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Items: 33

1.

High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach.

Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, De Meyts ER, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ.

J Infect Dis. 2019 Jun 28. pii: jiz318. doi: 10.1093/infdis/jiz318. [Epub ahead of print]

PMID:
31253993
2.

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries.

Asplund M, Kjartansdóttir KR, Mollerup S, Vinner L, Fridholm H, Herrera JAR, Friis-Nielsen J, Hansen TA, Jensen RH, Nielsen IB, Richter SR, Rey-Iglesia A, Matey-Hernandez ML, Alquezar-Planas DE, Olsen PVS, Sicheritz-Pontén T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ.

Clin Microbiol Infect. 2019 May 4. pii: S1198-743X(19)30206-X. doi: 10.1016/j.cmi.2019.04.028. [Epub ahead of print]

3.

Conflicting associations between dietary patterns and changes of anthropometric traits across subgroups of middle-aged women and men.

Jiang L, Audouze K, Romero Herrera JA, Ängquist LH, Kjærulff SK, Izarzugaza JMG, Tjønneland A, Halkjær J, Overvad K, Sørensen TIA, Brunak S.

Clin Nutr. 2019 Feb 14. pii: S0261-5614(19)30055-X. doi: 10.1016/j.clnu.2019.02.003. [Epub ahead of print]

4.

A Novel Familial Cardiac Arrhythmia Syndrome with Widespread ST-Segment Depression.

Bundgaard H, Jøns C, Lodder EM, Izarzugaza JMG, Romero Herrera JA, Pehrson S, Tfelt-Hansen J, Ahlberg G, Olesen MS, Holst AG, Wellens H, de Villiers C, Hastings R, Stuart G, Brunak S, Wilde AAM, Watkins H, Christensen AH.

N Engl J Med. 2018 Nov 1;379(18):1780-1781. doi: 10.1056/NEJMc1807668. No abstract available.

PMID:
30380381
5.

A generic deep convolutional neural network framework for prediction of receptor-ligand interactions-NetPhosPan: application to kinase phosphorylation prediction.

Fenoy E, Izarzugaza JMG, Jurtz V, Brunak S, Nielsen M.

Bioinformatics. 2019 Apr 1;35(7):1098-1107. doi: 10.1093/bioinformatics/bty715.

PMID:
30169744
6.

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.

Matey-Hernandez ML; Danish Pan Genome Consortium, Brunak S, Izarzugaza JMG.

BMC Bioinformatics. 2018 Jun 25;19(1):239. doi: 10.1186/s12859-018-2239-6.

7.

Retinoic Acid Signaling in Thymic Epithelial Cells Regulates Thymopoiesis.

Wendland K, Niss K, Kotarsky K, Wu NYH, White AJ, Jendholm J, Rivollier A, Izarzugaza JMG, Brunak S, Holländer GA, Anderson G, Sitnik KM, Agace WW.

J Immunol. 2018 Jul 15;201(2):524-532. doi: 10.4049/jimmunol.1800418. Epub 2018 May 30.

8.

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.

9.

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.

Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH.

Nature. 2017 Aug 3;548(7665):87-91. doi: 10.1038/nature23264. Epub 2017 Jul 26.

PMID:
28746312
10.

Cutavirus in Cutaneous Malignant Melanoma.

Mollerup S, Fridholm H, Vinner L, Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Herrera JA, Steiniche T, Mourier T, Brunak S, Willerslev E, Izarzugaza JM, Hansen AJ, Nielsen LP.

Emerg Infect Dis. 2017 Feb;23(2):363-365. doi: 10.3201/eid2302.161564.

11.

KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily.

Pons T, Vazquez M, Matey-Hernandez ML, Brunak S, Valencia A, Izarzugaza JM.

BMC Genomics. 2016 Jun 23;17 Suppl 2:396. doi: 10.1186/s12864-016-2723-1.

12.

How compelling are the data for Epstein-Barr virus being a trigger for systemic lupus and other autoimmune diseases?

Draborg A, Izarzugaza JM, Houen G.

Curr Opin Rheumatol. 2016 Jul;28(4):398-404. doi: 10.1097/BOR.0000000000000289. Review.

PMID:
26986247
13.

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.

Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JM, Brunak S.

Viruses. 2016 Feb 19;8(2). pii: E53. doi: 10.3390/v8020053.

14.

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing.

Mollerup S, Friis-Nielsen J, Vinner L, Hansen TA, Richter SR, Fridholm H, Herrera JA, Lund O, Brunak S, Izarzugaza JM, Mourier T, Nielsen LP, Hansen AJ.

J Clin Microbiol. 2016 Apr;54(4):980-7. doi: 10.1128/JCM.02723-15. Epub 2016 Jan 27.

15.

wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases.

Vazquez M, Pons T, Brunak S, Valencia A, Izarzugaza JM.

Hum Mutat. 2016 Jan;37(1):36-42. doi: 10.1002/humu.22914. Epub 2015 Oct 20.

PMID:
26443060
16.

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing.

Vinner L, Mourier T, Friis-Nielsen J, Gniadecki R, Dybkaer K, Rosenberg J, Langhoff JL, Cruz DF, Fonager J, Izarzugaza JM, Gupta R, Sicheritz-Ponten T, Brunak S, Willerslev E, Nielsen LP, Hansen AJ.

Sci Rep. 2015 Aug 19;5:13201. doi: 10.1038/srep13201.

17.

Traces of ATCV-1 associated with laboratory component contamination.

Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Mollerup S, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Sicheritz-Pontén T, Nielsen LP, Brunak S, Willerslev E, Izarzugaza JM, Hansen AJ.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):E925-6. doi: 10.1073/pnas.1423756112. Epub 2015 Feb 5. No abstract available.

18.

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios.

Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CN, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TI, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S.

Nat Commun. 2015 Jan 19;6:5969. doi: 10.1038/ncomms6969.

19.

wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases.

Izarzugaza JM, Vazquez M, del Pozo A, Valencia A.

BMC Bioinformatics. 2013 Nov 29;14:345. doi: 10.1186/1471-2105-14-345.

20.

Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations.

Birkbak NJ, Kochupurakkal B, Izarzugaza JM, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC.

PLoS One. 2013 Nov 12;8(11):e80023. doi: 10.1371/journal.pone.0080023. eCollection 2013.

21.

Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP.

Johansen MB, Izarzugaza JM, Brunak S, Petersen TN, Gupta R.

PLoS One. 2013 Jul 25;8(7):e68370. doi: 10.1371/journal.pone.0068370. Print 2013.

22.

Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining.

Izarzugaza JM, Krallinger M, Valencia A.

Front Physiol. 2012 Aug 22;3:323. doi: 10.3389/fphys.2012.00323. eCollection 2012.

23.

Prioritization of pathogenic mutations in the protein kinase superfamily.

Izarzugaza JM, del Pozo A, Vazquez M, Valencia A.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S3. doi: 10.1186/1471-2164-13-S4-S3.

24.

Characterization of pathogenic germline mutations in human protein kinases.

Izarzugaza JM, Hopcroft LE, Baresic A, Orengo CA, Martin AC, Valencia A.

BMC Bioinformatics. 2011;12 Suppl 4:S1. doi: 10.1186/1471-2105-12-S4-S1. Epub 2011 Jul 5.

25.

An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D.

Izarzugaza JM, Baresic A, McMillan LE, Yeats C, Clegg AB, Orengo CA, Martin AC, Valencia A.

BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S5. doi: 10.1186/1471-2105-10-S8-S5.

26.

Extraction of human kinase mutations from literature, databases and genotyping studies.

Krallinger M, Izarzugaza JM, Rodriguez-Penagos C, Valencia A.

BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S1. doi: 10.1186/1471-2105-10-S8-S1.

27.

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

Ezkurdia I, Graña O, Izarzugaza JM, Tress ML.

Proteins. 2009;77 Suppl 9:196-209. doi: 10.1002/prot.22554.

PMID:
19714769
28.

Cancer-associated mutations are preferentially distributed in protein kinase functional sites.

Izarzugaza JM, Redfern OC, Orengo CA, Valencia A.

Proteins. 2009 Dec;77(4):892-903. doi: 10.1002/prot.22512.

PMID:
19626714
29.

From cancer genomes to cancer models: bridging the gaps.

Baudot A, Real FX, Izarzugaza JM, Valencia A.

EMBO Rep. 2009 Apr;10(4):359-66. doi: 10.1038/embor.2009.46. Epub 2009 Mar 20. Review.

30.

Prediction of protein interaction based on similarity of phylogenetic trees.

Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A.

Methods Mol Biol. 2008;484:523-35. doi: 10.1007/978-1-59745-398-1_31.

PMID:
18592199
31.

Enhancing the prediction of protein pairings between interacting families using orthology information.

Izarzugaza JM, Juan D, Pons C, Pazos F, Valencia A.

BMC Bioinformatics. 2008 Jan 23;9:35. doi: 10.1186/1471-2105-9-35.

32.

Assessment of intramolecular contact predictions for CASP7.

Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND.

Proteins. 2007;69 Suppl 8:152-8.

PMID:
17671976
33.

TSEMA: interactive prediction of protein pairings between interacting families.

Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, Pazos F.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W315-9.

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