Browse by Research Team

Research Teams (202)
- Forslund, Sofia (MDC/ECRC) (202)

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Acta Physiologica

A gender perspective on diet, microbiome, and sex hormone interplay in cardiovascular disease.
Jovanovic, N. ORCID: https://orcid.org/0000-0001-6300-9705, Zach, V. ORCID: https://orcid.org/0000-0001-9555-0010, Crocini, C. ORCID: https://orcid.org/0000-0001-8231-2726, Bahr, L.S. ORCID: https://orcid.org/0000-0001-7932-8639, Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Franz, K. ORCID: https://orcid.org/0000-0002-3819-9671
Acta Physiologica 240 (11): e14228. November 2024

American Journal of Physiology Gastrointestinal and Liver Physiology

Gut microbiota differs between children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.
Knoll, R.L. ORCID: https://orcid.org/0000-0002-3496-345X, Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Kultima, J.R., Meyer, C.U., Kullmer, U., Sunagawa, S., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and Gehring, S.
American Journal of Physiology Gastrointestinal and Liver Physiology 312 (4): G327-G339. 1 April 2017

American Journal of Transplantation

Arthritis & Rheumatology

Shared and distinct gut microbiota in spondyloarthritis, acute anterior uveitis, and Crohn's disease.
Essex, M. ORCID: https://orcid.org/0000-0001-8758-7497, Rios Rodriguez, V., Rademacher, J., Proft, F., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Marko, L. ORCID: https://orcid.org/0000-0003-1888-5575, Pleyer, U., Strowig, T., Marchand, J., Kirwan, J.A. ORCID: https://orcid.org/0000-0002-5423-1651, Siegmund, B., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Poddubnyy, D.
Arthritis & Rheumatology 76 (1): 48-58. January 2024

BJPsych Open

The effect of stress on delay discounting in female patients with early-onset bulimia nervosa and alcohol use disorder: functional magnetic resonance imaging study.
Leenaerts, Nicolas ORCID: https://orcid.org/0000-0003-2421-6845, Ceccarini, Jenny, Weygandt, Martin ORCID: https://orcid.org/0000-0001-9962-4582, Sunaert, Stefan and Vrieze, Elske
BJPsych Open 11 (5): e207. 12 September 2025

BMC Bioinformatics

Domainoid: domain-oriented orthology inference.
Persson, E. ORCID: https://orcid.org/0000-0003-0532-8251, Kaduk, M., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
BMC Bioinformatics 20 (1): 523. 28 October 2019

Domain architecture conservation in orthologs.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Pekkari, I. and Sonnhammer, E.L.L.
BMC Bioinformatics 12 : 326. 5 August 2011

BMC Genomics

Orthology confers intron position conservation.
Henricson, A., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
BMC Genomics 11 : 412. 2 July 2010

BMC Microbiology

Resilience and stability of the CF- intestinal and respiratory microbiome during nutritional and exercise intervention.
Knoll, R.L. ORCID: https://orcid.org/0000-0002-3496-345X, Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Klopp, J., Kemper, A., Hilbert, K., Hillen, B., Pfirrmann, D., Simon, P., Bähner, V., Nitsche, O., Gehring, S., Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Poplawska, K.
BMC Microbiology 23 (1): 44. 21 February 2023

BMC Nutrition

Fasting, ketogenic, and anti-inflammatory diets in multiple sclerosis: a randomized controlled trial with 18-month follow-up.
Bahr, Lina S. ORCID: https://orcid.org/0000-0001-7932-8639, Bellmann-Strobl, Judith ORCID: https://orcid.org/0000-0003-2615-1643, Koppold, Daniela A., Rust, Rebekka, Schmitz-Hübsch, Tanja ORCID: https://orcid.org/0000-0003-4833-5937, Olszewska, Maja, Stadlbauer, Jean, Bock, Markus, Scheel, Michael, Chien, Claudia, Multmeier, Jan, Krannich, Alexander ORCID: https://orcid.org/0000-0002-4025-6495, Michalsen, Andreas, Paul, Friedemann ORCID: https://orcid.org/0000-0002-6378-0070 and Mähler, Anja ORCID: https://orcid.org/0000-0002-3904-5789
BMC Nutrition 11 (1): 167. 20 August 2025

BMJ Open

Sex hormone-dependent host-microbiome interactions and cardiovascular risk (XCVD): design of a longitudinal multi-omics cohort study.
Franz, K. ORCID: https://orcid.org/0000-0002-3819-9671, Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Mähler, A. ORCID: https://orcid.org/0000-0002-3904-5789, Chakaroun, R., Heinitz, S., Schlögl, H., Sacher, J., Steckhan, N. ORCID: https://orcid.org/0000-0003-0245-2046, Dechend, R. ORCID: https://orcid.org/0000-0001-6636-3080, Adams, N., Andersen, M., Glintborg, D., Viehweger, M., Bahr, L.S. ORCID: https://orcid.org/0000-0001-7932-8639 and Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
BMJ Open 15 (1): e087982. 9 January 2025

Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova, A., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Costea, P.I., Kozhakhmetov, S., Khassenbekova, Z., Urazova, M., Nurgozhin, T., Zhumadilov, Z., Benberin, V., Driessen, M., Hercog, R., Voigt, A.Y., Benes, V., Kandels-Lewis, S., Sunagawa, S., Letunic, I. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
BMJ Open 8 (7): e021682. 28 July 2018

BioEssays

Metagenomic insights into the human gut resistome and the forces that shape it.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Sunagawa, S., Coelho, L.P. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
BioEssays 36 (3): 316-329. March 2014

Bioinformatics

Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Pereira, C., Capella-Gutierrez, S., Sousa da Silva, A., Altenhoff, A., Huerta-Cepas, J., Muffato, M., Patricio, M., Vandepoele, K., Ebersberger, I., Blake, J., Fernández Breis, J.T., Boeckmann, B., Gabaldón, T., Sonnhammer, E., Dessimoz, C. and Lewis, S.
Bioinformatics 34 (2): 323-329. 15 January 2018

RTK: efficient rarefaction analysis of large datasets.
Saary, P., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and Hildebrand, F.
Bioinformatics 33 (16): 2594-2595. 15 August 2017

Benchmarking the next generation of homology inference tools.
Saripella, G.V., Sonnhammer, E.L.L. and Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993
Bioinformatics 32 (17): 2636-2641. 1 September 2016

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima, J.R., Coelho, L.P., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Huerta-Cepas, J., Li, S.S., Driessen, M., Voigt, A.Y., Zeller, G., Sunagawa, S. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Bioinformatics 32 (16): 2520-2523. 15 August 2016

Benchmarking homology detection procedures with low complexity filters.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
Bioinformatics 25 (19): 2500-2505. 1 October 2009

Predicting protein function from domain content.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
Bioinformatics 24 (15): 1681-1687. 1 August 2008

VisRD-visual recombination detection.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Huson, D.H. and Moulton, V.
Bioinformatics 20 (18): 3654-3655. 12 December 2004

Bioinformatics Advances

LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data.
Chen, C.Y. ORCID: https://orcid.org/0000-0003-1765-7132, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531 and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Bioinformatics Advances 3 (1): vbad063. 18 May 2023

Biological Psychiatry Global Open Science

Alteration of gut microbiome in patients with schizophrenia indicates links between bacterial tyrosine biosynthesis and cognitive dysfunction.
Thirion, F. ORCID: https://orcid.org/0000-0002-2310-5548, Speyer, H., Hansen, T.H., Nielsen, T., Fan, Y., Le Chatelier, E., Fromentin, S., Berland, M., Oñate, F.P., Pons, N., Galleron, N., Levenez, F., Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Birkner, T. ORCID: https://orcid.org/0000-0003-2656-2821, Jørgensen, T., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Vestergaard, H., Hansen, T., Nordentoft, M., Mors, O., Benros, M.E., Pedersen, O. and Ehrlich, S.D.
Biological Psychiatry Global Open Science 3 (2): 283-291. April 2023

Biotechnology for Biofuels

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate.
Gutmann, F. ORCID: https://orcid.org/0000-0001-6763-2270, Jann, C., Pereira, F., Johansson, A., Steinmetz, L.M. and Patil, K.R. ORCID: https://orcid.org/0000-0002-6166-8640
Biotechnology for Biofuels 14 (1): 41. 10 February 2021

Brain Research Bulletin

Exposure to a high-fat diet compromises gut health, behavior, and HPA axis function, with partial reversal when limited to adolescence.
Ott, Alexandra ORCID: https://orcid.org/0009-0000-4444-1834, Gül, Asude Zülal, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Birkner, Till ORCID: https://orcid.org/0000-0003-2656-2821, Popova, Elena ORCID: https://orcid.org/0000-0002-3043-9650, Winter, Christine and Hadar, Ravit
Brain Research Bulletin 239 : 111883. 1 June 2026

Briefings in Bioinformatics

OrthoDisease: tracking disease gene orthologs across 100 species.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Schreiber, F., Thanintorn, N. and Sonnhammer, E.L.L.
Briefings in Bioinformatics 12 (5): 463-473. September 2011

Cardiovascular Research

The effect of probiotic and synbiotic supplementation on lipid parameters among patients with cardiometabolic risk factors: a systematic review and meta-analysis of clinical trials.
Ghorbani, Z. ORCID: https://orcid.org/0000-0003-4230-5710, Kazemi, A. ORCID: https://orcid.org/0000-0001-5032-0078, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Martami, F., Noormohammadi, M., Salari, A., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Balou, H.A., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Mahdavi-Roshan, M.
Cardiovascular Research 119 (4): 933-956. April 2023

Blood pressure changes correlate with short-chain fatty acid production potential shifts under a synbiotic intervention.
Bartolomaeus, H. ORCID: https://orcid.org/0000-0003-4288-3828, Avery, E.G. ORCID: https://orcid.org/0000-0002-9094-1423, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Kozhakhmetov, S., Zhumadilov, Z., Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644, Wilck, N. ORCID: https://orcid.org/0000-0003-3189-5364, Kushugulova, A. and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Cardiovascular Research 116 (7): 1252-1253. June 2020

Hitchhiker's guide to microbiome studies.
Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184 and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Cardiovascular Research 116 (3): e44-e47. 1 March 2020

Cell

Rigorous science demands support of transgender scientists.
Aghi, K., Anderson, B.M., Castellano, B.M., Cunningham, A., Delano, M., Dickinson, E.S., von Diezmann, L., Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Grijseels, D.M., Groh, S.S., Guthman, E.M., Jayasinghe, I., Johnston, J., Long, S., McLaughlin, J.F., McLaughlin, M., Miyagi, M., Rajaraman, B., Sancheznieto, F., Scheim, A.I., Sun, S.E.D., Titmuss, F.D., Walsh, R.J. and Weinberg, Z.Y.
Cell 187 (6): 1327-1334. 14 March 2024

STEM pride: perspectives from transgender, nonbinary, and genderqueer scientists.
Armada-Moreira, A., Cizauskas, C., Fleury, G., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Guthman, E.M., Hanafiah, A., Hope, J.M., Jayasinghe, I., McSweeney, D. and Young, I.D.
Cell 184 (13): 3352-3355. 24 June 2021

Propionic acid shapes the multiple sclerosis disease course by an immunomodulatory mechanism.
Duscha, A., Gisevius, B., Hirschberg, S., Yissachar, N., Stangl, G.I., Eilers, E., Bader, V., Haase, S., Kaisler, J., David, C., Schneider, R., Troisi, R., Zent, D., Hegelmaier, T., Dokalis, N., Gerstein, S., Del Mare-Roumani, S., Amidror, S., Staszewski, O., Poschmann, G., Stühler, K., Hirche, F., Balogh, A. ORCID: https://orcid.org/0000-0001-8756-747X, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Träger, P., Zaiss, M.M., Holm, J.B., Massa, M.G., Nielsen, H.B., Faissner, A., Lukas, C., Gatermann, S.G., Scholz, M., Przuntek, H., Prinz, M., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Winklhofer, K.F., Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644, Linker, R.A., Gold, R. and Haghikia, A.
Cell 180 (6): 1067-1080. 19 March 2020

Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance.
Rubio-Cosials, A., Schulz, E.C., Lambertsen, L., Smyshlyaev, G., Rojas-Cordova, C., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Karaca, E., Bebel, A., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and Barabas, O.
Cell 173 (1): 208-220. 22 March 2018

Circulation

Circulation Research

Gut-heart axis: the role of gut microbiota and metabolites in heart failure.
Snelson, M. ORCID: https://orcid.org/0000-0003-4829-9550, Muralitharan, R.R. ORCID: https://orcid.org/0000-0002-7577-2123, Liu, C.F. ORCID: https://orcid.org/0000-0002-9383-341X, Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Marques, F.Z. ORCID: https://orcid.org/0000-0003-4920-9991 and Tang, W.H.W. ORCID: https://orcid.org/0000-0002-8335-735X
Circulation Research 136 (11): 1382-1406. 23 May 2025

Clinical and Translational Allergy

Communications Biology

Communications Medicine

EBioMedicine

Metabolic inflammation, brain age and cognitive functioning in short- and long-term clinical weight loss trials.
Maurer, Lukas, Kozarzewski, Leonard, Haberbosch, Linus, Flöel, Agnes, Haynes, John-Dylan, Spranger, Joachim ORCID: https://orcid.org/0000-0002-8900-4467, Mai, Knut and Weygandt, Martin ORCID: https://orcid.org/0000-0001-9962-4582
EBioMedicine 123 : 106064. January 2026

EClinicalMedicine

Intermittent fasting and health outcomes: an umbrella review of systematic reviews and meta-analyses of randomised controlled trials.
Sun, M.L., Yao, W., Wang, X.Y., Gao, S., Varady, K.A., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Zhang, M., Shi, Z.Y., Cao, F., Zou, B.J., Sun, M.H., Liu, K.X., Bao, Q., Xu, J., Qin, X., Xiao, Q., Wu, L., Zhao, Y.H., Zhang, D.Y., Wu, Q.J. and Gong, T.T
EClinicalMedicine 70 : 102519. April 2024

EMBO Reports

Biggest challenges in bioinformatics.
Fuller, J.C. ORCID: https://orcid.org/0000-0001-8801-149X, Khoueiry, P. ORCID: https://orcid.org/0000-0001-7643-3310, Dinkel, H. ORCID: https://orcid.org/0000-0002-9316-5204, Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Stamatakis, A., Barry, J., Budd, A. ORCID: https://orcid.org/0000-0003-0196-9051, Soldatos, T.G., Linssen, K. and Rajput, A.M.
EMBO Reports 14 (4): 302-304. 1 April 2013

ESC Heart Failure

An altered plasma lipidome-phenome network characterizes heart failure with preserved ejection fraction.
Jovanovic, N. ORCID: https://orcid.org/0000-0001-6300-9705, Foryst-Ludwig, A., Klose, C., da Conceicao, C.R., Alasfar, L. ORCID: https://orcid.org/0000-0001-8125-5723, Birkner, T. ORCID: https://orcid.org/0000-0003-2656-2821, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Kintscher, U. and Edelmann, F.
ESC Heart Failure 11 (3): 1553-1566. June 2024

Environment International

Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
Bengtsson-Palme, J. ORCID: https://orcid.org/0000-0002-6528-3158, Abramova, A., Berendonk, T.U., Coelho, L.P., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Gschwind, R., Heikinheimo, A., Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Khan, A.A., Klümper, U., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Nekoro, M., Osińska, A.D., Ugarcina Perovic, S., Pitkänen, T., Rødland, E.K., Ruppé, E., Wasteson, Y., Wester, A.L. and Zahra, R.
Environment International 178 : 108089. 5 July 2023

Environmental DNA

Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems.
Seeber, P.A. ORCID: https://orcid.org/0000-0003-4401-8248, Hippel, B., Kauserud, H., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Stoof‐Leichsenring, K.R., Herzschuh, U. and Epp, L.S.
Environmental DNA 4 (5): 1150-1163. September 2022

Environmental Science and Technology

Antibiotic resistance genes in river biofilms: a metagenomic approach toward the identification of sources and candidate hosts.
Kneis, D. ORCID: https://orcid.org/0000-0002-6048-6984, Berendonk, T.U., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Hess, S.
Environmental Science and Technology 56 (21): 14913-14922. 1 November 2022

European Journal of Anaesthesiology

Dopaminergic sub-network connectivity alterations are associated with postoperative cognitive dysfunction: results from the observational BioCog cohort study.
Lammers-Lietz, Florian, Borchers, Friedrich, Feinkohl, Insa ORCID: https://orcid.org/0000-0002-0307-1862, Kanar, Cicek, Krampe, Henning, Lichtner, Gregor, Sreekanth, Jayanth, Wiebach, Janine ORCID: https://orcid.org/0000-0002-7416-9859, Weygandt, Martin ORCID: https://orcid.org/0000-0001-9962-4582, Spies, Claudia, Winterer, Georg ORCID: https://orcid.org/0000-0002-3610-5029 and Paul, Friedemann ORCID: https://orcid.org/0000-0002-6378-0070
European Journal of Anaesthesiology 43 (7): 603-614. July 2026

European Journal of Heart Failure

Figshare

Phyloseq object.
Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184
[Dataset] 13 February 2024

qPCR_results.
Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184
[Dataset] 13 February 2024

Frontiers in Cellular and Infection Microbiology

Dynamic changes in microbiome composition following Mare's milk intake for prevention of collateral antibiotic effect.
Kushugulova, A., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Akpanova, S., Rysbekov, K., Kozhakhmetov, S., Khassenbekova, Z., Essex, M. ORCID: https://orcid.org/0000-0001-8758-7497, Nurgozhina, A., Nurgaziyev, M., Babenko, D., Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575 and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Frontiers in Cellular and Infection Microbiology 11 : 622735. 21 April 2021

Frontiers in Immunology

Outer retina micro-inflammation is driven by T cell responses prior to retinal degeneration in early age-related macular degeneration.
Stürzbecher, L. ORCID: https://orcid.org/0009-0001-6164-9060, Bartolomaeus, H. ORCID: https://orcid.org/0000-0003-4288-3828, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Bolz, S., Sekulic, A., Ueffing, M., Clark, S.J., Reichhart, N., Crespo-Garcia, S., Wilck, N. ORCID: https://orcid.org/0000-0003-3189-5364 and Strauß, O.
Frontiers in Immunology 16 : 1520188. 5 February 2025

A clinical protocol for a German birth cohort study of the Maturation of Immunity Against respiratory viral Infections (MIAI).
Hartmann, C.R., Khan, R., Schöning, J., Richter, M., Willers, M., Pirr, S., Heckmann, J., Dirks, J., Morbach, H., Konrad, M., Fries, E., Winkler, M., Büchel, J., Seidenspinner, S., Fischer, J., Vollmuth, C., Meinhardt, M., Marissen, J., Schmolke, M., Haid, S., Pietschmann, T., Backes, S., Dölken, L., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Keil, T., Heuschmann, P.U., Wöckel, A., Sagar, Dr., Ulas, T., Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Härtel, C. and Viemann, D.
Frontiers in Immunology 15 : 1443665. 17 September 2024

Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease.
Kayongo, A., Robertson, N.M., Siddharthan, T., Ntayi, M.L., Ndawula, J.C., Sande, O.J., Bagaya, B.S., Kirenga, B., Mayanja-Kizza, H., Joloba, M.L. and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Frontiers in Immunology 13 : 1085551. 17 January 2023

The gut microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS).
König, R.S., Albrich, W.C., Kahlert, C.R., Bahr, L.S. ORCID: https://orcid.org/0000-0001-7932-8639, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Vernazza, P., Scheibenbogen, C. and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Frontiers in Immunology 12 : 628741. 3 January 2022

Frontiers in Microbiology

The analysis of the gut microbiome during liver disease progression led to the identification of biomarkers for related mild cognitive impairment.
Giner-Pérez, Lola, Gallego, Juan-José, Gimènez-Garzó, Carla, Batallas, Daniela, Jarquín-Díaz, Víctor H. ORCID: https://orcid.org/0000-0003-3758-1091, Casanova-Ferrer, Franc, Fiorillo, Alessandra, Urios, Amparo, Martínez-Medina, Jennifer N. ORCID: https://orcid.org/0000-0003-3438-5730, López-Gramaje, Adrià, Arenas, Yaiza M, Escudero-García, Desamparados, Benlloch, Salvador, Salvador, Alicia, Felipo, Vicente, Forslund-Startceva, Sofia K. ORCID: https://orcid.org/0000-0003-4285-6993, Pérez Martínez, Gaspar and Montoliu, Carmina
Frontiers in Microbiology 16 : 1670512. 16 September 2025

Gastroenterology

S100A8 and S100A9 are important for postnatal development of gut microbiota and immune system in mice and infants.
Willers, M., Ulas, T. ORCID: https://orcid.org/0000-0002-9785-4197, Völlger, L., Vogl, T., Heinemann, A.S., Pirr, S. ORCID: https://orcid.org/0000-0002-3624-6251, Pagel, J., Fehlhaber, B., Halle, O., Schöning, J., Schreek, S., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Essex, M. ORCID: https://orcid.org/0000-0001-8758-7497, Hombach, P., Graspeuntner, S., Basic, M., Bleich, A., Cloppenborg-Schmidt, K., Künzel, S., Jonigk, D., Rupp, J., Hansen, G., Förster, R., Baines, J.F., Härtel, C., Schultze, J.L., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Roth, J. ORCID: https://orcid.org/0000-0001-7035-8348 and Viemann, D.
Gastroenterology 159 (6): 2130-2145. December 2020

Genome Biology

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.
Wirbel, J., Essex, M. ORCID: https://orcid.org/0000-0001-8758-7497, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Zeller, G. ORCID: https://orcid.org/0000-0003-1429-7485
Genome Biology 25 (1): 247. 25 September 2024

A novel exploratory method for visual recombination detection.
Strimmer, K. ORCID: https://orcid.org/0000-0001-7917-2056, Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Holland, B. ORCID: https://orcid.org/0000-0002-4628-7938 and Moulton, V.
Genome Biology 4 (5): R33. 2003

Genome Biology and Evolution

Quest for Orthologs entails quest for Tree of Life: in search of the gene stream.
Boeckmann, B., Marcet-Houben, M., Rees, J.A., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Huerta-Cepas, J., Muffato, M., Yilmaz, P., Xenarios, I., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Lewis, S.E. and Gabaldon, T.
Genome Biology and Evolution 7 (7): 1988-1999. 1 July 2015

Genome Medicine

The gut microbiota in multiple sclerosis varies with disease activity.
Thirion, F., Sellebjerg, F., Fan, Y., Lyu, L., Hansen, T.H., Pons, N., Levenez, F., Quinquis, B., Stankevic, E., Søndergaard, H.B., Dantoft, T.M., Poulsen, C.S., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Vestergaard, H., Hansen, T., Brix, S., Oturai, A., Sørensen, P.S., Ehrlich, S.D. and Pedersen, O. ORCID: https://orcid.org/0000-0002-3321-3972
Genome Medicine 15 (1): 1. 5 January 2023

Genome Research

Country-specific antibiotic use practices impact the human gut resistome.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Sunagawa, S., Kultima, J.R., Mende, D.R., Arumugam, M., Typas, A. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Research 23 (7): 1163-1169. July 2013

GitHub

IMMProveCF_public.
Knoll, Rebecca Luise ORCID: https://orcid.org/0000-0002-3496-345X
[Dataset] 14 August 2025

Gut

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.
Belda, E., Voland, L., Tremaroli, V., Falony, G. ORCID: https://orcid.org/0000-0003-2450-0782, Adriouch, S., Assmann, K.E., Prifiti, E., Aron-Wisnewsky, J., Debédat, J. ORCID: https://orcid.org/0000-0002-8377-5965, Le Roy, T. ORCID: https://orcid.org/0000-0002-0874-1490, Nielsen, T. ORCID: https://orcid.org/0000-0002-2066-7895, Amouyal, C., André, S., Andreelli, F., Blüher, M., Chakaroun, R. ORCID: https://orcid.org/0000-0001-9901-1815, Chilloux, J., Coelho, L.P., Dao, M.C., Das, P., Fellahi, S., Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Galleron, N., Hansen, T.H. ORCID: https://orcid.org/0000-0001-8748-3831, Holmes, B., Ji, B., Krogh Pedersen, H., Le, P., Le Chatelier, E., Lewinter, C., Mannerås-Holm, L., Marquet, F., Myridakis, A., Pelloux, V., Pons, N., Quinquis, B., Rouault, C., Roume, H., Salem, J.E., Sokolovska, N., Søndertoft, N.B., Touch, S., Vieira-Silva, S., Galan, P., Holst, J., Gøtze, J.P., Køber, L., Vestergaard, H., Hansen, T., Hercberg, S., Oppert, J.M., Nielsen, J., Letunic, I., Dumas, M.E. ORCID: https://orcid.org/0000-0001-9523-7024, Stumvoll, M., Pedersen, O.B., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Ehrlich, S.D., Zucker, J.D., Bäckhed, F. ORCID: https://orcid.org/0000-0002-4871-8818, Raes, J. and Clément, K. ORCID: https://orcid.org/0000-0002-2489-3355
Gut 71 (12): 2463-2480. 7 November 2022

Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.
Brial, F., Chilloux, J., Nielsen, T., Vieira-Silva, S., Falony, G., Andrikopoulos, P., Olanipekun, M., Hoyles, L., Djouadi, F., Neves, A.L., Rodriguez-Martinez, A., Mouawad, G.I., Pons, N., Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Le-Chatelier, E., Le Lay, A., Nicholson, J., Hansen, T., Hyötyläinen, T., Clément, K., Oresic, M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Ehrlich, S.D., Raes, J., Pedersen, O.B., Gauguier, D. and Dumas, M.E. ORCID: https://orcid.org/0000-0001-9523-7024
Gut 70 (11): 2105-2114. 7 October 2021

Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand, F. ORCID: https://orcid.org/0000-0002-0078-8948, Moitinho-Silva, L., Blasche, S., Jahn, M.T.T. ORCID: https://orcid.org/0000-0001-8322-9334, Gossmann, T.I., Heuerta Cepas, J., Hercog, R., Luetge, M., Bahram, M., Pryszlak, A., Alves, R.J., Waszak, S.M., Zhu, A., Ye, L., Costea, P.I., Aalvink, S., Belzer, C., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Sunagawa, S., Hentschel, U., Merten, C., Patil, K.R., Benes, V. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Gut 68 (10): 1781-1790. 9 September 2019

Gut Microbes

Hypertension

Effect of sunitinib treatment on skin sodium accumulation in patients with renal cancer: a pilot study.
Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Dörr, A., Linz, P. ORCID: https://orcid.org/0000-0002-8232-1443, van den Meiracker, A.H., Garrelds, I.M. ORCID: https://orcid.org/0000-0003-2061-6737, Kuehne, T. ORCID: https://orcid.org/0000-0003-1631-4824, Dechend, R. ORCID: https://orcid.org/0000-0001-6636-3080, Danser, A.H.J. ORCID: https://orcid.org/0000-0002-5052-3585, Flörcken, A. and Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644
Hypertension 79 (5): e103-e105. May 2022

Precarious symbiosis between host and microbiome in cardiovascular health.
Bartolomaeus, H. ORCID: https://orcid.org/0000-0003-4288-3828, Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Wilck, N. ORCID: https://orcid.org/0000-0003-3189-5364, Luft, F.C. ORCID: https://orcid.org/0000-0002-8635-1199, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Muller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644
Hypertension 73 (5): 926-935. May 2019

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Using unlabeled data to discover bivariate causality with deep restricted Boltzmann machines.
Sokolovska, N., Permiakova, O., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Zucker, J.D.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 17 (1): 358-364. January 2020

ISME Communications

Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.
Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Ferreira, S.C.M., Balard, A., Ďureje, L., Macholán, M., Piálek, J., Bengtsson-Palme, J., Kramer-Schadt, S., Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Heitlinger, E.
ISME Communications 4 (1): ycae053. 15 April 2024

ISME Journal

Cefiderocol resistance genes identified in environmental samples using functional metagenomics.
Gschwind, Remi ORCID: https://orcid.org/0000-0001-7741-9764, Bonnet, Mehdi, Abramova, Anna, Jarquín-Díaz, Victor Hugo ORCID: https://orcid.org/0000-0003-3758-1091, Wenne, Marcus, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Godron, Nicolas, Kampouris, Ioannis D., Tskhay, Faina, Nahid, Fouzia, Debroucker, Chloé, Bui-Hai, Maximilien, El Aiba, Inès, Klümper, Uli ORCID: https://orcid.org/0000-0002-4169-6548, Berendonk, Thomas U., Forslund-Startceva, Sofia K. ORCID: https://orcid.org/0000-0003-4285-6993, Zahra, Rabaab, Bengtsson-Palme, Johan ORCID: https://orcid.org/0000-0002-6528-3158 and Ruppé, Etienne
ISME Journal 20 (1): wrag010. January 2026

Insectes Sociaux

The gut microbiome is associated with behavioural task in honey bees.
Jones, J.C. ORCID: https://orcid.org/0000-0002-3557-1941, Fruciano, C., Marchant, J., Hildebrand, F., Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Engel, P. and Hughes, W.O.H.
Insectes Sociaux 65 (3): 419-429. August 2018

International Journal of Molecular Sciences

In vivo inhibition of TRPC6 by SH045 attenuates renal fibrosis in a New Zealand Obese (NZO) mouse model of metabolic syndrome.
Zheng, Z. ORCID: https://orcid.org/0000-0002-5114-3824, Xu, Y., Krügel, U. ORCID: https://orcid.org/0000-0002-2317-2302, Schaefer, M., Grune, T., Nürnberg, B. ORCID: https://orcid.org/0000-0002-5995-6555, Köhler, M.B., Gollasch, M. ORCID: https://orcid.org/0000-0003-2797-1934, Tsvetkov, D. ORCID: https://orcid.org/0000-0002-6472-971X and Marko, L. ORCID: https://orcid.org/0000-0003-1888-5575
International Journal of Molecular Sciences 23 (12): 6870. 20 June 2022

JAMA Pediatrics

Bifidobacterium and lactobacillus probiotics and gut dysbiosis in preterm infants: the PRIMAL randomized clinical trial.
Van Rossum, T., Haiß, A., Knoll, R.L. ORCID: https://orcid.org/0000-0002-3496-345X, Marißen, J., Podlesny, D., Pagel, J., Bleskina, M., Vens, M., Fortmann, I., Siller, B., Ricklefs, I., Klopp, J., Hilbert, K., Meyer, C., Thielemann, R., Goedicke-Fritz, S., Kuntz, M., Wieg, C., Teig, N., Körner, T., Kribs, A., Hudalla, H., Knuf, M., Stein, A., Gille, C., Bagci, S., Dohle, F., Proquitté, H., Olbertz, D.M., Schmidt, E., Koch, L., Pirr, S., Rupp, J., Spiegler, J., Kopp, M.V., Göpel, W., Herting, E., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Viemann, D., Zemlin, M., Bork, P., Gehring, S., König, I.R., Henneke, P. and Härtel, C.
JAMA Pediatrics 178 (10): 985-995. October 2024

JCI Insight

Endothelial deletion of adipose triglyceride lipase protects against heart failure with preserved ejection fraction.
Schwanbeck, J., Stahnke, M., Eberlein, A., Goeritzer, M., Schulze, A., Pernitsch, D., Kolb, D., Grabner, G.F., Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384, Schiattarella, G.G. ORCID: https://orcid.org/0000-0002-7582-7171, Cocera Ortega, L., López-Anguita, N. ORCID: https://orcid.org/0000-0003-3373-7191, Kershaw, E.E., Maatz, H. ORCID: https://orcid.org/0000-0002-9232-6272, Hübner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Zechner, R., Foryst-Ludwig, A. and Kintscher, U.
JCI Insight 10 (5): e187145. 10 March 2025

Journal of Allergy and Clinical Immunology

Effect of gestational age on lymphocyte phenotypes in hospitalized preterm infants.
Dirks, Johannes, Fortmann, Ingmar, Marißen, Janina, Pagel, Julia, Reichert, Lilith, Kipke, Henry, Dammann, Marie-Theres, Göpel, Wolfgang, Birkner, Till ORCID: https://orcid.org/0000-0003-2656-2821, Dahm, Kilian, Forslund-Startceva, Sofia Kirke ORCID: https://orcid.org/0000-0003-4285-6993, Viemann, Dorothee, Rupp, Jan, Morbach, Henner and Härtel, Christoph
Journal of Allergy and Clinical Immunology 157 (2): 506-516. February 2026

Journal of Clinical Periodontology

Oral microbiota of patients with phenylketonuria: a nation-based cross-sectional study.
Bingöl, M., Cardilli, A. ORCID: https://orcid.org/0000-0002-3470-4984, Bingöl, A.C., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Bang, C., Franke, A., Bartzela, T., Beblo, S., Mönch, E., Stolz, S., Schaefer, A.S. ORCID: https://orcid.org/0000-0001-5816-6765, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Richter, G.M. ORCID: https://orcid.org/0000-0002-4825-4670
Journal of Clinical Periodontology 51 (8): 1081-1092. August 2024

Journal of Extracellular Vesicles

Journal of Internal Medicine

Fasting intervention and its clinical effects on the human host and microbiome.
Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Journal of Internal Medicine 293 (2): 166-183. February 2023

Journal of Investigative Dermatology

Journal of Neurology

Anchor-based evaluation of digital motor biomarkers from a 2-year observation in 100 patients with multiple sclerosis.
Ellinghaus, Carla A. ORCID: https://orcid.org/0009-0007-6790-656X, Röhling, Hanna M., Dorsch, Eva-Maria, Sperber, Pia S. ORCID: https://orcid.org/0000-0002-9534-2374, Arsenova, Radina, Buenrostro, Gilberto Solorza, Rekers, Sophia, Usnich, Tatiana, Schindler, Patrick, Kroneberg, Daniel, Bellmann-Strobl, Judith ORCID: https://orcid.org/0000-0003-2615-1643, Oertel, Frederike C. ORCID: https://orcid.org/0000-0003-4906-5983, Brandt, Alexander U. ORCID: https://orcid.org/0000-0002-9768-014X, Weygandt, Martin ORCID: https://orcid.org/0000-0001-9962-4582, Paul, Friedemann ORCID: https://orcid.org/0000-0002-6378-0070, Piper, Sophie K. and Schmitz-Hübsch, Tanja ORCID: https://orcid.org/0000-0003-4833-5937
Journal of Neurology 273 (1): 4. 4 December 2025

Journal of Nutritional Biochemistry

UV light exposure versus vitamin D supplementation: a comparison of health benefits and vitamin D metabolism in a pig model.
Kühn, J., Brandsch, C., Bailer, A.C., Kiourtzidis, M., Hirche, F., Chen, C.Y. ORCID: https://orcid.org/0000-0003-1765-7132, Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Michel, S., Wensch-Dorendorf, M., Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Stangl, G.I.
Journal of Nutritional Biochemistry 134 : 109746. December 2024

Journal of Proteome Research

Comparing the extraction performance in mouse plasma of different biphasic methods for polar and nonpolar compounds.
Gutmann, F. ORCID: https://orcid.org/0000-0001-6763-2270, Fritsche-Guenther, R. ORCID: https://orcid.org/0000-0002-6965-0226, Dias, D.B. and Kirwan, J.A. ORCID: https://orcid.org/0000-0002-5423-1651
Journal of Proteome Research 23 (8): 2961-2969. 2 August 2024

Journal of Translational Medicine

The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life.
Kaczmarczyk, M., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Adamek, K., Węgrzyn, D., Skonieczna-Żydecka, K., Malinowski, D., Łoniewski, I., Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Ulas, T., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Łoniewska, B.
Journal of Translational Medicine 19 (1): 177. 28 April 2021

Journal of the American Society of Nephrology

Kidney International

Lecture Notes in Computer Science

A semi-supervised approach to discover bivariate causality in large biological data.
Sokolovska, N., Permiakova, O., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Zucker, J.D.
Lecture Notes in Computer Science 10934 : 406-420. 8 July 2018

Constructing phylogenetic supernetworks from quartets.
Grünewald, S., Spillner, A., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Moulton, V.
Lecture Notes in Computer Science 5251 : 284-295. 2008

Maternal Health Neonatology and Perinatology

Probiotic ice cream influences gut and vaginal microbiota in women at high risk of preterm birth: a randomized controlled study.
Borum, Leonora S. ORCID: https://orcid.org/0000-0002-4658-9362, Bartolomaeus, Theda U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Lamont, Ronald F., Bagge, Julie R., Markó, Lajos ORCID: https://orcid.org/0000-0003-1888-5575, Vinter, Christina A., Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Dechend, Ralf ORCID: https://orcid.org/0000-0001-6636-3080, Forslund-Startceva, Sofia K. ORCID: https://orcid.org/0000-0003-4285-6993 and Joergensen, Jan S.
Maternal Health Neonatology and Perinatology 11 (1): 43. 3 December 2025

Metabolites

A comparison of solvent-based extraction methods to assess the central carbon metabolites in mouse bone and muscle.
Dias, D.B., Fritsche-Guenther, R. ORCID: https://orcid.org/0000-0002-6965-0226, Gutmann, F. ORCID: https://orcid.org/0000-0001-6763-2270, Duda, G.N., Kirwan, J. ORCID: https://orcid.org/0000-0002-5423-1651 and Poh, P.S.P.
Metabolites 12 (5): 453. 18 May 2022

Methods in Ecology and Evolution

DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences.
Alquezar‐Planas, D.E. ORCID: https://orcid.org/0000-0001-5360-5263, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Cui, P., Quedenau, C. ORCID: https://orcid.org/0000-0002-6846-4915, Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627 and Greenwood, A.D. ORCID: https://orcid.org/0000-0002-8249-1565
Methods in Ecology and Evolution 22 September 2020

Methods in Molecular Biology

Evolution of protein domain architectures.
Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Kaduk, M. and Sonnhammer, E.L.L.
Methods in Molecular Biology 1910 : 469-504. 2019

Evolution of protein domain architectures.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
Methods in Molecular Biology 856 : 187-216. 2012

Microbial Ecology

Microbiome dynamics and functional composition in Coelopa frigida (Diptera, Coelopidae): insights into trophic specialization of kelp flies.
Bischof, P.S.P., Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531 and Bleidorn, C.
Microbial Ecology 87 (1): 91. 3 July 2024

Microbial Genomics

Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.
Ayala-Montaño, Stefany ORCID: https://orcid.org/0009-0009-1407-4397, Afolayan, Ayorinde O., Kociurzynski, Raisa, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531 and Reuter, Sandra ORCID: https://orcid.org/0000-0003-1672-5789
Microbial Genomics 12 (1): 001609. 22 January 2026

Microbiology Spectrum

Sputum microbiome and chronic obstructive pulmonary disease in a rural Ugandan cohort of well-controlled HIV infection.
Kayongo, A. ORCID: https://orcid.org/0000-0002-5338-3821, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Birkner, T. ORCID: https://orcid.org/0000-0003-2656-2821, Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Kigozi, E., Atugonza, C., Munana, R., Mawanda, D., Sekibira, R., Uwimaana, E., Alupo, P., Kalyesubula, R., Knauf, F., Siddharthan, T., Bagaya, B.S., Kateete, D.P., Joloba, M.L., Sewankambo, N.K., Jjingo, D., Kirenga, B., Checkley, W. and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Microbiology Spectrum 11 (2): e02139-21. April 2023

Microbiome

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host.
Midha, A., Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Ebner, F., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Hayani, R., Kundik, A., Cardilli, A. ORCID: https://orcid.org/0000-0002-3470-4984, Heitlinger, E., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Hartmann, S.
Microbiome 10 (1): 229. 16 December 2022

Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho, L.P. ORCID: https://orcid.org/0000-0002-9280-7885, Kultima, J.R., Costea, P.I., Fournier, C., Pan, Y., Czarnecki-Maulden, G., Hayward, M.R., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Schmidt, T.S.B., Descombes, P., Jackson, J.R., Li, Q. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Microbiome 6 (1): 72. 19 April 2018

Molecular Biology and Evolution

Ten years of collaborative progress in the quest for orthologs.
Linard, B. ORCID: https://orcid.org/0000-0002-5555-898X, Ebersberger, I., McGlynn, S.E. ORCID: https://orcid.org/0000-0002-8199-7011, Glover, N., Mochizuki, T., Patricio, M., Lecompte, O., Nevers, Y., Thomas, P.D., Gabaldón, T., Sonnhammer, E., Dessimoz, C. and Uchiyama, I.
Molecular Biology and Evolution 38 (8): 3033-3045. August 2021

Advances and applications in the quest for orthologs.
Glover, N., Dessimoz, C., Ebersberger, I., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Gabaldón, T., Huerta-Cepas, J., Martin, M.J., Muffato, M., Patricio, M., Pereira, C., Sousa da Silva, A., Wang, Y., Sonnhammer, E. and Thomas, P.D.
Molecular Biology and Evolution 36 (10): 2157-2164. October 2019

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. ORCID: https://orcid.org/0000-0003-4195-5025, Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Coelho, L.P., Szklarczyk, D., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017

Domain tree-based analysis of protein architecture evolution.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Henricson, A., Hollich, V. and Sonnhammer, E.L.L.
Molecular Biology and Evolution 25 (2): 254-264. 1 February 2008

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets.
Grünewald, S., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Dress, A. and Moulton, V.
Molecular Biology and Evolution 24 (2): 532-538. 1 February 2007

Molecular Ecology Resources

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes.
Seeber, P.A. ORCID: https://orcid.org/0000-0003-4401-8248, McEwen, G.K., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Förster, D.W., East, M.L., Melzheimer, J. and Greenwood, A.D. ORCID: https://orcid.org/0000-0002-8249-1565
Molecular Ecology Resources 19 (6): 1486-1496. November 2019

Molecular Nutrition & Food Research

Effects of a short-term vegan challenge in older adults on metabolic and inflammatory parameters - a randomized controlled crossover study.
Döschner, L., Schulze, K., Göger, L., Bosy-Westphal, A., Krüger, N., Franz, K. ORCID: https://orcid.org/0000-0002-3819-9671, Müller-Werdan, U., Herpich, C. ORCID: https://orcid.org/0000-0003-3059-1705 and Norman, K.
Molecular Nutrition & Food Research 68 (4): e2300623. February 2024

Molecular Systems Biology

Subspecies in the global human gut microbiome.
Costea, P.I. ORCID: https://orcid.org/0000-0003-1645-3947, Coelho, L.P., Sunagawa, S., Munch, R., Huerta-Cepas, J., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Hildebrand, F., Kushugulova, A., Zeller, G. ORCID: https://orcid.org/0000-0003-1429-7485 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Molecular Systems Biology 13 (12): 960. 14 December 2017

Multiple Sclerosis Journal

NPJ Biofilms and Microbiomes

Nature

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.
Vieira-Silva, S., Falony, G., Belda, E., Nielsen, T., Aron-Wisnewsky, J., Chakaroun, R., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Assmann, K., Valles-Colomer, M., Nguyen, T..D., Proost, S., Prifti, E., Tremaroli, V., Pons, N., Le Chatelier, E., Andreelli, F., Bastard, J.P., Coelho, L.P., Galleron, N., Hansen, T.H., Hulot, J.S., Lewinter, C., Pedersen, H.K., Quinquis, B., Rouault, C., Roume, H., Salem, J.E., Søndertoft, N.B., Touch, S., Dumas, M.E., Ehrlich, S.D., Galan, P., Gøtze, J.P., Hansen, T., Holst, J.J., Køber, L., Letunic, I., Nielsen, J., Oppert, J.M., Stumvoll, M., Vestergaard, H., Zucker, J.D., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Pedersen, O., Bäckhed, F., Clément, K. and Raes, J.
Nature 581 (7808): 310-315. 21 May 2020

Structure and function of the global topsoil microbiome.
Bahram, M., Hildebrand, F., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Anderson, J.L., Soudzilovskaia, N.A., Bodegom, P.M., Bengtsson-Palme, J., Anslan, S., Coelho, L.P., Harend, H., Huerta-Cepas, J., Medema, M.H., Maltz, M.R., Mundra, S., Olsson, P.A., Pent, M., Põlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nature 560 (7717): 233-237. 9 August 2018

Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen, H.K., Gudmundsdottir, V., Nielsen, H.B., Hyotylainen, T., Nielsen, T., Jensen, B.A.H., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D.R., Pöhö, P., Hellgren, L.I., Arumugam, M., Sunagawa, S., Vieira-Silva, S., Jørgensen, T., Holm, J.B., Trošt, K., Kristiansen, K., Brix, S., Raes, J., Wang, J., Hansen, T., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Brunak, S., Oresic, M., Ehrlich, S.D. and Pedersen, O.
Nature 535 (7612): 376-381. 21 July 2016

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Hildebrandt, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Pedersen, H.K., Arumugam, M., Kristiansen, K., Voigt, A.Y., Vestergaard, H., Hercog, R., Costea, P.I., Kultima, J.R., Li, J., Jørgensen, T., Levenez, F., Dore, J., Nielsen, H.B., Brunak, S., Raes, J., Hansen, T., Wang, J., Ehrlich, S.D., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and Pedersen, O.
Nature 528 (7581): 262-266. 10 December 2015

Nature Communications

A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.
Chechi, Kanta, Chakaroun, Rima, Myridakis, Antonis, Forslund-Startceva, Sofia K. ORCID: https://orcid.org/0000-0003-4285-6993, Fromentin, Sebastien, Nielsen, Trine, Aron-Wisneswky, Judith, Belda, Eugeni, Prifti, Edi, Lassen, Pierre Bel, Falony, Gwen, Vieira-Silva, Sara, Chilloux, Julien, Sonomura, Kazuhiro, Hoyles, Lesley, Martinez-Gili, Laura, Pallotti, Francesco, Andrikopoulos, Petros, Puig-Castellví, Francesc, Tapia, Romina Pacheco, Castro-Dionicio, Inés, Roume, Hugo, Pons, Nicolas, Le Chatelier, Emmanuelle, Quinquis, Benoit, Galleron, Nathalie, Berland, Magali, Olanipekun, Michael T., Jia, Manyi, Manolias, Angelos, Holmes, Bridget, Adriouch, Solia, Blüher, Matthias, Coelho, Luis Pedro, Da Silva, Kévin, Galan, Pilar, Ji, Boyang, Neves, Ana Luisa, Rouault, Christine, Salem, Joe-Elie, Tremaroli, Valentina, Hansen, Tue H., Søndertoft, Nadja B., Lewinter, Christian, Pedersen, Helle K., Mark, Peter D., Goetze, Jens P., Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Sato, Taka-Aki, Hercberg, Serge, Bäckhed, Fredrik, Letunic, Ivica, Oppert, Jean-Michel, Nielsen, Jens, Raes, Jeroen, Tzoulaki, Ioanna, Dehghan, Abbas, Zuber, Verena, Bouzigon, Emmanuelle, Lathrop, Mark, Raina, Parminder, Froguel, Philippe, Matsuda, Fumihiko, Demenais, Florence, Gauguier, Dominique, Stumvoll, Michael, Bork, Peer ORCID: https://orcid.org/0000-0002-2627-833X, Pedersen, Oluf, Ehrlich, S. Dusko, Clément, Karine and Dumas, Marc-Emmanuel
Nature Communications 17 (1): 3477. 14 April 2026

CFTR modulator therapy drives microbiome restructuring through improved host physiology in cystic fibrosis: the IMMProveCF phase IV trial.
Knoll, Rebecca Luise ORCID: https://orcid.org/0000-0002-3496-345X, Brauny, Melanie Meihu, Robert, Evelyn, Cloos, Louisa, Waser, Lydia, Hilbert, Katja, Ulmer, Nina, Hillen, Barlo, Birkner, Till ORCID: https://orcid.org/0000-0003-2656-2821, Bartolomaeus, Theda Ulrike Patricia ORCID: https://orcid.org/0000-0002-5156-7184, Nitsche, Oliver, Jarquín-Díaz, Víctor Hugo ORCID: https://orcid.org/0000-0003-3758-1091, Lynch, Susan, Gehring, Stephan, Maier, Lisa, Poplawska, Krystyna and Forslund-Startceva, Sofia Kirke ORCID: https://orcid.org/0000-0003-4285-6993
Nature Communications 16 (1): 10111. 18 November 2025

Elevated aldosterone and blood pressure in a mouse model of familial hyperaldosteronism with ClC-2 mutation.
Schewe, J., Seidel, E. ORCID: https://orcid.org/0000-0003-3334-3950, Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Marko, L. ORCID: https://orcid.org/0000-0003-1888-5575, Peters, J., Muller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644, Fahlke, C., Stölting, G. ORCID: https://orcid.org/0000-0002-2339-0545 and Scholl, U. ORCID: https://orcid.org/0000-0002-0309-8045
Nature Communications 10 (1): 5155. 14 November 2019

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.
Korpela, K., Salonen, A., Virta, L.J., Kekkonen, R.A., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and de Vos, W.M.
Nature Communications 7 : 10410. 26 January 2016

Nature Ecology & Evolution

Nature Medicine

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease.
Talmor-Barkan, Y., Bar, N., Shaul, A.A., Shahaf, N., Godneva, A., Bussi, Y., Lotan-Pompan, M., Weinberger, A., Shechter, A., Chezar-Azerrad, C., Arow, Z., Hammer, Y., Chechi, K., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Fromentin, S., Dumas, M.E., Ehrlich, S.D., Pedersen, O., Kornowski, R. and Segal, E.
Nature Medicine 28 (2): 295-302. February 2022

Reporting guidelines for human microbiome research: the STORMS checklist.
Mirzayi, C., Renson, A., Zohra, F., Elsafoury, S., Geistlinger, L., Kasselman, L.J., Eckenrode, K., van de Wijgert, J., Loughman, A., Marques, F.Z. ORCID: https://orcid.org/0000-0003-4920-9991, MacIntyre, D.A., Arumugam, M., Azhar, R., Beghini, F., Bergstrom, K., Bhatt, A., Bisanz, J.E., Braun, J., Bravo, H.C., Buck, G.A. ORCID: https://orcid.org/0000-0003-4621-3987, Bushman, F., Casero, D., Clarke, G., Collado, M.C., Cotter, P.D., Cryan, J.F., Demmer, R.T., Devkota, S., Elinav, E., Escobar, J.S., Fettweis, J., Finn, R.D., Fodor, A.A., Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Franke, A., Furlanello, C., Gilbert, J., Grice, E., Haibe-Kains, B., Handley, S., Herd, P., Holmes, S., Jacobs, J.P., Karstens, L., Knight, R., Knights, D., Koren, O., Kwon, D.S., Langille, M., Lindsay, B., McGovern, D., McHardy, A.C., McWeeney, S., Mueller, N.T., Nezi, L., Olm, M., Palm, N., Pasolli, E., Raes, J., Redinbo, M.R., Rühlemann, M., Balfour Sartor, R, Schloss, P.D., Schriml, L., Segal, E., Shardell, M., Sharpton, T., Smirnova, E., Sokol, H., Sonnenburg, J.L., Srinivasan, S., Thingholm, L.B., Turnbaugh, P.J., Upadhyay, V., Walls, R.L., Wilmes, P. ORCID: https://orcid.org/0000-0002-6478-2924, Yamada, T. ORCID: https://orcid.org/0000-0002-9622-1849, Zeller, G., Zhang, M., Zhao, N., Zhao, L., Bao, W., Culhane, A., Devanarayan, V., Dopazo, J., Fan, X., Fischer, M., Jones, W., Kusko, R., Mason, C.E., Mercer, T.R., Sansone, S.A., Scherer, A., Shi, L., Thakkar, S., Tong, W., Wolfinger, R., Hunter, C., Segata, N. ORCID: https://orcid.org/0000-0002-1583-5794, Huttenhower, C. ORCID: https://orcid.org/0000-0002-1110-0096, Dowd, J.B., Jones, H.E. ORCID: https://orcid.org/0000-0002-4285-3752 and Waldron, L. ORCID: https://orcid.org/0000-0003-2725-0694
Nature Medicine 27 (11): 1885-1892. November 2021

Nature Metabolism

Nature Methods

Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., DeLuca, T., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Lecompte, O., von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102, Xenarios, I., Sjölander, K., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, Martin, M.J., Muffato, M., Gabaldón, T., Lewis, S.E., Thomas, P.D., Sonnhammer, E. and Dessimoz, C.
Nature Methods 13 (5): 425-430. May 2016

Nature Microbiology

Nature Protocols

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen, H.K., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Gudmundsdottir, V., Petersen, A.Ø., Hildebrand, F., Hyötyläinen, T., Nielsen, T. ORCID: https://orcid.org/0000-0002-2066-7895, Hansen, T., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Ehrlich, S.D., Brunak, S., Oresic, M., Pedersen, O. and Nielsen, H.B.
Nature Protocols 13 (12): 2781-2800. December 2018

Nature Reviews Cardiology

Roadmap for alleviating the manifestations of ageing in the cardiovascular system.
Liberale, L., Tual-Chalot, S., Sedej, S., Ministrini, S., Georgiopoulos, G., Grunewald, M., Bäck, M., Bochaton-Piallat, M.L., Boon, R.A., Ramos, G.C., de Winther, M.P.J., Drosatos, K., Evans, P.C., Ferguson, J.F., Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Goettsch, C., Giacca, M., Haendeler, J., Kallikourdis, M., Ketelhuth, D.F.J., Koenen, R.R., Lacolley, P., Lutgens, E., Maffia, P., Miwa, S., Monaco, C., Montecucco, F., Norata, G.D., Osto, E., Richardson, G.D., Riksen, N.P., Soehnlein, O., Spyridopoulos, I., Van Linthout, S., Vilahur, G., Wentzel, J.J., Andrés, V., Badimon, L., Benetos, A., Binder, C.J., Brandes, R.P., Crea, F., Furman, D., Gorbunova, V., Guzik, T.J., Hill, J.A., Lüscher, T.F., Mittelbrunn, M., Nencioni, A., Netea, M.G., Passos, J.F., Stamatelopoulos, K.S., Tavernarakis, N., Ungvari, Z., Wu, J.C., Kirkland, J.L., Camici, G.G., Dimmeler, S., Kroemer, G., Abdellatif, M. and Stellos, K.
Nature Reviews Cardiology 22 (8): 577-605. August 2025

Nature Reviews Gastroenterology & Hepatology

Nucleic Acids Research

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S. ORCID: https://orcid.org/0000-0001-6606-2202, Smyshlyaev, G., Letunic, I. ORCID: https://orcid.org/0000-0003-3560-4288, Maistrenko, O.M. ORCID: https://orcid.org/0000-0003-1961-7548, Coelho, L.P., Orakov, A., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Hildebrand, F., Luetge, M., Schmidt, T.S.B., Barabas, O. ORCID: https://orcid.org/0000-0002-2873-5872 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nucleic Acids Research 50 (6): 3155-3168. 8 April 2022

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende, D.R. ORCID: https://orcid.org/0000-0001-6831-4557, Letunic, I., Maistrenko, O.M., Schmidt, T.S.B., Milanese, A., Paoli, L., Hernández-Plaza, A., Orakov, A.N., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Sunagawa, S., Zeller, G., Huerta-Cepas, J., Coelho, L.P. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nucleic Acids Research 48 (D1): D621-D625. 8 January 2020

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Cook, H., Mende, D.R., Letunic, I., Rattei, T., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nucleic Acids Research 47 (D1): D309-D314. 8 January 2019

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende, D.R. ORCID: https://orcid.org/0000-0001-6831-4557, Letunic, I. ORCID: https://orcid.org/0000-0003-3560-4288, Huerta-Cepas, J. ORCID: https://orcid.org/0000-0003-1731-9109, Li, S.S. ORCID: https://orcid.org/0000-0002-0073-3656, Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Sunagawa, S. ORCID: https://orcid.org/0000-0003-3065-0314 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nucleic Acids Research 45 (D1): D529-D534. 4 January 2017

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas, J., Szklarczyk, D., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Cook, H., Heller, D., Walter, M.C., Rattei, T., Mende, D.R., Sunagawa, S., Kuhn, M., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nucleic Acids Research 44 (D1): D286-D293. 4 January 2016

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., Kuhn, M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X and von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102
Nucleic Acids Research 43 (D1): D447-D452. January 2015

eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell, S., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nucleic Acids Research 42 (1): D231-D239. 1 January 2014

The Pfam protein families database.
Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E.L.L., Eddy, S.R., Bateman, A. and Finn, R.D.
Nucleic Acids Research 40 (D1): D290-D301. 1 January 2012

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
Ostlund, G., Schmitt, T., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Köstler, T., Messina, D.N., Roopra, S., Frings, O. and Sonnhammer, E.L.L.
Nucleic Acids Research 38 (Suppl 1): D196-D203. 1 January 2010

The Pfam protein families database.
Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Holm, L., Sonnhammer, E.L.L., Eddy, S.R. and Bateman, A.
Nucleic Acids Research 38 (Suppl 1): D211-D222. 1 January 2010

The Pfam protein families database.
Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Eddy, S.R., Sonnhammer, E.L.L. and Bateman, A.
Nucleic Acids Research 36 (Suppl 1): D281-D288. 1 January 2008

Nutrients

Mediterranean diet and atrial fibrillation: lessons learned from the AFHRI case-control study.
Neumann, F.A. ORCID: https://orcid.org/0000-0003-3107-075X, Jagemann, B., Makarova, N., Börschel, C.S., Aarabi, G., Gutmann, F. ORCID: https://orcid.org/0000-0001-6763-2270, Schnabel, R.B. ORCID: https://orcid.org/0000-0001-7170-9509 and Zyriax, B.C. ORCID: https://orcid.org/0000-0002-5377-5956
Nutrients 14 (17): 3615. 1 September 2022

Gut microbiome composition in obese and non-obese persons: a systematic review and meta-analysis.
Pinart, M. ORCID: https://orcid.org/0000-0002-8223-1325, Dötsch, A. ORCID: https://orcid.org/0000-0001-9086-2584, Schlicht, K., Laudes, M., Bouwman, J., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Pischon, T. ORCID: https://orcid.org/0000-0003-1568-767X and Nimptsch, K. ORCID: https://orcid.org/0000-0001-7877-205X
Nutrients 14 (1): 12. 1 January 2022

Obesity Reviews

PLoS ONE

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.
Trachana, K., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Larsson, T., Powell, S., Doerks, T., von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS ONE 9 (11): e111122. 4 November 2014

Parasites & Vectors

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations.
Vásquez-Aguilar, A.A., Barbachano-Guerrero, A., Angulo, D.F. and Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091
Parasites & Vectors 14 (1): 467. 14 September 2021

Parasites and Vectors

Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria).
Ferreira, S.C.M., Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091 and Heitlinger, E.
Parasites and Vectors 16 (1): 204. 17 June 2023

Parasitology Research

Dentition patterns and molecular diversity of Mastophorus muris (Gmelin, 1790) (Nematoda: Spiruroidea) support a host-associated subdivision.
Jost, J., Hirzmann, J., Ďureje, Ľ., Maaz, D., Martin, P., Stach, T. ORCID: https://orcid.org/0000-0001-5461-9069, Heitlinger, E. ORCID: https://orcid.org/0000-0002-7139-3425 and Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091
Parasitology Research 123 (6): 237. June 2024

Pharmacological Research

Reinforcing gut integrity: a systematic review and meta-analysis of clinical trials assessing probiotics, synbiotics, and prebiotics on intestinal permeability markers.
Ghorbani, Z., Shoaibinobarian, N., Noormohammadi, M., Taylor, K. ORCID: https://orcid.org/0000-0001-7491-4460, Kazemi, A., Bonyad, A., Khoshdooz, S., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531 and Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Pharmacological Research 216 : 107780. June 2025

The effect of probiotic and synbiotic supplementation on appetite-regulating hormones and desire to eat: a systematic review and meta-analysis of clinical trials.
Noormohammadi, M., Ghorbani, Z., Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Mahdavi-Roshan, M., Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Kazemi, A., Shoaibinobarian, N. and Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
Pharmacological Research 187 : 106614. January 2023

Phenomics

Human gut microbiome researches over the last decade: current challenges and future directions.
Wu, H., Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Wang, Z. and Zhao, G.
Phenomics 5 (1): 1-7. February 2025

Placenta

Commentary on a combined approach to the problem of developing biomarkers for the prediction of spontaneous preterm labor that leads to preterm birth.
Lamont, R.F., Richardson, L.S., Boniface, J.J., Cobo, T., Exner, M.M., Christensen, I.B., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Gaba, A., Helmer, H., Jørgensen, J.S., Khan, R.N., McElrath, T.F., Petro, K., Rasmussen, M., Singh, R., Tribe, R.M., Vink, J.S., Vinter, C.A., Zhong, N. and Menon, R.
Placenta 98 : 13-23. 1 September 2020

Proceedings of the National Academy of Sciences of the United States of America

Proceedings of the Royal Society of London Series B-Biological Sciences

Eco-evolutionary dynamics of host - microbiome interactions in a natural population of closely related mouse subspecies and their hybrids.
Ferreira, S.C.M., Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Planillo, A., Ďureje, L., Martincová, I., Kramer-Schadt, S. ORCID: https://orcid.org/0000-0002-9269-4446, Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Heitlinger, E.
Proceedings of the Royal Society of London Series B-Biological Sciences 291 (2037): 20241970. December 2024

Research Square

Modulating psoriasis microbiome: a clinical trial on mare's milk impact.
Colino, Silvia González ORCID: https://orcid.org/0009-0007-8959-9636, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Forslund, Sofia ORCID: https://orcid.org/0000-0003-4285-6993, Yermekbayeva, Bakytgul, Kozhakhmetov, Samat, Algazina, Togzhan, Touir, Gulnaz, Batpenova, Gulnar and Kushugulova, Almagul
Research Square : rs.3.rs-9814787/v1. 8 June 2026

Science & Healthcare

Science of the Total Environment

Host weight, seasonality and anthropogenic factors contribute to parasite community differences between urban and rural foxes.
Scholz, C., Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Planillo, A., Radchuk, V., Scherer, C., Schulze, C., Ortmann, S., Kramer-Schadt, S. and Heitlinger, E.
Science of the Total Environment 936 : 173355. August 2024

Scientific Reports

Rifaximin-induced changes in the gut microbiome associated to improvement of neurotransmission alterations and learning in rats with chronic liver disease.
Giner-Pérez, Lola, Jarquín-Díaz, Víctor Hugo ORCID: https://orcid.org/0000-0003-3758-1091, Leone, Paola, Giménez-Garzó, Carla, Mincheva, Gergana, Mira, Álex, Forslund-Startceva, Sofia Kirke ORCID: https://orcid.org/0000-0003-4285-6993, Rubio, Teresa, Felipo, Vicente, Pérez-Martínez, Gaspar and Llansola, Marta
Scientific Reports 15 (1): 34382. 2 October 2025

Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids.
Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091, Dayaram, A., Soilemetzidou, E.S., Desvars-Larrive, A., Bohner, J., Buuveibaatar, B., Kaczensky, P., Walzer, C., Greenwood, A.D. and Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531
Scientific Reports 15 (1): 2767. 22 January 2025

Role of TRPC6 in kidney damage after acute ischemic kidney injury.
Zheng, Z. ORCID: https://orcid.org/0000-0002-5114-3824, Tsvetkov, D. ORCID: https://orcid.org/0000-0002-6472-971X, Bartolomaeus, T.U.P. ORCID: https://orcid.org/0000-0002-5156-7184, Erdogan, C., Krügel, U., Schleifenbaum, J. ORCID: https://orcid.org/0000-0002-3195-1517, Schaefer, M., Nürnberg, B., Chai, X., Ludwig, F.A., N'diaye, G., Köhler, M.B., Wu, K., Gollasch, M. ORCID: https://orcid.org/0000-0003-2797-1934 and Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575
Scientific Reports 12 (1): 3038. 22 February 2022

TheScienceBreaker

Studies of the bugs within: telling sickness from cure.
Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Pedersen, O.
TheScienceBreaker 4 (1) 20 March 2018

Thrombosis and Haemostasis

Protease-activated receptor-1 IgG autoantibodies in patients with COVID-19.
Reinshagen, L., Nageswaran, V., Heidecke, H., Schulze-Forster, K., Wilde, A.C.B., Ramezani Rad, P., Poller, W., Asmus, E., Simmons, S., Kuebler, W.M., Witzenrath, M., Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Jakobs, K., Puccini, M., Leistner, D.M., Rauch-Kröhnert, U., Kränkel, N., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Landmesser, U., Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644 and Haghikia, A.
Thrombosis and Haemostasis 124 (12): 1164-1166. December 2024

Trials

Tolerance induction through early feeding to prevent food allergy in infants and children with sensitization against food allergens (TIFFANI): rationale, study design, and methods of a randomized controlled trial.
Kalb, B. ORCID: https://orcid.org/0000-0002-3104-6736, Meixner, L., Heller, S., Dölle-Bierke, S., Roll, S., Tissen-Diabaté, T., Lau, S., Forslund, S. ORCID: https://orcid.org/0000-0003-4285-6993, Marenholz, I. ORCID: https://orcid.org/0009-0007-6933-3849, Lee, Y.A. ORCID: https://orcid.org/0000-0002-1817-9163, Thiel, A., Babina, M., Scheffel, J., Worm, M. and Beyer, K.
Trials 25 : 272. 19 April 2024

Tolerance induction through non-avoidance to prevent persistent food allergy (TINA) in children and adults with peanut or tree nut allergy: rationale, study design and methods of a randomized controlled trial and observational cohort study.
Trendelenburg, V., Dölle-Bierke, S., Unterleider, N., Alexiou, A., Kalb, B. ORCID: https://orcid.org/0000-0002-3104-6736, Meixner, L., Heller, S., Lau, S., Lee, Y.A. ORCID: https://orcid.org/0000-0002-1817-9163, Fauchère, F., Braun, J., Babina, M., Altrichter, S., Birkner, T. ORCID: https://orcid.org/0000-0003-2656-2821, Roll, S., Dobbertin-Welsch, J., Worm, M. and Beyer, K. ORCID: https://orcid.org/0000-0003-1859-0419
Trials 23 (1): 236. 28 March 2022

Tolerance induction through early feeding to prevent food allergy in infants with eczema (TEFFA): rationale, study design, and methods of a randomized controlled trial.
Kalb, B., Meixner, L., Trendelenburg, V., Unterleider, N., Dobbertin-Welsch, J., Heller, S., Dölle-Bierke, S., Roll, S., Lau, S., Lee, Y.A. ORCID: https://orcid.org/0000-0002-1817-9163, Fauchère, F., Braun, J., Babina, M., Altrichter, S., Birkner, T. ORCID: https://orcid.org/0000-0003-2656-2821, Worm, M. and Beyer, K. ORCID: https://orcid.org/0000-0003-1859-0419
Trials 23 (1): 210. 12 March 2022

Zeitschrift fuer Herz-, Thorax- und Gefaesschirurgie

Die Effekte der Herz-Lungen-Maschine auf das intestinale Mikrobiom und die Relation zum postoperativen SIRS [The effects of the cardiopulmonary bypass on the gut microbiome and its contribution to postoperative SIRS].
Hinkov, H., Markó, L. ORCID: https://orcid.org/0000-0003-1888-5575, Nazari-Shafti, T.Z., Neuber, S., Meyborg, H., Krüger, K., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644, Falk, V., Emmert, M.Y. and Rodriguez, H.
Zeitschrift fuer Herz-, Thorax- und Gefaesschirurgie 37 (6): 315-323. December 2023

Zenodo

Metabolic inflammation, brain age and cognitive functioning in short- and long-term clinical weight loss trials.
Maurer, Lukas ORCID: https://orcid.org/0000-0002-5813-7910 and Weygandt, Martin ORCID: https://orcid.org/0000-0001-9962-4582
[Dataset] 1 December 2025

bioRxiv

Anthropogenic land use exerts selection pressures on the resistome of a wild rodent.
Gicquel, M. ORCID: https://orcid.org/0000-0002-0823-1239, Planillo, A. ORCID: https://orcid.org/0000-0001-6763-9923, Heitlinger, E. ORCID: https://orcid.org/0000-0002-7139-3425, Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Kramer-Schadt, S. ORCID: https://orcid.org/0000-0002-9269-4446, Ferreira, S.C.M. ORCID: https://orcid.org/0000-0003-0265-0210 and Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091
bioRxiv : 2025.12.12.693898. 12 December 2025

Global analysis of infant gut microbiota revealed distinctive maturation dynamics across lifestyles.
Bücking, Robert ORCID: https://orcid.org/0000-0002-0180-5551, Pasquali, Greta, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Buss, Claudia ORCID: https://orcid.org/0000-0002-8738-3133, Viemann, Dorothee ORCID: https://orcid.org/0000-0002-9009-3559, Jarquín-Díaz, Víctor Hugo ORCID: https://orcid.org/0000-0003-3758-1091 and Forslund-Startceva, Sofia Kirke ORCID: https://orcid.org/0000-0003-4285-6993
bioRxiv : 2025.12.11.693638. 11 December 2025

Interleukin enhancer binding factor 2 (Ilf2) and kidney epithelial stress resilience.
Cao, Shuang ORCID: https://orcid.org/0000-0001-7195-8193, López-Cayuqueo, Karen I. ORCID: https://orcid.org/0000-0001-8409-7345, Leiz, Janna ORCID: https://orcid.org/0000-0002-6531-7047, Boivin, Felix J. ORCID: https://orcid.org/0000-0003-2325-0830, Markó, Lajos ORCID: https://orcid.org/0000-0003-1888-5575, Hinze, Christian ORCID: https://orcid.org/0000-0003-2526-1621, Schmitz, Jessica, Bräsen, Jan Hinrich and Schmidt-Ott, Kai ORCID: https://orcid.org/0000-0002-7700-7142
bioRxiv : 2025.08.12.667599v3. 21 November 2025

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort.
Cusco, Anna ORCID: https://orcid.org/0000-0002-9574-5755, Duan, Yiqian ORCID: https://orcid.org/0000-0002-8046-9831, Gil, Fernando, Chklovski, Alexei, Kruthi, Nithya ORCID: https://orcid.org/0000-0002-4149-0400, Pan, Shaojun, Forslund, Sofia ORCID: https://orcid.org/0000-0003-4285-6993, Lau, Susanne ORCID: https://orcid.org/0000-0002-5189-4265, Löber, Ulrike ORCID: https://orcid.org/0000-0001-7468-9531, Zhao, Xinmging and Coelho, Luis Pedro ORCID: https://orcid.org/0000-0002-9280-7885
bioRxiv : 2025.09.17.676595. 17 September 2025

Baseline microbiome composition impacts resilience to and recovery following antibiotics.
Chen, C.Y. ORCID: https://orcid.org/0000-0003-1765-7132, Löber, U. ORCID: https://orcid.org/0000-0001-7468-9531, Bartolomaeus, H. ORCID: https://orcid.org/0000-0003-4288-3828, Maier, L., Müller, D.N. ORCID: https://orcid.org/0000-0003-3650-5644, Wilck, N. ORCID: https://orcid.org/0000-0003-3189-5364, Jarquín-Díaz, V.H. ORCID: https://orcid.org/0000-0003-3758-1091 and Forslund-Startceva, S.K. ORCID: https://orcid.org/0000-0003-4285-6993
bioRxiv : 2024.03.31.587491. 31 March 2024

Host genetic and environmental factors shape the human gut resistome.
Le Roy, C.I. ORCID: https://orcid.org/0000-0002-0341-751X, Bowyer, R.C.E. ORCID: https://orcid.org/0000-0002-6941-8160, Carr, V.R. ORCID: https://orcid.org/0000-0002-3038-8929, Costeira, R., Castillo-Fernandez, J.E.R., Martin, T.C. ORCID: https://orcid.org/0000-0001-9990-1455, Spector, T., Steves, C., Moyes, D. ORCID: https://orcid.org/0000-0002-1657-918X, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Bell, J.T. ORCID: https://orcid.org/0000-0002-3858-5986
bioRxiv : 2020.05.18.092973. 20 May 2020

mSphere

Meconium microbiome of very preterm infants across Germany.
Klopp, J. ORCID: https://orcid.org/0000-0001-9312-6398, Ferretti, P. ORCID: https://orcid.org/0000-0002-1707-9013, Meyer, C.U., Hilbert, K., Haiß, A., Marißen, J., Henneke, P., Hudalla, H., Pirr, S., Viemann, D., Zemlin, M., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Härtel, C., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Gehring, S. and Van Rossum, T. ORCID: https://orcid.org/0000-0002-3598-5001
mSphere 7 (1): e0080821. 23 February 2022

medRxiv

Plasma proteomics in acute heart failure: survival-associated protein signatures and 90-day trajectories.
Chitroceanu, Alexandra M., Fahjen, Pauline ORCID: https://orcid.org/0000-0002-5015-0643, Schulze, Daniel, Zach, Veronika, Alasfar, Lina, Ziehm, Matthias ORCID: https://orcid.org/0000-0001-7074-4054, Kirchner, Marieluise ORCID: https://orcid.org/0000-0002-7049-534X, Niquet, Sylvia, Dahmen, Jan-Niklas, Plappert, Carlos, Kretzler, Lucie, Kind, Andreas, Zurkan, Daniela, Pinto, Rafaela Maria, Reynolds, Edwardo, Trippel, Tobias D., Forslund, Sofia ORCID: https://orcid.org/0000-0003-4285-6993, Grittner, Ulrike, Mai, Knut, Gotthardt, Michael ORCID: https://orcid.org/0000-0003-1788-3172, Schiattarella, Gabriele G. ORCID: https://orcid.org/0000-0002-7582-7171, Kintscher, Ulrich, Ahmadi, Michael, Boldt, Leif-Hendrik, Buchmann, Nikolaus, Eckardt, Kai-Uwe, Endres, Matthias, Gerhardt, Holger ORCID: https://orcid.org/0000-0002-3030-0384, Hübner, Norbert ORCID: https://orcid.org/0000-0002-1218-6223, Kollmus-Heege, Jil, Landmesser, Ulf, Müller, Dominik N. ORCID: https://orcid.org/0000-0003-3650-5644, Nolte, Christian H., Piper, Sophie K., Rattan, Simrit, Rohrpasser-Napierkowski, Ira, Schönrath, Katharina, Schulz-Menger, Jeanette ORCID: https://orcid.org/0000-0003-3100-1092, Schweizerhof, Oliver, Pischon, Tobias ORCID: https://orcid.org/0000-0003-1568-767X, Pieske, Burkert ORCID: https://orcid.org/0000-0002-6466-5306, Weber, Joachim, Mertins, Philipp ORCID: https://orcid.org/0000-0002-2245-528X and Edelmann, Frank
medRxiv : 2025.12.01.25341310. 3 December 2025

This list was generated on Fri Jul 3 16:35:20 2026 UTC.