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Items: 37

1.

ZDOG: zooming in on dominating genes with mutations in cancer pathways.

Alberts R, Chen J, Zhang L.

BMC Bioinformatics. 2019 Dec 30;20(1):740. doi: 10.1186/s12859-019-3326-z.

2.

Correction to: The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.

Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vila AV, Collij V, Spekhorst LM, Van der Sloot KWJ, Peters V, Van Dullemen HM, Visschedijk MC, Festen EAM, Swertz MA, Dijkstra G, Weersma RK.

BMC Gastroenterol. 2019 Mar 27;19(1):44. doi: 10.1186/s12876-019-0938-8.

3.

The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.

Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vich Vila A, Collij V, Spekhorst LM, Van der Sloot KWJ, Peters V, Van Dullemen HM, Visschedijk MC, Festen EAM, Swertz MA, Dijkstra G, Weersma RK.

BMC Gastroenterol. 2019 Jan 8;19(1):5. doi: 10.1186/s12876-018-0917-5. Erratum in: BMC Gastroenterol. 2019 Mar 27;19(1):44.

4.

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.

Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK.

Sci Transl Med. 2018 Dec 19;10(472). pii: eaap8914. doi: 10.1126/scitranslmed.aap8914.

PMID:
30567928
5.

MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.

van der Velde KJ, Imhann F, Charbon B, Pang C, van Enckevort D, Slofstra M, Barbieri R, Alberts R, Hendriksen D, Kelpin F, de Haan M, de Boer T, Haakma S, Stroomberg C, Scholtens S, van de Geijn GJ, Festen EAM, Weersma RK, Swertz MA.

Bioinformatics. 2019 Mar 15;35(6):1076-1078. doi: 10.1093/bioinformatics/bty742.

6.

Genomic and Expression Analyses Identify a Disease-Modifying Variant for Fibrostenotic Crohn's Disease.

Visschedijk MC, Spekhorst LM, Cheng SC, van Loo ES, Jansen BHD, Blokzijl T, Kil H, de Jong DJ, Pierik M, Maljaars JPWJ, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Nieuwenhuijs VB, Imhann F, van Sommeren S, Alberts R, Xavier RJ, Dijkstra G, Nico Faber K, Aldaz CM, Weersma RK, Festen EAM.

J Crohns Colitis. 2018 Apr 27;12(5):582-588. doi: 10.1093/ecco-jcc/jjy001.

PMID:
29361163
7.

Genetic association analysis identifies variants associated with disease progression in primary sclerosing cholangitis.

Alberts R, de Vries EMG, Goode EC, Jiang X, Sampaziotis F, Rombouts K, Böttcher K, Folseraas T, Weismüller TJ, Mason AL, Wang W, Alexander G, Alvaro D, Bergquist A, Björkström NK, Beuers U, Björnsson E, Boberg KM, Bowlus CL, Bragazzi MC, Carbone M, Chazouillères O, Cheung A, Dalekos G, Eaton J, Eksteen B, Ellinghaus D, Färkkilä M, Festen EAM, Floreani A, Franceschet I, Gotthardt DN, Hirschfield GM, Hoek BV, Holm K, Hohenester S, Hov JR, Imhann F, Invernizzi P, Juran BD, Lenzen H, Lieb W, Liu JZ, Marschall HU, Marzioni M, Melum E, Milkiewicz P, Müller T, Pares A, Rupp C, Rust C, Sandford RN, Schramm C, Schreiber S, Schrumpf E, Silverberg MS, Srivastava B, Sterneck M, Teufel A, Vallier L, Verheij J, Vila AV, Vries B, Zachou K; International PSC Study Group, The UK PSC Consortium, Chapman RW, Manns MP, Pinzani M, Rushbrook SM, Lazaridis KN, Franke A, Anderson CA, Karlsen TH, Ponsioen CY, Weersma RK.

Gut. 2018 Aug;67(8):1517-1524. doi: 10.1136/gutjnl-2016-313598. Epub 2017 Aug 4.

8.

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.

Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK.

Gut. 2018 Jan;67(1):108-119. doi: 10.1136/gutjnl-2016-312135. Epub 2016 Oct 8.

9.

Drug Repositioning in Inflammatory Bowel Disease Based on Genetic Information.

Collij V, Festen EA, Alberts R, Weersma RK.

Inflamm Bowel Dis. 2016 Nov;22(11):2562-2570.

PMID:
27753694
10.

Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2.

Visschedijk MC, Alberts R, Mucha S, Deelen P, de Jong DJ, Pierik M, Spekhorst LM, Imhann F, van der Meulen-de Jong AE, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Dijkstra G, Ellinghaus D, Schreiber S, Wijmenga C; Initiative on Crohn and Colitis; Parelsnoer Institute, Rivas MA, Franke A, van Diemen CC, Weersma RK.

PLoS One. 2016 Aug 4;11(8):e0159609. doi: 10.1371/journal.pone.0159609. eCollection 2016.

11.

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.

Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A, Ripke S, Lee JC, Jostins L, Shah T, Abedian S, Cheon JH, Cho J, Dayani NE, Franke L, Fuyuno Y, Hart A, Juyal RC, Juyal G, Kim WH, Morris AP, Poustchi H, Newman WG, Midha V, Orchard TR, Vahedi H, Sood A, Sung JY, Malekzadeh R, Westra HJ, Yamazaki K, Yang SK; International Multiple Sclerosis Genetics Consortium; International IBD Genetics Consortium, Barrett JC, Alizadeh BZ, Parkes M, Bk T, Daly MJ, Kubo M, Anderson CA, Weersma RK.

Nat Genet. 2015 Sep;47(9):979-986. doi: 10.1038/ng.3359. Epub 2015 Jul 20.

12.

Performance of the Montreal classification for inflammatory bowel diseases.

Spekhorst LM, Visschedijk MC, Alberts R, Festen EA, van der Wouden EJ, Dijkstra G, Weersma RK; Dutch Initiative on Crohn and Colitis.

World J Gastroenterol. 2014 Nov 7;20(41):15374-81. doi: 10.3748/wjg.v20.i41.15374.

13.

Systems genetics of liver fibrosis: identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population.

Hall RA, Liebe R, Hochrath K, Kazakov A, Alberts R, Laufs U, Böhm M, Fischer HP, Williams RW, Schughart K, Weber SN, Lammert F.

PLoS One. 2014 Feb 28;9(2):e89279. doi: 10.1371/journal.pone.0089279. eCollection 2014.

14.

ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains.

Dogan A, Lasch P, Neuschl C, Millrose MK, Alberts R, Schughart K, Naumann D, Brockmann GA.

BMC Genomics. 2013 Jun 10;14:386. doi: 10.1186/1471-2164-14-386.

15.

Analysis of the lung transcriptome in Mycobacterium tuberculosis-infected mice reveals major differences in immune response pathways between TB-susceptible and resistant hosts.

Shepelkova G, Pommerenke C, Alberts R, Geffers R, Evstifeev V, Apt A, Schughart K, Wilk E.

Tuberculosis (Edinb). 2013 Mar;93(2):263-9. doi: 10.1016/j.tube.2012.11.007. Epub 2012 Dec 29.

PMID:
23276693
16.

Distinct gene loci control the host response to influenza H1N1 virus infection in a time-dependent manner.

Nedelko T, Kollmus H, Klawonn F, Spijker S, Lu L, Heßman M, Alberts R, Williams RW, Schughart K.

BMC Genomics. 2012 Aug 20;13:411. doi: 10.1186/1471-2164-13-411.

17.

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs.

Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der Velde KJ, Jansen RC, Schughart K.

Brief Bioinform. 2012 Mar;13(2):135-42. doi: 10.1093/bib/bbr026. Epub 2011 Jul 8. Review.

18.

Sirolimus conversion regimen versus continued calcineurin inhibitors in liver allograft recipients: a randomized trial.

Abdelmalek MF, Humar A, Stickel F, Andreone P, Pascher A, Barroso E, Neff GW, Ranjan D, Toselli LT, Gane EJ, Scarola J, Alberts RG, Maller ES, Lo CM; Sirolimus Liver Conversion Trial Study Group.

Am J Transplant. 2012 Mar;12(3):694-705. doi: 10.1111/j.1600-6143.2011.03919.x. Epub 2012 Jan 10.

19.

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease.

Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K.

BMC Genomics. 2011 Dec 19;12:610. doi: 10.1186/1471-2164-12-610.

20.

Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures.

Alberts R, Lu L, Williams RW, Schughart K.

Respir Res. 2011 May 2;12:61. doi: 10.1186/1465-9921-12-61. Erratum in: Respir Res. 2012;13(1):5.

21.

Cancer incidence and mortality among workers exposed to benzidine.

Brown SC, Alberts R, Schoenberg M.

Am J Ind Med. 2011 Apr;54(4):300-6. doi: 10.1002/ajim.20936. Epub 2011 Feb 15.

PMID:
21328418
22.

QTLminer: identifying genes regulating quantitative traits.

Alberts R, Schughart K.

BMC Bioinformatics. 2010 Oct 15;11:516. doi: 10.1186/1471-2105-11-516.

23.

A new mouse model reveals a critical role for host innate immunity in resistance to Rift Valley fever.

do Valle TZ, Billecocq A, Guillemot L, Alberts R, Gommet C, Geffers R, Calabrese K, Schughart K, Bouloy M, Montagutelli X, Panthier JJ.

J Immunol. 2010 Nov 15;185(10):6146-56. doi: 10.4049/jimmunol.1000949. Epub 2010 Oct 11.

24.

Data-driven assessment of eQTL mapping methods.

Michaelson JJ, Alberts R, Schughart K, Beyer A.

BMC Genomics. 2010 Sep 17;11:502. doi: 10.1186/1471-2164-11-502.

25.

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE; Coordination of Mouse Informatics Resources (CASIMIR); Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.

Genome Biol. 2010;11(3):R27. doi: 10.1186/gb-2010-11-3-r27. Epub 2010 Mar 9.

26.

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.

Gruenberger M, Alberts R, Smedley D, Swertz M, Schofield P; CASIMIR consortium, Schughart K.

BMC Res Notes. 2010 Jan 22;3:16. doi: 10.1186/1756-0500-3-16.

27.

Gene expression changes in the host response between resistant and susceptible inbred mouse strains after influenza A infection.

Alberts R, Srivastava B, Wu H, Viegas N, Geffers R, Klawonn F, Novoselova N, do Valle TZ, Panthier JJ, Schughart K.

Microbes Infect. 2010 Apr;12(4):309-18. doi: 10.1016/j.micinf.2010.01.008. Epub 2010 Jan 28.

PMID:
20114087
28.

affyGG: computational protocols for genetical genomics with Affymetrix arrays.

Alberts R, Vera G, Jansen RC.

Bioinformatics. 2008 Feb 1;24(3):433-4. Epub 2007 Dec 16.

PMID:
18086686
29.

Sequence polymorphisms cause many false cis eQTLs.

Alberts R, Terpstra P, Li Y, Breitling R, Nap JP, Jansen RC.

PLoS One. 2007 Jul 18;2(7):e622.

30.

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat.

Alberts R, Terpstra P, Hardonk M, Bystrykh LV, de Haan G, Breitling R, Nap JP, Jansen RC.

BMC Bioinformatics. 2007 Apr 20;8:132.

31.

A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays.

Alberts R, Terpstra P, Bystrykh LV, de Haan G, Jansen RC.

Genetics. 2005 Nov;171(3):1437-9. Epub 2005 Aug 3.

32.

Combining microarrays and genetic analysis.

Alberts R, Fu J, Swertz MA, Lubbers LA, Albers CJ, Jansen RC.

Brief Bioinform. 2005 Jun;6(2):135-45.

PMID:
15975223
33.

Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'.

Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke MP, de Haan G.

Nat Genet. 2005 Mar;37(3):225-32. Epub 2005 Feb 13.

PMID:
15711547
34.

Single-unit artificial intervertebral disc.

Alberts R, Patil AA, Zhou D.

J Neurosurg Spine. 2004 Jul;1(1):95-100.

PMID:
15291028
35.

Unusual sign of a Jefferson fracture. A case report.

Siegel M, Alberts R.

Spine (Phila Pa 1976). 1992 May;17(5):605-7. No abstract available.

PMID:
1621165
36.

Effect of aging on tensile mechanical properties of the rabbit distal femoral growth plate.

Guse RJ, Connolly JF, Alberts R, Lippiello L.

J Orthop Res. 1989;7(5):667-73.

PMID:
2760738
37.

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