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Items: 32

1.

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.

Pawlik A, van Gelder CWG, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Goble C.

F1000Res. 2017 Jul 3;6. pii: ELIXIR-1040. doi: 10.12688/f1000research.11718.1. eCollection 2017.

2.

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters.

de Jonge WJ, O'Duibhir E, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Kemmeren P, Holstege FC.

EMBO J. 2017 Feb 1;36(3):274-290. doi: 10.15252/embj.201695621. Epub 2016 Dec 15.

3.

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

Sameith K, Amini S, Groot Koerkamp MJ, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FC, Kemmeren P.

BMC Biol. 2015 Dec 23;13:112. doi: 10.1186/s12915-015-0222-5.

4.

FOXO target gene CTDSP2 regulates cell cycle progression through Ras and p21(Cip1/Waf1).

Kloet DE, Polderman PE, Eijkelenboom A, Smits LM, van Triest MH, van den Berg MC, Groot Koerkamp MJ, van Leenen D, Lijnzaad P, Holstege FC, Burgering BM.

Biochem J. 2015 Jul 15;469(2):289-98. doi: 10.1042/BJ20140831. Epub 2015 May 20.

5.

Cell cycle population effects in perturbation studies.

O'Duibhir E, Lijnzaad P, Benschop JJ, Lenstra TL, van Leenen D, Groot Koerkamp MJ, Margaritis T, Brok MO, Kemmeren P, Holstege FC.

Mol Syst Biol. 2014 Jun 21;10:732. doi: 10.15252/msb.20145172.

6.

Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC.

Cell. 2014 Apr 24;157(3):740-52. doi: 10.1016/j.cell.2014.02.054.

7.

A novel microscopy-based high-throughput screening method to identify proteins that regulate global histone modification levels.

Baas R, Lelieveld D, van Teeffelen H, Lijnzaad P, Castelijns B, van Schaik FM, Vermeulen M, Egan DA, Timmers HT, de Graaf P.

J Biomol Screen. 2014 Feb;19(2):287-96. doi: 10.1177/1087057113515024. Epub 2013 Dec 11.

PMID:
24334265
8.

Centromere binding and a conserved role in chromosome stability for SUMO-dependent ubiquitin ligases.

van de Pasch LA, Miles AJ, Nijenhuis W, Brabers NA, van Leenen D, Lijnzaad P, Brown MK, Ouellet J, Barral Y, Kops GJ, Holstege FC.

PLoS One. 2013 Jun 13;8(6):e65628. doi: 10.1371/journal.pone.0065628. Print 2013.

9.

A central role for TFIID in the pluripotent transcription circuitry.

Pijnappel WW, Esch D, Baltissen MP, Wu G, Mischerikow N, Bergsma AJ, van der Wal E, Han DW, Bruch Hv, Moritz S, Lijnzaad P, Altelaar AF, Sameith K, Zaehres H, Heck AJ, Holstege FC, Schöler HR, Timmers HT.

Nature. 2013 Mar 28;495(7442):516-9. doi: 10.1038/nature11970. Epub 2013 Mar 17.

PMID:
23503660
10.

The specificity and topology of chromatin interaction pathways in yeast.

Lenstra TL, Benschop JJ, Kim T, Schulze JM, Brabers NA, Margaritis T, van de Pasch LA, van Heesch SA, Brok MO, Groot Koerkamp MJ, Ko CW, van Leenen D, Sameith K, van Hooff SR, Lijnzaad P, Kemmeren P, Hentrich T, Kobor MS, Buratowski S, Holstege FC.

Mol Cell. 2011 May 20;42(4):536-49. doi: 10.1016/j.molcel.2011.03.026.

11.

Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs.

Daugeron MC, Lenstra TL, Frizzarin M, El Yacoubi B, Liu X, Baudin-Baillieu A, Lijnzaad P, Decourty L, Saveanu C, Jacquier A, Holstege FC, de Crécy-Lagard V, van Tilbeurgh H, Libri D.

Nucleic Acids Res. 2011 Aug;39(14):6148-60. doi: 10.1093/nar/gkr178. Epub 2011 Apr 1.

12.

Functional overlap and regulatory links shape genetic interactions between signaling pathways.

van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC.

Cell. 2010 Dec 10;143(6):991-1004. doi: 10.1016/j.cell.2010.11.021.

13.

A consensus of core protein complex compositions for Saccharomyces cerevisiae.

Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HW, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FC, Kemmeren P.

Mol Cell. 2010 Jun 25;38(6):916-28. doi: 10.1016/j.molcel.2010.06.002.

14.

Adaptable gene-specific dye bias correction for two-channel DNA microarrays.

Margaritis T, Lijnzaad P, van Leenen D, Bouwmeester D, Kemmeren P, van Hooff SR, Holstege FC.

Mol Syst Biol. 2009;5:266. doi: 10.1038/msb.2009.21. Epub 2009 Apr 28.

15.

On defining the dynamics of hydrophobic patches on protein surfaces.

Lijnzaad P, Feenstra KA, Heringa J, Holstege FC.

Proteins. 2008 Jul;72(1):105-14. doi: 10.1002/prot.21924.

PMID:
18186474
16.

Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA.

Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, van de Peppel J, Werner M, Holstege FC.

Mol Cell. 2006 Apr 21;22(2):179-92.

17.

Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.

Radonjic M, Andrau JC, Lijnzaad P, Kemmeren P, Kockelkorn TT, van Leenen D, van Berkum NL, Holstege FC.

Mol Cell. 2005 Apr 15;18(2):171-83.

18.

An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas.

Roepman P, Wessels LF, Kettelarij N, Kemmeren P, Miles AJ, Lijnzaad P, Tilanus MG, Koole R, Hordijk GJ, van der Vliet PC, Reinders MJ, Slootweg PJ, Holstege FC.

Nat Genet. 2005 Feb;37(2):182-6. Epub 2005 Jan 9.

PMID:
15640797
19.

The Ensembl genome database project.

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M.

Nucleic Acids Res. 2002 Jan 1;30(1):38-41.

20.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

Wang L, Rodriguez-Tomé P, Redaschi N, McNeil P, Robinson A, Lijnzaad P.

Genome Biol. 2000;1(5):RESEARCH0010. Epub 2000 Nov 6.

21.

RHdb: the Radiation Hybrid database.

Rodriguez-Tomé P, Lijnzaad P.

Nucleic Acids Res. 2001 Jan 1;29(1):165-6.

22.

RHdb: the radiation hybrid database.

Rodriguez-Tomé P, Lijnzaad P.

Nucleic Acids Res. 2000 Jan 1;28(1):146-7.

23.

A proposal for a standard CORBA interface for genome maps.

Barillot E, Leser U, Lijnzaad P, Cussat-Blanc C, Jungfer K, Guyon F, Vaysseix G, Helgesen C, Rodriguez-Tomé P.

Bioinformatics. 1999 Feb;15(2):157-69.

PMID:
10089201
24.

The radiation hybrid database.

Rodriguez-Tomé P, Lijnzaad P.

Nucleic Acids Res. 1999 Jan 1;27(1):115-8.

25.

A physical map of 30,000 human genes.

Deloukas P, Schuler GD, Gyapay G, Beasley EM, Soderlund C, Rodriguez-Tomé P, Hui L, Matise TC, McKusick KB, Beckmann JS, Bentolila S, Bihoreau M, Birren BB, Browne J, Butler A, Castle AB, Chiannilkulchai N, Clee C, Day PJ, Dehejia A, Dibling T, Drouot N, Duprat S, Fizames C, Fox S, Gelling S, Green L, Harrison P, Hocking R, Holloway E, Hunt S, Keil S, Lijnzaad P, Louis-Dit-Sully C, Ma J, Mendis A, Miller J, Morissette J, Muselet D, Nusbaum HC, Peck A, Rozen S, Simon D, Slonim DK, Staples R, Stein LD, Stewart EA, Suchard MA, Thangarajah T, Vega-Czarny N, Webber C, Wu X, Hudson J, Auffray C, Nomura N, Sikela JM, Polymeropoulos MH, James MR, Lander ES, Hudson TJ, Myers RM, Cox DR, Weissenbach J, Boguski MS, Bentley DR.

Science. 1998 Oct 23;282(5389):744-6.

26.

The Radiation Hybrid Database.

Lijnzaad P, Helgesen C, Rodriguez-Tomé P.

Nucleic Acids Res. 1998 Jan 1;26(1):102-5.

27.

Hydrophobic patches on protein subunit interfaces: characteristics and prediction.

Lijnzaad P, Argos P.

Proteins. 1997 Jul;28(3):333-43.

PMID:
9223180
28.

A CORBA server for the Radiation Hybrid DataBase.

Rodriguez-Tomé P, Helgesen C, Lijnzaad P, Jungfer K.

Proc Int Conf Intell Syst Mol Biol. 1997;5:250-3.

PMID:
9322045
29.

The Radiation Hybrid Database.

Rodriguez-Tomé P, Lijnzaad P.

Nucleic Acids Res. 1997 Jan 1;25(1):81-4.

30.

A method for detecting hydrophobic patches on protein surfaces.

Lijnzaad P, Berendsen HJ, Argos P.

Proteins. 1996 Oct;26(2):192-203.

PMID:
8916227
31.

Hydrophobic patches on the surfaces of protein structures.

Lijnzaad P, Berendsen HJ, Argos P.

Proteins. 1996 Jul;25(3):389-97.

PMID:
8844873
32.

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