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Items: 1 to 20 of 172

1.

Enhancer hubs and loop collisions identified from single-allele topologies.

Allahyar A, Vermeulen C, Bouwman BAM, Krijger PHL, Verstegen MJAM, Geeven G, van Kranenburg M, Pieterse M, Straver R, Haarhuis JHI, Jalink K, Teunissen H, Renkens IJ, Kloosterman WP, Rowland BD, de Wit E, de Ridder J, de Laat W.

Nat Genet. 2018 Jul 9. doi: 10.1038/s41588-018-0161-5. [Epub ahead of print]

PMID:
29988121
2.

Consensus molecular subtypes classification of colorectal adenomas.

Komor MA, Bosch LJ, Bounova G, Bolijn AS, van-Diemen PD, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, van Grieken NC, Carvalho B, Wessels LF, Jimenez CR, Fijneman RJ, Meijer GA; NGS-ProToCol Consortium, Dits N, Böttcher R, Hiemstra AC, Ylstra B, Sie D, van den Broek E, van der Meer D, Pepers F, Caldenhoven E, Janssen B, van Workum W, van Lieshout S, Bangma CH, van Leenders G, van de Werken H.

J Pathol. 2018 Jul 3. doi: 10.1002/path.5129. [Epub ahead of print]

PMID:
29968252
3.

Patterns of conservation and diversification in the fungal polarization network.

Diepeveen ET, Gehrmann T, Pourquié V, Abeel T, Laan L.

Genome Biol Evol. 2018 Jun 20. doi: 10.1093/gbe/evy121. [Epub ahead of print]

PMID:
29931311
4.

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer.

Vossen DM, Verhagen CVM, Verheij M, Wessels LFA, Vens C, van den Brekel MWM.

Oral Oncol. 2018 Jun;81:35-44. doi: 10.1016/j.oraloncology.2018.04.006. Epub 2018 Apr 13.

PMID:
29884412
5.

Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration.

Cioni B, Nevedomskaya E, Melis MHM, van Burgsteden J, Stelloo S, Hodel E, Spinozzi D, de Jong J, van der Poel H, de Boer JP, Wessels LFA, Zwart W, Bergman AM.

Mol Oncol. 2018 May 28. doi: 10.1002/1878-0261.12327. [Epub ahead of print]

6.

Integrating spatial-anatomical regularization and structure sparsity into SVM: Improving interpretation of Alzheimer's disease classification.

Sun Z, Qiao Y, Lelieveldt BPF, Staring M; Alzheimer's Disease NeuroImaging Initiative.

Neuroimage. 2018 Sep;178:445-460. doi: 10.1016/j.neuroimage.2018.05.051. Epub 2018 May 23.

PMID:
29802968
7.

A survey of functional genomic variation in domesticated chickens.

Derks MFL, Megens HJ, Bosse M, Visscher J, Peeters K, Bink MCAM, Vereijken A, Gross C, de Ridder D, Reinders MJT, Groenen MAM.

Genet Sel Evol. 2018 Apr 16;50(1):17. doi: 10.1186/s12711-018-0390-1.

8.

Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs.

Gehrmann T, Pelkmans JF, Ohm RA, Vos AM, Sonnenberg ASM, Baars JJP, Wösten HAB, Reinders MJT, Abeel T.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4429-4434. doi: 10.1073/pnas.1721381115. Epub 2018 Apr 11.

9.

Mass cytometry reveals innate lymphoid cell differentiation pathways in the human fetal intestine.

Li N, van Unen V, Höllt T, Thompson A, van Bergen J, Pezzotti N, Eisemann E, Vilanova A, Chuva de Sousa Lopes SM, Lelieveldt BPF, Koning F.

J Exp Med. 2018 May 7;215(5):1383-1396. doi: 10.1084/jem.20171934. Epub 2018 Mar 6.

PMID:
29511064
10.

Author Correction: Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy.

Doorenweerd N, Mahfouz A, van Putten M, Kaliyaperumal R, T' Hoen PAC, Hendriksen JGM, Aartsma-Rus AM, Verschuuren JJGM, Niks EH, Reinders MJT, Kan HE, Lelieveldt BPF.

Sci Rep. 2018 Mar 1;8(1):4058. doi: 10.1038/s41598-018-22154-7.

11.

Interactive Visual Exploration of 3D Mass Spectrometry Imaging Data Using Hierarchical Stochastic Neighbor Embedding Reveals Spatiomolecular Structures at Full Data Resolution.

Abdelmoula WM, Pezzotti N, Hölt T, Dijkstra J, Vilanova A, McDonnell LA, Lelieveldt BPF.

J Proteome Res. 2018 Mar 2;17(3):1054-1064. doi: 10.1021/acs.jproteome.7b00725. Epub 2018 Feb 15.

12.

Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer.

Severson TM, Kim Y, Joosten SEP, Schuurman K, van der Groep P, Moelans CB, Ter Hoeve ND, Manson QF, Martens JW, van Deurzen CHM, Barbe E, Hedenfalk I, Bult P, Smit VTHBM, Linn SC, van Diest PJ, Wessels L, Zwart W.

Nat Commun. 2018 Feb 2;9(1):482. doi: 10.1038/s41467-018-02856-2.

13.

Response to letter to the editor PD-17-0390, a comment on "Comparing methods for fetal fraction determination and quality control of NIPT samples".

van Beek DM, Straver R, Weiss MM, Boon EMJ, Huijsdens-van Amsterdam K, Oudejans CBM, Reinders MJT, Sistermans EA.

Prenat Diagn. 2017 Dec;37(12):1266-1267. doi: 10.1002/pd.5170. No abstract available.

14.

WISExome: a within-sample comparison approach to detect copy number variations in whole exome sequencing data.

Straver R, Weiss MM, Waisfisz Q, Sistermans EA, Reinders MJT.

Eur J Hum Genet. 2017 Dec;25(12):1354-1363. doi: 10.1038/s41431-017-0005-2. Epub 2017 Nov 8.

15.

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington's Disease.

Keo A, Aziz NA, Dzyubachyk O, van der Grond J, van Roon-Mom WMC, Lelieveldt BPF, Reinders MJT, Mahfouz A.

Front Mol Neurosci. 2017 Nov 30;10:399. doi: 10.3389/fnmol.2017.00399. eCollection 2017.

16.

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity.

Sachs N, de Ligt J, Kopper O, Gogola E, Bounova G, Weeber F, Balgobind AV, Wind K, Gracanin A, Begthel H, Korving J, van Boxtel R, Duarte AA, Lelieveld D, van Hoeck A, Ernst RF, Blokzijl F, Nijman IJ, Hoogstraat M, van de Ven M, Egan DA, Zinzalla V, Moll J, Boj SF, Voest EE, Wessels L, van Diest PJ, Rottenberg S, Vries RGJ, Cuppen E, Clevers H.

Cell. 2018 Jan 11;172(1-2):373-386.e10. doi: 10.1016/j.cell.2017.11.010. Epub 2017 Dec 7.

PMID:
29224780
17.

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types.

van Unen V, Höllt T, Pezzotti N, Li N, Reinders MJT, Eisemann E, Koning F, Vilanova A, Lelieveldt BPF.

Nat Commun. 2017 Nov 23;8(1):1740. doi: 10.1038/s41467-017-01689-9.

18.

An objective comparison of cell-tracking algorithms.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C.

Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30.

19.

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates.

Thijssen B, Dijkstra TMH, Heskes T, Wessels LFA.

Bioinformatics. 2018 Mar 1;34(5):803-811. doi: 10.1093/bioinformatics/btx666.

PMID:
29069283
20.

Reply to Lee and Howden.

Manson AL, Abeel T, Galagan J, Sundaramurthi JC, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM.

Clin Infect Dis. 2018 Jan 6;66(1):160-161. doi: 10.1093/cid/cix751. No abstract available.

PMID:
29040415

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