Browse by Research Team

Acta Physiologica

A gender perspective on diet, microbiome, and sex hormone interplay in cardiovascular disease.
Jovanovic, N., Zach, V., Crocini, C., Bahr, L.S., Forslund-Startceva, S.K. and Franz, K.
Acta Physiologica 12 September 2024 (In Press)

Metformin modulates microbiota and improves blood pressure and cardiac remodeling in a rat model of hypertension.
Wimmer, M.I., Bartolomaeus, H., Anandakumar, H., Chen, C.Y., Vecera, V., Kedziora, S., Kamboj, S., Schumacher, F., Pals, S., Rauch, A., Meisel, J., Potapenko, O., Yarritu, A., Bartolomaeus, T.U.P., Samaan, M., Thiele, A., Stürzbecher, L., Geisberger, S.Y., Kleuser, B., Oefner, P.J., Haase, N., Löber, U., Gronwald, W., Forslund-Startceva, S.K., Muller, D.N. and Wilck, N.
Acta Physiologica : e14226. 10 September 2024 (In Press)

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., Forslund, K., Kultima, J.R., Meyer, C.U., Kullmer, U., Sunagawa, S., Bork, P. and Gehring, S.
American Journal of Physiology Gastrointestinal and Liver Physiology 312 (4): G327-G339. 1 April 2017

Arthritis & Rheumatology

Shared and distinct gut microbiota in spondyloarthritis, acute anterior uveitis, and Crohn's disease.
Essex, M., Rios Rodriguez, V., Rademacher, J., Proft, F., Löber, U., Marko, L., Pleyer, U., Strowig, T., Marchand, J., Kirwan, J.A., Siegmund, B., Forslund, S.K. and Poddubnyy, D.
Arthritis & Rheumatology 76 (1): 48-58. January 2024

BMC Bioinformatics

Domainoid: domain-oriented orthology inference.
Persson, E., Kaduk, M., Forslund, S.K. and Sonnhammer, E.L.L.
BMC Bioinformatics 20 (1): 523. 28 October 2019

Domain architecture conservation in orthologs.
Forslund, K., 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. 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., Jarquín-Díaz, V.H., Klopp, J., Kemper, A., Hilbert, K., Hillen, B., Pfirrmann, D., Simon, P., Bähner, V., Nitsche, O., Gehring, S., Markó, L., Forslund, S.K. and Poplawska, K.
BMC Microbiology 23 (1): 44. 21 February 2023

BMJ Open

Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova, A., Forslund, S.K., 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.
BMJ Open 8 (7): e021682. 28 July 2018

BioEssays

Metagenomic insights into the human gut resistome and the forces that shape it.
Forslund, K., Sunagawa, S., Coelho, L.P. and Bork, P.
BioEssays 36 (3): 316-329. March 2014

Bioinformatics

Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund, K., 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., Bork, P. 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.
Bioinformatics 32 (17): 2636-2641. 1 September 2016

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima, J.R., Coelho, L.P., Forslund, K., Huerta-Cepas, J., Li, S.S., Driessen, M., Voigt, A.Y., Zeller, G., Sunagawa, S. and Bork, P.
Bioinformatics 32 (16): 2520-2523. 15 August 2016

Benchmarking homology detection procedures with low complexity filters.
Forslund, K. and Sonnhammer, E.L.L.
Bioinformatics 25 (19): 2500-2505. 1 October 2009

Predicting protein function from domain content.
Forslund, K. and Sonnhammer, E.L.L.
Bioinformatics 24 (15): 1681-1687. 1 August 2008

VisRD-visual recombination detection.
Forslund, K., 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., Löber, U. and Forslund, S.K.
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., 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., Birkner, T., Jørgensen, T., Forslund, S.K., 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., Jann, C., Pereira, F., Johansson, A., Steinmetz, L.M. and Patil, K.R.
Biotechnology for Biofuels 14 (1): 41. 10 February 2021

Briefings in Bioinformatics

OrthoDisease: tracking disease gene orthologs across 100 species.
Forslund, K., Schreiber, F., Thanintorn, N. and Sonnhammer, E.L.L.
Briefings in Bioinformatics 12 (5): 463-473. September 2011

Cardiovascular Research

VEGF-B hypertrophy predisposes to transition from diastolic to systolic heart failure in hypertensive rats.
Samuelsson, A.M., Bartolomaeus, T.U.P., Anandakumar, H., Thowsen, I., Nikpey, E., Han, J., Marko, L., Finne, K., Tenstad, O., Eckstein, J., Berndt, N., Kühne, T., Kedziora, S., Sultan, I., Skogstrand, T., Karlsen, T.V., Nurmi, H., Forslund, S.K., Bollano, E., Alitalo, K., Muller, D.N. and Wiig, H.
Cardiovascular Research 119 (7): 1553-1567. 4 July 2023

Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage.
Avery, E.G., Bartolomaeus, H., Rauch, A., Chen, C.Y., N'Diaye, G., Löber, U., Bartolomaeus, T.U.P., Fritsche-Guenther, R., Rodrigues, A.F., Yarritu, A., Zhong, C., Fei, L., Tsvetkov, D., Todiras, M., Park, J.K., Markó, L., Maifeld, A., Patzak, A., Bader, M., Kempa, S., Kirwan, J.A., Forslund, S.K., Müller, D.N. and Wilck, N.
Cardiovascular Research 119 (6): 1441-1452. May 2023

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., Kazemi, A., Bartolomaeus, T.U.P., Martami, F., Noormohammadi, M., Salari, A., Löber, U., Balou, H.A., Forslund, S.K. and Mahdavi-Roshan, M.
Cardiovascular Research 119 (4): 933-956. April 2023

Quantifying technical confounders in microbiome studies.
Bartolomaeus, T.U.P., Birkner, T., Bartolomaeus, H., Löber, U., Avery, E.G., Mähler, A., Weber, D., Kochlik, B., Balogh, A., Wilck, N., Boschmann, M., Müller, D.N., Markó, L. and Forslund, S.K.
Cardiovascular Research 117 (3): 863-875. 1 March 2021

Blood pressure changes correlate with short-chain fatty acid production potential shifts under a synbiotic intervention.
Bartolomaeus, H., Avery, E.G., Bartolomaeus, T.U.P., Kozhakhmetov, S., Zhumadilov, Z., Müller, D.N., Wilck, N., Kushugulova, A. and Forslund, S.K.
Cardiovascular Research 116 (7): 1252-1253. June 2020

B-cell lymphoma/leukemia 10 and angiotensin II-induced kidney injury.
Markó, L., Park, J.K., Henke, N., Rong, S., Balogh, A., Klamer, S., Bartolomaeus, H., Wilck, N., Ruland, J., Forslund, S.K., Luft, F.C., Dechend, R. and Müller, D.N.
Cardiovascular Research 116 (5): 1059-1070. 1 April 2020

Hitchhiker's guide to microbiome studies.
Bartolomaeus, T.U.P. and Forslund, S.K.
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., 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., 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., Kempa, S., 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., Winklhofer, K.F., Müller, D.N., 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., Karaca, E., Bebel, A., Bork, P. and Barabas, O.
Cell 173 (1): 208-220. 22 March 2018

Circulation

Mutant phosphodiesterase 3A protects from hypertension-induced cardiac damage.
Ercu, M., Mücke, M.B., Pallien, T., Markó, L., Sholokh, A., Schächterle, C., Aydin, A., Kidd, A., Walter, S., Esmati, Y., McMurray, B.J., Lato, D.F., Sunaga-Franze, D.Y., Dierks, P.H., Flores, B.I.M., Walker-Gray, R., Gong, M., Merticariu, C., Zühlke, K., Russwurm, M., Liu, T., Batolomaeus, T.U.P., Pautz, S., Schelenz, S., Taube, M., Napieczynska, H., Heuser, A., Eichhorst, J., Lehmann, M., Miller, D.C., Diecke, S., Qadri, F., Popova, E., Langanki, R., Movsesian, M.A., Herberg, F.W., Forslund, S.K., Müller, D.N., Borodina, T., Maass, P.G., Bähring, S., Hübner, N., Bader, M. and Klussmann, E.
Circulation 146 (23): 1758-1778. 6 December 2022

Salt transiently inhibits mitochondrial energetics in mononuclear phagocytes.
Geisberger, S., Bartolomaeus, H., Neubert, P., Willebrand, R., Zasada, C., Bartolomaeus, T., McParland, V., Swinnen, D., Geuzens, A., Maifeld, A., Krampert, L., Vogl, M., Mähler, A., Wilck, N., Marko, L., Tilic, E., Forslund, S.K., Binger, K.J., Stegbauer, J., Dechend, R., Kleinewietfeld, M., Jantsch, J., Kempa, S. and Müller, D.N.
Circulation 144 (2): 144-158. 13 July 2021

Phosphodiesterase 3A and arterial hypertension.
Ercu, M., Markó, L., Schächterle, C., Tsvetkov, D., Cui, Y., Maghsodi, S., Bartolomaeus, T.U.P., Maass, P.G., Zühlke, K., Gregersen, N., Hübner, N., Hodge, R., Mühl, A., Pohl, B., Molé-Illas, R., Geelhaar, A., Walter, S., Napieczynska, H., Schelenz, S., Taube, M., Heuser, A., Anistan, Y.M., Qadri, F., Todiras, M., Plehm, R., Popova, E., Langanki, R., Eichhorst, J., Lehmann, M., Wiesner, B., Russwurm, M., Forslund, S.K., Kamer, I., Müller, D.N., Gollasch, M., Aydin, A., Bähring, S., Bader, M., Luft, F.C. and Klussmann, E.
Circulation 142 (2): 133-149. 14 July 2020

Short-chain fatty acid propionate protects from hypertensive cardiovascular damage.
Bartolomaeus, H., Balogh, A., Yakoub, M., Homann, S., Markó, L., Höges, S., Tsvetkov, D., Krannich, A., Wundersitz, S., Avery, E.G., Haase, N., Kräker, K., Hering, L., Maase, M., Kusche-Vihrog, K., Grandoch, M., Fielitz, J., Kempa, S., Gollasch, M., Zhumadilov, Z., Kozhakhmetov, S., Kushugulova, A., Eckardt, K.U., Dechend, R., Rump, L.C., Forslund, S.K., Müller, D.N., Stegbauer, J. and Wilck, N.
Circulation 139 (11): 1407-1421. 12 March 2019

Circulation Research

The gut microbiome in hypertension: recent advances and future perspectives.
Avery, E.G., Bartolomaeus, H., Maifeld, A., Marko, L., Wiig, H., Wilck, N., Rosshart, S.P., Forslund, S.K. and Muller, D.N.
Circulation Research 128 (7): 934-950. 2 April 2021

Clinical and Translational Allergy

An interdisciplinary approach to characterize peanut-allergic patients - first data from the FOOD@ consortium.
Worm, M., Alexiou, A., Höfer, V., Birkner, T., Jeanrenaud, A.C.S.N., Fauchère, F., Pazur, K., Steinert, C., Arnau-Soler, A., Banerjee, P., Diefenbach, A., Dobbertin-Welsch, J., Dölle-Bierke, S., Francuzik, W., Ghauri, A., Heller, S., Kalb, B., Löber, U., Marenholz, I., Markó, L., Scheffel, J., Potapenko, O., Roll, St., Lau, S., Lee, Y.A., Braun, J., Thiel, A., Babina, M., Altrichter, S., Forslund, S.K. and Beyer, K.
Clinical and Translational Allergy 12 (10): e12197. October 2022

Communications Biology

Genomic attributes of airway commensal bacteria and mucosa.
Cuthbertson, L., Löber, U., Ish-Horowicz, J.S., McBrien, C.N., Churchward, C., Parker, J.C., Olanipekun, M.T., Burke, C., McGowan, A., Davies, G.A., Lewis, K.E., Hopkin, J.M., Chung, K.F., O'Carroll, O., Faul, J., Creaser-Thomas, J., Andrews, M., Ghosal, R., Piatek, S., Willis-Owen, S.A.G., Bartolomaeus, T.U.P., Birkner, T., Dwyer, S., Kumar, N., Turek, E.M., William Musk, A, Hui, J., Hunter, M., James, A., Dumas, M.E., Filippi, S., Cox, M.J., Lawley, T.D., Forslund, S.K., Moffatt, M.F. and Cookson, W.O.C.
Communications Biology 7 (1): 171. 12 February 2024

EBioMedicine

Gut microbiome and atrial fibrillation - results from a large population-based study.
Palmu, J., Börschel, C.S., Ortega-Alonso, A., Markó, L., Inouye, M., Jousilahti, P., Salido, R.A., Sanders, K., Brennan, C., Humphrey, G.C., Sanders, J.G., Gutmann, F., Linz, D., Salomaa, V., Havulinna, A.S., Forslund, S.K., Knight, R., Lahti, L., Niiranen, T. and Schnabel, R.B.
EBioMedicine 91 : 104583. May 2023

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., 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., Khoueiry, P., Dinkel, H., Forslund, K., Stamatakis, A., Barry, J., Budd, A., 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., Foryst-Ludwig, A., Klose, C., da Conceicao, C.R., Alasfar, L., Birkner, T., Forslund, S.K., 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., Abramova, A., Berendonk, T.U., Coelho, L.P., Forslund, S.K., Gschwind, R., Heikinheimo, A., Jarquín-Díaz, V.H., Khan, A.A., Klümper, U., Löber, U., 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., Hippel, B., Kauserud, H., Löber, U., 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., Berendonk, T.U., Forslund, S.K. and Hess, S.
Environmental Science and Technology 56 (21): 14913-14922. 1 November 2022

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., Akpanova, S., Rysbekov, K., Kozhakhmetov, S., Khassenbekova, Z., Essex, M., Nurgozhina, A., Nurgaziyev, M., Babenko, D., Markó, L. and Forslund, S.K.
Frontiers in Cellular and Infection Microbiology 11 : 622735. 21 April 2021

Frontiers in Immunology

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.
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., Löber, U., Vernazza, P., Scheibenbogen, C. and Forslund, S.K.
Frontiers in Immunology 12 : 628741. 3 January 2022

Gastroenterology

S100A8 and S100A9 are important for postnatal development of gut microbiota and immune system in mice and infants.
Willers, M., Ulas, T., Völlger, L., Vogl, T., Heinemann, A.S., Pirr, S., Pagel, J., Fehlhaber, B., Halle, O., Schöning, J., Schreek, S., Löber, U., Essex, M., 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., Roth, J. and Viemann, D.
Gastroenterology 159 (6): 2130-2145. December 2020

Genome Biology

A novel exploratory method for visual recombination detection.
Strimmer, K., Forslund, K., Holland, B. 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., Huerta-Cepas, J., Muffato, M., Yilmaz, P., Xenarios, I., Bork, P., 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., Vestergaard, H., Hansen, T., Brix, S., Oturai, A., Sørensen, P.S., Ehrlich, S.D. and Pedersen, O.
Genome Medicine 15 (1): 1. 5 January 2023

Genome Research

Country-specific antibiotic use practices impact the human gut resistome.
Forslund, K., Sunagawa, S., Kultima, J.R., Mende, D.R., Arumugam, M., Typas, A. and Bork, P.
Genome Research 23 (7): 1163-1169. July 2013

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., Adriouch, S., Assmann, K.E., Prifiti, E., Aron-Wisnewsky, J., Debédat, J., Le Roy, T., Nielsen, T., Amouyal, C., André, S., Andreelli, F., Blüher, M., Chakaroun, R., Chilloux, J., Coelho, L.P., Dao, M.C., Das, P., Fellahi, S., Forslund, S., Galleron, N., Hansen, T.H., 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., Stumvoll, M., Pedersen, O.B., Bork, P., Ehrlich, S.D., Zucker, J.D., Bäckhed, F., Raes, J. and Clément, K.
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., Le-Chatelier, E., Le Lay, A., Nicholson, J., Hansen, T., Hyötyläinen, T., Clément, K., Oresic, M., Bork, P., Ehrlich, S.D., Raes, J., Pedersen, O.B., Gauguier, D. and Dumas, M.E.
Gut 70 (11): 2105-2114. 7 October 2021

Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand, F., Moitinho-Silva, L., Blasche, S., Jahn, M.T.T., 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., Sunagawa, S., Hentschel, U., Merten, C., Patil, K.R., Benes, V. and Bork, P.
Gut 68 (10): 1781-1790. 9 September 2019

Hypertension

Effect of sunitinib treatment on skin sodium accumulation in patients with renal cancer: a pilot study.
Markó, L., Dörr, A., Linz, P., van den Meiracker, A.H., Garrelds, I.M., Kuehne, T., Dechend, R., Danser, A.H.J., Flörcken, A. and Müller, D.N.
Hypertension 79 (5): e103-e105. May 2022

Precarious symbiosis between host and microbiome in cardiovascular health.
Bartolomaeus, H., Markó, L., Wilck, N., Luft, F.C., Forslund, S.K. and Muller, D.N.
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. 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., Ferreira, S.C.M., Balard, A., Ďureje, L., Macholán, M., Piálek, J., Bengtsson-Palme, J., Kramer-Schadt, S., Forslund-Startceva, S.K. and Heitlinger, E.
ISME Communications 4 (1): ycae053. 15 April 2024

Insectes Sociaux

The gut microbiome is associated with behavioural task in honey bees.
Jones, J.C., Fruciano, C., Marchant, J., Hildebrand, F., Forslund, S., Bork, P., 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., Xu, Y., Krügel, U., Schaefer, M., Grune, T., Nürnberg, B., Köhler, M.B., Gollasch, M., Tsvetkov, D. and Marko, L.
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., 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., Viemann, D., Zemlin, M., Bork, P., Gehring, S., König, I.R., Henneke, P. and Härtel, C.
JAMA Pediatrics 5 August 2024 (In Press)

Journal of Clinical Periodontology

Oral microbiota of patients with phenylketonuria: a nation-based cross-sectional study.
Bingöl, M., Cardilli, A., Bingöl, A.C., Löber, U., Bang, C., Franke, A., Bartzela, T., Beblo, S., Mönch, E., Stolz, S., Schaefer, A.S., Forslund, S.K. and Richter, G.M.
Journal of Clinical Periodontology 51 (8): 1081-1092. August 2024

Journal of Internal Medicine

Fasting intervention and its clinical effects on the human host and microbiome.
Forslund, S.K.
Journal of Internal Medicine 293 (2): 166-183. February 2023

Journal of Investigative Dermatology

Skin sodium accumulates in psoriasis and reflects disease severity.
Maifeld, A., Wild, J., Karlsen, T.V., Rakova, N., Wistorf, E., Linz, P., Jung, R., Birukov, A., Gimenez-Rivera, V.A., Wilck, N., Bartolomaeus, T., Dechend, R., Kleinewietfeld, M., Forslund, S.K., Krause, A., Kokolakis, G., Philipp, S., Clausen, B.E., Brand, A., Waisman, A., Kurschus, F.C., Wegner, J., Schultheis, M., Luft, F.C., Boschmann, M., Kelm, M., Wiig, H., Kuehne, T., Müller, D.N., Karbach, S. and Markó, L.
Journal of Investigative Dermatology 142 (1): 166-178. January 2022

Journal of Nutritional Biochemistry

UV light exposure vs. 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., Markó, L., Bartolomaeus, T.U.P., Löber, U., Michel, S., Wensch-Dorendorf, M., Forslund-Startceva, S.K. and Stangl, G.I.
Journal of Nutritional Biochemistry : 109746. 22 August 2024 (In Press)

Journal of Proteome Research

Comparing the extraction performance in mouse plasma of different biphasic methods for polar and nonpolar compounds.
Gutmann, F., Fritsche-Guenther, R., Dias, D.B. and Kirwan, J.A.
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., Adamek, K., Węgrzyn, D., Skonieczna-Żydecka, K., Malinowski, D., Łoniewski, I., Markó, L., Ulas, T., Forslund, S.K. and Łoniewska, B.
Journal of Translational Medicine 19 (1): 177. 28 April 2021

Journal of the American Society of Nephrology

Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance.
Holle, J., Bartolomaeus, H., Löber, U., Behrens, F., Bartolomaeus, T.U.P., Anandakumar, H., Wimmer, M., Vu, D.L., Kuhring, M., Brüning, U., Maifeld, A., Geisberger, S., Kempa, S., Schumacher, F., Kleuser, B., Bufler, P., Querfeld, U., Kitschke, S., Engler, D., Kuhrt, L.D., Drechsel, O., Eckardt, K.U., Forslund, S., Thürmer, A., McParland, V., Kirwan, J., Wilck, N. and Mueller, D.
Journal of the American Society of Nephrology 33 (12): 2259-2275. December 2022

Kidney International

Mutant phosphodiesterase 3A protects the kidney from hypertension-induced damage.
Sholokh, A., Walter, S., Markó, L., McMurray, B.J., Sunaga-Franze, D.Y., Xu, M., Zühlke, K., Russwurm, M., Bartolomaeus, T.U.P., Langanki, R., Qadri, F., Heuser, A., Patzak, A., Forslund, S.K., Bähring, S., Borodina, T., Persson, P.B., Maass, P.G., Bader, M. and Klussmann, E.
Kidney International 104 (2): 388-393. August 2023

Lecture Notes in Computer Science

A semi-supervised approach to discover bivariate causality in large biological data.
Sokolovska, N., Permiakova, O., Forslund, S.K. 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. and Moulton, V.
Lecture Notes in Computer Science 5251 : 284-295. 2008

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., Gutmann, F., Duda, G.N., Kirwan, J. 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., Löber, U., Cui, P., Quedenau, C., Chen, W. and Greenwood, A.D.
Methods in Ecology and Evolution 22 September 2020

Methods in Molecular Biology

Evolution of protein domain architectures.
Forslund, S.K., Kaduk, M. and Sonnhammer, E.L.L.
Methods in Molecular Biology 1910 : 469-504. 2019

Evolution of protein domain architectures.
Forslund, K. 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., Löber, U. and Bleidorn, C.
Microbial Ecology 87 (1): 91. 3 July 2024

Microbiology Spectrum

Sputum microbiome and chronic obstructive pulmonary disease in a rural Ugandan cohort of well-controlled HIV infection.
Kayongo, A., Bartolomaeus, T.U.P., Birkner, T., Markó, L., Löber, U., 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.
Microbiology Spectrum : e0213921. 15 February 2023 (In Press)

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., Ebner, F., Löber, U., Hayani, R., Kundik, A., Cardilli, A., Heitlinger, E., Forslund, S.K. 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., Kultima, J.R., Costea, P.I., Fournier, C., Pan, Y., Czarnecki-Maulden, G., Hayward, M.R., Forslund, S.K., Schmidt, T.S.B., Descombes, P., Jackson, J.R., Li, Q. and Bork, P.
Microbiome 6 (1): 72. 19 April 2018

Molecular Biology and Evolution

Ten years of collaborative progress in the quest for orthologs.
Linard, B., Ebersberger, I., McGlynn, S.E., 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., 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., Forslund, K., Coelho, L.P., Szklarczyk, D., Jensen, L.J., von Mering, C. and Bork, P.
Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017

Domain tree-based analysis of protein architecture evolution.
Forslund, K., 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., 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., McEwen, G.K., Löber, U., Förster, D.W., East, M.L., Melzheimer, J. and Greenwood, A.D.
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., Müller-Werdan, U., Herpich, C. 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., Coelho, L.P., Sunagawa, S., Munch, R., Huerta-Cepas, J., Forslund, K., Hildebrand, F., Kushugulova, A., Zeller, G. and Bork, P.
Molecular Systems Biology 13 (12): 960. 14 December 2017

NPJ Biofilms and Microbiomes

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.
Essex, M., Millet Pascual-Leone, B.L., Löber, U., Kuhring, M., Zhang, B., Brüning, U., Fritsche-Guenther, R., Krzanowski, M., Fiocca Vernengo, F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thibeault, C., Corman, V.M., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
NPJ Biofilms and Microbiomes 10 (1): 66. 1 August 2024

Nature

Towards the biogeography of prokaryotic genes.
Coelho, L.P., Alves, R., Del Río, Á.R., Myers, P.N., Cantalapiedra, C.P., Giner-Lamia, J., Schmidt, T.S., Mende, D.R., Orakov, A., Letunic, I., Hildebrand, F., Van Rossum, T., Forslund, S.K., Khedkar, S., Maistrenko, O.M., Pan, S., Jia, L., Ferretti, P., Sunagawa, S., Zhao, X.M., Nielsen, H.B., Huerta-Cepas, J. and Bork, P.
Nature 601 (7892): 252-256. 13 January 2022

Combinatorial, additive and dose-dependent drug-microbiome associations.
Forslund, S.K., Chakaroun, R., Zimmermann-Kogadeeva, M., Markó, L., Aron-Wisnewsky, J., Nielsen, T., Moitinho-Silva, L., Schmidt, T.S.B., Falony, G., Vieira-Silva, S., Adriouch, S., Alves, R.J., Assmann, K., Bastard, J.P., Birkner, T., Caesar, R., Chilloux, J., Coelho, L.P., Fezeu, L., Galleron, N., Helft, G., Isnard, R., Ji, B., Kuhn, M., Le Chatelier, E., Myridakis, A., Olsson, L., Pons, N., Prifti, E., Quinquis, B., Roume, H., Salem, J.E., Sokolovska, N., Tremaroli, V., Valles-Colomer, M., Lewinter, C., Søndertoft, N.B., Pedersen, H.K., Hansen, T.H., Gøtze, J.P., Køber, L., Vestergaard, H., Hansen, T., Zucker, J.D., Hercberg, S., Oppert, J.M., Letunic, I., Nielsen, J., Bäckhed, F., Ehrlich, S.D., Dumas, M.E., Raes, J., Pedersen, O., Clément, K., Stumvoll, M. and Bork, P.
Nature 600 : 500-505. 16 December 2021

Unravelling the collateral damage of antibiotics on gut bacteria.
Maier, L., Goemans, C.V., Wirbel, J., Kuhn, M., Eberl, C., Pruteanu, M., Müller, P., Garcia-Santamarina, S., Cacace, E., Zhang, B., Gekeler, C., Banerjee, T., Anderson, E.E., Milanese, A., Löber, U., Forslund, S.K., Patil, K.R., Zimmermann, M., Stecher, B., Zeller, G., Bork, P. and Typas, A.
Nature 599 : 120-124. 4 November 2021

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., 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., 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., 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.
Nature 560 (7717): 233-237. 9 August 2018

Salt-responsive gut commensal modulates T(H)17 axis and disease.
Wilck, N., Matus, M.G., Kearney, S.M., Olesen, S.W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., Vvedenskaya, O., Kleiner, F.H., Tsvetkov, D., Klug, L., Costea, P.I., Sunagawa, S., Maier, L., Rakova, N., Schatz, V., Neubert, P., Frätzer, C., Krannich, A., Gollasch, M., Grohme, D.A., Côrte-Real, B.F., Gerlach, R.G., Basic, M., Typas, A., Wu, C., Titze, J.M., Jantsch, J., Boschmann, M., Dechend, R., Kleinewietfeld, M., Kempa, S., Bork, P., Linker, R.A., Alm, E.J. and Müller, D.N.
Nature 551 (7682): 585-589. 30 November 2017

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., 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., 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., 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. and Pedersen, O.
Nature 528 (7581): 262-266. 10 December 2015

Nature Communications

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung.
Dörner, P.J., Anandakumar, H., Röwekamp, I., Fiocca Vernengo, F., Millet Pascual-Leone, B., Krzanowski, M., Sellmaier, J., Brüning, U., Fritsche-Guenther, R., Pfannkuch, L., Kurth, F., Milek, M., Igbokwe, V., Löber, U., Gutbier, B., Holstein, M., Heinz, G.A., Mashreghi, M.F., Schulte, L.N., Klatt, A.B., Caesar, S., Wienhold, S.M., Offermanns, S., Mack, M., Witzenrath, M., Jordan, S., Beule, D., Kirwan, J.A., Forslund, S.K., Wilck, N., Bartolomaeus, H., Heimesaat, M.M. and Opitz, B.
Nature Communications 15 (1): 2788. 30 March 2024

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide.
Andrikopoulos, P., Aron-Wisnewsky, J., Chakaroun, R., Myridakis, A., Forslund, S.K., Nielsen, T., Adriouch, S., Holmes, B., Chilloux, J., Vieira-Silva, S., Falony, G., Salem, J.E., Andreelli, F., Belda, E., Kieswich, J., Chechi, K., Puig-Castellvi, F., Chevalier, M., Le Chatelier, E., Olanipekun, M.T., Hoyles, L., Alves, R., Helft, G., Isnard, R., Køber, L., Coelho, L.P., Rouault, C., Gauguier, D., Gøtze, J.P., Prifti, E., Froguel, P., Zucker, J.D., Bäckhed, F., Vestergaard, H., Hansen, T., Oppert, J.M., Blüher, M., Nielsen, J., Raes, J., Bork, P., Yaqoob, M.M., Stumvoll, M., Pedersen, O., Ehrlich, S.D., Clément, K. and Dumas, M.E.
Nature Communications 14 (1): 5843. 20 September 2023

The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis.
Schoeler, M., Ellero-Simatos, S., Birkner, T., Mayneris-Perxachs, J., Olsson, L., Brolin, H., Löber, U., Kraft, J.D., Polizzi, A., Martí-Navas, M., Puig, J., Moschetta, A., Montagner, A., Gourdy, P., Heymes, C., Guillou, H., Tremaroli, V., Fernández-Real, J.M., Forslund, S.K., Burcelin, R. and Caesar, R.
Nature Communications 14 (1): 5329. 1 September 2023

Fasting alters the gut microbiome reducing blood pressure and body weight in metabolic syndrome patients.
Maifeld, A., Bartolomaeus, H., Löber, U., Avery, E.G., Steckhan, N., Markó, L., Wilck, N., Hamad, I., Šušnjar, U., Mähler, A., Hohmann, C., Chen, C.Y., Cramer, H., Dobos, G., Lesker, T.R., Strowig, T., Dechend, R., Bzdok, D., Kleinewietfeld, M., Michalsen, A., Müller, D.N. and Forslund, S.K.
Nature Communications 12 (1): 1970. 30 March 2021

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.
Molinaro, A., Bel Lassen, P., Henricsson, M., Wu, H., Adriouch, S., Belda, E., Chakaroun, R., Nielsen, T., Bergh, P.O., Rouault, C., André, S., Marquet, F., Andreelli, F., Salem, J.E., Assmann, K., Bastard, J.P., Forslund, S., Le Chatelier, E., Falony, G., Pons, N., Prifti, E., Quinquis, B., Roume, H., Vieira-Silva, S., Hansen, T.H., Pedersen, H.K., Lewinter, C., Sønderskov, N.B., Køber, L., Vestergaard, H., Hansen, T., Zucker, J.D., Galan, P., Dumas, M.E., Raes, J., Oppert, J.M., Letunic, I., Nielsen, J., Bork, P., Ehrlich, S.D., Stumvoll, M., Pedersen, O., Aron-Wisnewsky, J., Clément, K. and Bäckhed, F.
Nature Communications 11 (1): 5881. 18 November 2020

Elevated aldosterone and blood pressure in a mouse model of familial hyperaldosteronism with ClC-2 mutation.
Schewe, J., Seidel, E., Forslund, S., Marko, L., Peters, J., Muller, D.N., Fahlke, C., Stölting, G. and Scholl, U.
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., Bork, P. and de Vos, W.M.
Nature Communications 7 : 10410. 26 January 2016

Nature Ecology & Evolution

Ecological factors influence balancing selection on leaf chemical profiles of a wildflower.
Carley, L.N., Mojica, J.P., Wang, B., Chen, C.Y., Lin, Y.P., Prasad, K.V.S.K, Chan, E., Hsu, C.W., Keith, R., Nuñez, C.L., Olson-Manning, C.F., Rushworth, C.A., Wagner, M.R., Wang, J., Yeh, P.M., Reichelt, M., Ghattas, K., Gershenzon, J., Lee, C.R. and Mitchell-Olds, T.
Nature Ecology & Evolution 5 : 1135-1144. August 2021

Nature Medicine

Microbiome and metabolome features of the cardiometabolic disease spectrum.
Fromentin, S., Forslund, S.K., Chechi, K., Aron-Wisnewsky, J., Chakaroun, R., Nielsen, T., Tremaroli, V., Ji, B., Prifti, E., Myridakis, A., Chilloux, J., Andrikopoulos, P., Fan, Y., Olanipekun, M.T., Alves, R., Adiouch, S., Bar, N., Talmor-Barkan, Y., Belda, E., Caesar, R., Coelho, L.P., Falony, G., Fellahi, S., Galan, P., Galleron, N., Helft, G., Hoyles, L., Isnard, R., Le Chatelier, E., Julienne, H., Olsson, L., Pedersen, H.K., Pons, N., Quinquis, B., Rouault, C., Roume, H., Salem, J.E., Schmidt, T.S.B., Vieira-Silva, S., Li, P., Zimmermann-Kogadeeva, M., Lewinter, C., Søndertoft, N.B., Hansen, T.H., Gauguier, D., Gøtze, J.P., Køber, L., Kornowski, R., Vestergaard, H., Hansen, T., Zucker, J.D., Hercberg, S., Letunic, I., Bäckhed, F., Oppert, J.M., Nielsen, J., Raes, J., Bork, P., Stumvoll, M., Segal, E., Clément, K., Dumas, M.E., Ehrlich, S.D. and Pedersen, O.
Nature Medicine 28 (2): 303-314. 17 February 2022

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., 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., MacIntyre, D.A., Arumugam, M., Azhar, R., Beghini, F., Bergstrom, K., Bhatt, A., Bisanz, J.E., Braun, J., Bravo, H.C., Buck, G.A., 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., 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., Yamada, T., 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., Huttenhower, C., Dowd, J.B., Jones, H.E. and Waldron, L.
Nature Medicine 27 (11): 1885-1892. November 2021

Nature Methods

Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., Jensen, L.J., 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

Recovery of gut microbiota of healthy adults following antibiotic exposure.
Palleja, A., Mikkelsen, K.H., Forslund, S.K., Kashani, A., Allin, K.H., Nielsen, T., Hansen, T.H., Liang, S., Feng, Q., Zhang, C., Pyl, P.T., Coelho, L.P., Yang, H., Wang, J., Typas, A., Nielsen, M.F., Nielsen, H.B., Bork, P., Wang, J., Vilsbøll, T., Hansen, T., Knop, F.K., Arumugam, M. and Pedersen, O.
Nature Microbiology 3 : 1255-1265. November 2018

Nature Protocols

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen, H.K., Forslund, S.K., Gudmundsdottir, V., Petersen, A.Ø., Hildebrand, F., Hyötyläinen, T., Nielsen, T., Hansen, T., Bork, P., Ehrlich, S.D., Brunak, S., Oresic, M., Pedersen, O. and Nielsen, H.B.
Nature Protocols 13 (12): 2781-2800. December 2018

Nucleic Acids Research

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S., Smyshlyaev, G., Letunic, I., Maistrenko, O.M., Coelho, L.P., Orakov, A., Forslund, S.K., Hildebrand, F., Luetge, M., Schmidt, T.S.B., Barabas, O. and Bork, P.
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., Letunic, I., Maistrenko, O.M., Schmidt, T.S.B., Milanese, A., Paoli, L., Hernández-Plaza, A., Orakov, A.N., Forslund, S.K., Sunagawa, S., Zeller, G., Huerta-Cepas, J., Coelho, L.P. and Bork, P.
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., Cook, H., Mende, D.R., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C. and Bork, P.
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., Letunic, I., Huerta-Cepas, J., Li, S.S., Forslund, K., Sunagawa, S. and Bork, P.
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., Cook, H., Heller, D., Walter, M.C., Rattei, T., Mende, D.R., Sunagawa, S., Kuhn, M., Jensen, L.J., von Mering, C. and Bork, P.
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., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., Kuhn, M., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 43 (D1): D447-D452. January 2015

eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J., von Mering, C. and Bork, P.
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., 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., 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., 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., 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., Jagemann, B., Makarova, N., Börschel, C.S., Aarabi, G., Gutmann, F., Schnabel, R.B. and Zyriax, B.C.
Nutrients 14 (17): 3615. 1 September 2022

Increased salt intake decreases diet-induced thermogenesis in healthy volunteers: a randomized placebo-controlled study.
Mähler, A., Klamer, S., Maifeld, A., Bartolomaeus, H., Markó, L., Chen, C.Y., Forslund, S.K., Boschmann, M., Müller, D.N. and Wilck, N.
Nutrients 14 (2): 253. 7 January 2022

Gut microbiome composition in obese and non-obese persons: a systematic review and meta-analysis.
Pinart, M., Dötsch, A., Schlicht, K., Laudes, M., Bouwman, J., Forslund, S.K., Pischon, T. and Nimptsch, K.
Nutrients 14 (1): 12. 1 January 2022

Identification and characterization of human observational studies in nutritional epidemiology on gut microbiomics for joint data analysis.
Pinart, M., Nimptsch, K., Forslund, S.K., Schlicht, K., Gueimonde, M., Brigidi, P., Turroni, S., Ahrens, W., Hebestreit, A., Wolters, M., Dötsch, A., Nöthlings, U., Oluwagbemigun, K., Cuadrat, R.R.C., Schulze, M.B., Standl, M., Schloter, M., De Angelis, M., Iozzo, P., Guzzardi, M.A., Vlaemynck, G., Penders, J., Jonkers, D.M.A.E., Stemmer, M., Chiesa, G., Cavalieri, D., De Filippo, C., Ercolini, D., De Filippis, F., Ribet, D., Achamrah, N., Tavolacci, M.P., Déchelotte, P., Bouwman, J., Laudes, M. and Pischon, T.
Nutrients 13 (9): 3292. September 2021

Protein intake, metabolic status and the gut microbiota in different ethnicities: results from two independent cohorts.
Bel Lassen, P., Attaye, I., Adriouch, S., Nicolaou, M., Aron-Wisnewsky, J., Nielsen, T., Chakaroun, R., Le Chatelier, E., Forslund, S., Belda, E., Bork, P., Bäckhed, F., Stumvoll, M., Pedersen, O., Herrema, H., Groen, A., Pinto-Sietsma, S.J., Zwinderman, A., Nieuwdorp, M. and Clement, K.
Nutrients 13 (9): 3159. September 2021

PLoS ONE

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.
Trachana, K., Forslund, K., Larsson, T., Powell, S., Doerks, T., von Mering, C. and Bork, P.
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.
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. 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., Heitlinger, E. and Jarquín-Díaz, V.H.
Parasitology Research 123 (6): 237. June 2024

Pharmacological Research

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., Mahdavi-Roshan, M., Bartolomaeus, T.U.P., Kazemi, A., Shoaibinobarian, N. and Forslund, S.K.
Pharmacological Research 187 : 106614. January 2023

Phenomics

Human gut microbiome researches over the last decade: current challenges and future directions.
Wu, H., Forslund, S., Wang, Z. and Zhao, G.
Phenomics 23 October 2023 (In Press)

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., 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

A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea.
Mottaghinia, S., Stenzel, S., Tsangaras, K., Nikolaidis, N., Laue, M., Müller, K., Hölscher, H., Löber, U., McEwen, G.K., Donnellan, S.C., Rowe, K.C., Aplin, K.P., Goffinet, C. and Greenwood, A.D.
Proceedings of the National Academy of Sciences of the United States of America 121 (6): e2220392121. 1 February 2024

Enhanced Ca(2+) signaling, mild primary aldosteronism, and hypertension in a familial hyperaldosteronism mouse model (Cacna1h(M1560V/+)).
Seidel, E., Schewe, J., Zhang, J., Dinh, H.A., Forslund, S.K., Markó, L., Hellmig, N., Peters, J., Muller, D.N., Lifton, R.P., Nottoli, T., Stölting, G. and Scholl, U.I.
Proceedings of the National Academy of Sciences of the United States of America 118 (17): e2014876118. 27 April 2021

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., 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

Role of TRPC6 in kidney damage after acute ischemic kidney injury.
Zheng, Z., Tsvetkov, D., Bartolomaeus, T.U.P., Erdogan, C., Krügel, U., Schleifenbaum, J., Schaefer, M., Nürnberg, B., Chai, X., Ludwig, F.A., N'diaye, G., Köhler, M.B., Wu, K., Gollasch, M. and Markó, L.
Scientific Reports 12 (1): 3038. 22 February 2022

TheScienceBreaker

Studies of the bugs within: telling sickness from cure.
Forslund, S.K. 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., Marko, L., Jakobs, K., Leistner, D.M., Rauch-Kröhnert, U., Kränkel, N., Forslund, S.K., Landmesser, U., Müller, D.N. and Haghikia, A.
Thrombosis and Haemostasis 6 November 2023 (In Press)

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., Meixner, L., Heller, S., Dölle-Bierke, S., Roll, S., Tissen-Diabaté, T., Lau, S., Forslund, S., Marenholz, I., Lee, Y.A., 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., Meixner, L., Heller, S., Lau, S., Lee, Y.A., Fauchère, F., Braun, J., Babina, M., Altrichter, S., Birkner, T., Roll, S., Dobbertin-Welsch, J., Worm, M. and Beyer, K.
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., Fauchère, F., Braun, J., Babina, M., Altrichter, S., Birkner, T., Worm, M. and Beyer, K.
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., Nazari-Shafti, T.Z., Neuber, S., Meyborg, H., Krüger, K., Forslund, S.K., Müller, D.N., Falk, V., Emmert, M.Y. and Rodriguez, H.
Zeitschrift fuer Herz-, Thorax- und Gefaesschirurgie December 2023

bioRxiv

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M., Pascual-Leone, B.M., Löber, U., Kuhring, M., Zhang, B., Bruening, U., Fritsche-Guenther, R., Krzanowski, M., Vernengo, F.F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thiebeault, C., Corman, V., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 December 2022

Host genetic and environmental factors shape the human gut resistome.
Le Roy, C.I., Bowyer, R.C.E., Carr, V.R., Costeira, R., Castillo-Fernandez, J.E.R., Martin, T.C., Spector, T., Steves, C., Moyes, D., Forslund, S.K. and Bell, J.T.
bioRxiv : 2020.05.18.092973. 20 May 2020

Microbiome determinants and physiological effects of the benzoate-hippurate microbial-host co-metabolic pathway.
Brial, F., Chilloux, J., Nielsen, T., Vieira-Silva, S., Falony, G., Hoyles, L., Neves, A.L., Rodriguez-Martinez, A., Mouawad, G.I., Pons, N., Forslund, S., Le Chatelier, E., Le Lay, A.M., Nicholson, J.K., Hansen, T., Clément, K., Bork, P., Ehrlich, S.D., Raes, J., Pedersen, O., Gauguier, D. and Dumas, M.E.
bioRxiv : 2019.12.15.876672. 16 December 2019

mSphere

Meconium microbiome of very preterm infants across Germany.
Klopp, J., Ferretti, P., Meyer, C.U., Hilbert, K., Haiß, A., Marißen, J., Henneke, P., Hudalla, H., Pirr, S., Viemann, D., Zemlin, M., Forslund, S.K., Härtel, C., Bork, P., Gehring, S. and Van Rossum, T.
mSphere 7 (1): e0080821. 23 February 2022