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Mårten Lindqvist

Position: Researcher School/office: School of Medical Sciences

Email: bWFydGVuLmxpbmRxdmlzdDtvcnUuc2U=

Phone: +46 19 301273

Room: -

Research subject

Medicine

About Mårten Lindqvist

Mårten Lindqvist is postdoctoral research fellow in the group of functional bioinformatics. He holds a PhD in molecular medicine from Uppsala University (2016) where he was part of the team that made the first Swedish human whole genome sequencing, sequenced and analyzed in Sweden. Previously he studied mathematics (BSc, University of Bergen 2006) and computer science/Industrial engineering (MSc Linköping University/CERN 2011).

Carl Mårten has focused his research on methods using data from whole genome sequencing and targeted deep sequencing. At Örebro University these methods are applied to metagenomic samples, together with additional data, to assess functional profiles and predict clinical outcome. He is involved in the medical education as assisting course coordinator for semester 5.

Active projects

Research groups

Publications

Articles in journals | Conference papers | Manuscripts |

Articles in journals

Pertsinidou, E. , Salomon, B. , Bergemalm, D. , Salihovic, S. , Hedin, C. R. H. , Ling Lundström, M. , Keita, Å. V. , Magnusson, M. K. & et al. (2025). Anti-integrin αvβ6 IgG antibody as a diagnostic and prognostic marker in ulcerative colitis: A cross-sectional and longitudinal study defining a specific disease phenotype. Journal of Crohn's & Colitis, 19 (5). [BibTeX]
Salomon, B. , Sudhakar, P. , Bergemalm, D. , Andersson, E. , Grännö, O. , Carlson, M. , Hedin, C. R. H. , Söderholm, J. D. & et al. (2025). Characterization of Inflammatory Bowel Disease Heterogeneity Using Serum Proteomics: A multicenter study. Journal of Crohn's & Colitis, 19 (5). [BibTeX]
Asghar, N. , Jaafar, R. , Valko, A. , Merinder, O. , Ljungberg, K. , Lindqvist, C. M. & Johansson, M. (2025). Development of Langat virus infectious clones as a platform for live-attenuated tick-borne encephalitis vaccine. Npj viruses, 3 (1). [BibTeX]
Grännö, O. , Bergemalm, D. , Salomon, B. , Lindqvist, C. M. , Hedin, C. R. H. , Carlson, M. , Dannenberg, K. , Andersson, E. & et al. (2025). Preclinical protein signatures of Crohn's disease and ulcerative colitis: A nested case-control study within large population-based cohorts. Gastroenterology, 168 (4), 741-753. [BibTeX]
Ling Lundström, M. , Peterson, C. , Hedin, C. R. H. , Bergemalm, D. , Lampinen, M. , Magnusson, M. K. , Keita, Å. V. , Kruse, R. & et al. (2024). Faecal biomarkers for diagnosis and prediction of disease course in treatment-naïve patients with IBD. Alimentary Pharmacology and Therapeutics, 60 (6), 765-777. [BibTeX]
Salihovic, S. , Nyström, N. , Mathisen, C. B. , Kruse, R. , Olbjørn, C. , Andersen, S. , Noble, A. J. , Dorn-Rasmussen, M. & et al. (2024). Identification and validation of a blood- based diagnostic lipidomic signature of pediatric inflammatory bowel disease. Nature Communications, 15 (1). [BibTeX]
Koskela, A. , Lindqvist, C. M. , Asghar, N. , Johansson, M. , Sundqvist, M. , Mölling, P. & Stenmark, B. (2023). Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization. Scientific Reports, 13 (1). [BibTeX]
Lundström, M. L. , Peterson, C. , Lampinen, M. , Hedin, C. R. H. , Keita, Å. V. , Kruse, R. , Magnusson, M. K. , Lindqvist, C. M. & et al. (2023). Fecal Biomarkers of Neutrophil and Eosinophil Origin Reflect the Response to Biological Therapy and Corticosteroids in Patients With Inflammatory Bowel Disease. Clinical and Translational Gastroenterology, 14 (8). [BibTeX]
Juzenas, S. , Hübenthal, M. , Lindqvist, C. M. , Kruse, R. , Steiert, T. A. , Degenhardt, F. , Schulte, D. , Nikolaus, S. & et al. (2022). Detailed transcriptional landscape of peripheral blood points to increased neutrophil activation in treatment-naïve inflammatory bowel disease. Journal of Crohn's & Colitis, 16 (7), 1097-1109. [BibTeX]
Moraes Holst, L. , Halfvarson, J. , Carlson, M. , Hedin, C. , Kruse, R. , Lindqvist, C. M. , Bergemalm, D. , Almér, S. & et al. (2022). Downregulated Mucosal Autophagy, Alpha Kinase-1 and IL-17 Signaling Pathways in Active and Quiescent Ulcerative Colitis. Clinical and Experimental Gastroenterology, 15, 129-144. [BibTeX]
Casado-Bedmar, M. , de-Faria, F. M. , Biskou, O. , Lindqvist, C. M. , Ranasinghe, P. D. , Bednarska, O. , Peterson, C. , Walter, S. A. & et al. (2022). Elevated F-EDN correlates with mucosal eosinophil degranulation in patients with IBS: A possible association with microbiota?. Journal of Leukocyte Biology, 111 (3), 655-665. [BibTeX]
Fart, F. , Tingö, L. , Engelheart, S. , Lindqvist, C. M. , Brummer, R. J. , Kihlgren, A. & Schoultz, I. (2022). Gut Health and Its Association with Wellbeing and Nutrient Intake in Community-Dwelling Older Adults. Gastroenterology Insights, 13 (4), 349-364. [BibTeX]
de-Faria, F. M. , Casado-Bedmar, M. , Lindqvist, C. M. , Jones, M. P. , Walter, S. A. & Keita, Å. V. (2021). Altered interaction between enteric glial cells and mast cells in the colon of women with irritable bowel syndrome. Neurogastroenterology and Motility, 33 (11). [BibTeX]
Holster, S. , Repsilber, D. , Geng, D. , Hyötyläinen, T. , Salonen, A. , Lindqvist, C. M. , Rajan, S. K. , de Vos, W. M. & et al. (2021). Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. Beneficial Microbes, 12 (1), 17-30. [BibTeX]
Juzenas, S. , Lindqvist, C. M. , Ito, G. , Dolshanskaya, Y. , Halfvarson, J. , Franke, A. & Hemmrich-Stanisak, G. (2020). Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries. NAR Genomics and Bioinformatics, 2 (1). [BibTeX]
Fart, F. , Rajan, S. K. , Wall, R. , Rangel, I. , Ganda Mall, J. P. , Tingö, L. , Brummer, R. J. , Repsilber, D. & et al. (2020). Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults. Nutrients, 12 (9). [BibTeX]
Ganda Mall, J. P. , Fart, F. , Sabet, J. A. , Lindqvist, C. M. , Nestestog, R. , Hegge, F. T. , Keita, Å. V. , Brummer, R. J. & et al. (2020). Effects of Dietary Fibres on Acute Indomethacin-Induced Intestinal Hyperpermeability in the Elderly: A Randomised Placebo Controlled Parallel Clinical Trial. Nutrients, 12 (7). [BibTeX]
Vatn, S. , Carstens, A. , Kristoffersen, A. B. , Bergemalm, D. , Casén, C. , Moen, A. E. F. , Tannaes, T. M. , Lindstrøm, J. & et al. (2020). Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character). Scandinavian Journal of Gastroenterology, 55 (10), 1146-1156. [BibTeX]
Rajan, S. K. , Lindqvist, C. M. , Brummer, R. J. , Schoultz, I. & Repsilber, D. (2019). Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method. PLOS ONE, 14 (9). [BibTeX]
Holster, S. , Lindqvist, C. M. , Repsilber, D. , Salonen, A. , de Vos, W. , König, J. & Brummer, R. J. (2019). The Effect of Allogenic Versus Autologous Fecal Microbiota Transfer on Symptoms, Visceral Perception and Fecal and Mucosal Microbiota in Irritable Bowel Syndrome: A Randomized Controlled Study. Clinical and Translational Gastroenterology, 10 (4). [BibTeX]
Carstens, A. , Dicksved, J. , Nelson, R. , Lindqvist, C. M. , Andreasson, A. , Bohr, J. , Tysk, C. , Talley, N. J. & et al. (2019). The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis. Clinical and Translational Gastroenterology, 10 (7). [BibTeX]
Ganda Mall, J. , Östlund-Lagerström, L. , Lindqvist, C. M. , Algilani, S. , Rasoal, D. , Repsilber, D. , Brummer, R. J. , V. Keita, Å. & et al. (2018). Are self-reported gastrointestinal symptoms among older adults associated with increased intestinal permeability and psychological distress?. BMC Geriatrics, 18 (1). [BibTeX]
Ganda Mall, J. P. , Löfvendahl, L. , Lindqvist, C. M. , Brummer, R. J. , Keita, Å. V. & Schoultz, I. (2018). Differential effects of dietary fibres on colonic barrier function in elderly individuals with gastrointestinal symptoms. Scientific Reports, 8 (1). [BibTeX]
Keita, Å. V. , Lindqvist, C. M. , Öst, Å. , Magana, C. D. L. , Schoultz, I. & Halfvarson, J. (2018). Gut barrier dysfunction: a primary defect in twins with Crohn's disease predominantly caused by genetic predisposition. Journal of Crohn's & Colitis, 12 (10), 1200-1209. [BibTeX]

Conference papers

Visuri, I. , Dannenberg, K. , Salomon, B. , Lundström, M. L. , Bergemalm, D. , Eriksson, C. , Lindqvist, M. , Keita, Å. V. & et al. (2025). Correlations of clinical characteristics and serum proteins with drug levels: A multicentre cohort study of patients with inflammatory bowel disease starting biologics. In: Journal of Crohn's & Colitis. Oxford University Press. [BibTeX]
Smeds, P. , Almlöf, J. , Munters, A. , Mähler, N. , Nordin, J. , Melin, M. , Köhn, L. , Mesilaakso, L. & et al. (2024). Hydra-genetics, a modular framework for bioinformatics pipeline development. In: European Journal of Human Genetics. Paper presented at 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, Scotland, June 10-13, 2023. (pp. 675-676). Nature Portfolio. [BibTeX]
Koskela, A. , Lindqvist, C. M. , Asghar, N. , Johansson, M. , Sundqvist, M. , Mölling, P. & Stenmark, B. (2023). Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization. Paper presented at Smögen Virology Symposium 2023, Smögen, Sweden, August 24-26, 2023. [BibTeX]
Asghar, N. , Jaafar, R. , Lindqvist, C. M. , Ljunberg, K. & Johansson, M. (2023). Design, rescue, and characterization of Langat virus infectious clone by next generation sequencing. Paper presented at 20th Smögen Summer Symposium on Virology, Smögen, August 24-26, 2023. (pp. 51-51). [BibTeX]
Koskela, A. , Qvick, A. , Jakobsen, I. , Lindqvist, C. M. , Farkas, S. A. , Green, A. , Isaksson, H. S. , Holmgren, B. & et al. (2022). Evaluation of Microsatellite instability score from GMS560 DNA panel. Paper presented at Cutting-Edge Implementation of Precision Medicine in Europe, Stockholm, Sweden, September 22-23, 2022. [BibTeX]
Juzenas, S. , Hübenthal, M. , Zeissig, S. , Strüning, N. , Keller, A. , Schulte, D. , D'Amato, M. , Lindqvist, C. M. & et al. (2019). Sequencing-based hematopoietic miRNA landscape reveals common and distinct features of autoimmune inflammatory phenotypes. In: Journal of Crohn's & Colitis. Oxford University Press. [BibTeX]
Keita, A. V. , Lindqvist, C. M. , Ost, A. , Magana, C. D. L. , Schoultz, I. & Halfvarson, J. (2018). Gut barrier dysfunction: a primary defect in twins with Crohn's disease predominantly caused by genetic predisposition. In: Journal of Crohn's & Colitis. Oxford University Press. [BibTeX]

Manuscripts

Grännö, O. , Bergemalm, D. , Lindqvist, C. M. , Hedin, C. R. H. , Carlson, M. , Dannenberg, K. , Andersson, E. , Strid, H. & et al. A protein signature for prediction of disease course in newly diagnosed ulcerative colitis. [BibTeX]
Holster, S. , Repsilber, D. , Geng, D. , Hyötyläinen, T. , Salonen, A. , Lindqvist, C. M. , Rajan, S. K. , De Vos, W. M. & et al. Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. [BibTeX]
Visuri, I. , Dannenberg, K. , Salomon, B. , Ling Lundström, M. , Bergemalm, D. , Eriksson, C. , Lindqvist, C. M. , Keita, Å. V. & et al. Correlations of clinical characteristics and serum proteins with drug levels : A multicentre cohort study of patients with inflammatory bowel disease starting biologics. [BibTeX]
Ganda Mall, J. , Fart, F. , Sabet, J. , Lindqvist, C. , Keita, Å. V. , Brummer, R. J. & Schoultz, I. Effects of dietary fibres on indomethacin-induced intestinal permeability in elderly : A randomised placebo controlled parallel clinical trial. [BibTeX]
Holster, S. , Repsilber, D. , Geng, D. , Hyötyläinen, T. , Lindqvist, C. M. , de Vos, W. , Brummer, R. J. & König, J. Faecal microbiota transfer in irritable bowel syndrome results inaltered correlations between the gut microbiota and its metabolites. [BibTeX]
Rajan, S. K. , Lindqvist, C. M. , Sihlbom, C. , Olsson, B. , Brummer, R. J. , Schoultz, I. & Repsilber, D. Functional proteomics profiles in faecal sample microbiomes : Validating NGS-based predictions with LC-MS proteomics. [BibTeX]
Fart, F. , Tingö, L. , Engelheart, S. , Lindqvist, C. M. , Brummer, R. J. , Kihlgren, A. & Schoultz, I. Gut Health and its Associations to Well-being and Nutrient intake in Community-Dwelling Older Adults. [BibTeX]
Carstens, A. , Björkqvist, O. , Lindqvist, C. M. , Rangel, I. , Repsilber, D. , Eriksson, C. , Bergemalm, D. , Bresso, F. & et al. Gut microbiota associated with treatment outcome to biological treatment in inflammatory bowel disease. [BibTeX]
Grännö, O. , Thunberg, J. , Ludvigsson, J. F. , Kuja-Halkola, R. , Lindqvist, C. M. & Halfvarson, J. Heritability of Crohn’s disease and ulcerative colitis : A Swedish nationwide population-based twin study. [BibTeX]
Fart, F. , Amcoff, K. , Bergemalm, D. , Andersson, E. , Kalla, R. , Satsangi, J. , Lindqvist, C. M. , Halfvarson, J. & et al. Loss of tolerance to microbial antigens in preclinical Crohn’s disease differs with age at diagnosis : A twin study. [BibTeX]
Qvick, A. , Adolfsson, E. , Tornéus, L. , Lindqvist, C. M. , Carlsson, J. , Stenmark, B. , Karlsson, C. & Helenius, G. Methylation patterns in cell-free DNA for pan-cancer detection. [BibTeX]
Grännö, O. , Lindqvist, C. M. , Bergemalm, D. , Salomon, B. , Hedin, C. , Carlson, M. , Dannenberg, K. , Strid, H. & et al. The mucosa-associated gut microbiome in newly diagnosed inflammatory bowel disease. [BibTeX]