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Items: 1 to 50 of 101

1.

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O.

Cell. 2018 Mar 22;173(1):208-220.e20. doi: 10.1016/j.cell.2018.02.032. Epub 2018 Mar 15.

2.

Subspecies in the global human gut microbiome.

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P.

Mol Syst Biol. 2017 Dec 14;13(12):960. doi: 10.15252/msb.20177589.

3.

Salt-responsive gut commensal modulates TH17 axis and disease.

Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN.

Nature. 2017 Nov 30;551(7682):585-589. doi: 10.1038/nature24628. Epub 2017 Nov 15.

4.

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 JT; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S.

Bioinformatics. 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]

5.

Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O.

Nature. 2017 May 3;545(7652):116. doi: 10.1038/nature22318. No abstract available.

PMID:
28470190
6.

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P.

Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. doi: 10.1093/molbev/msx148.

7.

RTK: efficient rarefaction analysis of large datasets.

Saary P, Forslund K, Bork P, Hildebrand F.

Bioinformatics. 2017 Aug 15;33(16):2594-2595. doi: 10.1093/bioinformatics/btx206.

8.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534. doi: 10.1093/nar/gkw989. Epub 2016 Oct 24.

9.

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.

Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S.

Am J Physiol Gastrointest Liver Physiol. 2017 Apr 1;312(4):G327-G339. doi: 10.1152/ajpgi.00293.2016. Epub 2016 Dec 30.

10.

Human gut microbes impact host serum metabolome and insulin sensitivity.

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O.

Nature. 2016 Jul 21;535(7612):376-81. Epub 2016 Jul 13.

PMID:
27409811
11.

Benchmarking the next generation of homology inference tools.

Saripella GV, Sonnhammer EL, Forslund K.

Bioinformatics. 2016 Sep 1;32(17):2636-41. doi: 10.1093/bioinformatics/btw305. Epub 2016 Jun 1.

12.

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.

Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183. Epub 2016 Apr 8.

13.

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

14.

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM.

Nat Commun. 2016 Jan 26;7:10410. doi: 10.1038/ncomms10410.

15.

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O.

Nature. 2015 Dec 10;528(7581):262-266. doi: 10.1038/nature15766. Epub 2015 Dec 2. Erratum in: Nature. 2017 May 3;545(7652):116.

16.

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 MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93. doi: 10.1093/nar/gkv1248. Epub 2015 Nov 17.

17.

Ambulance clinicians' experiences of relationships with patients and significant others.

Holmberg M, Wahlberg AC, Fagerberg I, Forslund K.

Nurs Crit Care. 2016 Jul;21(4):e16-23. doi: 10.1111/nicc.12196. Epub 2015 Jul 17.

PMID:
26184114
18.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group.

Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121.

19.

The relationship with the ambulance clinicians as experienced by significant others.

Holmberg M, Forslund K, Wahlberg AC, Fagerberg I.

Nurs Crit Care. 2016 Jul;21(4):e1-8. doi: 10.1111/nicc.12144. Epub 2015 Jan 9.

PMID:
25571767
20.

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, Bork P.

PLoS One. 2014 Nov 4;9(11):e111122. doi: 10.1371/journal.pone.0111122. eCollection 2014.

21.

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 KP, Kuhn M, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003. Epub 2014 Oct 28.

22.

Individuality and temporal stability of the human gut microbiome.

Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, Bork P.

Cent Asian J Glob Health. 2014 Mar 27;2(Suppl):120. doi: 10.5195/cajgh.2013.120. eCollection 2013.

23.

Metagenomic insights into the human gut resistome and the forces that shape it.

Forslund K, Sunagawa S, Coelho LP, Bork P.

Bioessays. 2014 Mar;36(3):316-29. doi: 10.1002/bies.201300143. Epub 2014 Jan 29. Review.

PMID:
24474281
24.

eggNOG v4.0: nested orthology inference across 3686 organisms.

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1.

25.

To surrender in dependence of another: the relationship with the ambulance clinicians as experienced by patients.

Holmberg M, Forslund K, Wahlberg AC, Fagerberg I.

Scand J Caring Sci. 2014 Sep;28(3):544-51. doi: 10.1111/scs.12079. Epub 2013 Sep 20.

PMID:
24067194
26.

[Swedish forensic psychiatry changing. Comprehensive proposal for legislative changes in the Psychiatry Law Inquiry report].

Hedlund J, Kristiansson M, Forslund K.

Lakartidningen. 2013 Jun 18-Jul 2;110(25-26):1223-6. Review. Swedish. No abstract available.

PMID:
23865263
27.

Country-specific antibiotic use practices impact the human gut resistome.

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P.

Genome Res. 2013 Jul;23(7):1163-9. doi: 10.1101/gr.155465.113. Epub 2013 Apr 8.

28.

Biggest challenges in bioinformatics.

Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM; HUB Participants.

EMBO Rep. 2013 Apr;14(4):302-4. doi: 10.1038/embor.2013.34. Epub 2013 Mar 15.

29.

Evolution of protein domain architectures.

Forslund K, Sonnhammer EL.

Methods Mol Biol. 2012;856:187-216. doi: 10.1007/978-1-61779-585-5_8. Review.

PMID:
22399460
30.

How to think about interprofessional competence: a metacognitive model.

Wilhelmsson M, Pelling S, Uhlin L, Owe Dahlgren L, Faresjö T, Forslund K.

J Interprof Care. 2012 Mar;26(2):85-91. doi: 10.3109/13561820.2011.644644. Epub 2012 Jan 11.

PMID:
22236489
31.

The Pfam protein families database.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065. Epub 2011 Nov 29.

32.

Domain architecture conservation in orthologs.

Forslund K, Pekkari I, Sonnhammer EL.

BMC Bioinformatics. 2011 Aug 5;12:326. doi: 10.1186/1471-2105-12-326.

33.

OrthoDisease: tracking disease gene orthologs across 100 species.

Forslund K, Schreiber F, Thanintorn N, Sonnhammer EL.

Brief Bioinform. 2011 Sep;12(5):463-73. doi: 10.1093/bib/bbr024. Epub 2011 May 12. Review.

PMID:
21565935
34.

CSF 5-HIAA and exposure to and expression of interpersonal violence in suicide attempters.

Moberg T, Nordström P, Forslund K, Kristiansson M, Asberg M, Jokinen J.

J Affect Disord. 2011 Jul;132(1-2):173-8. doi: 10.1016/j.jad.2011.01.018. Epub 2011 Feb 26.

PMID:
21356560
35.

Karolinska Interpersonal Violence Scale predicts suicide in suicide attempters.

Jokinen J, Forslund K, Ahnemark E, Gustavsson JP, Nordström P, Asberg M.

J Clin Psychiatry. 2010 Aug;71(8):1025-32. doi: 10.4088/JCP.09m05944blu.

PMID:
20797380
36.

Orthology confers intron position conservation.

Henricson A, Forslund K, Sonnhammer EL.

BMC Genomics. 2010 Jul 2;11:412. doi: 10.1186/1471-2164-11-412.

37.

Low cortisol levels in blood from dairy cows with ketosis: a field study.

Forslund KB, Ljungvall OA, Jones BV.

Acta Vet Scand. 2010 May 20;52:31. doi: 10.1186/1751-0147-52-31.

38.

The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.

39.

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer EL.

Nucleic Acids Res. 2010 Jan;38(Database issue):D196-203. doi: 10.1093/nar/gkp931. Epub 2009 Nov 5.

40.

Benchmarking homology detection procedures with low complexity filters.

Forslund K, Sonnhammer EL.

Bioinformatics. 2009 Oct 1;25(19):2500-5. doi: 10.1093/bioinformatics/btp446. Epub 2009 Jul 20.

PMID:
19620098
41.

Suicide risk after homicide in Sweden.

Jokinen J, Forslund K, Nordström AL, Lindqvist P, Nordström P.

Arch Suicide Res. 2009;13(3):297-301. doi: 10.1080/13811110903044609.

PMID:
19591003
42.

Acute chest pain emergencies - spouses' prehospital experiences.

Forslund K, Quell R, Sørlie V.

Int Emerg Nurs. 2008 Oct;16(4):233-40. doi: 10.1016/j.ienj.2008.07.001. Epub 2008 Aug 28.

PMID:
18929341
43.

An observational study on early-lactation metabolic profiles in Swedish organically and conventionally managed dairy cows.

Fall N, Gröhn YT, Forslund K, Essen-Gustafsson B, Niskanen R, Emanuelson U.

J Dairy Sci. 2008 Oct;91(10):3983-92. doi: 10.3168/jds.2008-1099.

PMID:
18832222
44.

Predicting protein function from domain content.

Forslund K, Sonnhammer EL.

Bioinformatics. 2008 Aug 1;24(15):1681-7. doi: 10.1093/bioinformatics/btn312. Epub 2008 Jun 30. Erratum in: Bioinformatics. 2009 May 1;25(9):1214.

PMID:
18591194
45.

The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8. Epub 2007 Nov 26.

46.

Domain tree-based analysis of protein architecture evolution.

Forslund K, Henricson A, Hollich V, Sonnhammer EL.

Mol Biol Evol. 2008 Feb;25(2):254-64. Epub 2007 Nov 19.

PMID:
18025066
47.

DST non-suppression predicts suicide after attempted suicide.

Jokinen J, Carlborg A, Mårtensson B, Forslund K, Nordström AL, Nordström P.

Psychiatry Res. 2007 Apr 15;150(3):297-303. Epub 2007 Feb 20.

PMID:
17316825
48.

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets.

Grünewald S, Forslund K, Dress A, Moulton V.

Mol Biol Evol. 2007 Feb;24(2):532-8. Epub 2006 Nov 21.

PMID:
17119010
49.

Mastitis and related management factors in certified organic dairy herds in Sweden.

Hamilton C, Emanuelson U, Forslund K, Hansson I, Ekman T.

Acta Vet Scand. 2006 Jul 17;48:11.

50.

Experiences of adding nurses to increase medical competence at an emergency medical dispatch centre.

Forslund K, Kihlgren M, Sorlie V.

Accid Emerg Nurs. 2006 Oct;14(4):230-6. Epub 2006 Sep 1.

PMID:
16949825

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