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Items: 19

1.

CiliaCarta: An integrated and validated compendium of ciliary genes.

van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li C, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, van Reeuwijk J, Wheway G, Knapp B, Scheel JF, Franco B, Mans DA, van Wijk E, Képès F, Slaats GG, Toedt G, Kremer H, Omran H, Szymanska K, Koutroumpas K, Ueffing M, Nguyen TT, Letteboer SJF, Oud MM, van Beersum SEC, Schmidts M, Beales PL, Lu Q, Giles RH, Szklarczyk R, Russell RB, Gibson TJ, Johnson CA, Blacque OE, Wolfrum U, Boldt K, Roepman R, Hernandez-Hernandez V, Huynen MA.

PLoS One. 2019 May 16;14(5):e0216705. doi: 10.1371/journal.pone.0216705. eCollection 2019.

2.

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists.

van Hooff JJE, Tromer E, van Dam TJP, Kops GJPL, Snel B.

Bioessays. 2019 May;41(5):e1900006. doi: 10.1002/bies.201900006.

PMID:
31026339
3.

Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites.

Meerstein-Kessel L, van der Lee R, Stone W, Lanke K, Baker DA, Alano P, Silvestrini F, Janse CJ, Khan SM, van de Vegte-Bolmer M, Graumans W, Siebelink-Stoter R, Kooij TWA, Marti M, Drakeley C, Campo JJ, van Dam TJP, Sauerwein R, Bousema T, Huynen MA.

Sci Rep. 2018 Jan 11;8(1):410. doi: 10.1038/s41598-017-18840-7.

4.

The Gene Ontology of eukaryotic cilia and flagella.

Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J.

Cilia. 2017 Nov 16;6:10. doi: 10.1186/s13630-017-0054-8. eCollection 2017.

5.

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts.

van der Lee R, Wiel L, van Dam TJP, Huynen MA.

Nucleic Acids Res. 2017 Oct 13;45(18):10634-10648. doi: 10.1093/nar/gkx704.

6.

The Role of Efflux Pumps in Tuberculosis Treatment and Their Promise as a Target in Drug Development: Unraveling the Black Box.

Te Brake LHM, de Knegt GJ, de Steenwinkel JE, van Dam TJP, Burger DM, Russel FGM, van Crevel R, Koenderink JB, Aarnoutse RE.

Annu Rev Pharmacol Toxicol. 2018 Jan 6;58:271-291. doi: 10.1146/annurev-pharmtox-010617-052438. Epub 2017 Jul 17. Review.

PMID:
28715978
7.

Interspecies differences in PTH-mediated PKA phosphorylation of the epithelial calcium channel TRPV5.

van Goor MK, Verkaart S, van Dam TJ, Huynen MA, van der Wijst J.

Pflugers Arch. 2017 Oct;469(10):1301-1311. doi: 10.1007/s00424-017-1996-9. Epub 2017 May 22.

8.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJ, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJ, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R; UK10K Rare Diseases Group.

Nat Commun. 2016 May 13;7:11491. doi: 10.1038/ncomms11491.

9.

KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome.

Sanders AA, de Vrieze E, Alazami AM, Alzahrani F, Malarkey EB, Sorusch N, Tebbe L, Kuhns S, van Dam TJ, Alhashem A, Tabarki B, Lu Q, Lambacher NJ, Kennedy JE, Bowie RV, Hetterschijt L, van Beersum S, van Reeuwijk J, Boldt K, Kremer H, Kesterson RA, Monies D, Abouelhoda M, Roepman R, Huynen MH, Ueffing M, Russell RB, Wolfrum U, Yoder BK, van Wijk E, Alkuraya FS, Blacque OE.

Genome Biol. 2015 Dec 29;16:293. doi: 10.1186/s13059-015-0858-z.

10.

OFIP/KIAA0753 forms a complex with OFD1 and FOR20 at pericentriolar satellites and centrosomes and is mutated in one individual with oral-facial-digital syndrome.

Chevrier V, Bruel AL, Van Dam TJ, Franco B, Lo Scalzo M, Lembo F, Audebert S, Baudelet E, Isnardon D, Bole A, Borg JP, Kuentz P, Thevenon J, Burglen L, Faivre L, Rivière JB, Huynen MA, Birnbaum D, Rosnet O, Thauvin-Robinet C.

Hum Mol Genet. 2016 Feb 1;25(3):497-513. doi: 10.1093/hmg/ddv488. Epub 2015 Dec 7.

PMID:
26643951
11.

TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome.

Lambacher NJ, Bruel AL, van Dam TJ, Szymańska K, Slaats GG, Kuhns S, McManus GJ, Kennedy JE, Gaff K, Wu KM, van der Lee R, Burglen L, Doummar D, Rivière JB, Faivre L, Attié-Bitach T, Saunier S, Curd A, Peckham M, Giles RH, Johnson CA, Huynen MA, Thauvin-Robinet C, Blacque OE.

Nat Cell Biol. 2016 Jan;18(1):122-31. doi: 10.1038/ncb3273. Epub 2015 Nov 23.

12.

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes.

Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TT, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, Horn N, Boldt K, Parry DA, Letteboer SJF, Roosing S, Adams M, Bell SM, Bond J, Higgins J, Morrison EE, Tomlinson DC, Slaats GG, van Dam TJP, Huang L, Kessler K, Giessl A, Logan CV, Boyle EA, Shendure J, Anazi S, Aldahmesh M, Al Hazzaa S, Hegele RA, Ober C, Frosk P, Mhanni AA, Chodirker BN, Chudley AE, Lamont R, Bernier FP, Beaulieu CL, Gordon P, Pon RT, Donahue C, Barkovich AJ, Wolf L, Toomes C, Thiel CT, Boycott KM, McKibbin M, Inglehearn CF; UK10K Consortium; University of Washington Center for Mendelian Genomics, Stewart F, Omran H, Huynen MA, Sergouniotis PI, Alkuraya FS, Parboosingh JS, Innes AM, Willoughby CE, Giles RH, Webster AR, Ueffing M, Blacque O, Gleeson JG, Wolfrum U, Beales PL, Gibson T, Doherty D, Mitchison HM, Roepman R, Johnson CA.

Nat Cell Biol. 2015 Aug;17(8):1074-1087. doi: 10.1038/ncb3201. Epub 2015 Jul 13.

13.

The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium.

van Dam TJ, Wheway G, Slaats GG; SYSCILIA Study Group, Huynen MA, Giles RH.

Cilia. 2013 May 31;2(1):7. doi: 10.1186/2046-2530-2-7.

14.

Evolution of modular intraflagellar transport from a coatomer-like progenitor.

van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6943-8. doi: 10.1073/pnas.1221011110. Epub 2013 Apr 8.

15.

The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.

Suijkerbuijk SJ, van Dam TJ, Karagöz GE, von Castelmur E, Hubner NC, Duarte AM, Vleugel M, Perrakis A, Rüdiger SG, Snel B, Kops GJ.

Dev Cell. 2012 Jun 12;22(6):1321-9. doi: 10.1016/j.devcel.2012.03.009.

16.

Evolution of the TOR pathway.

van Dam TJ, Zwartkruis FJ, Bos JL, Snel B.

J Mol Evol. 2011 Oct;73(3-4):209-20. doi: 10.1007/s00239-011-9469-9. Epub 2011 Nov 5.

17.

Evolution of the Ras-like small GTPases and their regulators.

van Dam TJ, Bos JL, Snel B.

Small GTPases. 2011 Jan;2(1):4-16.

18.

Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi.

van Dam TJ, Rehmann H, Bos JL, Snel B.

Cell Signal. 2009 Nov;21(11):1579-85. doi: 10.1016/j.cellsig.2009.06.004. Epub 2009 Jun 28.

PMID:
19567266
19.

Protein complex evolution does not involve extensive network rewiring.

van Dam TJ, Snel B.

PLoS Comput Biol. 2008 Jul 25;4(7):e1000132. doi: 10.1371/journal.pcbi.1000132.

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