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Tag tf [219 articles]

Recent papers classified by the tag tf.
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  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to microarray motif tf by xwbcn on 2006-04-05 03:17:26 as ** along with 9 people and 5 groups tharris ana adepace nickluscombe noano koller jrest phoenixzxl klo C. elegans / WormBase structural_bioinformatics Bioinformatics EisenLab EBI-regulation
  • Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data
    BMC Bioinformatics, Vol. 7 (04 July 2006), 330.
    by Seon-Young Kim, Yongsung Kim
    posted to tf promoter microarray mammal human_genome genome expression chip by xwbcn on 2007-01-13 04:28:37 as ** along with 3 people heliopais jfr Ao_Li2007
  • Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.
    Proc Natl Acad Sci U S A (31 July 2006)
    by Celine Moorman, Ling V V Sun, Junbai Wang, Elzo de Wit, Wendy Talhout, Lucas D D Ward, Frauke Greil, Xiang-Jun J Lu, Kevin P P White, Harmen J J Bussemaker, Bas van Steensel
    posted to interaction pathway tf transcriptome by xwbcn on 2006-10-12 13:20:52 as ** along with 4 people and 4 groups ana indigoviolet johncumbers wrowell structural_bioinformatics Bioinformatics EisenLab Cline_lab
  • Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.
    Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 7145-7150.
    by X Xie, TS Mikkelsen, A Gnirke, K Lindblad-Toh, M Kellis, ES Lander
    posted to genome_alignment human human_genome mammal motif networks tf by xwbcn on 2007-05-11 09:54:09 as ** along with 5 people and 1 group cisevol aprasad olympos rschulz bpcusack JacksonLab
  • Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
    Nat Genet, Vol. 35, No. 1. (2003), pp. 57-64.
    by Gael Yvert, Rachel B Brem, Jacqueline Whittle, Joshua M Akey, Eric Foss, Erin N Smith, Rachel Mackelprang, Leonid Kruglyak
    posted to tf trans-regulatory yeast by xwbcn on 2007-05-23 09:59:14 as ** along with 3 people and 1 group RMGraze oannes lp2 Regulomics_UCHSC
  • Identifying regulatory networks by combinatorial analysis of promoter elements.
    Nat Genet, Vol. 29, No. 2. (October 2001), pp. 153-159.
    by Y Pilpel, P Sudarsanam, GM Church
    posted to microarray motif tf by xwbcn on 2006-04-05 03:16:44 as ** along with 6 people and 1 group imouthesmp troels_marstrand wnpx noano koller windman83 Bioinformatics
  • Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.
    Proc Natl Acad Sci U S A (31 March 2006)
    by Ji-Young Y Lee, Juliette Colinas, Jean Y Y Wang, Daniel Mace, Uwe Ohler, Philip N N Benfey
    posted to arabidopsis microarray mirna motif tf by xwbcn on 2006-04-05 02:16:36 as *** along with 2 people and 1 group cdawson dlmace GIG
  • High-throughput Biochemical Analysis of in-vivo Location Data Reveals Novel Classes of POU5F1(Oct4)/DNA complexes.
    Genome Res (22 January 2008)
    by Dean Tantin, Matt Gemberling, Catherine Callister, Will Fairbrother
    posted to chip methods pou5f1 tf by xingxu on 2008-05-19 20:20:46 as ** along with 2 people maximilianh caseybrown
  • Identification of transcription factor binding sites with variable-order Bayesian networks.
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2657-2666.
    by I Ben-Gal, A Shani, A Gohr, J Grau, S Arviv, A Shmilovici, S Posch, I Grosse
    posted to bayesian bayesnet tf by wnpx on 2006-01-05 22:36:49 as ** along with 1 person troels_marstrand
  • ETS transcription factors and regulation of immunity
    Archivum Immunologiae et Therapiae Experimentalis, Vol. 54, No. 3. (23 June 2006), pp. 149-163.
    by Sarah Gallant, Gary Gilkeson
    posted to immunology mastitis saureus tf by waszak on 2008-05-21 16:28:18 as **
  • Changes in the Expression of Many Ets Family Transcription Factors and of Potential Target Genes in Normal Mammary Tissue and Tumors
    J. Biol. Chem., Vol. 279, No. 12. (19 March 2004), pp. 11281-11292.
    by Christina K Galang, William J Muller, Gabriele Foos, Robert G Oshima, Craig A Hauser
    posted to ets mastitis tf by waszak on 2008-05-15 21:38:56 as **
  • NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
    Nucleic Acids Research, Vol. 33, No. 5. (2005), pp. 1445-1453.
    by Thomas A Down, Tim J Hubbard
    posted to mcmc nestedsampling tf by waszak on 2008-06-30 01:08:45 as ** along with 4 people and 1 group emptyhb lyongu dpollard dquest EisenLab
  • Design Logic of a Cannabinoid Receptor Signaling Network That Triggers Neurite Outgrowth
    Science, Vol. 320, No. 5878. (16 May 2008), pp. 903-909.
    by Kenneth D Bromberg, Avi Ma'ayan, Susana R Neves, Ravi Iyengar
    posted to microarray networks tf by waszak on 2008-05-17 11:24:08 as ** along with 3 people AlexanderPico caseybrown oelemento
  • notes Discerning static and causal interactions in genome-wide reverse engineering problems.
    Bioinformatics (Oxford, England) (8 May 2008)
    by M Zampieri, N Soranzo, C Altafini
    posted to causal correlation distance metrics protein tf by verdicchio on 2008-08-04 21:31:02 as ** along with 4 people roys guhjy tmmurali balicea
  • Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. 4925-4936.
    by Yu, Xueping, Lin, Jimmy, Zack, J Donald, Qian, Jiang
    posted to interaction tf tissue-specific by snow_dragon on 2008-08-12 15:26:16 as read along with 1 person olympos
  • Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae
    Nucleic Acids Research, Vol. 34, No. 3. (2006), pp. 917-927.
    by Xueping Yu, Jimmy Lin, Tomohiro Masuda, Noriko Esumi, Donald J Zack, Jiang Qian
    posted to co-regulation of tf yeast by snow_dragon on 2008-08-12 15:30:49 as read along with 2 people hplatero olympos
  • The effect of experience on the test-driven development process
    Empirical Software Engineering, Vol. 12, No. 6. (1 December 2007), pp. 593-615.
    by Matthias Müller, Andreas Höfer
    posted to experiment observatory testing tf by smogit on 2008-06-13 15:31:44 as ** along with 1 person fabul
  • Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor.
    BMC Genomics, Vol. 9 (12 February 2008), 79.
    by Emma Laing, Khushwant Sidhu, Simon J Hubbard
    posted to operons regulation tf tfbs by sdyxz on 2008-02-20 15:08:19 as * along with 1 person msuarezdiez
  • Integrated Assessment and Prediction of Transcription Factor Binding
    PLoS Computational Biology, Vol. 2, No. 6. (1 June 2006), e70.
    by Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker
    posted to prediction target tf transcription by samal on 2006-08-22 07:03:55 as ** along with 7 people and 1 group nklee jfr balajis wnpx emilyhare reidy Ao_Li2007 EisenLab
  • Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
    Nature, Vol. 440, No. 7087., pp. 1050-1053.
    by Benjamin Prud'homme, Nicolas Gompel, Antonis Rokas, Victoria A Kassner, Thomas M Williams, Shu-Dan Yeh, John R True, Sean B Carroll
    posted to phenotype regulation tf by ranb on 2006-04-20 04:56:52 as ** along with 9 people and 1 group carlfulp RMGraze dpollard balicea tny adepace Garamonfok blobbybirdman emptyhb EisenLab
  • Transcription Factor Map Alignment of Promoter Regions
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e49.
    by Enrique Blanco, Xavier Messeguer, Temple F Smith, Roderic Guigó
    posted to algorithm modules reg-class tf by ranb on 2006-05-26 19:54:07 as **** along with 2 people brixtonmc oscarluoinau
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to tf tool by ranb on 2006-04-14 02:28:09 as read along with 29 people and 6 groups daforerog yylin cambray emptyhb bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Model-based identification of cis-acting elements from microarray data
    Genomics, Vol. In Press, Corrected Proof
    by Yunlong Liu, Milton W Taylor, Howard J Edenberg
    posted to algorithm model tf by ranb on 2006-05-30 18:02:55 as *****
  • Expression profiling in primates reveals a rapid evolution of human transcription factors
    Nature, Vol. 440, No. 7081. (March 2006), pp. 242-245.
    by Yoav Gilad, Alicia Oshlack, Gordon K Smyth, Terence P Speed, Kevin P White
    posted to evolution expression primates tf by ranb on 2006-04-14 02:17:30 as read along with 15 people and 4 groups stevanspringer ccots eckart_bindewald dchughes tabu nirfriedman nickluscombe johncumbers djkt nicg mikaelhuss JeffR100 candypmcg emarker emptyhb FAB-lab G4ID EBI-regulation Genetics-of-Gambling
  • Integrated Assessment and Prediction of Transcription Factor Binding
    PLoS Computational Biology, Vol. preprint, No. 2006. (1 May 2006)
    by Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey G Ideker
    posted to algorithm model prediction tf by ranb on 2006-05-30 18:22:18 as **** along with 2 people alokm brixtonmc
  • Identifying transcription factor functions and targets by phenotypic activation.
    Proc Natl Acad Sci U S A, Vol. 103, No. 32. (8 August 2006), pp. 12045-12050.
    by G Chua, QD Morris, R Sopko, MD Robinson, O Ryan, ET Chan, BJ Frey, BJ Andrews, C Boone, TR Hughes
    posted to yeast transcription tf regulation network motif expression by raiyar on 2008-11-06 10:41:59 as ** along with 4 people and 1 group siebert indigoviolet koller hplatero EisenLab
  • Global and Local Architecture of the Mammalian microRNA-Transcription Factor Regulatory Network.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Reut Shalgi, Daniel Lieber, Moshe Oren, Yitzhak Pilpel
    posted to factor mirna network tf transcription by rahulthadani on 2007-07-19 05:06:12 as * along with 13 people and 2 groups mtagaya jfr andersbj rdiaz sebastien_vigneau ealloza zwang bootsy cabbagezs heliopais ale maralena OriginalLurch Bioinformatics microRNA
  • Alpha particle loss and neutral beam current drive in fusion plasma with central current hole
    Plasma Physics and Controlled Fusion, Vol. 46, No. 7. (2004), pp. S95-S105.
    by K Tobita, T Ozeki, Y Nakamura
    posted to advanced by configuration energetic in induced loss particle ripple tf tokamak by qgao on 2008-05-28 03:08:28 as ****
  • Physics of energetic particles in ITER
    Nuclear Fusion, Vol. 38, No. 9. (1998), pp. 1275-1281.
    by SV Putvinski
    posted to energetic particle ripple tf by qgao on 2008-05-28 03:35:37 as **
  • Requirement for T-bet in the aberrant differentiation of unhelped memory CD8+ T cells
    J. Exp. Med., Vol. 204, No. 9. (4 September 2007), pp. 2015-2021.
    by Andrew M Intlekofer, Naofumi Takemoto, Charlly Kao, Arnob Banerjee, Felix Schambach, John K Northrop, Hao Shen, John E Wherry, Steven L Reiner
    posted to unhelped transcription tf tcell t-bet memory help factor differentiation cd8 cd4 by qeimmu on 2008-10-14 04:56:25 as **
  • Transcription factors: the right combination for the DNA lock.
    Curr Biol, Vol. 9, No. 12. (17 June 1999)
    by S Khorasanizadeh, F Rastinejad
    posted to tf by nickluscombe on 2007-05-23 13:00:54 as ** along with 1 group EBI-regulation
  • Homeodomain interactions.
    Curr Opin Struct Biol, Vol. 6, No. 1. (February 1996), pp. 62-68.
    by C Wolberger
    posted to tf by nickluscombe on 2007-05-23 12:45:40 as ** along with 1 group EBI-regulation
  • An overview of the basic helix-loop-helix proteins.
    Genome Biol, Vol. 5, No. 6. (2004)
    by S Jones
    posted to tf by nickluscombe on 2007-05-23 12:23:33 as ** along with 1 person and 1 group guhjy EBI-regulation
  • Homeodomain revisited: a lesson from disease-causing mutations.
    Hum Genet, Vol. 116, No. 6. (May 2005), pp. 433-444.
    by YI Chi
    posted to tf by nickluscombe on 2007-05-23 12:59:31 as ** along with 1 group EBI-regulation
  • LIM-homeodomain genes in mammalian development and human disease.
    Mol Biol Rep, Vol. 32, No. 2. (June 2005), pp. 67-77.
    by CS Hunter, SJ Rhodes
    posted to tf by nickluscombe on 2007-05-23 12:58:08 as ** along with 1 group EBI-regulation
  • Genetic reconstruction of a functional transcriptional regulatory network.
    Nat Genet (8 April 2007)
    by Zhanzhi Hu, Patrick J J Killion, Vishwanath R R Iyer
    posted to expression tf yeast by nickluscombe on 2007-06-13 09:45:15 as ** along with 13 people and 6 groups akraemer behindtherabbit ptrobajo dpollard xico zwang lizabeth dejori xingxu naegele czeller mapplab siebert Bioinformatics EisenLab WetBiology EBI-regulation ic4 generif_paper
  • The genesis and evolution of homeobox gene clusters
    Nature Reviews Genetics, Vol. 6, No. 12. (10 November 2005), pp. 881-892.
    by Jordi Garcia-Fernàndez
    posted to tf by nickluscombe on 2007-05-23 13:01:51 as ** along with 7 people and 2 groups brant balicea emilyhare BioMaxi timflutre blobbybirdman blackm0k EisenLab EBI-regulation
  • Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters.
    Genome Res, Vol. 13, No. 6A. (June 2003), pp. 1097-1110.
    by M Shannon, AT Hamilton, L Gordon, E Branscomb, L Stubbs
    posted to human tf by nickluscombe on 2006-08-17 14:46:24 as ** along with 1 group EBI-regulation
  • Deregulated homeobox gene expression in cancer: cause or consequence?
    Nat Rev Cancer, Vol. 2, No. 10. (October 2002), pp. 777-785.
    by C Abate-Shen
    posted to tf by nickluscombe on 2007-05-23 13:02:40 as ** along with 1 group EBI-regulation
  • Recognition of specific DNA sequences.
    Mol Cell, Vol. 8, No. 5. (November 2001), pp. 937-946.
    by CW Garvie, C Wolberger
    posted to tf by nickluscombe on 2007-05-23 12:24:41 as ** along with 1 group EBI-regulation
  • The Evolution of Transcriptional Regulation in Eukaryotes
    Mol Biol Evol, Vol. 20, No. 9. (1 September 2003), pp. 1377-1419.
    by Gregory A Wray, Matthew W Hahn, Ehab Abouheif, James P Balhoff, Margaret Pizer, Matthew V Rockman, Laura A Romano
    posted to evolution tf by nickluscombe on 2007-05-23 12:27:04 as ** along with 8 people and 5 groups ana dpollard adepace anatiferous mimulus_99 cisevol emptyhb emmahe structural_bioinformatics Bioinformatics EisenLab EBI-regulation cis-regulatory-evolution
  • KRAB-containing zinc-finger repressor proteins
    Genome Biology, Vol. 4, No. 10. (2003)
    by Raul Urrutia
    posted to tf by nickluscombe on 2007-05-23 12:40:23 as ** along with 1 group EBI-regulation
  • Transcription factors in hematopoietic malignancies
    Current Opinion in Genetics & Development, Vol. 17, No. 1. (February 2007), pp. 78-83.
    by Sigal Gery, Phillip H Koeffler
    posted to tf cancer by nickluscombe on 2007-02-05 14:07:12 as ** along with 1 group EBI-regulation
  • Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms.
    Mol Cell Biol, Vol. 20, No. 2. (January 2000), pp. 429-440.
    by ME Massari, C Murre
    posted to tf by nickluscombe on 2007-05-23 12:25:52 as ** along with 4 people and 1 group guhjy tuck balicea heliopais EBI-regulation
  • Yeast transcriptional regulatory mechanisms.
    Annu Rev Genet, Vol. 29 (1995), pp. 651-674.
    by K Struhl
    posted to tf yeast by nickluscombe on 2007-05-23 12:28:53 as ** along with 1 group EBI-regulation
  • Combinatorial transcription factors.
    Curr Opin Genet Dev, Vol. 8, No. 5. (October 1998), pp. 552-559.
    by C Wolberger
    posted to tf by nickluscombe on 2007-05-23 12:44:09 as ** along with 1 group EBI-regulation
  • Epigenetic Control of the foxp3 Locus in Regulatory T Cells
    PLoS Biology, Vol. 5, No. 2. (1 February 2007), e38.
    by Stefan Floess, Jennifer Freyer, Christiane Siewert, Udo Baron, Sven Olek, Julia Polansky, Kerstin Schlawe, Hyun-Dong Chang, Tobias Bopp, Edgar Schmitt, Stefan Klein-Hessling, Edgar Serfling, Alf Hamann, Jochen Huehn
    posted to transcription tf regulation mammals by nickluscombe on 2007-01-31 15:47:41 as ** along with 1 group EBI-regulation
  • The T-box family
    Genome Biology, Vol. 3, No. 6. (2002), pp. reviews3008.1-reviews3008.7.
    by Val Wilson, Frank Conlon
    posted to tf by nickluscombe on 2007-05-23 12:41:09 as ** along with 1 group EBI-regulation
  • Transcriptional activation by recruitment.
    Nature, Vol. 386, No. 6625. (10 April 1997), pp. 569-577.
    by M Ptashne, A Gann
    posted to tf by nickluscombe on 2007-05-23 12:29:19 as ** along with 1 group EBI-regulation
  • Multiprotein-DNA complexes in transcriptional regulation.
    Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 29-56.
    by C Wolberger
    posted to tf by nickluscombe on 2007-05-23 12:43:00 as ** along with 1 person and 3 groups barry structural_bioinformatics Bioinformatics EBI-regulation
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