Browse by Research Team

2023

Mutant phosphodiesterase 3A protects the kidney from hypertension-induced damage.
Sholokh, A. and Walter, S. and Markó, L. and McMurray, B.J. and Sunaga-Franze, D.Y. and Xu, M. and Zühlke, K. and Russwurm, M. and Bartolomaeus, T.U.P. and Langanki, R. and Qadri, F. and Heuser, A. and Patzak, A. and Forslund, S.K. and Bähring, S. and Borodina, T. and Persson, P.B. and Maass, P.G. and Bader, M. and Klussmann, E.
Kidney International 25 May 2023 (In Press)

LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data.
Chen, C.Y. and Löber, U. and Forslund, S.K.
Bioinformatics Advances : vbad063. 18 May 2023 (In Press)

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

Alteration of gut microbiome in patients with schizophrenia indicates links between bacterial tyrosine biosynthesis and cognitive dysfunction.
Thirion, F. and Speyer, H. and Hansen, T.H. and Nielsen, T. and Fan, Y. and Le Chatelier, E. and Fromentin, S. and Berland, M. and Oñate, F.P. and Pons, N. and Galleron, N. and Levenez, F. and Markó, L. and Birkner, T. and Jørgensen, T. and Forslund, S.K. and Vestergaard, H. and Hansen, T. and Nordentoft, M. and Mors, O. and Benros, M.E. and Pedersen, O. and Ehrlich, S.D.
Biological Psychiatry Global Open Science 3 (2): 283-291. April 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. and Kazemi, A. and Bartolomaeus, T.U.P. and Martami, F. and Noormohammadi, M. and Salari, A. and Löber, U. and Balou, H.A. and Forslund, S.K. and Mahdavi-Roshan, M.
Cardiovascular Research 119 (4): 933-956. April 2023

VEGF-B hypertrophy predisposes to transition from diastolic to systolic heart failure in hypertensive rats.
Samuelsson, A.M. and Bartolomaeus, T.U.P. and Anandakumar, H. and Thowsen, I. and Nikpey, E. and Han, J. and Marko, L. and Finne, K. and Tenstad, O. and Eckstein, J. and Berndt, N. and Kühne, T. and Kedziora, S. and Sultan, I. and Skogstrand, T. and Karlsen, T.V. and Nurmi, H. and Forslund, S.K. and Bollano, E. and Alitalo, K. and Muller, D.N. and Wiig, H.
Cardiovascular research 23 March 2023 (In Press)

Resilience and stability of the CF- intestinal and respiratory microbiome during nutritional and exercise intervention.
Knoll, R.L. and Jarquín-Díaz, V.H. and Klopp, J. and Kemper, A. and Hilbert, K. and Hillen, B. and Pfirrmann, D. and Simon, P. and Bähner, V. and Nitsche, O. and Gehring, S. and Markó, L. and Forslund, S.K. and Poplawska, K.
BMC Microbiology 23 (1): 44. 21 February 2023

Sputum microbiome and chronic obstructive pulmonary disease in a rural Ugandan cohort of well-controlled HIV infection.
Kayongo, A. and Bartolomaeus, T.U.P. and Birkner, T. and Markó, L. and Löber, U. and Kigozi, E. and Atugonza, C. and Munana, R. and Mawanda, D. and Sekibira, R. and Uwimaana, E. and Alupo, P. and Kalyesubula, R. and Knauf, F. and Siddharthan, T. and Bagaya, B.S. and Kateete, D.P. and Joloba, M.L. and Sewankambo, N.K. and Jjingo, D. and Kirenga, B. and Checkley, W. and Forslund, S.K.
Microbiology Spectrum : e0213921. 15 February 2023 (In Press)

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

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

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

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

2022

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host.
Midha, A. and Jarquín-Díaz, V.H. and Ebner, F. and Löber, U. and Hayani, R. and Kundik, A. and Cardilli, A. and Heitlinger, E. and Forslund, S.K. and Hartmann, S.
Microbiome 10 (1): 229. 16 December 2022

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

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

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.
Belda, E. and Voland, L. and Tremaroli, V. and Falony, G. and Adriouch, S. and Assmann, K.E. and Prifiti, E. and Aron-Wisnewsky, J. and Debédat, J. and Le Roy, T. and Nielsen, T. and Amouyal, C. and André, S. and Andreelli, F. and Blüher, M. and Chakaroun, R. and Chilloux, J. and Coelho, L.P. and Dao, M.C. and Das, P. and Fellahi, S. and Forslund, S. and Galleron, N. and Hansen, T.H. and Holmes, B. and Ji, B. and Krogh Pedersen, H. and Le, P. and Le Chatelier, E. and Lewinter, C. and Mannerås-Holm, L. and Marquet, F. and Myridakis, A. and Pelloux, V. and Pons, N. and Quinquis, B. and Rouault, C. and Roume, H. and Salem, J.E. and Sokolovska, N. and Søndertoft, N.B. and Touch, S. and Vieira-Silva, S. and Galan, P. and Holst, J. and Gøtze, J.P. and Køber, L. and Vestergaard, H. and Hansen, T. and Hercberg, S. and Oppert, J.M. and Nielsen, J. and Letunic, I. and Dumas, M.E. and Stumvoll, M. and Pedersen, O.B. and Bork, P. and Ehrlich, S.D. and Zucker, J.D. and Bäckhed, F. and Raes, J. and Clément, K.
Gut 71 (12): 2463-2480. 7 November 2022

Antibiotic resistance genes in river biofilms: a metagenomic approach toward the identification of sources and candidate hosts.
Kneis, D. and Berendonk, T.U. and Forslund, S.K. and Hess, S.
Environmental Science and Technology 56 (21): 14913-14922. 1 November 2022

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

Mediterranean diet and atrial fibrillation: lessons learned from the AFHRI case-control study.
Neumann, F.A. and Jagemann, B. and Makarova, N. and Börschel, C.S. and Aarabi, G. and Gutmann, F. and Schnabel, R.B. and Zyriax, B.C.
Nutrients 14 (17): 3615. 1 September 2022

Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems.
Seeber, P.A. and Hippel, B. and Kauserud, H. and Löber, U. and Stoof‐Leichsenring, K.R. and Herzschuh, U. and Epp, L.S.
Environmental DNA 4 (5): 1150-1163. September 2022

Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage.
Avery, E.G. and Bartolomaeus, H. and Rauch, A. and Chen, C.Y. and N'Diaye, G. and Löber, U. and Bartolomaeus, T.U.P. and Fritsche-Guenther, R. and Rodrigues, A.F. and Yarritu, A. and Zhong, C. and Fei, L. and Tsvetkov, D. and Todiras, M. and Park, J.K. and Markó, L. and Maifeld, A. and Patzak, A. and Bader, M. and Kempa, S. and Kirwan, J.A. and Forslund, S.K. and Müller, D.N. and Wilck, N.
Cardiovascular Research : cvac121. 29 July 2022 (In Press)

In vivo inhibition of TRPC6 by SH045 attenuates renal fibrosis in a New Zealand Obese (NZO) mouse model of metabolic syndrome.
Zheng, Z. and Xu, Y. and Krügel, U. and Schaefer, M. and Grune, T. and Nürnberg, B. and Köhler, M.B. and Gollasch, M. and Tsvetkov, D. and Marko, L.
International Journal of Molecular Sciences 23 (12): 6870. 20 June 2022

A comparison of solvent-based extraction methods to assess the central carbon metabolites in mouse bone and muscle.
Dias, D.B. and Fritsche-Guenther, R. and Gutmann, F. and Duda, G.N. and Kirwan, J. and Poh, P.S.P.
Metabolites 12 (5): 453. 18 May 2022

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

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S. and Smyshlyaev, G. and Letunic, I. and Maistrenko, O.M. and Coelho, L.P. and Orakov, A. and Forslund, S.K. and Hildebrand, F. and Luetge, M. and Schmidt, T.S.B. and Barabas, O. and Bork, P.
Nucleic Acids Research 50 (6): 3155-3168. 8 April 2022

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. and Dölle-Bierke, S. and Unterleider, N. and Alexiou, A. and Kalb, B. and Meixner, L. and Heller, S. and Lau, S. and Lee, Y.A. and Fauchère, F. and Braun, J. and Babina, M. and Altrichter, S. and Birkner, T. and Roll, S. and Dobbertin-Welsch, J. and 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. and Meixner, L. and Trendelenburg, V. and Unterleider, N. and Dobbertin-Welsch, J. and Heller, S. and Dölle-Bierke, S. and Roll, S. and Lau, S. and Lee, Y.A. and Fauchère, F. and Braun, J. and Babina, M. and Altrichter, S. and Birkner, T. and Worm, M. and Beyer, K.
Trials 23 (1): 210. 12 March 2022

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

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

Microbiome and metabolome features of the cardiometabolic disease spectrum.
Fromentin, S. and Forslund, S.K. and Chechi, K. and Aron-Wisnewsky, J. and Chakaroun, R. and Nielsen, T. and Tremaroli, V. and Ji, B. and Prifti, E. and Myridakis, A. and Chilloux, J. and Andrikopoulos, P. and Fan, Y. and Olanipekun, M.T. and Alves, R. and Adiouch, S. and Bar, N. and Talmor-Barkan, Y. and Belda, E. and Caesar, R. and Coelho, L.P. and Falony, G. and Fellahi, S. and Galan, P. and Galleron, N. and Helft, G. and Hoyles, L. and Isnard, R. and Le Chatelier, E. and Julienne, H. and Olsson, L. and Pedersen, H.K. and Pons, N. and Quinquis, B. and Rouault, C. and Roume, H. and Salem, J.E. and Schmidt, T.S.B. and Vieira-Silva, S. and Li, P. and Zimmermann-Kogadeeva, M. and Lewinter, C. and Søndertoft, N.B. and Hansen, T.H. and Gauguier, D. and Gøtze, J.P. and Køber, L. and Kornowski, R. and Vestergaard, H. and Hansen, T. and Zucker, J.D. and Hercberg, S. and Letunic, I. and Bäckhed, F. and Oppert, J.M. and Nielsen, J. and Raes, J. and Bork, P. and Stumvoll, M. and Segal, E. and Clément, K. and Dumas, M.E. and 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. and Bar, N. and Shaul, A.A. and Shahaf, N. and Godneva, A. and Bussi, Y. and Lotan-Pompan, M. and Weinberger, A. and Shechter, A. and Chezar-Azerrad, C. and Arow, Z. and Hammer, Y. and Chechi, K. and Forslund, S.K. and Fromentin, S. and Dumas, M.E. and Ehrlich, S.D. and Pedersen, O. and Kornowski, R. and Segal, E.
Nature Medicine 28 (2): 295-302. February 2022

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

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

The gut microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS).
König, R.S. and Albrich, W.C. and Kahlert, C.R. and Bahr, L.S. and Löber, U. and Vernazza, P. and Scheibenbogen, C. and Forslund, S.K.
Frontiers in Immunology 12 : 628741. 3 January 2022

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

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

2021

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

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

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

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

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

Identification and characterization of human observational studies in nutritional epidemiology on gut microbiomics for joint data analysis.
Pinart, M. and Nimptsch, K. and Forslund, S.K. and Schlicht, K. and Gueimonde, M. and Brigidi, P. and Turroni, S. and Ahrens, W. and Hebestreit, A. and Wolters, M. and Dötsch, A. and Nöthlings, U. and Oluwagbemigun, K. and Cuadrat, R.R.C. and Schulze, M.B. and Standl, M. and Schloter, M. and De Angelis, M. and Iozzo, P. and Guzzardi, M.A. and Vlaemynck, G. and Penders, J. and Jonkers, D.M.A.E. and Stemmer, M. and Chiesa, G. and Cavalieri, D. and De Filippo, C. and Ercolini, D. and De Filippis, F. and Ribet, D. and Achamrah, N. and Tavolacci, M.P. and Déchelotte, P. and Bouwman, J. and 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. and Attaye, I. and Adriouch, S. and Nicolaou, M. and Aron-Wisnewsky, J. and Nielsen, T. and Chakaroun, R. and Le Chatelier, E. and Forslund, S. and Belda, E. and Bork, P. and Bäckhed, F. and Stumvoll, M. and Pedersen, O. and Herrema, H. and Groen, A. and Pinto-Sietsma, S.J. and Zwinderman, A. and Nieuwdorp, M. and Clement, K.
Nutrients 13 (9): 3159. September 2021

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

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

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

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

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. and Löber, U. and Adamek, K. and Węgrzyn, D. and Skonieczna-Żydecka, K. and Malinowski, D. and Łoniewski, I. and Markó, L. and Ulas, T. and Forslund, S.K. and Łoniewska, B.
Journal of Translational Medicine 19 (1): 177. 28 April 2021

Enhanced Ca(2+) signaling, mild primary aldosteronism, and hypertension in a familial hyperaldosteronism mouse model (Cacna1h(M1560V/+)).
Seidel, E. and Schewe, J. and Zhang, J. and Dinh, H.A. and Forslund, S.K. and Markó, L. and Hellmig, N. and Peters, J. and Muller, D.N. and Lifton, R.P. and Nottoli, T. and 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

Dynamic changes in microbiome composition following Mare's milk intake for prevention of collateral antibiotic effect.
Kushugulova, A. and Löber, U. and Akpanova, S. and Rysbekov, K. and Kozhakhmetov, S. and Khassenbekova, Z. and Essex, M. and Nurgozhina, A. and Nurgaziyev, M. and Babenko, D. and Markó, L. and Forslund, S.K.
Frontiers in Cellular and Infection Microbiology 11 : 622735. 21 April 2021

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

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

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

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate.
Gutmann, F. and Jann, C. and Pereira, F. and Johansson, A. and Steinmetz, L.M. and Patil, K.R.
Biotechnology for Biofuels 14 (1): 41. 10 February 2021

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. and Löber, U. and Adamek, K. and Węgrzyn, D. and Skonieczna-Żydecka, K. and Malinowski, D. and Łoniewski, I. and Markó, L. and Ulas, T. and Forslund, S.K. and Łoniewska, B.
Research Square : rs.3.rs-154335/v1. 29 January 2021

2020

S100A8 and S100A9 are important for postnatal development of gut microbiota and immune system in mice and infants.
Willers, M. and Ulas, T. and Völlger, L. and Vogl, T. and Heinemann, A.S. and Pirr, S. and Pagel, J. and Fehlhaber, B. and Halle, O. and Schöning, J. and Schreek, S. and Löber, U. and Essex, M. and Hombach, P. and Graspeuntner, S. and Basic, M. and Bleich, A. and Cloppenborg-Schmidt, K. and Künzel, S. and Jonigk, D. and Rupp, J. and Hansen, G. and Förster, R. and Baines, J.F. and Härtel, C. and Schultze, J.L. and Forslund, S.K. and Roth, J. and Viemann, D.
Gastroenterology 159 (6): 2130-2145. December 2020

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

DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences.
Alquezar‐Planas, D.E. and Löber, U. and Cui, P. and Quedenau, C. and Chen, W. and Greenwood, A.D.
Methods in Ecology and Evolution 22 September 2020

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. and Richardson, L.S. and Boniface, J.J. and Cobo, T. and Exner, M.M. and Christensen, I.B. and Forslund, S.K. and Gaba, A. and Helmer, H. and Jørgensen, J.S. and Khan, R.N. and McElrath, T.F. and Petro, K. and Rasmussen, M. and Singh, R. and Tribe, R.M. and Vink, J.S. and Vinter, C.A. and Zhong, N. and Menon, R.
Placenta 98 : 13-23. 1 September 2020

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

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

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

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

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

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

Hitchhiker's guide to microbiome studies.
Bartolomaeus, T.U.P. and Forslund, S.K.
Cardiovascular Research 116 (3): e44-e47. 1 March 2020

Fasting alters the gut microbiome with sustained blood pressure and body weight reduction in metabolic syndrome patients.
Balogh, A. and Bartolomaeus, H. and Löber, U. and Avery, E.G. and Steckhan, N. and Markó, L. and Wilck, N. and Hamad, I. and Šušnjar, U. and Mähler, A. and Hohmann, C. and Cramer, H. and Dobos, G. and Lesker, T.R. and Strowig, T. and Dechend, R. and Bzdok, D. and Kleinewietfeld, M. and Michalsen, A. and Müller, D.N. and Forslund, S.K.
medRxiv : 2020.02.23.20027029. 25 February 2020

Dissecting the collateral damage of antibiotics on gut microbes.
Maier, L. and Goemans, C.V. and Pruteanu, M. and Wirbel, J. and Kuhn, M. and Cacace, E. and Banerjee, T. and Anderson, E.E. and Milanese, A. and Löber, U. and Forslund, S.K. and Patil, K.R. and Zeller, G. and Bork, P. and Typas, A.
bioRxiv : 2020.01.09.893560. 9 January 2020

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende, D.R. and Letunic, I. and Maistrenko, O.M. and Schmidt, T.S.B. and Milanese, A. and Paoli, L. and Hernández-Plaza, A. and Orakov, A.N. and Forslund, S.K. and Sunagawa, S. and Zeller, G. and Huerta-Cepas, J. and Coelho, L.P. and Bork, P.
Nucleic Acids Research 48 (D1): D621-D625. 8 January 2020

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

2019

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

Elevated aldosterone and blood pressure in a mouse model of familial hyperaldosteronism with ClC-2 mutation.
Schewe, J. and Seidel, E. and Forslund, S. and Marko, L. and Peters, J. and Muller, D.N. and Fahlke, C. and Stölting, G. and Scholl, U.
Nature Communications 10 (1): 5155. 14 November 2019

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes.
Seeber, P.A. and McEwen, G.K. and Löber, U. and Förster, D.W. and East, M.L. and Melzheimer, J. and Greenwood, A.D.
Molecular Ecology Resources 19 (6): 1486-1496. November 2019

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

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

Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand, F. and Moitinho-Silva, L. and Blasche, S. and Jahn, M.T.T. and Gossmann, T.I. and Heuerta Cepas, J. and Hercog, R. and Luetge, M. and Bahram, M. and Pryszlak, A. and Alves, R.J. and Waszak, S.M. and Zhu, A. and Ye, L. and Costea, P.I. and Aalvink, S. and Belzer, C. and Forslund, S.K. and Sunagawa, S. and Hentschel, U. and Merten, C. and Patil, K.R. and Benes, V. and Bork, P.
Gut 68 (10): 1781-1790. 9 September 2019

Precarious symbiosis between host and microbiome in cardiovascular health.
Bartolomaeus, H. and Markó, L. and Wilck, N. and Luft, F.C. and Forslund, S.K. and Muller, D.N.
Hypertension 73 (5): 926-935. May 2019

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

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J. and Szklarczyk, D. and Heller, D. and Hernández-Plaza, A. and Forslund, S.K. and Cook, H. and Mende, D.R. and Letunic, I. and Rattei, T. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 47 (D1): D309-D314. 8 January 2019

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

2018

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

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

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

The gut microbiome is associated with behavioural task in honey bees.
Jones, J.C. and Fruciano, C. and Marchant, J. and Hildebrand, F. and Forslund, S. and Bork, P. and Engel, P. and Hughes, W.O.H.
Insectes Sociaux 65 (3): 419-429. August 2018

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

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

Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho, L.P. and Kultima, J.R. and Costea, P.I. and Fournier, C. and Pan, Y. and Czarnecki-Maulden, G. and Hayward, M.R. and Forslund, S.K. and Schmidt, T.S.B. and Descombes, P. and Jackson, J.R. and Li, Q. and Bork, P.
Microbiome 6 (1): 72. 19 April 2018

Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance.
Rubio-Cosials, A. and Schulz, E.C. and Lambertsen, L. and Smyshlyaev, G. and Rojas-Cordova, C. and Forslund, K. and Karaca, E. and Bebel, A. and Bork, P. and Barabas, O.
Cell 173 (1): 208-220. 22 March 2018

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

2017

Subspecies in the global human gut microbiome.
Costea, P.I. and Coelho, L.P. and Sunagawa, S. and Munch, R. and Huerta-Cepas, J. and Forslund, K. and Hildebrand, F. and Kushugulova, A. and Zeller, G. and Bork, P.
Molecular Systems Biology 13 (12): 960. 14 December 2017

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

RTK: efficient rarefaction analysis of large datasets.
Saary, P. and Forslund, K. and Bork, P. and Hildebrand, F.
Bioinformatics 33 (16): 2594-2595. 15 August 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. and Forslund, K. and Coelho, L.P. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P.
Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017

Gut microbiota differs between children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.
Knoll, R.L. and Forslund, K. and Kultima, J.R. and Meyer, C.U. and Kullmer, U. and Sunagawa, S. and Bork, P. and Gehring, S.
American Journal of Physiology Gastrointestinal and Liver Physiology 312 (4): G327-G339. 1 April 2017

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende, D.R. and Letunic, I. and Huerta-Cepas, J. and Li, S.S. and Forslund, K. and Sunagawa, S. and Bork, P.
Nucleic Acids Research 45 (D1): D529-D534. 4 January 2017

2016

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. and Forslund, K. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P.
bioRxiv : 076331. 22 September 2016

Benchmarking the next generation of homology inference tools.
Saripella, G.V. and 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. and Coelho, L.P. and Forslund, K. and Huerta-Cepas, J. and Li, S.S. and Driessen, M. and Voigt, A.Y. and Zeller, G. and Sunagawa, S. and Bork, P.
Bioinformatics 32 (16): 2520-2523. 15 August 2016

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

Standardized benchmarking in the quest for orthologs.
Altenhoff, A.M. and Boeckmann, B. and Capella-Gutierrez, S. and Dalquen, D.A. and DeLuca, T. and Forslund, K. and Huerta-Cepas, J. and Linard, B. and Pereira, C. and Pryszcz, L.P. and Schreiber, F. and da Silva, A.S. and Szklarczyk, D. and Train, C.M. and Bork, P. and Lecompte, O. and von Mering, C. and Xenarios, I. and Sjölander, K. and Jensen, L.J. and Martin, M.J. and Muffato, M. and Gabaldón, T. and Lewis, S.E. and Thomas, P.D. and Sonnhammer, E. and Dessimoz, C.
Nature Methods 13 (5): 425-430. May 2016

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.
Korpela, K. and Salonen, A. and Virta, L.J. and Kekkonen, R.A. and Forslund, K. and Bork, P. and de Vos, W.M.
Nature Communications 7 : 10410. 26 January 2016

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas, J. and Szklarczyk, D. and Forslund, K. and Cook, H. and Heller, D. and Walter, M.C. and Rattei, T. and Mende, D.R. and Sunagawa, S. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 44 (D1): D286-D293. 4 January 2016

2015

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

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

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk, D. and Franceschini, A. and Wyder, S. and Forslund, K. and Heller, D. and Huerta-Cepas, J. and Simonovic, M. and Roth, A. and Santos, A. and Tsafou, K.P. and Kuhn, M. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 43 (D1): D447-D452. January 2015

2014

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.
Trachana, K. and Forslund, K. and Larsson, T. and Powell, S. and Doerks, T. and von Mering, C. and Bork, P.
PLoS ONE 9 (11): e111122. 4 November 2014

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

eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell, S. and Forslund, K. and Szklarczyk, D. and Trachana, K. and Roth, A. and Huerta-Cepas, J. and Gabaldon, T. and Rattei, T. and Creevey, C. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 42 (1): D231-D239. 1 January 2014

2013

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

Biggest challenges in bioinformatics.
Fuller, J.C. and Khoueiry, P. and Dinkel, H. and Forslund, K. and Stamatakis, A. and Barry, J. and Budd, A. and Soldatos, T.G. and Linssen, K. and Rajput, A.M.
EMBO Reports 14 (4): 302-304. 1 April 2013

2012

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

Evolution of protein domain architectures.
Forslund, K. and Sonnhammer, E.L.L.
Methods in Molecular Biology 856 : 187-216. 2012

2011

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

Domain architecture conservation in orthologs.
Forslund, K. and Pekkari, I. and Sonnhammer, E.L.L.
BMC Bioinformatics 12 : 326. 5 August 2011

2010

Orthology confers intron position conservation.
Henricson, A. and Forslund, K. and Sonnhammer, E.L.L.
BMC Genomics 11 : 412. 2 July 2010

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
Ostlund, G. and Schmitt, T. and Forslund, K. and Köstler, T. and Messina, D.N. and Roopra, S. and 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. and Mistry, J. and Tate, J. and Coggill, P. and Heger, A. and Pollington, J.E. and Gavin, O.L. and Gunasekaran, P. and Ceric, G. and Forslund, K. and Holm, L. and Sonnhammer, E.L.L. and Eddy, S.R. and Bateman, A.
Nucleic Acids Research 38 (Suppl 1): D211-D222. 1 January 2010

2009

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

2008

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

Domain tree-based analysis of protein architecture evolution.
Forslund, K. and Henricson, A. and Hollich, V. and Sonnhammer, E.L.L.
Molecular Biology and Evolution 25 (2): 254-264. 1 February 2008

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

Constructing phylogenetic supernetworks from quartets.
Grünewald, S. and Spillner, A. and Forslund, K. and Moulton, V.
Lecture Notes in Computer Science 5251 : 284-295. 2008

2007

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

2004

VisRD-visual recombination detection.
Forslund, K. and Huson, D.H. and Moulton, V.
Bioinformatics 20 (18): 3654-3655. 12 December 2004

2003

A novel exploratory method for visual recombination detection.
Strimmer, K. and Forslund, K. and Holland, B. and Moulton, V.
Genome Biology 4 (5): R33. 2003