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Items: 20

1.

Transcriptomic and molecular genetic analysis of the cell wall salvage response of Aspergillus niger to the absence of galactofuranose synthesis.

Park J, Hulsman M, Arentshorst M, Breeman M, Alazi E, Lagendijk EL, Rocha MC, Malavazi I, Nitsche BM, van den Hondel CA, Meyer V, Ram AF.

Cell Microbiol. 2016 Jun 5. doi: 10.1111/cmi.12624. [Epub ahead of print]

PMID:
27264789
2.

Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots.

Scholma J, Fuhler GM, Joore J, Hulsman M, Schivo S, List AF, Reinders MJ, Peppelenbosch MP, Post JN.

Sci Rep. 2016 May 26;6:26695. doi: 10.1038/srep26695.

3.

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.

Gritsenko AA, Hulsman M, Reinders MJ, de Ridder D.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004336. doi: 10.1371/journal.pcbi.1004336. eCollection 2015 Aug.

4.

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.

Babaei S, Mahfouz A, Hulsman M, Lelieveldt BP, de Ridder J, Reinders M.

PLoS Comput Biol. 2015 May 12;11(5):e1004221. doi: 10.1371/journal.pcbi.1004221. eCollection 2015 May.

5.

Switching from a unicellular to multicellular organization in an Aspergillus niger hypha.

Bleichrodt RJ, Hulsman M, Wösten HA, Reinders MJ.

MBio. 2015 Mar 3;6(2):e00111. doi: 10.1128/mBio.00111-15.

6.

Analysis of high-throughput screening reveals the effect of surface topographies on cellular morphology.

Hulsman M, Hulshof F, Unadkat H, Papenburg BJ, Stamatialis DF, Truckenmüller R, van Blitterswijk C, de Boer J, Reinders MJ.

Acta Biomater. 2015 Mar;15:29-38. doi: 10.1016/j.actbio.2014.12.019. Epub 2014 Dec 30.

PMID:
25554402
7.

FluG affects secretion in colonies of Aspergillus niger.

Wang F, Krijgsheld P, Hulsman M, de Bekker C, Müller WH, Reinders M, de Vries RP, Wösten HA.

Antonie Van Leeuwenhoek. 2015 Jan;107(1):225-40. doi: 10.1007/s10482-014-0321-2. Epub 2014 Nov 5.

PMID:
25370014
8.

Scale-space measures for graph topology link protein network architecture to function.

Hulsman M, Dimitrakopoulos C, de Ridder J.

Bioinformatics. 2014 Jun 15;30(12):i237-45. doi: 10.1093/bioinformatics/btu283.

9.

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis.

Holstege H, Pfeiffer W, Sie D, Hulsman M, Nicholas TJ, Lee CC, Ross T, Lin J, Miller MA, Ylstra B, Meijers-Heijboer H, Brugman MH, Staal FJ, Holstege G, Reinders MJ, Harkins TT, Levy S, Sistermans EA.

Genome Res. 2014 May;24(5):733-42. doi: 10.1101/gr.162131.113. Epub 2014 Apr 23.

10.

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging.

van den Akker EB, Passtoors WM, Jansen R, van Zwet EW, Goeman JJ, Hulsman M, Emilsson V, Perola M, Willemsen G, Penninx BW, Heijmans BT, Maier AB, Boomsma DI, Kok JN, Slagboom PE, Reinders MJ, Beekman M.

Aging Cell. 2014 Apr;13(2):216-25. doi: 10.1111/acel.12160. Epub 2013 Nov 19.

11.

Molecular mechanisms of biomaterial-driven osteogenic differentiation in human mesenchymal stromal cells.

Barradas AM, Monticone V, Hulsman M, Danoux C, Fernandes H, Tahmasebi Birgani Z, Barrère-de Groot F, Yuan H, Reinders M, Habibovic P, van Blitterswijk C, de Boer J.

Integr Biol (Camb). 2013 Jul 24;5(7):920-31. doi: 10.1039/c3ib40027a. Epub 2013 Jun 11.

PMID:
23752904
12.

Predicting the therapeutic efficacy of MSC in bone tissue engineering using the molecular marker CADM1.

Mentink A, Hulsman M, Groen N, Licht R, Dechering KJ, van der Stok J, Alves HA, Dhert WJ, van Someren EP, Reinders MJ, van Blitterswijk CA, de Boer J.

Biomaterials. 2013 Jun;34(19):4592-601. doi: 10.1016/j.biomaterials.2013.03.001. Epub 2013 Mar 26.

PMID:
23541110
13.

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.

Babaei S, Hulsman M, Reinders M, de Ridder J.

BMC Bioinformatics. 2013 Jan 23;14:29. doi: 10.1186/1471-2105-14-29.

14.

High content imaging in the screening of biomaterial-induced MSC behavior.

Unadkat HV, Groen N, Doorn J, Fischer B, Barradas AM, Hulsman M, van de Peppel J, Moroni L, van Leeuwen JP, Reinders MJ, van Blitterswijk CA, de Boer J.

Biomaterials. 2013 Feb;34(5):1498-505. doi: 10.1016/j.biomaterials.2012.10.035. Epub 2012 Nov 23.

PMID:
23182347
15.

A modular versatile chip carrier for high-throughput screening of cell-biomaterial interactions.

Unadkat HV, Rewagad RR, Hulsman M, Hulshof GF, Truckenmüller RK, Stamatialis DF, Reinders MJ, Eijkel JC, van den Berg A, van Blitterswijk CA, de Boer J.

J R Soc Interface. 2013 Jan 6;10(78):20120753. doi: 10.1098/rsif.2012.0753.

16.

Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger.

van den Berg BA, Reinders MJ, Hulsman M, Wu L, Pel HJ, Roubos JA, de Ridder D.

PLoS One. 2012;7(10):e45869. doi: 10.1371/journal.pone.0045869. Epub 2012 Oct 1.

17.

A mesenchymal stromal cell gene signature for donor age.

Alves H, van Ginkel J, Groen N, Hulsman M, Mentink A, Reinders M, van Blitterswijk C, de Boer J.

PLoS One. 2012;7(8):e42908. doi: 10.1371/journal.pone.0042908. Epub 2012 Aug 23.

18.

An algorithm-based topographical biomaterials library to instruct cell fate.

Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Carpenter AE, Wessling M, Post GF, Uetz M, Reinders MJ, Stamatialis D, van Blitterswijk CA, de Boer J.

Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16565-70. doi: 10.1073/pnas.1109861108. Epub 2011 Sep 26. Erratum in: Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5731. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5905. Carpenter, Anne E [added]; Wessling, Matthias [added].

19.

Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization.

Hulsman M, Mentink A, van Someren EP, Dechering KJ, de Boer J, Reinders MJ.

BMC Bioinformatics. 2010 Mar 26;11:156. doi: 10.1186/1471-2105-11-156.

20.

Evolutionary optimization of kernel weights improves protein complex comembership prediction.

Hulsman M, Reinders MJ, de Ridder D.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):427-37. doi: 10.1109/TCBB.2008.137.

PMID:
19644171
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