lusk's inside [55 articles] Export

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	A systems view of Drosophila segmentation [My Copy] Genome Biology, Vol. 9 (11 February 2008), 207. by Mike Levine posted to inside segmentation by lusk on 2008-04-30 04:49:19 as along with 1 person grahamc
	Sequence Context affects the rate of short insertions and deletions in flies and primates [My Copy] Genome Biology, Vol. 9 (21 February 2008), R37. by Amos Tanay, Eric D. Siggia posted to deletion insertion inside organization_paper by lusk on 2008-04-15 02:02:12 as along with 8 people emptyhb timflutre bpcusack djkt biomcgary gjuggler brant aprasad
	Transcriptional regulation of a pair-rule stripe in Drosophila. [My Copy] Genes Dev, Vol. 5, No. 5. (May 1991), pp. 827-839. by S. Small, R. Kraut, T. Hoey, R. Warrior, M. Levine posted to eve flies inside by lusk on 2008-04-13 01:46:37 as along with 1 person and 1 group dpollard EisenLab
	Extensive low-affinity transcriptional interactions in the yeast genome. [My Copy] Genome Res (29 June 2006) by Amos Tanay posted to inside by lusk on 2007-09-25 03:01:44 as along with 6 people and 2 groups devin indigoviolet dpollard balicea koller emptyhb TranscriptionalRegulationWithThermodynamicModels EisenLab
	From promoter sequence to expression: a probabilistic framework [My Copy] In RECOMB 2002 by Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Koller edited by Sorin Istrail, Michael S. Waterman, Andrew G. Clark posted to inside by lusk on 2007-09-25 02:59:55 as
	A feature-based approach to modeling protein-DNA interactions [My Copy] In RECOMB 2007 by E. Sharon, E. Segal edited by T. Speed, H. Huang posted to inside by lusk on 2007-09-25 02:54:17 as
	Coherence and Timing of Cell Cycle Start Examined at Single-Cell Resolution [My Copy] Molecular Cell, Vol. 21, No. 1. (6 January 2006), pp. 3-14. by James M. Bean, Eric D. Siggia, Frederick R. Cross posted to flow_cytometry inside by lusk on 2007-05-08 01:30:44 as along with 1 person balabu
	SCPD: a promoter database of the yeast Saccharomyces cerevisiae. [My Copy] Bioinformatics, Vol. 15, No. 7-8. (g 1999), pp. 607-611. by J. Zhu, M. Q. Zhang posted to inside by lusk on 2007-05-04 04:00:44 as along with 4 people chad_davis xiaobeizhao nklee njcitulike
	Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both. [My Copy] Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402. by T. Vavouri, G. Elgar posted to inside by lusk on 2007-05-03 17:49:54 as along with 6 people and 2 groups troels_marstrand kaspermunch dpollard adepace Stew brant Bioinformatics EisenLab
	DNA binding sites: representation and discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 16, No. 1. (January 2000), pp. 16-23. by G. D. Stormo posted to inside review by lusk on 2007-05-03 17:49:30 as along with 9 people and 1 group yylin Stew emptyhb isimpson kaarsinogen mbj dquest ezralanglois xili03 Bioinformatics - CRUK
	A probabilistic method to detect regulatory modules. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by S. Sinha, E. van Nimwegen, E. D. Siggia posted to inside by lusk on 2007-05-03 17:49:04 as along with 4 people and 2 groups maximilianh indigoviolet dquest cisevol EisenLab cis-regulatory-evolution
	PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. [My Copy] BMC Bioinformatics, Vol. 5 (28 October 2004) by S. Sinha, M. Blanchette, M. Tompa posted to inside by lusk on 2007-05-03 17:48:44 as along with 5 people mgledi eckart_bindewald dquest adsmitty xili03
	PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. [My Copy] PLoS computational biology, Vol. 1, No. 7. (December 2005) by Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen posted to inside by lusk on 2007-05-03 17:48:21 as along with 17 people and 3 groups farhat wowalz aprasad cajunsushi treangen druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lilou idonaldson yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
	Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments [My Copy] BMC Bioinformatics, Vol. 7 (14 August 2006), 376. by Daniel A. Pollard, Alan M. Moses, Venky N. Iyer, Michael B. Eisen posted to inside by lusk on 2007-05-03 17:48:02 as along with 6 people and 2 groups aprasad dpollard Garamonfok lilou cisevol emptyhb EisenLab cis-regulatory-evolution
	Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 44. (1 November 2005), pp. 15936-15941. by V. Mustonen, M. Lässig posted to inside by lusk on 2007-05-03 17:47:26 as along with 4 people and 2 groups kaarsinogen dpollard cisevol emptyhb EisenLab cis-regulatory-evolution
	Large-scale turnover of functional transcription factor binding sites in Drosophila. [My Copy] PLoS Comput Biol, Vol. 2, No. 10. (October 2006) by A. M. Moses, D. A. Pollard, D. A. Nix, et al.V. N. Iyer, X. Y. Li, M. D. Biggin, M. B. Eisen posted to inside by lusk on 2007-05-03 17:47:01 as along with 6 people and 2 groups caseybrown adepace eukfn maximilianh cisevol emptyhb EisenLab cis-regulatory-evolution
	MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. [My Copy] Genome Biol, Vol. 5, No. 12. (2004) by A. M. Moses, D. Y. Chiang, D. A. Pollard, V. N. Iyer, M. B. Eisen posted to inside by lusk on 2007-05-03 17:46:39 as along with 4 people and 2 groups tuck indigoviolet Garamonfok cisevol EisenLab cis-regulatory-evolution
	Position specific variation in the rate of evolution in transcription factor binding sites. [My Copy] BMC Evol Biol, Vol. 3, No. 1. (28 August 2003) by A. M. Moses, D. Y. Chiang, M. Kellis, E. S. Lander, M. B. Eisen posted to inside organization_paper by lusk on 2007-05-03 17:46:18 as along with 6 people and 2 groups briann dpollard adepace nklee cisevol emptyhb EisenLab cis-regulatory-evolution
	Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. [My Copy] Pac Symp Biocomput (2004), pp. 324-335. by A. M. Moses, D. Y. Chiang, M. B. Eisen posted to inside by lusk on 2007-05-03 17:45:55 as along with 3 people eckart_bindewald dquest wenhan
	Analysis of computational approaches for motif discovery [My Copy] Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8. by Nan Li, Martin Tompa posted to inside review by lusk on 2007-05-03 17:45:28 as along with 11 people and 2 groups wowalz yevishere ana barry tuck chad_davis dquest nklee maximilianh xi03 csdhwang structural_bioinformatics Bioinformatics
	Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. [My Copy] J Mol Evol, Vol. 22, No. 2. (1985), pp. 160-174. by M. Hasegawa, H. Kishino, T. Yano posted to hky inside organization_paper by lusk on 2007-05-03 17:45:03 as along with 4 people aprasad alexeid AaronDarling Natasha
	Transcriptional regulatory code of a eukaryotic genome [My Copy] Nature, Vol. 431, No. 7004. (02 September 2004), pp. 99-104. by Christopher T. Harbison, D. Benjamin Gordon, Tong I. Lee, et al.Nicola J. Rinaldi, Kenzie D. Macisaac, Timothy W. Danford, Nancy M. Hannett, Jean-Bosco Tagne, David B. Reynolds, Jane Yoo, Ezra G. Jennings, Julia Zeitlinger, Dmitry K. Pokholok, Manolis Kellis, P. Alex Rolfe, Ken T. Takusagawa, Eric S. Lander, David K. Gifford, Ernest Fraenkel, Richard A. Young posted to inside by lusk on 2007-05-03 17:43:35 as along with 29 people and 8 groups viren4388 daveGerrard Dulce talponer wowalz siebert alokm tuck lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller nklee cisevol njcitulike xili03 brant mariakmejia kristallreiner snow_dragon aalibes Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
	Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. [My Copy] Mol Biol Evol, Vol. 15, No. 7. (July 1998), pp. 910-917. by A. L. Halpern, W. J. Bruno posted to inside organization_paper by lusk on 2007-05-03 17:42:54 as along with 2 people and 1 group emptyhb dpollard EisenLab
	Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi [My Copy] PLoS Biol, Vol. 2, No. 12. (9 November 2004), e398. by Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen posted to inside by lusk on 2007-05-03 17:42:35 as along with 6 people and 3 groups roys matted mbeisen tsackton nickluscombe cisevol EisenLab EBI-regulation cis-regulatory-evolution
	Searching for regulatory elements in human noncoding sequences. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 3. (June 1997), pp. 399-406. by L. Duret, P. Bucher posted to inside review by lusk on 2007-05-03 17:42:03 as along with 2 people nklee chad_davis
	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 identification inside by lusk on 2007-05-03 17:41:41 as along with 3 people and 1 group dpollard dquest nklee EisenLab
	Computational prediction of transcription-factor binding site locations [My Copy] Genome Biology, Vol. 5, No. 1. (2003), 201. by Martha Bulyk posted to inside review by lusk on 2007-05-03 17:41:14 as along with 9 people and 1 group Baschl marti tkmaia kaarsinogen Stew nklee yevishere xili03 aalibes EisenLab
	LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731. by M. Brudno, C. B. Do, G. M. Cooper, et al.M. F. Kim, E. Davydov, E. D. Green, A. Sidow, S. Batzoglou, posted to alignment inside by lusk on 2007-05-03 17:40:50 as along with 14 people and 1 group treangen operon balajis dpollard xwbcn dquest adepace hdopazo Garamonfok adijr natstreet nklee Neeperando kcrawlik EisenLab
	Determining the requirements for cooperative DNA binding by Swi5p and Pho2p (Grf10p/Bas2p) at the HO promoter. [My Copy] J Biol Chem, Vol. 270, No. 49. (8 December 1995), pp. 29151-29161. by R. M. Brazas, L. T. Bhoite, M. D. Murphy, et al.Y. Yu, Y. Chen, D. W. Neklason, D. J. Stillman posted to bibus inside by lusk on 2007-05-03 17:40:23 as
	Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. [My Copy] EMBO J, Vol. 17, No. 21. (2 November 1998), pp. 6327-6336. by P. L. Blaiseau, D. Thomas posted to bibus inside by lusk on 2007-05-03 17:39:57 as
	Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. [My Copy] Journal of molecular biology, Vol. 193, No. 4. (20 February 1987), pp. 723-750. by O. G. Berg, P. H. von Hippel posted to bibus inside by lusk on 2007-05-03 17:39:37 as along with 9 people and 2 groups mox emptyhb jjray indigoviolet discreteonyxorb cisevol Ema brant zambujo EisenLab cis-regulatory-evolution
	Fitting a mixture model by expectation maximization to discover motifs in biopolymers. [My Copy] Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, Vol. 2 (1994), pp. 28-36. by T. L. Bailey, C. Elkan posted to bibus inside by lusk on 2007-05-03 17:39:10 as along with 3 people hendrik85 bjbecerra dquest
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to bibus inside by lusk on 2007-05-03 17:38:42 as along with 77 people and 6 groups VGreiff richter80 krapnik azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog mcbla coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 14. (15 July 2006) by Barrett C. Foat, Alexandre V. Morozov, Harmen J. Bussemaker posted to affinity inside by lusk on 2007-05-02 03:37:15 as along with 5 people mox absterga yevishere dquest xili03
	Identifying DNA and protein patterns with statistically significant alignments of multiple sequences [My Copy] Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577. by G. Z. Hertz, G. D. Stormo posted to inside by lusk on 2007-04-25 21:47:19 as along with 8 people and 1 group megraw tonamswish wowalz yylin tuck indigoviolet dquest chad_davis EisenLab
	Improved tools for biological sequence comparison. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 8. (April 1988), pp. 2444-2448. by W. R. Pearson, D. J. Lipman posted to inside by lusk on 2007-04-25 21:45:51 as along with 15 people and 2 groups rshe maria_hauser pachorip parnell carlosviana cawelsh9 arcticrasta ffranca gurkanbebek bsmagic CitoJam cjeans sujaikumar Ema bozdagd Bioinformatics bioinplant
	A Genomic Regulatory Network for Development [My Copy] Science, Vol. 295, No. 5560. (1 March 2002), pp. 1669-1678. by Eric H. Davidson, Jonathan P. Rast, Paola Oliveri, et al.Andrew Ransick, Cristina Calestani, Chiou-Hwa Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, Cesar Arenas-Mena, Ochan Otim, C. Titus Brown, Carolina B. Livi, Pei Y. Lee, Roger Revilla, Alistair G. Rust, Zheng Pan, Maria J. Schilstra, Peter J. C. Clarke, Maria I. Arnone, Lee Rowen, R. Andrew Cameron, David R. McClay, Leroy Hood, Hamid Bolouri posted to inside network sea_urchin by lusk on 2007-04-25 21:41:04 as along with 11 people and 2 groups antonkratz emptyhb yyfwuhan dlobo balajis adepace margaritis ccr edvin dquest lukaswindhager GEB EisenLab
	On the power of profiles for transcription factor binding site detection. [My Copy] Statistical applications in genetics and molecular biology, Vol. 2 (2003) by S. Rahmann, T. Müller, M. Vingron posted to inside by lusk on 2007-04-25 21:34:47 as along with 2 people megraw bluto
	Constructing transcriptional regulatory networks [My Copy] Genes & Development, Vol. 19, No. 13. (1 July 2005), pp. 1499-1511. by Alexandre Blais, Brian D. Dynlacht posted to inside review by lusk on 2007-04-25 21:11:37 as along with 9 people and 3 groups sergiun fenghezi vertikalist brant balicea xico tabu braingrind jtomasch BTS-PT-AS-CS EisenLab WetBiology
	Computational methods for transcriptional regulation [My Copy] Current Opinion in Genetics & Development In Chromosomes and expression mechanisms, Vol. 15, No. 2. (April 2005), pp. 214-221. by Eric D. Siggia posted to inside review by lusk on 2007-04-25 21:08:54 as
	cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. [My Copy] Mol Cell Biol, Vol. 25, No. 9. (May 2005), pp. 3411-3420. by M. M. Kulkarni, D. N. Arnosti posted to inside organization_paper by lusk on 2007-04-21 18:30:27 as along with 2 people and 1 group adepace olympos EisenLab
	Gene expression from random libraries of yeast promoters. [My Copy] Genetics, Vol. 172, No. 4. (April 2006), pp. 2113-2122. by M. Ligr, R. Siddharthan, F. R. Cross, E. D. Siggia posted to inside random_library by lusk on 2007-04-21 18:28:38 as along with 1 person tresch
	Conserved sequences and the evolution of gene regulatory signals. [My Copy] Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633. by M. D. Adams posted to inside review by lusk on 2007-04-21 18:12:02 as along with 2 people and 1 group dpollard cconboy EisenLab
	Doxycycline, the drug used to control the tet-regulatable promoter system, has no effect on global gene expression in Saccharomyces cerevisiae. [My Copy] Yeast, Vol. 22, No. 7. (May 2005), pp. 565-569. by J. A. Wishart, A. Hayes, L. Wardleworth, N. Zhang, S. G. Oliver posted to inside methods by lusk on 2007-04-17 21:23:32 as
	De novo cis-regulatory module elicitation for eukaryotic genomes [My Copy] PNAS, Vol. 102, No. 20. (17 May 2005), pp. 7079-7084. by Mayetri Gupta, Jun S. Liu posted to inside module_inference by lusk on 2007-04-13 20:13:18 as along with 2 people and 1 group tuck indigoviolet EisenLab
	A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis [My Copy] BMC Evolutionary Biology, Vol. 6 (22 November 2006), 99. by David A. Fitzpatrick, Mary E. Logue, Jason E. Stajich, Geraldine Butler posted to fungal_phylogeny inside by lusk on 2007-04-13 19:45:55 as along with 6 people and 1 group tomt21 dpollard stajich cmzmasek kiekyon druvus EisenLab
	Functional variation and evolution of non-coding DNA [My Copy] Current Opinion in Genetics & Development In Genomes and evolution, Vol. 16, No. 6. (December 2006), pp. 559-564. by C. Bird, B. Stranger, E. Dermitzakis posted to inside review by lusk on 2007-02-13 23:45:16 as along with 9 people and 4 groups jrhill jameswasmuth dpollard dchughes adepace sujaikumar candypmcg Stew cisevol EisenLab G4ID Genetics-of-Gambling cis-regulatory-evolution
	The molecular population genetics of regulatory genes [My Copy] Molecular Ecology, Vol. 9, No. 10. (2000), pp. 1451-1461. by Michael D. Purugganan posted to inside popgen review by lusk on 2007-02-13 23:43:42 as
	The transcriptional regulatory code of eukaryotic cells - insights from genome-wide analysis of chromatin organization and transcription factor binding [My Copy] Current Opinion in Cell Biology In Nucleus and gene expression, Vol. 18, No. 3. (June 2006), pp. 291-298. by Leah O. Barrera, Bing Ren posted to inside review by lusk on 2007-02-13 23:42:55 as along with 4 people and 4 groups dchughes cmm oannes vietanh0 FAB-lab G4ID Regulomics_UCHSC Genetics-of-Gambling
	Evolution of cis-regulatory regions versus codifying regions. [My Copy] Int J Dev Biol, Vol. 47, No. 7-8. (2003), pp. 665-673. by F. Rodríguez-Trelles, R. Tarrío, F. J. Ayala posted to inside review by lusk on 2007-02-13 23:36:06 as

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outside	69
inside	55
organization_paper	34
review	30
impact	25
methods	23
eisen_journal_club	18
specificity	15
affin_cut	12
cutoff_model	11
proteomic	11
round_robin	10
structure	10
jc	8
spacing	8
bibus	5
sm_mol	5
cancer	4
deletion	4
evolution	4
regulon	4
rich_presented	4
stuart_presented	4
colin_presented	3
cooperativity	3
devin_presented	3
e3	3
flies	3
information	3
motif	3
next_project	3
nucleosome	3
null	3
290	2
angela_presented	2
brant_presented	2
danr_presented	2
drosophila	2
eve	2
gam1	2
g_protein	2
in_depth	2
insertion	2
integrated	2
mcm1	2
module_inference	2
random_library	2
sequencing	2
skn7	2
sumo	2
turnover_rate	2
2d_gel	1
activity	1
affinity	1
alanine_scanning	1
alignment	1
amplification	1
binding	1
confocal	1
consensus	1
dna	1
emily_presented	1
fkh1	1
flow_cytometry	1
fret	1
fungal_phylogeny	1
genny	1
grammar	1
hek293	1
hky	1
identification	1
illumina	1
knockout	1
landscape	1
method	1
microarray	1
mouse	1
ndd1	1
network	1
neutral	1
overlap	1
pias	1
plant	1
plants	1
popgen	1
promoter	1
pseudocounts	1
purification	1
ranbp2	1
rap1	1
reb1	1
replication	1
rnai	1
ryan_presented	1
sea_urchin	1
segmentation	1
selection	1
senescence	1
stewart_presented	1
tfbs	1
theory	1
transplantation	1
tss	1
weighted_average	1
yap1	1

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