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Items: 1 to 50 of 326

1.

A Brief History of Protein Sorting Prediction.

Nielsen H, Tsirigos KD, Brunak S, von Heijne G.

Protein J. 2019 May 22. doi: 10.1007/s10930-019-09838-3. [Epub ahead of print] Review.

PMID:
31119599
2.

Bifidobacterium breve Bif195 Protects Against Small-intestinal Damage Caused by Acetylsalicylic Acid in Healthy Volunteers.

Mortensen B, Murphy C, O'Grady J, Lucey M, Elsafi G, Barry L, Westphal V, Wellejus A, Lukjancenko O, Eklund AC, Nielsen HB, Baker A, Damholt A, van Hylckama Vlieg JET, Shanahan F, Buckley M.

Gastroenterology. 2019 May 13. pii: S0016-5085(19)40880-9. doi: 10.1053/j.gastro.2019.05.008. [Epub ahead of print]

3.

Seroprevalence of Toxoplasma gondii in domestic pigs, sheep, cattle, wild boars, and moose in the Nordic-Baltic region: A systematic review and meta-analysis.

Olsen A, Berg R, Tagel M, Must K, Deksne G, Enemark HL, Alban L, Johansen MV, Nielsen HV, Sandberg M, Lundén A, Stensvold CR, Pires SM, Jokelainen P.

Parasite Epidemiol Control. 2019 Mar 4;5:e00100. doi: 10.1016/j.parepi.2019.e00100. eCollection 2019 May. Review.

4.

Risk of inflammatory bowel disease after Campylobacter jejuni and Campylobacter concisus infection: a population-based cohort study.

Nielsen HL, Dalager-Pedersen M, Nielsen H.

Scand J Gastroenterol. 2019 Mar;54(3):265-272. doi: 10.1080/00365521.2019.1578406. Epub 2019 Mar 24.

PMID:
30905214
5.

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.

Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sønderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcatili P.

Proteins. 2019 Jun;87(6):520-527. doi: 10.1002/prot.25674. Epub 2019 Mar 9.

PMID:
30785653
6.

SignalP 5.0 improves signal peptide predictions using deep neural networks.

Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H.

Nat Biotechnol. 2019 Apr;37(4):420-423. doi: 10.1038/s41587-019-0036-z. Epub 2019 Feb 18.

PMID:
30778233
7.

Valaciclovir therapy for herpes encephalitis: caution advised.

Bodilsen J, Nielsen H, Whitley RJ.

J Antimicrob Chemother. 2019 Jun 1;74(6):1467-1468. doi: 10.1093/jac/dky568.

PMID:
30668736
8.

SIRT7-Dependent Deacetylation of Fibrillarin Controls Histone H2A Methylation and rRNA Synthesis during the Cell Cycle.

Iyer-Bierhoff A, Krogh N, Tessarz P, Ruppert T, Nielsen H, Grummt I.

Cell Rep. 2018 Dec 11;25(11):2946-2954.e5. doi: 10.1016/j.celrep.2018.11.051.

9.

Predicting eukaryotic protein secretion without signals.

Nielsen H, Petsalaki EI, Zhao L, Stühler K.

Biochim Biophys Acta Proteins Proteom. 2018 Dec 4. pii: S1570-9639(18)30209-7. doi: 10.1016/j.bbapap.2018.11.011. [Epub ahead of print] Review.

PMID:
30529297
10.

Sequencing-based methods for detection and quantitation of ribose methylations in RNA.

Krogh N, Nielsen H.

Methods. 2019 Mar 1;156:5-15. doi: 10.1016/j.ymeth.2018.11.017. Epub 2018 Nov 29. Review.

PMID:
30503826
11.

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.

Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB.

Nat Protoc. 2018 Dec;13(12):2781-2800. doi: 10.1038/s41596-018-0064-z.

PMID:
30382244
12.

Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment.

Andersen KL, Nielsen H.

Biomolecules. 2018 Oct 30;8(4). pii: E128. doi: 10.3390/biom8040128.

13.

Positive predictive value of ICD-10 diagnosis codes for brain abscess in the Danish National Patient Registry.

Bodilsen J, Dalager-Pedersen M, Kjærgaard N, van de Beek D, Brouwer MC, Nielsen H.

Clin Epidemiol. 2018 Oct 12;10:1503-1508. doi: 10.2147/CLEP.S176072. eCollection 2018.

14.

Recovery of gut microbiota of healthy adults following antibiotic exposure.

Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O.

Nat Microbiol. 2018 Nov;3(11):1255-1265. doi: 10.1038/s41564-018-0257-9. Epub 2018 Oct 22.

PMID:
30349083
15.

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows.

Difford GF, Plichta DR, Løvendahl P, Lassen J, Noel SJ, Højberg O, Wright AG, Zhu Z, Kristensen L, Nielsen HB, Guldbrandtsen B, Sahana G.

PLoS Genet. 2018 Oct 12;14(10):e1007580. doi: 10.1371/journal.pgen.1007580. eCollection 2018 Oct.

16.

Motility and biofilm formation of the emerging gastrointestinal pathogen Campylobacter concisus differs under microaerophilic and anaerobic environments.

Ovesen S, Durack J, Kirk KF, Nielsen HL, Nielsen H, Lynch SV.

Gut Microbes. 2019;10(1):34-44. doi: 10.1080/19490976.2018.1472201. Epub 2018 Sep 25.

PMID:
30252590
17.

Incidence and predictors of intravenous acyclovir-induced nephrotoxicity.

Richelsen RKB, Jensen SB, Nielsen H.

Eur J Clin Microbiol Infect Dis. 2018 Oct;37(10):1965-1971. doi: 10.1007/s10096-018-3332-5. Epub 2018 Aug 7.

PMID:
30083888
18.

Isavuconazole in a Successful Combination Treatment of Disseminated Mucormycosis in a Child with Acute Lymphoblastic Leukaemia and Generalized Haemochromatosis: A Case Report and Review of the Literature.

Pomorska A, Malecka A, Jaworski R, Radon-Proskura J, Hare RK, Nielsen HV, Andersen LO, Jensen HE, Arendrup MC, Irga-Jaworska N.

Mycopathologia. 2019 Feb;184(1):81-88. doi: 10.1007/s11046-018-0287-0. Epub 2018 Jul 23. Review.

PMID:
30039238
19.

Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential.

Gemmell MR, Berry S, Mukhopadhya I, Hansen R, Nielsen HL, Bajaj-Elliott M, Nielsen H, Hold GL.

Emerg Microbes Infect. 2018 Jun 26;7(1):116. doi: 10.1038/s41426-018-0118-x.

20.

Characteristics of the bacterial microbiome in association with common intestinal parasites in irritable bowel syndrome.

Krogsgaard LR, Andersen LO', Johannesen TB, Engsbro AL, Stensvold CR, Nielsen HV, Bytzer P.

Clin Transl Gastroenterol. 2018 Jun 19;9(6):161. doi: 10.1038/s41424-018-0027-2.

21.

Anti-infective treatment of brain abscess.

Bodilsen J, Brouwer MC, Nielsen H, Van De Beek D.

Expert Rev Anti Infect Ther. 2018 Jul;16(7):565-578. doi: 10.1080/14787210.2018.1489722. Epub 2018 Jul 5. Review.

PMID:
29909695
22.

Adventure tourism and schistosomiasis: serology and clinical findings in a group of Danish students after white-water rafting in Uganda.

Röser D, Bjerrum S, Helleberg M, Nielsen HV, David KP, Thybo S, Stensvold CR.

JMM Case Rep. 2018 Feb 2;5(4):e005141. doi: 10.1099/jmmcr.0.005141. eCollection 2018 Apr.

23.

Community-acquired meningitis in adults caused by Escherichia coli in Denmark and The Netherlands.

Bodilsen J, Brouwer MC, Kjærgaard N, Sirks MJ, van der Ende A, Nielsen H, van de Beek D; DASGIB study group.

J Infect. 2018 Jul;77(1):25-29. doi: 10.1016/j.jinf.2018.05.009. Epub 2018 Jun 1.

PMID:
29859862
24.

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.

RNA Biol. 2018;15(6):829-831. doi: 10.1080/15476286.2018.1460996. Epub 2018 May 9.

25.

In Reply-Statin Use Associated With a Decreased Risk of Community-Acquired Staphylococcus aureus Bacteremia.

Smit J, Schønheyder HC, Nielsen H, Søgaard M, López-Cortés LE, Rodríguez-Baño J, Thomsen RW, Frøslev T.

Mayo Clin Proc. 2018 Apr;93(4):542. doi: 10.1016/j.mayocp.2017.12.023. No abstract available.

PMID:
29622103
26.

Analysis of a gene panel for targeted sequencing of colorectal cancer samples.

Jensen KH, Izarzugaza JMG, Juncker AS, Hansen RB, Hansen TF, Timshel P, Blondal T, Jensen TS, Rygaard-Hjalsted E, Mouritzen P, Thorsen M, Wernersson R, Nielsen HB, Jakobsen A, Brunak S, Sørensen FB.

Oncotarget. 2018 Jan 10;9(10):9043-9060. doi: 10.18632/oncotarget.24138. eCollection 2018 Feb 6.

27.

Cerebrospinal fluid lactate as a marker to differentiate between community-acquired acute bacterial meningitis and aseptic meningitis/encephalitis in adults: a Danish prospective observational cohort study.

Buch K, Bodilsen J, Knudsen A, Larsen L, Helweg-Larsen J, Storgaard M, Brandt C, Wiese L, Østergaard C, Nielsen H, Lebech AM; Danish Study Group for Infections in the Brain.

Infect Dis (Lond). 2018 Jul;50(7):514-521. doi: 10.1080/23744235.2018.1441539. Epub 2018 Feb 28.

PMID:
29490540
28.

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease.

Kirk KF, Méric G, Nielsen HL, Pascoe B, Sheppard SK, Thorlacius-Ussing O, Nielsen H.

Sci Rep. 2018 Jan 30;8(1):1902. doi: 10.1038/s41598-018-20135-4.

29.

Sero-prevalence of Toxoplasma gondii in Danish pigs.

Kofoed KG, Vorslund-Kiær M, Nielsen HV, Alban L, Johansen MV.

Vet Parasitol Reg Stud Reports. 2017 Dec;10:136-138. doi: 10.1016/j.vprsr.2017.10.004. Epub 2017 Oct 17.

PMID:
31014586
30.

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial.

Roager HM, Vogt JK, Kristensen M, Hansen LBS, Ibrügger S, Mærkedahl RB, Bahl MI, Lind MV, Nielsen RL, Frøkiær H, Gøbel RJ, Landberg R, Ross AB, Brix S, Holck J, Meyer AS, Sparholt MH, Christensen AF, Carvalho V, Hartmann B, Holst JJ, Rumessen JJ, Linneberg A, Sicheritz-Pontén T, Dalgaard MD, Blennow A, Frandsen HL, Villas-Bôas S, Kristiansen K, Vestergaard H, Hansen T, Ekstrøm CT, Ritz C, Nielsen HB, Pedersen OB, Gupta R, Lauritzen L, Licht TR.

Gut. 2019 Jan;68(1):83-93. doi: 10.1136/gutjnl-2017-314786. Epub 2017 Nov 1.

31.

Substoichiometric ribose methylations in spliceosomal snRNAs.

Krogh N, Kongsbak-Wismann M, Geisler C, Nielsen H.

Org Biomol Chem. 2017 Oct 31;15(42):8872-8876. doi: 10.1039/c7ob02317k.

PMID:
29048444
32.

DeepLoc: prediction of protein subcellular localization using deep learning.

Almagro Armenteros JJ, Sønderby CK, Sønderby SK, Nielsen H, Winther O.

Bioinformatics. 2017 Nov 1;33(21):3387-3395. doi: 10.1093/bioinformatics/btx431. Erratum in: Bioinformatics. 2017 Sep 19;:.

PMID:
29036616
33.

DeepLoc: prediction of protein subcellular localization using deep learning.

Almagro Armenteros JJ, Sønderby CK, Sønderby SK, Nielsen H, Winther O.

Bioinformatics. 2017 Dec 15;33(24):4049. doi: 10.1093/bioinformatics/btx548. No abstract available.

PMID:
29028934
34.

Statin Use and Risk of Community-Acquired Staphylococcus aureus Bacteremia: A Population-Based Case-Control Study.

Smit J, López-Cortés LE, Thomsen RW, Schønheyder HC, Nielsen H, Frøslev T, Rodríguez-Bãno J, Søgaard M.

Mayo Clin Proc. 2017 Oct;92(10):1469-1478. doi: 10.1016/j.mayocp.2017.07.008.

PMID:
28982483
35.

An introduction to deep learning on biological sequence data: examples and solutions.

Jurtz VI, Johansen AR, Nielsen M, Almagro Armenteros JJ, Nielsen H, Sønderby CK, Winther O, Sønderby SK.

Bioinformatics. 2017 Nov 15;33(22):3685-3690. doi: 10.1093/bioinformatics/btx531.

36.

Morbo Serpentino.

Nielsen HM, Shakar S, Weinreich U, Hansen M, Fisker R, Nielsen H, Baudendistel TE, Aronowitz P.

J Hosp Med. 2017 Sep;12(9):755-759. doi: 10.12788/jhm.2821. No abstract available.

PMID:
28914283
37.

Schistosomiasis in European Travelers and Migrants: Analysis of 14 Years TropNet Surveillance Data.

Lingscheid T, Kurth F, Clerinx J, Marocco S, Trevino B, Schunk M, Muñoz J, Gjørup IE, Jelinek T, Develoux M, Fry G, Jänisch T, Schmid ML, Bouchaud O, Puente S, Zammarchi L, Mørch K, Björkman A, Siikamäki H, Neumayr A, Nielsen H, Hellgren U, Paul M, Calleri G, Kosina P, Myrvang B, Ramos JM, Just-Nübling G, Beltrame A, Saraiva da Cunha J, Kern P, Rochat L, Stich A, Pongratz P, Grobusch MP, Suttorp N, Witzenrath M, Hatz C, Zoller T; TropNet Schistosomiasis Investigator Group.

Am J Trop Med Hyg. 2017 Aug;97(2):567-574. doi: 10.4269/ajtmh.17-0034. Epub 2017 Jul 19.

38.

Protein Sorting Prediction.

Nielsen H.

Methods Mol Biol. 2017;1615:23-57. doi: 10.1007/978-1-4939-7033-9_2. Review.

PMID:
28667600
39.

Campylobacter fetus impairs barrier function in HT-29/B6 cells through focal tight junction alterations and leaks.

Bücker R, Krug SM, Fromm A, Nielsen HL, Fromm M, Nielsen H, Schulzke JD.

Ann N Y Acad Sci. 2017 Oct;1405(1):189-201. doi: 10.1111/nyas.13406. Epub 2017 Jun 29.

PMID:
28662272
40.

[More of something good is not always better].

Nielsen HI.

Ugeskr Laeger. 2017 Jun 12;179(24). pii: V69192. Danish. No abstract available.

PMID:
28606293
41.

Adherence to local antimicrobial guidelines for initial treatment of community-acquired infections.

Hagen TL, Hertz MA, Uhrin GB, Dalager-Pedersen M, Schønheyder HC, Nielsen H.

Dan Med J. 2017 Jun;64(6). pii: A5381.

PMID:
28566116
42.

The disease burden of congenital toxoplasmosis in Denmark, 2014.

Nissen J, Jokelainen P, Stensvold CR, Trevisan C, Fuchs J, Burgdorf KS, Nielsen HV, Pires SM.

PLoS One. 2017 May 30;12(5):e0178282. doi: 10.1371/journal.pone.0178282. eCollection 2017.

43.

The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls.

Ring HC, Thorsen J, Saunte DM, Lilje B, Bay L, Riis PT, Larsen N, Andersen LO, Nielsen HV, Miller IM, Bjarnsholt T, Fuursted K, Jemec GB.

JAMA Dermatol. 2017 Sep 1;153(9):897-905. doi: 10.1001/jamadermatol.2017.0904.

44.

Clinical epidemiology in the era of big data: new opportunities, familiar challenges.

Ehrenstein V, Nielsen H, Pedersen AB, Johnsen SP, Pedersen L.

Clin Epidemiol. 2017 Apr 27;9:245-250. doi: 10.2147/CLEP.S129779. eCollection 2017.

45.

The identification and functional annotation of RNA structures conserved in vertebrates.

Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2017 Aug;27(8):1371-1383. doi: 10.1101/gr.208652.116. Epub 2017 May 9.

46.

Predicting Secretory Proteins with SignalP.

Nielsen H.

Methods Mol Biol. 2017;1611:59-73. doi: 10.1007/978-1-4939-7015-5_6.

PMID:
28451972
47.

RiboMeth-seq: Profiling of 2'-O-Me in RNA.

Krogh N, Birkedal U, Nielsen H.

Methods Mol Biol. 2017;1562:189-209. doi: 10.1007/978-1-4939-6807-7_13.

PMID:
28349462
48.

Retrospective PCR-based species identification of Leishmania in two patients with visceral leishmaniasis in Serbia.

Dakić Z, Nielsen HV, Pavlović M, Poluga J, Stevanović G, Lavadinović L, Milošević B, Pelemiš M, Urošević A, Jovanović S, Stensvold CR.

JMM Case Rep. 2016 Oct 20;3(5):e005063. doi: 10.1099/jmmcr.0.005063. eCollection 2016 Oct.

49.

Reducing socioeconomic inequalities in COPD care in the hospital outpatient setting - A nationwide initiative.

Tøttenborg SS, Lange P, Thomsen RW, Nielsen H, Johnsen SP.

Respir Med. 2017 Apr;125:19-23. doi: 10.1016/j.rmed.2017.02.016. Epub 2017 Feb 22.

50.

Dientamoeba fragilis, a Commensal in Children in Danish Day Care Centers.

Jokelainen P, Hebbelstrup Jensen B, Andreassen BU, Petersen AM, Röser D, Krogfelt KA, Nielsen HV, Stensvold CR.

J Clin Microbiol. 2017 Jun;55(6):1707-1713. doi: 10.1128/JCM.00037-17. Epub 2017 Mar 22.

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