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Jonas Halfvarson

Title: Professor School/office: School of Medical Sciences

Email:

Phone: +46 19 303000, +46 738 082361

Room: C2212

Jonas Halfvarson

Research Subject

Research environments

About Jonas Halfvarson

 

In Sweden more than 61 000 individuals are affected by inflammatory bowel disease (IBD), including the predominant forms Crohn’s disease and ulcerative colitis. In the absence of a prevention strategies and curative treatment, the disease has a major impact on many affected individuals, including life-long medication, hospitalizations, recurring sick-leaves, and often a need for surgical intervention. IBD has a high and escalating incidence throughout the world, especially among teenagers and elderly, reflecting the strategic importance for the society at large, both from patient and health care perspectives. My research goal is to improve the healthcare for individuals affected by IBD and thereby increasing their quality of life. I aim to accomplish this by identifying biomarkers that can be used to diagnose the diseases (diagnostic biomarkers) and to foresee who will progress to a severe disease status (prognostic biomarkers). Individuals who will progress to a severe disease status are in need of treatment with biologics already at diagnosis. Therefore, I aim to identify biomarkers that can be used to foresee who will respond from a specific treatment (predictive biomarkers) and who will benefit from taking the drug over a longer period of time (prognostic biomarkers).

 

Research Projects

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Publications

Publications

Articles in journals |  Articles, reviews/surveys |  Chapters in books |  Conference papers |  Manuscripts | 

Articles in journals

Björkqvist, O. , Repsilber, D. , Seifert, M. , Brislawn, C. , Jansson, J. , Engstrand, L. , Rangel, I. & Halfvarson, J. (2019). Alterations in the relative abundance of Faecalibacterium prausnitzii correlate with changes in fecal calprotectin in patients with ileal Crohn's disease: a longitudinal study. Scandinavian Journal of Gastroenterology.
Visuri, I. , Eriksson, C. , Mårdberg, E. , Grip, O. , Gustavsson, A. , Hjortswang, H. , Karling, P. , Montgomery, S. & et al. (2019). Anti-TNF agent drug survival in patients with IBD: real-world comparisons of individual anti-TNF agents based on the Swedish National Quality Registry for IBD (SWIBREG). Journal of Crohn's & Colitis, 13 (Suppl. 1), S443-S444.
Weimers, P. , Halfvarson, J. , Sachs, M. C. , Ludvigsson, J. F. , Peter, I. , Olén, O. & Burisch, J. (2019). Association between inflammatory bowel disease and Parkinson's disease: seek and you shall find?. Gut, 68 (1), 175-176.
Butwicka, A. , Olén, O. , Larsson, H. , Halfvarson, J. , Almqvist, C. , Lichtenstein, P. , Serlachius, E. , Frisén, L. & et al. (2019). Association of Childhood-Onset Inflammatory Bowel Disease With Risk of Psychiatric Disorders and Suicide Attempt. JAMA pediatrics.
Walker, G. J. , Harrison, J. W. , Heap, G. A. , Voskuil, M. D. , Andersen, V. , Anderson, C. A. , Ananthakrishnan, A. N. , Barrett, J. C. & et al. (2019). Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease. Journal of the American Medical Association (JAMA), 321 (8), 773-785.
Everhov, Å. H. , Sachs, M. C. , Malmborg, P. , Nordenvall, C. , Myrelid, P. , Khalili, H. , Elmberg, M. , Ekbom, A. & et al. (2019). Changes in inflammatory bowel disease subtype during follow-up and over time in 44,302 patients. Scandinavian Journal of Gastroenterology, 54 (1), 55-63.
Burisch, J. , Vardi, H. , Schwartz, D. , Krznaric, Z. , Lakatos, P. L. , Fumery, M. , Kupcinskas, L. , Magro, F. & et al. (2019). Cost analysis in a prospective European population-based inception cohort: is there a cost-saving effect of biological therapy?. Journal of Crohn's & Colitis, 13 (Suppl. 1), S9-S10.
Burisch, J. , Chetcuti Zammit, S. , Ellul, P. , Turcan, S. , Duricova, D. , Bortlik, M. , Winther Andersen, K. , Andersen, V. & et al. (2019). Disease course of inflammatory bowel disease unclassified in a European population-based inception cohort: an Epi-IBD study. Journal of Gastroenterology and Hepatology, 34 (6), 996-1003.
Yzet, C. , Ungaro, R. , Bossuyt, P. , Baert, F. , Vanasek, T. , D'Haens, G. , Joustra, V. , Panaccione, R. & et al. (2019). Endoscopic and deep remission at 1 year prevents disease progression in early Crohn's disease: long-term data from CALM. Journal of Crohn's & Colitis, 13 (Suppl. 1), S24-S25.
Örtqvist, A. K. , Lundholm, C. , Halfvarson, J. , Ludvigsson, J. F. & Almqvist, C. (2019). Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study. Gut, 68 (2), 218-225.
Eriksson, C. , Rundquist, S. , Cao, Y. , Montgomery, S. & Halfvarson, J. (2019). Impact of thiopurines on the natural history and surgical outcome of ulcerative colitis: a cohort study. Gut, 68 (4), 623-632.
Weimers, P. , Halfvarson, J. , Sachs, M. C. , Saunders-Pullman, R. , Ludvigsson, J. F. , Peter, I. , Burisch, J. & Olén, O. (2019). Inflammatory Bowel Disease and Parkinson's Disease: A Nationwide Swedish Cohort Study. Inflammatory Bowel Diseases, 25 (1), 111-123.
Weimers, P. , Halfvarson, J. , Saunders-Pullman, R. , Ludvigsson, J. F. , Peter, I. , Olén, O. & Burisch, J. (2019). Inflammatory Bowel Disease and Parkinson's Disease: A Reply to Letter to the Editor of Shih-Wei Lai. Inflammatory Bowel Diseases.
Burisch, J. , Kiudelis, G. , Kupcinskas, L. , Kievit, H. A. L. , Andersen, K. W. , Andersen, V. , Salupere, R. , Pedersen, N. & et al. (2019). Natural disease course of Crohn's disease during the first 5 years after diagnosis in a European population-based inception cohort: an Epi-IBD study. Gut, 68 (3), 423-433.
Burisch, J. , Katsanos, K. H. , Christodoulou, D. K. , Barros, L. , Magro, F. , Pedersen, N. , Kjeldsen, J. , Vegh, Z. & et al. (2019). Natural Disease Course of Ulcerative Colitis During the First Five Years of Follow-up in a European Population-based Inception Cohort-An Epi-IBD Study. Journal of Crohn's & Colitis, 13 (2), 198-208.
Butwicka, A. , Sariaslan, A. , Larsson, H. , Halfvarson, J. , Myrelid, P. E. , Olén, O. , Frisen, L. , Lichtenstein, P. & et al. (2019). No association between urbanisation, neighbourhood deprivation and IBD: a population-based study of 4 million individuals. Gut, 68 (5), 947-948.
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. Journal of Crohn's & Colitis, 13 (Suppl. 1), S614-S614.
Shubhakar, A. , Jansen, B. , Adams, A. , Reiding, K. , Ventham, N. , Bergemalm, D. , Urbanowicz, P. , Gardner, R. & et al. (2019). Serum N-glycomic biomarkers predict treatment escalation in inflammatory bowel disease. Journal of Crohn's & Colitis, 13 (Suppl. 1), S32-S33.
Drobin, K. , Assadi, G. , Hong, M. , Andersson, E. , Fredolini, C. , Forsström, B. , Reznichenko, A. , Akhter, T. & et al. (2019). Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci. Inflammatory Bowel Diseases, 25 (2), 306-316.
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).
King, J. A. , Underwood, F. E. , Panaccione, N. , Quan, J. , Windsor, J. W. , Kotze, P. G. , Ng, S. C. , Ghosh, S. & et al. (2019). Trends in hospitalisation rates for inflammatory bowel disease in western versus newly industrialised countries: a population-based study of countries in the Organisation for Economic Co-operation and Development. The Lancet Gastroenterology & Hepatology, 4 (4), 287-295.
Danese, S. , Allez, M. , van Bodegraven, A. A. , Dotan, I. , Gisbert, J. P. , Hart, A. , Lakatos, P. L. , Magro, F. & et al. (2019). Unmet Medical Needs in Ulcerative Colitis: An Expert Group Consensus. Digestive Diseases, 37 (4), 266-283.
Everhov, Å. H. , Khalili, H. , Askling, J. , Myrelid, P. , Ludvigsson, J. F. , Halfvarson, J. , Nordenvall, C. , Neovius, M. & et al. (2019). Work Loss Before and After Diagnosis of Crohn's Disease. Inflammatory Bowel Diseases, 25 (7), 1237-1247.
Rundquist, S. , Eriksson, C. , Nilsson, L. , Angelison, L. , Jäghult, S. , Björk, J. , Grip, O. , Hjortswang, H. & et al. (2018). Clinical effectiveness of golimumab in Crohn's disease: an observational study based on the Swedish National Quality Registry for Inflammatory Bowel Disease (SWIBREG). Scandinavian Journal of Gastroenterology, 53 (10-11), 1257-1263.
Eriksson, C. , Bergemalm, D. , Vigren, L. , Nilsson, L. , Visuri, I. , Hjortswang, H. , Udumyan, R. , Almer, S. & et al. (2018). Clinical effectiveness of golimumab: Interim analysis of the observational study of patients with ulcerative colitis on golimumab in the Swedish National Quality Registry for IBD-GO-SWIBREG. Journal of Crohn's & Colitis, 12 (Suppl. 1), S409-S410.
Eriksson, C. , Rundquist, S. , Lykiardopoulos, V. , Karlen, P. , Grip, O. , Söderman, C. , Almer, S. , Hertervig, E. & et al. (2018). Clinical effectiveness of vedolizumab: Interim analysis of the Swedish observational study on vedolizumab assessing effectiveness and healthcare resource utilisation in patients with Crohn's disease (SVEAH CD). Journal of Crohn's & Colitis, 12 (Suppl. 1), S494-S495.
Eriksson, C. , Rundquist, S. , Lykiardopoulos, V. , Karlen, P. , Grip, O. , Söderman, C. , Almer, S. , Hertervig, E. & et al. (2018). Clinical effectiveness of vedolizumab: Interim analysis of the Swedish observational study on vedolizumab assessing effectiveness and healthcare resource utilisation in patients with ulcerative colitis (SVEAH UC). Journal of Crohn's & Colitis, 12 (Suppl. 1), S382-S383.
Siegel, C. A. , Whitman, C. B. , Spiegel, B. M. R. , Feagan, B. , Sands, B. , Loftus, E. V. , Panaccione, R. , D'Haens, G. & et al. (2018). Development of an index to define overall disease severity in IBD. Gut, 67 (2), 244-254.
Carstens, A. , Roos, A. , Andreasson, A. , Magnuson, A. , Agréus, L. , Halfvarson, J. & Engstrand, L. (2018). Differential clustering of faecal and mucosa-associated microbiota in healthy individuals. Journal of Digestive Diseases, 19 (12), 745-752.
Vatn, S. , Karlsson, M. C. , Carstens, A. , Detlie, T. E. , Ricanek, P. , Bergemalm, D. , Lindquist, C. M. , Jahnsen, J. & et al. (2018). Faecal microbiota in newly diagnosed Crohn's disease and its relation to treatment escalation. Journal of Crohn's & Colitis, 12 (Suppl. 1), S555-S555.
Vatn, S. , Karlsson, M. C. , Carstens, A. , Detlie, T. E. , Ricanek, P. , Lindquist, C. M. , Bergemalm, D. , Jahnsen, J. & et al. (2018). Faecal microbiota in treatment-naive ulcerative colitis and its relation to treatment escalation. Journal of Crohn's & Colitis, 12 (Suppl. 1), S557-S557.
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. Journal of Crohn's & Colitis, 12 (Suppl. 1), S1-S1.
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.
Burisch, J. , Andersen, V. , Cukovic-Cavka, S. , Lakatos, P. L. , D'Inca, R. , Magro, F. , Arebi, N. , Kievit, L. & et al. (2018). Immunomodulators reduce the risk of surgery and hospitalisation in Crohn's disease in a prospective European population-based inception cohort: the Epi-IBD cohort. Journal of Crohn's & Colitis, 12 (Suppl. 1), S42-S43.
Everhov, Å. H. , Halfvarson, J. , Myrelid, P. , Sachs, M. C. , Nordenvall, C. , Söderling, J. , Ekbom, A. , Neovius, M. & et al. (2018). Incidence and Treatment of Patients Diagnosed With Inflammatory Bowel Diseases at 60 Years or Older in Sweden. Gastroenterology, 154 (3), 518-528.
Eriksson, C. , Henriksson, I. , Brus, O. , Zhulina, Y. , Nyhlin, N. , Tysk, C. , Montgomery, S. & Halfvarson, J. (2018). Incidence, prevalence and clinical outcome of anaemia in inflammatory bowel disease: a population-based cohort study. Alimentary Pharmacology and Therapeutics, 48 (6), 638-645.
Björkqvist, O. , Repsilber, D. , Seifert, M. , Engstrand, L. , Rangel, I. & Halfvarson, J. (2018). Increasing abundance of faecalibacterium prausnitzii is associated with decreased intestinal inflammation in Crohn's disease: A longitudinal study. Journal of Crohn's & Colitis, 12 (Suppl. 1), S468-S469.
Burisch, J. , Ellul, P. , Arebi, N. , Kaimakliotis, I. , D'Inca, R. , Andersen, V. , Belousova, E. , Hernandez, V. & et al. (2018). Natural disease course of inflammatory bowel disease unclassified in a prospective European population-based inception cohort-the Epi-IBD cohort. Journal of Crohn's & Colitis, 12 (Suppl. 1), S523-S524.
Amcoff, K. , Cao, Y. , Zhulina, Y. , Lampinen, M. , Halfvarson, J. & Carlson, M. (2018). Prognostic significance of eosinophil granule proteins in inflammatory bowel disease. Journal of Crohn's & Colitis, 12 (Suppl. 1), S181-S182.
Melinder, C. , Hiyoshi, A. , Kasiga, T. , Halfvarson, J. , Fall, K. & Montgomery, S. (2018). Resilience to stress and risk of gastrointestinal infections. European Journal of Public Health, 28 (2), 364-369.
Hedin, C. & Halfvarson, J. (2018). Should we use vedolizumab as mono or combo therapy in ulcerative colitis?. Baillière's Best Practice & Research: Clinical Gastroenterology, 32-33, 27-34.
Everhov, Å. H. , Khalili, H. , Askling, J. , Myrelid, P. , Ludvigsson, J. F. , Halfvarson, J. , Nordenvall, C. , Söderling, J. & et al. (2018). Sick Leave and Disability Pension in Prevalent Patients With Crohn's Disease. Journal of Crohn's & Colitis, 12 (12), 1418-1428.
Eriksson, C. , Rundquist, S. , Cao, Y. , Montgomery, S. & Halfvarson, J. (2018). The impact of thiopurine drugs on the natural history and surgical outcome of ulcerative colitis: A cohort study. Journal of Crohn's & Colitis, 12 (Suppl. 1), S481-S481.
Svensson, M. , Bergman, D. , Olén, O. , Myrelid, P. , Bohr, J. , Wickbom, A. , Khalili, H. , Münch, A. & et al. (2018). Validating microscopic colitis (MC) in Swedish pathology registers. Scandinavian Journal of Gastroenterology.
Zammit, S. C. , Ellul, P. , Girardin, G. , Valpiani, D. , Nielsen, K. R. , Olsen, J. , Goldis, A. , Lazar, D. & et al. (2018). Vitamin D deficiency in a European inflammatory bowel disease inception cohort: an Epi-IBD study. European Journal of Gastroenterology and Hepathology, 30 (11), 1297-1303.
Eriksson, C. , Rundquist, S. , Lykiardopoulos, B. , Karlén, P. , Grip, O. , Söderman, C. , Almer, S. , Hertervig, E. & et al. (2017). A Swedish observational study (SVEAH) on vedolizumab assessing effectiveness and healthcare resource utilization in patients with inflammatory bowel disease. Journal of Crohn's & Colitis, 11 (Suppl. 1), S262-S263.
Kuja-Halkola, R. , Lebwohl, B. , Halfvarson, J. , Emilsson, L. , Magnusson, P. K. & Ludvigsson, J. F. (2017). Birth weight, sex, and celiac disease: a nationwide twin study. Clinical Epidemiology, 9, 567-577.
Burisch, J. , Halfvarson, J. , Kupcinskas, L. , Hernandez, V. , Kaimakliotis, I. , Valpiani, D. , Pedersen, N. , Duricova, D. & et al. (2017). Change in Crohn's disease behavior in a prospective European population-based inception cohort - the ECCO-EpiCom cohort. Journal of Crohn's & Colitis, 11 (Suppl. 1), S452-S453.
Eriksson, C. , Cao, Y. , Rundquist, S. , Zhulina, Y. , Henriksson, I. , Montgomery, S. & Halfvarson, J. (2017). Changes in medical management and colectomy rates: a population-based cohort study on the epidemiology and natural history of ulcerative colitis in Orebro, Sweden, 1963-2010. Alimentary Pharmacology and Therapeutics, 46 (8), 748-757.
Amcoff, K. , Stridsberg, M. , Lampinen, M. , Magnuson, A. , Carlson, M. & Halfvarson, J. (2017). Clinical implications of assay specific differences in f-calprotectin when monitoring inflammatory bowel disease activity over time. Scandinavian Journal of Gastroenterology, 52 (3), 344-350.
Rencz, F. , Gulácsi, L. , Péntek, M. , Gecse, K. B. , Dignass, A. , Halfvarson, J. , Gomollón, F. , Baji, P. & et al. (2017). Cost-utility of biological treatment sequences for luminal Crohn's disease in Europe. Expert review of pharmacoeconomics & outcomes research, 17 (6), 597-606.
Westerlind, H. , Mellander, M. , Bresso, F. , Munch, A. , Bonfiglio, F. , Assadi, G. , Rafter, J. , Huebenthal, M. & et al. (2017). Dense genotyping of immune-related loci identifies HLA variants associated with increased risk of collagenous colitis. Gut, 66 (3), 421-428.
Burisch, J. , Halfvarson, J. , Kupcinskas, L. , Hernandez, V. , Kaimakliotis, I. , Valpiani, D. , Pedersen, N. , Duricova, D. & et al. (2017). Disease course during the first five years following diagnosis in a prospective European population-based inception cohort - the ECCO-EpiCom cohort. Journal of Crohn's & Colitis, 11 (Suppl. 1), S435-S436.
Halfvarson, J. , Brislawn, C. J. , Lamendella, R. , Vázquez-Baeza, Y. , Walters, W. A. , Bramer, L. M. , D'Amato, M. , Bonfiglio, F. & et al. (2017). Dynamics of the human gut microbiome in inflammatory bowel disease. Nature Microbiology, 2 (5).
Eriksson, C. , Cao, Y. , Rundquist, S. , Zhulina, Y. , Henriksson, I. , Montgomery, S. & Halfvarson, J. (2017). Editorial: do thiopurines and biologics decrease the risk of colectomy? Authors' reply. Alimentary Pharmacology and Therapeutics, 46 (9), 897-898.
Bergemalm, D. , Kruse, R. , Sapnara, M. , Halfvarson, J. & Hultgren Hörnquist, E. (2017). Elevated fecal peptidase D at onset of colitis in Galphai2(-/-) mice, a mouse model of IBD. PLoS ONE, 12 (3).
Adams, A. , Kalla, R. , Vatn, S. , Bonfiglio, F. , Nimmo, E. , Kennedy, N. , Ventham, N. , Vatn, M. & et al. (2017). Epigenetic alterations at diagnosis predict susceptibility, prognosis and treatment escalation in inflammatory bowel disease - IBD Character. Journal of Crohn's & Colitis, 11 (Suppl. 1), S108-S108.
Kalla, R. , Adams, A. T. , Vatn, S. , Bonfiglio, F. , Nimmo, E. R. , Kennedy, N. A. , Ventham, N. , Vatn, M. H. & et al. (2017). Epigenetic alterations at diagnosis predict susceptibility, prognosis and treatment escalation in inflammatory bowel disease – ibd character. Gut, 66 (Suppl. 2), A24-A25.
Kalla, R. , Adams, A. , Nimmo, E. , Kennedy, N. , Ventham, N. , Vatn, M. , Jahnsen, J. , Ricanek, P. & et al. (2017). Epigenetic alterations in inflammatory bowel disease: the complex interplay between genome-wide methylation alterations, germline variation, and gene expression. The Lancet, 389 (Suppl. 1), 52-52.
Huang, H. , Halfvarson, J. & Barrett, J. C. (2017). Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature, 547 (7662), 173-+.
Eriksson, C. , Marsal, J. , Bergemalm, D. , Vigren, L. , Björk, J. , Eberhardson, M. , Karling, P. , Söderman, C. & et al. (2017). Long-term effectiveness of vedolizumab in inflammatory bowel disease: a national study based on the Swedish National Quality Registry for Inflammatory Bowel Disease (SWIBREG). Scandinavian Journal of Gastroenterology, 52 (6-7), 722-729.
Angelison, L. , Almer, S. , Eriksson, A. , Karling, P. , Fagerberg, U. , Halfvarson, J. , Thörn, M. , Björk, J. & et al. (2017). Long-term outcome of infliximab treatment in chronic active ulcerative colitis: a Swedish multicentre study of 250 patients. Alimentary Pharmacology and Therapeutics, 45 (4), 519-532.
Ricanek, P. , Rahul, K. , Ber, Y. , Vatn, S. , Finnby, L. , Lindahl, T. , Bergemalm, D. , Carstens, A. & et al. (2017). Microbiota related disease activity and distribution in subgroups of inflammatory bowel disease. Journal of Crohn's & Colitis, 11 (Suppl. 1), S483-S484.
Burisch, J. , Vegh, Z. , Katsanos, K. H. , Christodoulou, D. K. , Lazar, D. , Goldis, A. , O'Morain, C. , Fernandez, A. & et al. (2017). Occurrence of anaemia in the first year of inflammatory bowel disease in a European population-based inception cohort: An ECCO-EpiCom study. Journal of Crohn's & Colitis, 11 (10), 1213-1222.
Kalla, R. , Adams, A. T. , Vatn, S. , Bergemalm, D. , Ricanek, P. , Lindstrom, J. C. , Ocklind, A. , Nordberg, N. & et al. (2017). Proximity extension assay based proteins show immune cell specificity and can diagnose and predict outcomes in inflammatory bowel diseases: ibd character study. Gut, 66 (Suppl. 2), A202-A203.
Kalla, R. , Adams, A. , Vatn, S. , Bergemalm, D. , Ricanek, P. , Lindström, J. , Ocklind, A. , Nordberg, N. & et al. (2017). Proximity extension assay based proteins show immune cell specificity and can diagnose and predict outcomes in inflammatory bowel diseases: IBD Character study. Journal of Crohn's & Colitis, 11 (Suppl. 1), S13-S13.
Andersson, E. , Bergemalm, D. , Kruse, R. , Neumann, G. , D'Amato, M. , Repsilber, D. & Halfvarson, J. (2017). Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profiles. PLoS ONE, 12 (10).
Burisch, J. , Halfvarson, J. , Kupcinskas, L. , Hernandez, V. , Kaimakliotis, I. , Valpiani, D. , Pedersen, N. , Duricova, D. & et al. (2017). The risk of proximal disease extension in patients with limited ulcerative colitis in a prospective European population-based inception cohort - the ECCO-EpiCom cohort. Journal of Crohn's & Colitis, 11 (Suppl. 1), S436-S436.
Jakobsson, G. L. , Sternegård, E. , Olén, O. , Myrelid, P. , Ljung, R. , Strid, H. , Halfvarson, J. & Ludvigsson, J. F. (2017). Validating inflammatory bowel disease (IBD) in the Swedish National Patient Register and the Swedish Quality Register for IBD (SWIBREG). Scandinavian Journal of Gastroenterology, 52 (2), 216-221.
Bodea, C. A. , Neale, B. M. , Ripke, S. , International IBD Genetics Consortium, G. a. , Daly, M. J. , Devlin, B. & Roeder, K. (2016). A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies. American Journal of Human Genetics, 98 (5), 857-868.
Li, D. , Achkar, J. , Haritunians, T. , Jacobs, J. P. , Hui, K. Y. , D'Amato, M. , Brand, S. , Radford-Smith, G. & et al. (2016). A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition. Gastroenterology, 151 (4), 724-732.
Rivas, M. A. , Graham, D. , Sulem, P. , Stevens, C. , Desch, A. N. , Goyette, P. , Gudbjartsson, D. , Jonsdottir, I. & et al. (2016). A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nature Communications, 7.
Ellinghaus, D. , Jostins, L. , Spain, S. L. , Cortes, A. , Bethune, J. , Han, B. , Park, Y. R. , Raychaudhuri, S. & et al. (2016). Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nature Genetics, 48 (5), 510-518.
Heap, G. A. , Halfvarson, J. & Ahmad, T. (2016). Clinical Features and HLA Association of 5-Aminosalicylate (5-ASA)-induced Nephrotoxicity in Inflammatory Bowel Disease. Journal of Crohn's & Colitis, 10 (2), 149-158.
Amcoff, K. , Joossens, M. , Pierik, M. J. , Jonkers, D. , Bohr, J. , Joossens, S. , Romberg-Camps, M. , Nyhlin, N. & et al. (2016). Concordance in Anti-OmpC and Anti-I2 Indicate the Influence of Genetic Predisposition: Results of a European Study of Twins with Crohn's Disease. Journal of Crohn's & Colitis, 10 (6), 695-702.
Zhulina, Y. , Cao, Y. , Amcoff, K. , Carlson, M. , Tysk, C. & Halfvarson, J. (2016). Faecal calprotectin for the prediction of relapse in inactive inflammatory bowel disease: - authors' reply. Alimentary Pharmacology and Therapeutics, 44 (7), 770-771.
Burisch, J. , Gerdes, U. , Almer, S. , Cukovic-Cavka, S. , Sebastian, S. , Kaimakliotis, I. , Duricova, D. , Pedersen, N. & et al. (2016). Frequency of anaemia and anaemia subtypes in east-west European inception cohort: an ECCO-EpiCom cohort study. Journal of Crohn's & Colitis, 10 (Suppl. 1), S453-S454.
Assadi, G. , Vesterlund, L. , Bonfiglio, F. , Mazzurana, L. , Cordeddu, L. , Schepis, D. , Mjösberg, J. , Ruhrmann, S. & et al. (2016). Functional Analyses of the Crohn's Disease Risk Gene LACC1. PLoS ONE, 11 (12).
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Einarsdottir, E. , Koskinen, L. L. E. , Dukes, E. , Kainu, K. , Suomela, S. , Lappalainen, M. , Ziberna, F. , Korponay-Szabo, I. R. & et al. (2009). IL23R in the Swedish, Finnish, Hungarian and Italian populations: association with IBD and psoriasis, and linkage to celiac disease. BMC Medical Genetics, 10 (8).
Jansson, J. , Willing, B. , Lucio, M. , Fekete, A. , Dicksved, J. , Halfvarson, J. , Tysk, C. & Schmitt-Kopplin, P. (2009). Metabolomics reveals metabolic biomarkers of Crohn's disease. PloS one, 4 (7), e6386.
Almer, S. , Befrits, R. , Eriksson, A. S. , Halfvarson, J. , Hindorf, U. & Löfberg, R. (2009). Modern läkemedelsterapi vid Crohn  [Current drug therapy in Crohn disease]: nationella riktlinjer [national guidelines]. Läkartidningen, 106 (45), 2988-2993.
Zucchelli, M. , Torkvist, L. , Halfvarson, J. , Söderhäll, C. , Lee, Y. , Löfberg, R. , Kere, J. & D ´Amato, M. (2009). No association between the eczema genes COL29A1 and IL31 and inflammatory bowel disease. Inflammatory Bowel Diseases, 15 (7), 961-962.
Zucchelli, M. , Torkvist, L. , Bresso, F. , Halfvarson, J. , Hellquist, A. , Anedda, F. , Assadi, G. , Lindgren, G. B. & et al. (2009). PepT1 oligopeptide transporter (SLC15A1) gene polymorphism in inflammatory bowel disease. Inflammatory Bowel Diseases, 15 (10), 1562-1569.
Verberkmoes, N. C. , Russell, A. L. , Shah, M. , Godzik, A. , Rosenquist, M. , Halfvarson, J. , Lefsrud, M. G. , Apajalahti, J. & et al. (2009). Shotgun metaproteomics of the human distal gut microbiota. ISME Journal, 3 (2), 179-189.
Zhulina, Y. , Carlson, M. , Peterson, C. G. , Tysk, C. , Gustavsson, A. , Bohr, J. , Bodin, L. & Halfvarson, J. (2009). Subclinical inflammation due to environmental exposure in health co-twins to twins with inflammatory bowel disease. Gastroenterology, 136 (5), A20-A20.
Halfvarson, J. & Järnerot, G. (2009). Treatment of choice for acute severe steroid-refractory ulcerative colitis is remicade. Inflammatory Bowel Diseases, 15 (1), 143-145.
Willing, B. , Halfvarson, J. , Dicksved, J. , Rosenquist, M. , Järnerot, G. , Engstrand, L. , Tysk, C. & Jansson, J. K. (2009). Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflammatory Bowel Diseases, 15 (5), 653-660.
Halfvarson, J. , Dicksved, J. , Rosenquist, M. , Willing, E. , Järnerot, G. , Engstrand, L. , Jansson, J. K. & Tysk, C. (2008). Bakteriefloran hos tvillingar med Crohns sjukdom. Gastrokuriren, 13 (29 PO-08).
Gustavsson, A. , Järnerot, G. , Hertervig, E. , Friis-Liby, I. , Blomquist, L. , Karlen, P. , Grännö, C. , Vilien, M. & et al. (2008). Colectomy after rescue therapy for intravenous-steroid resistant acute ulcerative colitis: a 3-year follow-up study of the Swedish-Danish infliximab/placebo trial. Gut, 57(Suppl 1), A79-A79.
Vandewalle-El Khoury, P. , Colombel, J. , Joossens, S. , Standaert-Vitse, A. , Collot, M. , Halfvarson, J. , Ayadi, A. , Landers, C. J. & et al. (2008). Detection of antisynthetic mannoside antibodies (ASigmaMA) reveals heterogeneity in the ASCA response of Crohn's disease patients and contributes to differential diagnosis, stratification, and prediction. American Journal of Gastroenterology, 103 (4), 949-957.
Schoultz, I. , Verma, D. , Törkvist, L. , Halfvarson, J. , Lerm, M. , Söderkvist, P. & Söderholm, J. D. (2008). M2080 Compound Polymorphisms in CARD8 and CIAS1 Predispose to Crohn's Disease in a Swedish Cohort. Gastroenterology, 134 (4), A464-A465.
Dicksved, J. , Halfvarson, J. , Rosenquist, M. , Järnerot, G. , Tysk, C. , Apajalahti, J. , Engstrand, L. & Jansson, J. K. (2008). Molecular analysis of the gut microbiota of identical twins with Crohn's disease. The ISME journal, 2 (7), 716-727.
Walch, A. , Sjöberg, M. , Meshkat, M. , Gustavsson, A. , Järnerot, G. , Vogelsang, H. , Hertervig, E. , Novacek, G. & et al. (2008). Outcome of rescue therapy in steroid-resistant ulcerative colitis: a retrospective study comparing cyclosporine and infliximab. Gut, 57(Suppl II), A265.
Nyhlin, N. , Bergman, J. , Bohr, J. , Gustavsson, A. , Halfvarson, J. , Salén, E. , Sandberg Gertzén, H. & Tysk, C. (2008). Plasmaferes vid svår läkemedelsutlöst kolestas. Gastrokuriren, 13 (33), PO-16.
Halfvarson, J. , Dicksved, J. , Rosenquist, M. , Järnerot, G. , Tysk, C. , Engstrand, L. & Jansson, J. K. (2008). W1182 molecular fingerprinting of the gut microbiota of twins reveals differences according to Crohn's disease. Gastroenterology, 134 (4, Supplement 1), A-650-A-650.
Gustavsson, A. , Jaenerot, G. , Hertervig, E. , Friis-Iiby, I. , Blomquist, L. , Karlen, P. , Granno, C. , Vilien, M. & et al. (2007). A 2-year follow-up of the swedish-danish Infliximab/Placebo trial in steroid resistant acute ulcerative colitis. Gastroenterology, 132 (4), A146-A147.
Halfvarson, J. , Jess, T. , Bodin, L. , Järnerot, G. , Munkholm, P. , Binder, V. & Tysk, C. (2007). Longitudinal concordance for clinical characteristics in a Swedish-Danish twin population with inflammatory bowel disease. Inflammatory Bowel Diseases, 13 (12), 1536-1544.
Gustavsson, A. , Halfvarson, J. , Magnuson, A. , Sandberg-Gertzén, H. , Tysk, C. & Järnerot, G. (2007). Long-term colectomy rate after intensive intravenous corticosteroid therapy for ulcerative colitis prior to the immunosuppressive treatment era. American Journal of Gastroenterology, 102 (11), 2513-2519.
Järnerot, G. , Halfvarson, J. & Tysk, C. (2007). Twin studies in inflammatory bowel disease: a review. Austral - Asian Journal of Cancer, 6 (1), 29-33.
Bodger, K. , Halfvarson, J. , Dodson, A. R. , Campbell, F. , Wilson, S. , Lee, R. , Lindberg, E. , Järnerot, G. & et al. (2006). Altered colonic glycoprotein expression in unaffected monozygotic twins of inflammatory bowel disease patients. Gut, 55 (7), 973-977.
Halfvarson, J. , Jess, T. , Magnuson, A. , Montgomery, S. M. , Orholm, M. , Tysk, C. , Binder, V. & Järnerot, G. (2006). Environmental factors in inflammatory bowel disease: a co-twin control study of a Swedish-Danish twin population. Inflammatory Bowel Diseases, 12 (10), 925-933.
Halfvarson, J. (2006). Infliximab är indicerat även vid ulcerös kolit. Läkartidningen, 103 (13), 1013-1013.
Järnerot, G. , Halfvarson, J. & Tysk, C. (2006). Twin studies in inflammatory bowel disease: a review. Recent Advances and Research Updates (7), 143-7.
Joossens, S. , Halfvarson, J. , Camps, M. , Vermeire, S. , Jarnerot, G. , Stockbrugger, R. , Bossuyt, X. , Rutgeerts, P. & et al. (2005). A panel of serologic markers in twins with inflammatory bowel disease. Gut (Suppl.).
Halfvarson, J. , Standaert-Vitse, A. , Järnerot, G. , Sendid, B. , Jouault, T. , Bodin, L. , Duhamel, A. , Colombel, J. F. & et al. (2005). Anti-Saccharomyces cerevisiae antibodies in twins with inflammatory bowel disease. Gut, 54 (9), 1237-1243.
Halfvarson, J. , Bresso, F. , D ´Amato, M. , Järnerot, G. , Pettersson, S. & Tysk, C. (2005). CARD15/NOD2 polymorphisms do not explain concordance of Crohn´s disease in Swedish monozygotic twins. Digestive and Liver Disease, 37 (10), 768-762.
Tamboli, C. , Attaluri, A. , Yan, J. , Duke, A. , Colombel, J. F. , Silverberg, M. , McLeod, R. , Jewell, D. & et al. (2005). Phenotypic concordance and time clustering of diagnosis in multiply affected ibd families: the IOIBD Multiplex Family Collaborative Project, phases I & II. Gut, Suppl.
Halfvarson, J. , Jess, T. , Jespersgaard, C. , Riis, L. , Tysk, C. , Järnerot, G. , Skytt Andersen, P. & Munkholm, P. (2005). Prevalence of Toll-like receptor 2 and 4 polymorphisms in twins with inflammatory bowel disease: a population based Danish Swedish cohort study. Gut.
Gustavsson, A. , Halfvarson, J. , Sandberg-Gertzén, H. , Tysk, C. & Järnerot, G. (2005). Tio års uppföljning av patienter behandlade för svår attack av ulcerös kolit. Sv Läkaresällskapets Handl, Hygiea.
Jess, T. , Halfvarson, J. , Bodin, L. , Tysk, C. , Järnerot, G. & Binder, V. (2004). Concordance for Vienna Classification Characteristics in monozygotic twins with Crohn’s disease: a Danish-Swedish cohort study of IBD twins. Gut, 53 (Suppl VI), A140-A140.
Halfvarson, J. , Jess, T. , Bodin, L. , Tysk, C. , Binder, V. & Järnerot, G. (2004). Concordance in phenotype in ulcerative colitis: a study in monozygotic twins. Gut, 53 (Suppl VI), A145-A145.
Halfvarson, J. , Tysk, C. & Jarnerot, G. (2004). Decreasing pair concordance in monozygotic twins with Crohn's disease. Gastroenterology, 126 (4), A45-A45.
Halfvarson, J. , Bresso, F. , Tysk, C. , Pettersson, S. & Jarnerot, G. (2004). Genetic Crohn's disease: A different entity than sporadic. A study in monozygotic twins. Gastroenterology, 126 (4), A359-A360.
Halfvarson, J. , Jess, T. , Bodin, L. , Tysk, C. , Binder, V. & Jarnerot, G. (2004). Phenotypic concordance in monozygotic twin pairs with ulcerative colitis. Gastroenterology, 126 (4), A356-A356.
Jess, T. , Halfvarson, J. , Bodin, L. , Tysk, C. , Jarnerot, G. & Binder, V. (2004). Strong genetic influence on longitudinal changes in Vienna Classification characteristics: a Danish-Swedish cohort study of IBD twins. Gastroenterology, 126 (4), A469-A469.
Halfvarson, J. , Bodin, L. , Tysk, C. , Lindberg, E. & Järnerot, G. (2003). Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics. Gastroenterology, 124 (7), 1767-1773.
Halfvarson, J. (2002). Stor och tung men med bra tangentbord [Big and heavy but the keyboard is good]. Läkartidningen, 99 (13), 1478-1478.
Halfvarson, J. , Heijne, N. , Ljungman, P. , Ham, M. N. , Holmgren, G. & Tomson, G. (2000). Knowing when but not how!: mothers' perceptions and use of antibiotics in a rural area of Viet Nam. Tropical doctor, 30 (1), 6-10.
Halfvarson, J. & Loogna, P. (1997). Svårt avgöra om full och arg har skallskada [Difficult to diagnose head injuries in drunk and violent persons]. Läkartidningen, 94 (42), 3719-3722.

Articles, reviews/surveys

Ludvigsson, J. F. , Andersson, M. , Bengtsson, J. , Eberhardson, M. , Fagerberg, U. L. , Grip, O. , Halfvarson, J. , Hjortswang, H. & et al. (2019). Swedish Inflammatory Bowel Disease Register (SWIBREG): a nationwide quality register. Scandinavian Journal of Gastroenterology, 1-13.
Halfvarson, J. , Cummings, F. , Grip, O. & Savoye, G. (2018). Inflammatory bowel disease registries for collection of patient iron parameters in Europe. World Journal of Gastroenterology, 24 (10), 1063-1071.
Ek, W. E. , D'Amato, M. & Halfvarson, J. (2014). The history of genetics in inflammatory bowel disease. Annals of Gastroenterology, 27 (4), 294-303.

Chapters in books

Halfvarson, J. (2013). Genetic epidemiology of inflammatory bowel disease, early twin and family studies. In: D’Amato M, Rioux J., Molecular Genetics of Inflammatory Bowel Disease (pp. 23-43). USA: Springer.
Halfvarson, J. (2009). Ulcerös kolit. In: Utdrag ur Medicinska mag- och tarmsjukdomar. Lund: Studentlitteratur AB.
Halfvarson, J. (2008). Ulcerös kolit. In: Henry Nyhlin, Medicinska mag- och tarmsjukdomar (pp. 371-382). Lund: Studentlitteratur.

Conference papers

Rundquist, S. , Eriksson, C. , Nilsson, L. , Angelison, L. , Jäghult, S. , Björk, J. , Grip, O. , Hjortswang, H. & et al. (2018). Clinical effectiveness of golimumab in Crohn´s disease – an observational study based on the Swedish National Quality Registry for Inflammatory Bowel Disease (SWIBREG). Paper presented at 26th United European Gastroenterology Week, Vienna, Austria, October 20-24, 2018.
Eriksson, C. , Bergenmalm, D. , Vigren, L. , Nilsson, L. , Visuri, I. , Hjortswang, H. , Udumyan, R. , Almer, S. & et al. (2018). Golimumab är effektivt vid ulcerös kolit under svenska förhållanden. Interimsanalys av en svensk prospektiv multi-centerstudie, GO-SWIBREG. Paper presented at Gastrodagarna 2018, Falun, Sweden, 16-18 maj, 2018.
Göranzon, C. , Hultgren Hörnquist, E. , Kumawat, A. K. , Halfvarson, J. , Tysk, C. , Eriksson, S. , Bohr, J. & Nyhlin, N. (2010). Immunohistochemical characterization of lymphocytes in microscopic colitis. Paper presented at 18th United European Gastroenterology Week, Barcelona, Oct, 2010.
Jansson, J. K. , Willing, B. , Dicksved, J. , Halfvarson, J. , Andersson, A. , Rosenquist, M. , Järnerot, G. , Tysk, C. & et al. (2008). Molecular fingerprinting of twins with Crohn's disease reveals the importance of dysbiosis of the gut microbiota. Paper presented at American Society of Microbiology: 2nd conference on beneficial host-microbial interactions, San Diego 12-16 October 2008.
Willing, B. , Halfvarson, J. , Dicksved, J. , Rosenquist, M. , Järnerot, G. , Engstrand, L. , Tysk, C. & Jansson, J. K. (2008). Studying discordant monozygotic twins reveals differences in mucosa-associated microbiota depending on Crohn's disease phenotype. Paper presented at INRA-RRI 2008 Symposium, Clermont-Ferrand, Frankrike, 18-20 Juni, 2008.
Halfvarson, J. , Ahmad, T. , Daperno, M. , Jewell, D. , Järnerot, G. & Tysk, C. (2003). Inflytandet av CARD15/NOD2 samt IBD5 bland svenska tvåäggstvillingar.

Manuscripts

Amcoff, K. , Cao, Y. , Zhulina, Y. , Lampinen, M. , Halfvarson, J. & Carlson, M. Prognostic significance of eosinophile granule proteins in inflammatory bowel disease.
Zhulina, Y. , Cao, Y. , Amcoff, K. , Carlsson, M. , Tysk, C. & Halfvarson, J. Prognostic significance of faecal calprotectin in patients with inactive inflammatory bowel disease.
Melinder, C. , Hiyoshi, A. , Kasiga, T. , Halfvarson, J. , Fall, K. & Montgomery, S. Resilience to stress and risk of gastrointestinal infections.
Gustavsson, A. , Magnuson, A. , Blomberg, B. , Andersson, M. , Halfvarson, J. & Tysk, C. Smoking is a risk factor for recurrence of intestinal stricture after endoscopic dilation in Crohn’s disease.