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Items: 17


Antisense transcriptional interference mediates condition-specific gene repression in budding yeast.

Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G.

Nucleic Acids Res. 2018 Jul 6;46(12):6009-6025. doi: 10.1093/nar/gky342.


Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast.

Peña-Castillo L, Badis G.

Methods Mol Biol. 2016;1361:203-25. doi: 10.1007/978-1-4939-3079-1_12.


Yeast ribosomal protein L7 and its homologue Rlp7 are simultaneously present at distinct sites on pre-60S ribosomal particles.

Babiano R, Badis G, Saveanu C, Namane A, Doyen A, Díaz-Quintana A, Jacquier A, Fromont-Racine M, de la Cruz J.

Nucleic Acids Res. 2013 Nov;41(20):9461-70. doi: 10.1093/nar/gkt726. Epub 2013 Aug 13.


Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences.

Santos MA, Turinsky AL, Ong S, Tsai J, Berger MF, Badis G, Talukder S, Gehrke AR, Bulyk ML, Hughes TR, Wodak SJ.

Nucleic Acids Res. 2010 Dec;38(22):7927-42. doi: 10.1093/nar/gkq714. Epub 2010 Aug 12.


Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.

Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J.

EMBO J. 2010 Jul 7;29(13):2147-60. doi: 10.1038/emboj.2010.106. Epub 2010 Jun 1.


Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.


TFCat: the curated catalog of mouse and human transcription factors.

Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R.

Genome Biol. 2009;10(3):R29. doi: 10.1186/gb-2009-10-3-r29. Epub 2009 Mar 12.


A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.


Predicting the binding preference of transcription factors to individual DNA k-mers.

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR.

Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16.


Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.


Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer.

Sandhu C, Hewel JA, Badis G, Talukder S, Liu J, Hughes TR, Emili A.

J Proteome Res. 2008 Apr;7(4):1529-41. doi: 10.1021/pr700836q. Epub 2008 Feb 27.


Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription.

Berger AB, Decourty L, Badis G, Nehrbass U, Jacquier A, Gadal O.

Mol Cell Biol. 2007 Nov;27(22):8015-26. Epub 2007 Sep 17.


Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase.

Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A.

Cell. 2005 Jun 3;121(5):725-37.


The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae.

Torchet C, Badis G, Devaux F, Costanzo G, Werner M, Jacquier A.

RNA. 2005 Jun;11(6):928-38.


Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae.

Boyer J, Badis G, Fairhead C, Talla E, Hantraye F, Fabre E, Fischer G, Hennequin C, Koszul R, Lafontaine I, Ozier-Kalogeropoulos O, Ricchetti M, Richard GF, Thierry A, Dujon B.

Genome Biol. 2004;5(9):R72. Epub 2004 Aug 31.


Targeted mRNA degradation by deadenylation-independent decapping.

Badis G, Saveanu C, Fromont-Racine M, Jacquier A.

Mol Cell. 2004 Jul 2;15(1):5-15.


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