 2019-04-05]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Gene fusion involving the insulin-like growth factor 1 receptor in an ALK-negative inflammatory myofibroblastic tumour.
Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F
Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing.
Ku A, Ravi N, Yang M, ..., Lilja H, Ceder Y
PLoS ONE 14 (5) e0217507 [2019-05-29; online 2019-05-29]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.
Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K
Nat Commun 10 (1) 1519 [2019-04-03; online 2019-04-03]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Global Proteomics and Proteogenomics [Technology development]

Year 2018

PubMed DOI Crossref
Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.
Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY
Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers.
Valind A, Wessman S, Pal N, ..., Sandstedt B, Gisselsson D
Pediatr Blood Cancer 65 (11) e27301 [2018-11-00; online 2018-07-03]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Neuroblastoma with flat genomic profile: a question of representativity?
Valind A, Öra I, Mertens F, Gisselsson D
BMJ Case Reports 2018 (-) bcr-2018-225568 [2018-09-08; online 2018-09-08]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury.
Kapur R, Kim M, Rebetz J, ..., Speck ER, Semple JW
Blood Adv 2 (13) 1651-1663 [2018-07-10; online 2018-07-12]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling.
Roswall P, Bocci M, Bartoschek M, ..., Eriksson U, Pietras K
Nat. Med. 24 (4) 463-473 [2018-05-00; online 2018-03-12]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative.
Brueffer C, Vallon-Christersson J, Grabau D, ..., Borg Å, Saal LH
JCO Precision Oncology 2 (2) 1-18 [2018-03-09; online 2018-03-09]
Clinical Genomics Lund [Service]
PubMed DOI Crossref
Isolated myelosarcoma is characterized by recurrent NFE2 mutations and concurrent preleukemic clones in the bone marrow.
Lazarevic V, Orsmark-Pietras C, Lilljebjörn H, ..., Juliusson G, Fioretos T
Blood 131 (5) 577-581 [2018-02-01; online 2017-11-30]
Clinical Genomics Lund [Collaborative]
PubMed DOI Crossref
Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.
Rydén L, Loman N, Larsson C, ..., Saal LH, Borg Å
Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Collaborative]

Year 2017

PubMed DOI Crossref
New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia.
Lilljebjörn H, Fioretos T
Blood 130 (12) 1395-1401 [2017-09-21; online 2017-08-04]
Clinical Genomics Lund [Collaborative]
PubMed DOI Crossref
Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification
Karlsson A, Brunnström H, Micke P, ..., Planck M, Staaf J
Journal of Thoracic Oncology 12 (8) 1257-1267 [2017-08-00; online 2017-08-00]
Clinical Genomics Lund [Service] Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Davies H, Glodzik D, Morganella S, ..., Stratton MR, Nik-Zainal S
Nat. Med. 23 (4) 517-525 [2017-04-00; online 2017-03-13]
Clinical Genomics Lund [Collaborative]
PubMed DOI Crossref
Identification of two distinct mesenchymal stromal cell populations in human malignant glioma.
Svensson A, Ramos-Moreno T, Eberstål S, Scheding S, Bengzon J
J. Neurooncol. 131 (2) 245-254 [2017-01-00; online 2016-10-18]
Clinical Genomics Lund [Service]

Year 2016

PubMed DOI Crossref
Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia.
Lilljebjörn H, Henningsson R, Hyrenius-Wittsten A, ..., Fontes M, Fioretos T
Nat Commun 7 (-) 11790 [2016-06-06; online 2016-06-06]
Clinical Genomics Lund [Collaborative]

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