Tag footprinting [40 articles] Export

Recent papers classified by the tag footprinting.

	Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. [My Copy] Molecular biology and evolution, Vol. 23, No. 6. (June 2006), pp. 1293-1303. by S. De Bodt, G. Theissen, Y. Van de Peer posted to promoters footprinting by orzenil on 2009-09-15 01:28:07 as along with 2 people mlog maximilianh
	Mapping Protein−Protein Interactions with a Library of Tethered Cutting Reagents: The Binding Site of σ70 on Escherichia coli RNA Polymerase† [My Copy] Biochemistry, Vol. 38, No. 14. (1 April 1999), pp. 4259-4265. by Stacey L. Traviglia, Saul A. Datwyler, Claude F. Meares posted to ppi footprinting by timg on 2009-08-24 14:14:26 as
	Hydroxyl Radical Footprinting [My Copy] DNA-Protein Interactions (2001), pp. 49-61. by Evgeny Zaychikov, Peter Schickor, Ludmilla Denissova, Hermann Heumann posted to dna footprinting rna techniques by gonzalez on 2009-06-09 17:25:27 as
	Phylogeny based discovery of regulatory elements. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by J. Gertz, J. C. Fay, B. A. Cohen posted to crm footprinting hky85 motif phylogeny pwm regulation tfbs by pradiptaray on 2009-05-23 05:26:04 as along with 4 people and 2 groups druvus indigoviolet dquest cisevol EisenLab cis-regulatory-evolution
	Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. [My Copy] Journal of molecular biology, Vol. 203, No. 2. (20 September 1988), pp. 439-455. by D. A. Tagle, B. F. Koop, M. Goodman, J. L. Slightom, D. L. Hess, R. T. Jones posted to comparative conserved footprinting by maximilianh on 2009-04-23 14:08:28 as
	Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 218-223. by Nicholas T. Ingolia, Sina Ghaemmaghami, John R. S. Newman, Jonathan S. Weissman posted to footprinting genomewide profiling protein proteomics ribosome translation by fpattyn on 2009-04-15 16:52:21 as along with 18 people and 3 groups hzoltan jwfoley yyfwuhan gbloeb guhjy dpollard fenghezi gangcai idonaldson coela jbhiatt kshundyak absterga myzhang bertelsen VGreiff provero kinestetika RockmanLab NYU Journal Review microbiology_nijmegen
	Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. [My Copy] Nature methods, Vol. 6, No. 4. (22 April 2009), pp. 283-289. by Jay R. Hesselberth, Xiaoyu Chen, Zhihong Zhang, et al.Peter J. Sabo, Richard Sandstrom, Alex P. Reynolds, Robert E. Thurman, Shane Neph, Michael S. Kuehn, William S. Noble, Stanley Fields, John A. Stamatoyannopoulos posted to chip digital dnasei footprinting genome genomic mapping proteindna by fpattyn on 2009-04-15 16:15:00 as along with 8 people absterga inesdesantiago kmdaily humburg emptyhb roys coela jbhiatt
	Analysis of RNA polymerase-promoter complex formation. [My Copy] Methods (San Diego, Calif.), Vol. 47, No. 1. (January 2009), pp. 13-24. by W. Ross, R. L. Gourse posted to 5 footprinting gel_mobility primer_extension race transcription by shana on 2009-02-10 12:07:12 as
	Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes [My Copy] PLoS Comput Biol, Vol. 4, No. 4. (18 April 2008), e1000067. by Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis posted to footprinting by xili03 on 2008-10-08 08:20:40 as along with 1 person dakelley
	Discovering regulatory motifs in the Plasmodium genome using comparative genomics [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 17. (1 September 2008), pp. 1843-1849. by Jie Wu, Douglas H. Sieglaff, Joshua Gervin, Xiaohui S. Xie posted to footprinting by xili03 on 2008-10-07 07:27:57 as along with 5 people idonaldson APRegier semrich Neeperando neils
	Algorithms for phylogenetic footprinting. [My Copy] J Comput Biol, Vol. 9, No. 2. (2002), pp. 211-223. by M. Blanchette, B. Schwikowski, M. Tompa posted to comparative footprinting genomic by nklee on 2008-09-30 04:43:53 as along with 2 people chad_davis dquest
	Cooperative binding of [lambda] repressors to sites separated by integral turns of the DNA helix [My Copy] Cell, Vol. 44, No. 5. (14 March 1986), pp. 681-687. by A. Hochschild, M. Ptashne posted to dna-loop footprinting by icq242500260 on 2008-09-12 17:15:48 as
	FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by D. L. Corcoran, E. Feingold, P. V. Benos posted to dna footprinting phylogenetic regions regulatory by bryankr on 2008-09-02 12:46:41 as along with 1 person wowalz
	Nuclease activity of 1,10-phenanthroline-copper: sequence-specific targeting [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 83, No. 19., pp. 7147-7151. by C. H. Chen, D. S. Sigman posted to footprinting by icq242500260 on 2008-08-14 12:50:06 as
	Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution [My Copy] BMC Bioinformatics, Vol. 9 (23 January 2008), 37. by Rekin's Janky, Jacques van Helden posted to footprinting by xili03 on 2008-08-11 08:58:36 as along with 2 people and 1 group druvus cisevol cis-regulatory-evolution
	Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. [My Copy] Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 774-782. by L. McCue, W. Thompson, C. Carmack, et al.M. P. Ryan, J. S. Liu, V. Derbyshire, C. E. Lawrence posted to bacteria footprinting motif phylogeny prokaryote regulation tfbs by pradiptaray on 2008-08-07 16:23:07 as along with 4 people and 1 group azazello dquest adepace nklee EisenLab
	DNA sequencing by the chemical method: a 10 minute procedure for the G+A reaction [My Copy] Trends in Genetics, Vol. 9, No. 10. (October 1993), pp. 337-338. by Andrés F. Muro, Gustavo C. Pesce, Alberto R. Kornblibhtt posted to footprinting method by icq242500260 on 2008-07-01 11:02:06 as
	The OhrR repressor senses organic hydroperoxides by reversible formation of a cysteine-sulfenic acid derivative [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 10. (14 May 2002), pp. 6690-6695. by Mayuree Fuangthong, John D. Helmann posted to footprinting method by icq242500260 on 2008-07-01 10:33:38 as
	High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis [My Copy] Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), e63. by Somdeb Mitra, Inna V. Shcherbakova, Russ B. Altman, Michael Brenowitz, Alain Laederach posted to analysis footprinting by fpattyn on 2008-06-24 16:28:01 as
	Transcriptional analysis of the hmw gene cluster of Mycoplasma pneumoniae. [My Copy] Journal of bacteriology, Vol. 181, No. 16. (August 1999), pp. 4978-4985. by R. H. Waldo, P. L. Popham, C. E. Romero-Arroyo, E. A. Mothershed, K. K. Lee, D. C. Krause posted to footprinting mycoplasma primer_extension promoters transcription by shana on 2008-06-24 03:29:48 as
	CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. [My Copy] PLoS computational biology, Vol. 4, No. 6. (6 June 2008), e1000090. by P. Ray, S. Shringarpure, M. Kolar, E. P. Xing posted to comparative detection footprinting genomics motif phylogenetic by Stew on 2008-06-14 14:43:13 as along with 7 people and 1 group dquest emptyhb madreach xili03 djkt cisevol Ema cis-regulatory-evolution
	Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements. [My Copy] Bioinformatics (18 March 2008) by R Satija, L Pachter, J Hein posted to alignment cis-regulatory drosophila footprinting phylogenetic prediction regulatory by Stew on 2008-06-06 08:24:29 as along with 6 people jo_davies druvus eckart_bindewald maximilianh gjuggler Ema
	Footprint of the sigma protein: A re-examination [My Copy] Biochemical and Biophysical Research Communications, Vol. 177, No. 1. (31 May 1991), pp. 140-144. by Arthur Wellman, Claude F. Meares posted to footprinting sigma by shana on 2008-05-03 23:43:51 as
	Multi-species sequence comparison: the next frontier in genome annotation [My Copy] Genome Biology, Vol. 4, No. 12. (2003) by Inna Dubchak, Kelly Frazer posted to footprinting by nklee on 2008-02-19 23:06:17 as
	A novel approach to identifying regulatory motifs in distantly related genomes [My Copy] Genome Biology, Vol. 6, No. 13. (2005) by Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer, Kathleen Marchal posted to clustering comparative footprinting genomic by nklee on 2008-01-31 04:19:31 as along with 1 person wowalz
	A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. [My Copy] J Mol Biol, Vol. 284, No. 2. (27 November 1998), pp. 241-254. by K. Robison, A. M. McGuire, G. M. Church posted to comparative ecoli footprinting genomic by nklee on 2008-01-02 23:09:01 as along with 2 people medic0747 kaarsinogen
	Prediction of synergistic transcription factors by function conservation [My Copy] Genome Biology, Vol. 8, No. 12. (2007) by Zihua Hu, Boyu Hu, James Collins posted to footprinting by nklee on 2007-12-19 21:16:32 as along with 3 people and 1 group cjeans maximilianh ale cis-regulatory-evolution
	Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 319-328. by E. Barta posted to alignment conserved footprinting scanning by maximilianh on 2007-11-27 13:04:18 as
	Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements. [My Copy] Methods Mol Biol, Vol. 395 (2007), pp. 425-436. by P. V. Benos, D. L. Corcoran, E. Feingold posted to alignment cns footprinting scanning by maximilianh on 2007-11-27 13:02:58 as
	PhyloScan: Identification of transcription factor binding sites using cross-species evidence [My Copy] Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1. by Steven C. Carmack, Lee A. Mccue, Lee A. Newberg, Charles E. Lawrence posted to footprinting by nklee on 2007-11-27 06:16:56 as along with 3 people and 1 group dpollard dquest lusk EisenLab
	Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. [My Copy] Genome Res, Vol. 11, No. 7. (July 2001), pp. 1175-1186. by P. F. Cliften, L. W. Hillier, L. Fulton, et al.T. Graves, T. Miner, W. R. Gish, R. H. Waterston, M. Johnston posted to footprinting yeast by nklee on 2007-10-29 05:16:18 as along with 2 people evaf kaarsinogen
	Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. [My Copy] Proc Natl Acad Sci U S A (29 March 2007) by Alona Sosinsky, Barry Honig, Richard S S. Mann, Andrea Califano posted to cis-regulatory drosophila footprinting phlyogenetic prediction by Stew on 2007-10-19 00:42:18 as along with 4 people and 2 groups dpollard maximilianh cisevol isimpson EisenLab cis-regulatory-evolution
	Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos. [My Copy] Methods, Vol. 39, No. 3. (July 2006), pp. 212-219. by M. L. Allende, M. Manzanares, J. J. Tena, C. G. Feijóo, J. L. Gómez-Skarmeta posted to prediction phlyogenetic frog footprinting fish cis-regulatory by Stew to the group EisenLab on 2007-09-18 01:19:46 as
	Constitutive Nucleosome Depletion and Ordered Factor Assembly at the GRP78 Promoter Revealed by Single Molecule Footprinting [My Copy] PLoS Genetics, Vol. 2, No. 9. (1 October 2006), e160. by Einav N. Gal-Yam, Shinwu Jeong, Amos Tanay, Gerda Egger, Amy S. Lee, Peter A. Jones posted to footprinting molecule single by brant on 2006-10-11 16:23:49 as along with 1 group EisenLab
	Close sequence comparisons are sufficient to identify human cis-regulatory elements. [My Copy] Genome Res (12 June 2006) by Shyam Prabhakar, Francis Poulin, Malak Shoukry, et al.Veena Afzal, Edward M M. Rubin, Olivier Couronne, Len A A. Pennacchio posted to alignment annotation conserved constraint evolution footprinting human mammal mammals prediction rate selection tfbs transcription turnover by samal on 2006-08-22 05:18:32 as along with 8 people and 2 groups indigoviolet dpollard nickluscombe olympos emptyhb bpcusack mariakmejia kcrawlik EisenLab EBI-regulation
	FootPrinter: A program designed for phylogenetic footprinting. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3840-3842. by M. Blanchette, M. Tompa posted to factor footprinting phylogenetic transcription by kaur on 2005-10-09 17:10:05 as along with 2 people chad_davis balajis
	Chromatin structure at the flanking regions of the human beta-globin locus control region DNase I hypersensitive site-2: proposed nucleosome positioning by DNA-binding proteins including GATA-1. [My Copy] Biochim Biophys Acta, Vol. 1679, No. 3. (17 September 2004), pp. 201-213. by N. Davies, J. Freebody, V. Murray posted to b-globin footprinting human by forluvoft on 2005-03-03 00:42:21 as
	Functional genomics via metabolic footprinting: monitoring metabolite secretion by [My Copy] Comparative and Functional Genomics, Vol. 4, No. 4. (18 July 2003), pp. 376-391. by Naheed N. Kaderbhai, David I. Broadhurst, David I. Ellis, Royston Goodacre, Douglas B. Kell posted to footprinting metabolic metabolomics by rmj001 on 2005-01-19 11:40:20 as along with 1 person die95
	High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. [My Copy] Nat Biotechnol, Vol. 21, No. 6. (June 2003), pp. 692-696. by J. Allen, H. M. Davey, D. Broadhurst, et al.J. K. Heald, J. J. Rowland, S. G. Oliver, D. B. Kell posted to footprinting metabolic metabolomics by dbk on 2004-11-13 13:16:32 along with 4 people and 3 groups peterli irenas raiyar katerinakal streptomyces dbk-lab steinmetzlab
	Discrimination of modes of action of antifungal substances by use of metabolic footprinting. [My Copy] Appl Environ Microbiol, Vol. 70, No. 10. (October 2004), pp. 6157-6165. by J. Allen, H. M. Davey, D. Broadhurst, J. J. Rowland, S. G. Oliver, D. B. Kell posted to footprinting metabolic metabolomics by dbk to the group dbk-lab on 2004-11-11 23:37:22 along with 1 group streptomyces

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metabolic	8
metabolomics	8
comparative	6
transcription	6
alignment	5
genomic	5
prediction	5
tfbs	5
cis-regulatory	4
motif	4
phylogenetic	4
conserved	3
genome	3
mammals	3
method	3
phlyogenetic	3
conservation	2
dna	2
drosophila	2
fish	2
frog	2
human	2
mapping	2
molecule	2
mouse	2
phylogeny	2
primer_extension	2
promoters	2
protein	2
regulation	2
regulatory	2
ribosome	2
rna	2
scanning	2
single	2
yeast	2
5	1
algorithm	1
analysis	1
annotation	1
b-globin	1
bacteria	1
chip	1
chromatin	1
clustering	1
cns	1
coli	1
constraint	1
crm	1
detection	1
digital	1
dna-loop	1
dnasei	1
ecoli	1
escherichia	1
evolution	1
factor	1
folding	1
ftir	1
gel_mobility	1
genetic	1
genomewide	1
genomics	1
hky85	1
hydroxyl	1
hydroxyradical	1
icq	1
in-vivo	1
interactions	1
mammal	1
mass	1
metabolome	1
mycoplasma	1
noalignment	1
ppi	1
profile	1
profiling	1
prokaryote	1
proteindna	1
proteomics	1
pwm	1
race	1
radical	1
rate	1
regions	1
ribosomal	1
rnaprotein	1
selection	1
sigma	1
spectrometry	1
spectroscopy	1
structure	1
structure_comparison	1
techniques	1
translation	1
tryptophan	1
turnover	1

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