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Items: 39

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.

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.

3.

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.

4.

NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish.

Dona M, Bachmann-Gagescu R, Texier Y, Toedt G, Hetterschijt L, Tonnaer EL, Peters TA, van Beersum SE, Bergboer JG, Horn N, de Vrieze E, Slijkerman RW, van Reeuwijk J, Flik G, Keunen JE, Ueffing M, Gibson TJ, Roepman R, Boldt K, Kremer H, van Wijk E.

PLoS Genet. 2015 Oct 20;11(10):e1005574. doi: 10.1371/journal.pgen.1005574. eCollection 2015 Oct.

5.

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.

6.

Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry.

Texier Y, Toedt G, Gorza M, Mans DA, van Reeuwijk J, Horn N, Willer J, Katsanis N, Roepman R, Gibson TJ, Ueffing M, Boldt K.

Mol Cell Proteomics. 2014 May;13(5):1382-91. doi: 10.1074/mcp.O113.033233. Epub 2014 Feb 21.

7.

Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma.

Wu H, Haag D, Muley T, Warth A, Zapatka M, Toedt G, Pscherer A, Hahn M, Rieker RJ, Wachter DL, Meister M, Schnabel P, Müller-Decker K, Rogers MA, Hoffmann H, Lichter P.

Genes Chromosomes Cancer. 2013 Mar;52(3):250-64. doi: 10.1002/gcc.22025. Epub 2012 Oct 17.

PMID:
23074073
8.

A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins.

Jiang K, Toedt G, Montenegro Gouveia S, Davey NE, Hua S, van der Vaart B, Grigoriev I, Larsen J, Pedersen LB, Bezstarosti K, Lince-Faria M, Demmers J, Steinmetz MO, Gibson TJ, Akhmanova A.

Curr Biol. 2012 Oct 9;22(19):1800-7. doi: 10.1016/j.cub.2012.07.047. Epub 2012 Aug 9.

9.

Nos2 inactivation promotes the development of medulloblastoma in Ptch1(+/-) mice by deregulation of Gap43-dependent granule cell precursor migration.

Haag D, Zipper P, Westrich V, Karra D, Pfleger K, Toedt G, Blond F, Delhomme N, Hahn M, Reifenberger J, Reifenberger G, Lichter P.

PLoS Genet. 2012;8(3):e1002572. doi: 10.1371/journal.pgen.1002572. Epub 2012 Mar 15.

10.

Downregulation of PRDX1 by promoter hypermethylation is frequent in 1p/19q-deleted oligodendroglial tumours and increases radio- and chemosensitivity of Hs683 glioma cells in vitro.

Dittmann LM, Danner A, Gronych J, Wolter M, Stühler K, Grzendowski M, Becker N, Bageritz J, Goidts V, Toedt G, Felsberg J, Sabel MC, Barbus S, Reifenberger G, Lichter P, Tews B.

Oncogene. 2012 Jul 19;31(29):3409-18. doi: 10.1038/onc.2011.513. Epub 2011 Dec 12.

PMID:
22158042
11.

ELM--the database of eukaryotic linear motifs.

Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51. doi: 10.1093/nar/gkr1064. Epub 2011 Nov 21.

12.

RNAi screening in glioma stem-like cells identifies PFKFB4 as a key molecule important for cancer cell survival.

Goidts V, Bageritz J, Puccio L, Nakata S, Zapatka M, Barbus S, Toedt G, Campos B, Korshunov A, Momma S, Van Schaftingen E, Reifenberger G, Herold-Mende C, Lichter P, Radlwimmer B.

Oncogene. 2012 Jul 5;31(27):3235-43. doi: 10.1038/onc.2011.490. Epub 2011 Nov 7.

PMID:
22056879
13.

FSTL5 is a marker of poor prognosis in non-WNT/non-SHH medulloblastoma.

Remke M, Hielscher T, Korshunov A, Northcott PA, Bender S, Kool M, Westermann F, Benner A, Cin H, Ryzhova M, Sturm D, Witt H, Haag D, Toedt G, Wittmann A, Schöttler A, von Bueren AO, von Deimling A, Rutkowski S, Scheurlen W, Kulozik AE, Taylor MD, Lichter P, Pfister SM.

J Clin Oncol. 2011 Oct 10;29(29):3852-61. doi: 10.1200/JCO.2011.36.2798. Epub 2011 Sep 12.

PMID:
21911727
14.

Attributes of short linear motifs.

Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ.

Mol Biosyst. 2012 Jan;8(1):268-81. doi: 10.1039/c1mb05231d. Epub 2011 Sep 12.

PMID:
21909575
15.

Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data.

Becker N, Toedt G, Lichter P, Benner A.

BMC Bioinformatics. 2011 May 9;12:138. doi: 10.1186/1471-2105-12-138.

16.

Inflammatory cytokines and signaling pathways are associated with survival of primary chronic lymphocytic leukemia cells in vitro: a dominant role of CCL2.

Schulz A, Toedt G, Zenz T, Stilgenbauer S, Lichter P, Seiffert M.

Haematologica. 2011 Mar;96(3):408-16. doi: 10.3324/haematol.2010.031377. Epub 2010 Dec 6.

17.

Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain.

Stange DE, Engel F, Longerich T, Koo BK, Koch M, Delhomme N, Aigner M, Toedt G, Schirmacher P, Lichter P, Weitz J, Radlwimmer B.

Gut. 2010 Sep;59(9):1236-44. doi: 10.1136/gut.2009.195701. Epub 2010 May 17.

PMID:
20479215
18.

Molecular signatures classify astrocytic gliomas by IDH1 mutation status.

Toedt G, Barbus S, Wolter M, Felsberg J, Tews B, Blond F, Sabel MC, Hofmann S, Becker N, Hartmann C, Ohgaki H, von Deimling A, Wiestler OD, Hahn M, Lichter P, Reifenberger G, Radlwimmer B.

Int J Cancer. 2011 Mar 1;128(5):1095-103. doi: 10.1002/ijc.25448.

19.

Recurrent copy number gain of transcription factor SOX2 and corresponding high protein expression in oral squamous cell carcinoma.

Freier K, Knoepfle K, Flechtenmacher C, Pungs S, Devens F, Toedt G, Hofele C, Joos S, Lichter P, Radlwimmer B.

Genes Chromosomes Cancer. 2010 Jan;49(1):9-16. doi: 10.1002/gcc.20714.

PMID:
19787784
20.

High-resolution genomic profiling of childhood T-ALL reveals frequent copy-number alterations affecting the TGF-beta and PI3K-AKT pathways and deletions at 6q15-16.1 as a genomic marker for unfavorable early treatment response.

Remke M, Pfister S, Kox C, Toedt G, Becker N, Benner A, Werft W, Breit S, Liu S, Engel F, Wittmann A, Zimmermann M, Stanulla M, Schrappe M, Ludwig WD, Bartram CR, Radlwimmer B, Muckenthaler MU, Lichter P, Kulozik AE.

Blood. 2009 Jul 30;114(5):1053-62. doi: 10.1182/blood-2008-10-186536. Epub 2009 Apr 30.

21.

penalizedSVM: a R-package for feature selection SVM classification.

Becker N, Werft W, Toedt G, Lichter P, Benner A.

Bioinformatics. 2009 Jul 1;25(13):1711-2. doi: 10.1093/bioinformatics/btp286. Epub 2009 Apr 27.

PMID:
19398451
22.

Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci.

Pfister S, Remke M, Benner A, Mendrzyk F, Toedt G, Felsberg J, Wittmann A, Devens F, Gerber NU, Joos S, Kulozik A, Reifenberger G, Rutkowski S, Wiestler OD, Radlwimmer B, Scheurlen W, Lichter P, Korshunov A.

J Clin Oncol. 2009 Apr 1;27(10):1627-36. doi: 10.1200/JCO.2008.17.9432. Epub 2009 Mar 2.

PMID:
19255330
23.

BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas.

Pfister S, Janzarik WG, Remke M, Ernst A, Werft W, Becker N, Toedt G, Wittmann A, Kratz C, Olbrich H, Ahmadi R, Thieme B, Joos S, Radlwimmer B, Kulozik A, Pietsch T, Herold-Mende C, Gnekow A, Reifenberger G, Korshunov A, Scheurlen W, Omran H, Lichter P.

J Clin Invest. 2008 May;118(5):1739-49. doi: 10.1172/JCI33656.

24.

Etiology-dependent molecular mechanisms in human hepatocarcinogenesis.

Schlaeger C, Longerich T, Schiller C, Bewerunge P, Mehrabi A, Toedt G, Kleeff J, Ehemann V, Eils R, Lichter P, Schirmacher P, Radlwimmer B.

Hepatology. 2008 Feb;47(2):511-20.

PMID:
18161050
25.

Supratentorial primitive neuroectodermal tumors of the central nervous system frequently harbor deletions of the CDKN2A locus and other genomic aberrations distinct from medulloblastomas.

Pfister S, Remke M, Toedt G, Werft W, Benner A, Mendrzyk F, Wittmann A, Devens F, von Hoff K, Rutkowski S, Kulozik A, Radlwimmer B, Scheurlen W, Lichter P, Korshunov A.

Genes Chromosomes Cancer. 2007 Sep;46(9):839-51.

PMID:
17592618
26.

Cytogenetic and molecular genetic analyses of giant cell glioblastoma multiforme reveal distinct profiles in giant cell and non-giant cell subpopulations.

Martinez R, Roggendorf W, Baretton G, Klein R, Toedt G, Lichter P, Schackert G, Joos S.

Cancer Genet Cytogenet. 2007 May;175(1):26-34.

PMID:
17498554
27.

DNA microarray analysis identifies candidate regions and genes in unexplained mental retardation.

Engels H, Brockschmidt A, Hoischen A, Landwehr C, Bosse K, Walldorf C, Toedt G, Radlwimmer B, Propping P, Lichter P, Weber RG.

Neurology. 2007 Mar 6;68(10):743-50.

PMID:
17339581
28.

Hypermethylation and transcriptional downregulation of the CITED4 gene at 1p34.2 in oligodendroglial tumours with allelic losses on 1p and 19q.

Tews B, Roerig P, Hartmann C, Hahn M, Felsberg J, Blaschke B, Sabel M, Kunitz A, Toedt G, Neben K, Benner A, von Deimling A, Reifenberger G, Lichter P.

Oncogene. 2007 Jul 26;26(34):5010-6. Epub 2007 Feb 19.

PMID:
17311001
29.

Gene expression signature predicting pathologic complete response with gemcitabine, epirubicin, and docetaxel in primary breast cancer.

Thuerigen O, Schneeweiss A, Toedt G, Warnat P, Hahn M, Kramer H, Brors B, Rudlowski C, Benner A, Schuetz F, Tews B, Eils R, Sinn HP, Sohn C, Lichter P.

J Clin Oncol. 2006 Apr 20;24(12):1839-45.

PMID:
16622258
30.

Identification of gains on 1q and epidermal growth factor receptor overexpression as independent prognostic markers in intracranial ependymoma.

Mendrzyk F, Korshunov A, Benner A, Toedt G, Pfister S, Radlwimmer B, Lichter P.

Clin Cancer Res. 2006 Apr 1;12(7 Pt 1):2070-9.

31.

Identification of novel oligodendroglioma-associated candidate tumor suppressor genes in 1p36 and 19q13 using microarray-based expression profiling.

Tews B, Felsberg J, Hartmann C, Kunitz A, Hahn M, Toedt G, Neben K, Hummerich L, von Deimling A, Reifenberger G, Lichter P.

Int J Cancer. 2006 Aug 15;119(4):792-800.

32.

High-resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer.

Stange DE, Radlwimmer B, Schubert F, Traub F, Pich A, Toedt G, Mendrzyk F, Lehmann U, Eils R, Kreipe H, Lichter P.

Clin Cancer Res. 2006 Jan 15;12(2):345-52.

33.

Isochromosome breakpoints on 17p in medulloblastoma are flanked by different classes of DNA sequence repeats.

Mendrzyk F, Korshunov A, Toedt G, Schwarz F, Korn B, Joos S, Hochhaus A, Schoch C, Lichter P, Radlwimmer B.

Genes Chromosomes Cancer. 2006 Apr;45(4):401-10.

PMID:
16419060
34.

Recurrent coamplification of cytoskeleton-associated genes EMS1 and SHANK2 with CCND1 in oral squamous cell carcinoma.

Freier K, Sticht C, Hofele C, Flechtenmacher C, Stange D, Puccio L, Toedt G, Radlwimmer B, Lichter P, Joos S.

Genes Chromosomes Cancer. 2006 Feb;45(2):118-25.

PMID:
16235239
35.

Patient-based cross-platform comparison of oligonucleotide microarray expression profiles.

Schlingemann J, Habtemichael N, Ittrich C, Toedt G, Kramer H, Hambek M, Knecht R, Lichter P, Stauber R, Hahn M.

Lab Invest. 2005 Aug;85(8):1024-39.

36.

FACT--a framework for the functional interpretation of high-throughput experiments.

Kokocinski F, Delhomme N, Wrobel G, Hummerich L, Toedt G, Lichter P.

BMC Bioinformatics. 2005 Jun 28;6:161.

37.

Detection of chromosomal imbalances in retinoblastoma by matrix-based comparative genomic hybridization.

Zielinski B, Gratias S, Toedt G, Mendrzyk F, Stange DE, Radlwimmer B, Lohmann DR, Lichter P.

Genes Chromosomes Cancer. 2005 Jul;43(3):294-301.

PMID:
15834944
38.

Effective transcriptome amplification for expression profiling on sense-oriented oligonucleotide microarrays.

Schlingemann J, Thuerigen O, Ittrich C, Toedt G, Kramer H, Hahn M, Lichter P.

Nucleic Acids Res. 2005 Feb 17;33(3):e29.

39.

Site-specific protein modification to identify the MutL interface of MutH.

Toedt GH, Krishnan R, Friedhoff P.

Nucleic Acids Res. 2003 Feb 1;31(3):819-25.

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