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Article

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

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 : gkz1002. 24 October 2019 (In Press)

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

B-cell lymphoma/leukemia 10 (Bcl10) 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 26 June 2019 (In Press)

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

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

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 5 November 2018 (In Press)

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

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

Benchmarking the next generation of homology inference tools.
Saripella, G.V.a 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

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

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

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

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

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

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

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

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

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

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

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

Review

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

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

Editorial

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

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

Preprint

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

This list was generated on Sun Dec 15 02:21:19 2019 CET.
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