dquest's library 397 articles Export

	Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1831-1832. by Aziz Mithani, Gail M. Preston, Jotun Hein posted to pathways by dquest on 2009-07-24 15:41:17 as along with 3 people JeremyZucker poirel renatomilani
	OWL Web Ontology Language Guide [My Copy] (2004) edited by Michael K. Smith, Chris Welty, Deborah L. Mcguinness posted to descriptionlogics knowledgebase ontology owl by dquest on 2009-07-23 15:04:31 as
	Predicting functionality of protein-DNA interactions by integrating diverse evidence [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i137-144. by Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy, Christopher T. Workman posted to motifpaper motifsampling by dquest on 2009-07-09 19:29:04 as along with 3 people ashishanand TRHvidsten scjparker
	Proteome coverage prediction with infinite Markov models [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i154-160. by Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann posted to lcmsms by dquest on 2009-07-09 19:28:22 as along with 3 people and 1 group kiekyon AlexBateman roys Journal picks
	DISCOVER: a feature-based discriminative method for motif search in complex genomes. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i321-329. by Wenjie Fu, Pradipta Ray, Eric P. Xing posted to motifpaper motifsampling by dquest on 2009-07-09 19:23:09 as along with 5 people and 1 group guhjy Stew idonaldson thegoose maximilianh Bioinformatics - CRUK
	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 motifpaper motifsampling by dquest on 2009-07-09 19:21:05 as along with 7 people and 1 group emptyhb madreach xili03 djkt cisevol Stew Ema cis-regulatory-evolution
	BioFilter: an architecture for parallel deployment and dynamic chaining of standalone bioinformatics tools [My Copy] In 19th IEEE International Parallel and Distributed Processing Symposium, 2005. Proceedings (2005) by T. Brettin, A. Kewalramani posted to file-import-09-07-06 by dquest on 2009-07-06 19:43:41 as
	Pattern-oriented software architecture: a system of patterns [My Copy] (2002) by F. Buschmann posted to softwareengineering by dquest on 2009-07-06 19:41:19 as
	MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications [My Copy] Nucl. Acids Res., Vol. 35, No. Supplement 1. (7 November 2006), pp. gkl791-D394. by C. E. Zhou, J. Smith, M. Lam, A. Zemla, M. D. Dyer, T. Slezak posted to biosites by dquest on 2009-06-30 21:04:43 as along with 1 person druvus
	Alignment of the UMLS semantic network with BioTop: methodology and assessment. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i69-76. by Stefan Schulz, Elena Beisswanger, László van den Hoek, Olivier Bodenreider, Erik M. van Mulligen posted to ontology by dquest on 2009-06-26 17:06:14 as along with 5 people and 1 group guhjy sobolevnrm fgibson allysonlister dullhunk baker-group
	Efficient exact motif discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i356-364. by T. Marschall, S. Rahmann posted to motifpaper by dquest on 2009-06-26 16:39:33 as along with 4 people wowalz nuin idonaldson maximilianh
	Assessing phylogenetic motif models for predicting transcription factor binding sites [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i339-347. by John Hawkins, Charles Grant, William S. Noble, Timothy L. Bailey posted to benchmark motifpaper motifsampling by dquest on 2009-06-26 16:08:38 as along with 8 people and 3 groups Stew marti Lombardo_7 megraw operon nuin AlexBateman scjparker EisenLab Bioinformatics - CRUK Journal picks
	Toward a gold standard for promoter prediction evaluation. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. i313-320. by Thomas Abeel, Yves Van de Peer, Yvan Saeys posted to benchmark human promoter by dquest on 2009-06-26 15:56:05 as along with 6 people and 1 group daforerog marti druvus AlexBateman tonamswish djkt Journal picks
	Integrating systems biology data repositories to improve cis-regulatory motif characterization and discovery [My Copy] (1 May 2009) by Daniel Quest posted to motifpaper thesis by dquest on 2009-06-17 16:57:26 as
	Discovering <italic>cis-</italic>Regulatory RNAs in <italic>Shewanella</italic> Genomes by Support Vector Machines [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000338. by Xing Xu, Yongmei Ji, Gary D. Stormo posted to regulatorynetworks rna by dquest on 2009-04-03 16:30:58 as along with 1 person mhamada
	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R25. by Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg posted to algorithms alignment by dquest on 2009-04-02 20:32:23 as along with 33 people and 4 groups darshan fstrozzi adijr debasis bozdagd polivares torfinnnome n00c talponer jmcq rschulz ghattem operon humburg idonaldson mmartin skembel heliopais djkt GeeSharpMinor bertelsen darian semrich dakelley idoerg vmsr hpaces admash pdexheimer mhamada fpattyn natstreet druvus BergmanLab SIMR bioinformatics iSEEM Notre Dame Bioinformatics
	Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 82. by Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn posted to motifpaper by dquest on 2009-03-11 15:53:05 as along with 9 people and 2 groups daveGerrard ilyashl svenrahmann idonaldson maximilianh bmajoros nuin idoerg cisevol cis-regulatory-evolution BergmanLab
	Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. [My Copy] BMC genomics, Vol. 9 (16 December 2008), 609. by K. Hannay, E. M. Marcotte, C. Vogel posted to geneduplicationandloss by dquest on 2009-03-02 03:09:27 as along with 9 people michaelbarton gurprit_raunu bpcusack biomcgary sylvainforet natstreet JustinCrocker druvus tny
	SeqAn - An efficient, generic C++ library for sequence analysis [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Andreas Doring, David Weese, Tobias Rausch, Knut Reinert posted to libraries by dquest on 2009-02-26 18:51:27 as along with 15 people MarcelSchulz n00c druvus mmartin daforerog groepl guhjy chad_davis laughcry ryanraaum nklee barriot mailund magusina reyez
	MUSCLE: multiple sequence alignment with high accuracy and high throughput [My Copy] Nucl. Acids Res., Vol. 32, No. 5. (19 March 2004), pp. 1792-1797. by Robert C. Edgar posted to multiplesequencealignment by dquest on 2009-02-26 17:20:58 as along with 29 people and 2 groups mgomes jeargle tomjad foxpowa esyoun natstreet BioNica gjuggler edvin yylin treangen sebk agustinarce fhsantanna nachtalp bpb chrn jwm Haggan sanchezbuelna timflutre olympos martainn newton1234 skumagai bmaust sconlan dmp kcrawlik Radiation_Damage Stressosome
	Ortholog detection using the reciprocal smallest distance algorithm. [My Copy] Methods Mol Biol, Vol. 396 (2007), pp. 95-110. by D. P. Wall, T. Deluca posted to orthalog by dquest on 2009-02-24 00:36:12 as along with 4 people pansapiens maximilianh operon cerca
	PAML 4: phylogenetic analysis by maximum likelihood. [My Copy] Molecular biology and evolution, Vol. 24, No. 8. (1 August 2007), pp. 1586-1591. by Ziheng Yang posted to phylogenetics by dquest on 2009-02-24 00:25:01 as along with 13 people and 1 group ckenaley biomcgary michaelbarton druvus operon akifumi hdopazo BioNica stajich ryanraaum RamuAnandakrishnan CharlesM Ema Mycology
	Assessing performance of orthology detection strategies applied to eukaryotic genomes. [My Copy] PLoS ONE, Vol. 2 (2007) by F. Chen, A. J. Mackey, J. K. Vermunt, D. S. Roos posted to orthalog by dquest on 2009-02-24 00:21:13 as along with 14 people and 3 groups richardbickerton treangen cgaugain druvus icases operon rvosa indigoviolet stajich cjeans winterschlaefer bpcusack cerca natstreet EisenLab FAB-lab TNT
	MetaCyc: a multiorganism database of metabolic pathways and enzymes. [My Copy] Nucleic acids research, Vol. 32, No. Database issue. (1 January 2004) by Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, et al.Alfred Wang, Suzanne Paley, Martha Arnaud, John Pick, Seung Y. Rhee, Peter D. Karp posted to databases regulatorynetworks by dquest on 2009-02-22 22:37:59 as along with 2 people irenas kuhn
	Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology. [My Copy] Biochemical Society transactions, Vol. 34, No. Pt 1. (February 2006), pp. 104-107. by T. W. Overton, L. Griffiths, M. D. Patel, et al.J. L. Hobman, C. W. Penn, J. A. Cole, C. Constantinidou posted to regulatorynetworks by dquest on 2009-02-16 03:59:06 as
	Co-operative interactions between the catabolite gene activator protein and the lac repressor at the lactose promoter. [My Copy] Journal of molecular biology, Vol. 214, No. 2. (20 July 1990), pp. 381-396. by J. M. Hudson, M. G. Fried posted to regulatorynetworks by dquest on 2009-02-16 03:45:18 as
	Evidence for “Pre-recruitment” as a New Mechanism of Transcription Activation in Escherichia coli: The Large Excess of SoxS Binding Sites per Cell Relative to the Number of SoxS Molecules per Cell [My Copy] Biochemical and Biophysical Research Communications, Vol. 291, No. 4. (8 March 2002), pp. 979-986. by K. Griffith posted to regulatorynetworks by dquest on 2009-02-15 23:00:18 as
	Ortholog Detection Using the Reciprocal Smallest Distance Algorithm [My Copy] Comparative Genomics (2008), pp. 95-110. by Dennis P. Wall, Todd Deluca posted to orthalog by dquest on 2008-12-31 18:40:09 as along with 1 person cerca
	Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques [My Copy] Genome Research, Vol. 16, No. 12. (19 December 2006), pp. 1455-1464. by Laura Elnitski, Victor X. Jin, Peggy J. Farnham, Steven J. M. Jones posted to regulatorynetworks by dquest on 2008-09-29 17:19:10 as along with 11 people and 2 groups matted gdb wowalz Stew heliopais bryankr giovanni lusk SeungjoonOh cabbagezs maximilianh Bioinformatics - CRUK GeschwindLab
	MTAP: The Motif Tool Assessment Platform [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 9. (2008) by Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham Ali posted to motifpaper by dquest on 2008-08-31 18:39:26 as along with 5 people wowalz nklee cassj YuvalTabach Stew
	ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters [My Copy] Cell, Vol. 131, No. 5. (30 November 2007), pp. 831-832. by Christoph D. Schmid, Philipp Bucher posted to chipseq by dquest on 2008-07-28 23:50:58 as along with 4 people ewilban1 polivares mikaelhuss vega
	Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing [My Copy] Nature Methods, Vol. 4, No. 8. (11 June 2007), pp. 651-657. by Gordon Robertson, Martin Hirst, Matthew Bainbridge, et al.Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L. Griffith, Ann He, Marco Marra, Michael Snyder, Steven Jones posted to chipseq by dquest on 2008-07-28 23:48:51 as along with 13 people and 1 group absterga samanthacooper stubrown ewilban1 fpattyn polivares caseybrown guhjy vega kengg ghattem slevy03 raiyar Plantandetc
	Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse [My Copy] Cell, Vol. 120, No. 2. (28 January 2005), pp. 169-181. by Bradley E. Bernstein, Michael Kamal, Kerstin Lindblad-Toh, et al.Stefan Bekiranov, Dione K. Bailey, Dana J. Huebert, Scott Mcmahon, Elinor K. Karlsson, Edward J. Kulbokas, Thomas R. Gingeras, Stuart L. Schreiber, Eric S. Lander posted to chipseq by dquest on 2008-07-28 23:47:08 as along with 5 people antonkratz olympos caseybrown jasonflannick inesdesantiago
	High-resolution profiling of histone methylations in the human genome. [My Copy] Cell, Vol. 129, No. 4. (18 May 2007), pp. 823-837. by Artem Barski, Suresh Cuddapah, Kairong Cui, et al.Tae-Young Y. Roh, Dustin E. Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, Keji Zhao posted to chipseq by dquest on 2008-07-28 23:46:03 as along with 22 people and 2 groups rsaito darian tonamswish stubrown fpattyn hagechouchin443 absterga ewilban1 suizifish jochenG caseybrown raylim jernst giovenko guhjy kengg sebastien_vigneau jackjackjjj ghattem epigenetics ksha inesdesantiago JLab Plantandetc
	Genome-Wide Mapping of in Vivo Protein-DNA Interactions [My Copy] Science, Vol. 316, No. 5830. (8 June 2007), pp. 1497-1502. by David S. Johnson, Ali Mortazavi, Richard M. Myers, Barbara Wold posted to chipseq by dquest on 2008-07-28 23:45:13 as along with 23 people and 5 groups daforerog tonamswish ewilban1 aprasad jo_davies aalibes balicea andersbj JeremyZucker aswin kengg giovanni cjeans ghattem zwang epigenetics biomcgary george_g cabbagezs Jporci blobbybirdman caseybrown emptyhb Bioinformatics microRNA Marcotte_Lab UH - Computational Biology Myxo group
	Transcriptional Regulatory Networks in Saccharomyces cerevisiae [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804. by Tong I. Lee, Nicola J. Rinaldi, Francois Robert, et al.Duncan T. Odom, Ziv Bar-Joseph, Georg K. Gerber, Nancy M. Hannett, Christopher T. Harbison, Craig M. Thompson, Itamar Simon, Julia Zeitlinger, Ezra G. Jennings, Heather L. Murray, D. Benjamin Gordon, Bing Ren, John J. Wyrick, Jean-Bosco Tagne, Thomas L. Volkert, Ernest Fraenkel, David K. Gifford, Richard A. Young posted to chipchip by dquest on 2008-07-28 23:36:19 as along with 31 people and 2 groups mjoach kmdaily kinop junehlee lillo80 camster snuppepuppan icases forluvoft ggrot alokm opheliav samal sameetmehta cconboy koller jguinney franklin timflutre jpoyatos lusk nklee karfunkel mimulus_99 roys njcitulike brant kristallreiner Borelli Takayuki siebert dbk-lab TNT
	Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. [My Copy] Nature, Vol. 409, No. 6819. (25 January 2001), pp. 533-538. by V. R. Iyer, C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, P. O. Brown posted to chipchip by dquest on 2008-07-28 23:35:06 as along with 1 person kaarsinogen
	Genome-Wide Location and Function of DNA Binding Proteins [My Copy] Science, Vol. 290, No. 5500. (22 December 2000), pp. 2306-2309. by Bing Ren, Francois Robert, John J. Wyrick, et al.Oscar Aparicio, Ezra G. Jennings, Itamar Simon, Julia Zeitlinger, Jorg Schreiber, Nancy Hannett, Elenita Kanin, Thomas L. Volkert, Christopher J. Wilson, Stephen P. Bell, Richard A. Young posted to chipchip by dquest on 2008-07-28 23:34:01 as along with 8 people aprasad miguel kaarsinogen johncumbers tvdbulck epigenetics yevishere kristallreiner
	Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. [My Copy] Nature genetics, Vol. 28, No. 4. (August 2001), pp. 327-334. by J. D. Lieb, X. Liu, D. Botstein, P. O. Brown posted to chipchip by dquest on 2008-07-28 23:32:59 as
	Evolution of Evolvability in Gene Regulatory Networks [My Copy] PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000112. by Anton Crombach, Paulien Hogeweg posted to bioregulationoverview by dquest on 2008-07-15 21:29:45 as along with 18 people and 1 group tomhebbron roys mjoach semrich wangbo kaarsinogen renatomilani aramesh2 erel10 Ema jdiezperezj bootsy dlobo Stew djkt shoshin rebeccamancy Borelli GEB
	Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. [My Copy] Genome research, Vol. 18, No. 6. (June 2008), pp. 900-910. by B. K. Cho, E. M. Knight, C. L. Barrett, B. Ø. Palsson posted to bioregulationoverview by dquest on 2008-07-03 22:55:23 as
	YaeL (EcfE) activates the sigma E pathway of stress response through a site-2 cleavage of anti-sigma E, RseA [My Copy] Genes Dev., Vol. 16, No. 16. (15 August 2002), pp. 2147-2155. by Kazue Kanehara, Koreaki Ito, Yoshinori Akiyama posted to bioregulationoverview by dquest on 2008-07-03 20:01:16 as
	A new mechanism for coactivation of transcription initiation: repositioning of an activator triggered by the binding of a second activator. [My Copy] Cell, Vol. 66, No. 6. (20 September 1991), pp. 1185-1195. by E. Richet, D. Vidal-Ingigliardi, O. Raibaud posted to bioregulationoverview by dquest on 2008-07-01 19:02:48 as
	Determinants of the C-Terminal Domain of the Escherichia coli RNA Polymerase alpha Subunit Important for Transcription at Class I Cyclic AMP Receptor Protein-Dependent Promoters [My Copy] J. Bacteriol., Vol. 184, No. 8. (15 April 2002), pp. 2273-2280. by Nigel J. Savery, Georgina S. Lloyd, Stephen J. Busby, Mark S. Thomas, Richard H. Ebright, Richard L. Gourse posted to bioregulationoverview by dquest on 2008-06-26 21:34:12 as
	Prokaryotic Gene Expression [My Copy] (1999) edited by Simon Baumberg posted to bioregulationoverview by dquest on 2008-06-26 20:11:59 as
	A Genetic Switch Phage Lambda Revisited [My Copy] (2004) by Mark Ptashne posted to bioregulationoverview by dquest on 2008-06-25 21:45:38 as
	An Introduction to Systems Biology Design Principles of Biological Circuits [My Copy] (2007) by Uri Alon posted to bioregulationoverview by dquest on 2008-06-25 20:49:22 as
	Genomic analysis of the hierarchical structure of regulatory networks [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 40. (3 October 2006), pp. 14724-14731. by Haiyuan Yu, Mark Gerstein posted to bioregulationoverview by dquest on 2008-06-20 01:25:03 as along with 6 people arjun_citeulike carlk jiny hplatero bootsy RobMills
	An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs [My Copy] Nucl. Acids Res., Vol. 32, No. 22. (16 December 2004), pp. 6643-6649. by Hong-Wu Ma, Bharani Kumar, Uta Ditges, Florian Gunzer, Jan Buer, An-Ping Zeng posted to bioregulationoverview by dquest on 2008-06-20 01:24:17 as
	Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (2004) by Hong W. Ma, Jan Buer, An P. Zeng posted to bioregulationoverview by dquest on 2008-06-20 01:19:10 as along with 2 people balabu hustwj

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motifpaper	167
grammarpaper	63
motifsampling	38
regulatorynetworks	31
bioregulationoverview	27
microarrayanalysis	15
rnai	10
basedonbaldietal	9
proteinnetworks	7
rnastructure	6
algorithms	5
chipseq	5
databases	5
orthalog	5
chipchip	4
histones	4
rnafolding	4
sirna	4
baysian	3
microarray	3
phylogenetics	3
transcriptionbasics	3
transcriptregulation	3
visualization	3
analysis	2
benchmark	2
mirna	2
multiplesequencealignment	2
networkmotifs	2
ontology	2
staph	2
timecoursemicroarray	2
3d	1
alignment	1
bacteriainfoandalgs	1
bioinformaticscoursematerial_sequences	1
biosites	1
bsub	1
centraldogmarevisited	1
descriptionlogics	1
ecoli	1
enzymes	1
file-import-09-07-06	1
geneduplicationandloss	1
geneprediction	1
general	1
human	1
imunology	1
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methalation	1
microrna	1
organals	1
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parallel	1
pathways	1
phylogeneticprofiling	1
prediction	1
prokaryotes	1
promoter	1
proteindocking	1
proteinmotiffinding	1
proteinstructure	1
questpapers	1
repeatmasking	1
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ribozymes	1
rna	1
software	1
softwareengineering	1
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thesis	1
transcriptfeedbackloops	1

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