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	Assessing phylogenetic motif models for predicting transcription factor binding sites [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i339-347. by John Hawkins, Charles Grant, William S. Noble, Timothy L. Bailey posted to binding binding-sites factor motif phylogen prediction tfbs transcription by Stew to the group EisenLab on 2009-06-17 15:29:29 as along with 9 people and 2 groups bsamal dquest marti Lombardo_7 megraw operon nuin AlexBateman scjparker Bioinformatics - CRUK Journal picks
	Local DNA topography correlates with functional noncoding regions of the human genome. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. Parker, Loren Hansen, Hatice Ozel O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted to conservation noncoding_dna structure by dpollard to the group EisenLab on 2009-03-24 00:19:35 as along with 41 people and 5 groups arthegall provero rsaito daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre stajich bpcusack jbhiatt djkt dhlbh friendpine inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab cis-regulatory-evolution
	Mapping short DNA sequencing reads and calling variants using mapping quality scores [My Copy] Genome Research by Heng Li, J. Ruan, R. Durbin posted to bioinformatics methods nextgensequencing shortread solexa by stajich to the group EisenLab on 2008-09-01 06:21:33 as along with 1 person and 1 group GustavoLacerda Mycology
	Genomic Analysis of Adaptive Differentiation in Drosophila melanogaster [My Copy] Genetics, Vol. 179, No. 1. (1 May 2008), pp. 455-473. by Thomas L. Turner, Mia T. Levine, Melissa L. Eckert, David J. Begun posted to adaptation clinal drosophila by stajich to the group EisenLab on 2008-05-21 04:40:09 as along with 2 people and 1 group emptyhb pradiptaray Mycology
	Levers and fulcrums: progress in cis-regulatory motif models [My Copy] Nature Methods, Vol. 5, No. 4., pp. 297-298. by Ewan Birney posted to cis-regulatory comparative_genomics methods motif prediction by stajich to the group EisenLab on 2008-04-07 16:11:40 as along with 3 people and 1 group emptyhb pradiptaray isimpson Mycology
	Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome [My Copy] Genome Research, Vol. 17, No. 12. (7 December 2007), pp. 1755-1762. by Peter Andolfatto posted to drosophila hitchhiking positive_selection by dpollard to the group EisenLab on 2008-02-13 06:38:24 as along with 5 people druvus djkt usagi-kirin mimulus_99 emptyhb
	Gene network inference via structural equation modeling in genetical genomics experiments. [My Copy] Genetics, Vol. 178, No. 3. (3 March 2008), pp. 1763-1776. by B. Liu, A. de la Fuente, I. Hoeschele posted to eqtl method network system by dpollard to the group EisenLab on 2008-02-12 23:12:26 as along with 8 people roys Scis0000002 orzenil raiyar xingxu caseybrown smgomez guhjy
	Multi-scale correlations in continuous genomic data. [My Copy] Pac Symp Biocomput (2008), pp. 201-215. by R. E. Thurman, W. S. Noble, J. A. Stamatoyannopoulos posted to correlation histone hypersensitive nucleosome by dpollard to the group EisenLab on 2008-02-01 07:05:30 as along with 5 people sebastien_vigneau timflutre Eroslavochka guhjy operon
	Using DNA duplex stability information for transcription factor binding site discovery. [My Copy] Pac Symp Biocomput (2008), pp. 453-464. by R. Gordân, A. J. Hartemink posted to binding_site biophysical_model method motif_detection prediction transcription_factor by dpollard to the group EisenLab on 2008-02-01 06:21:42 as along with 1 person bootsy
	Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. [My Copy] Pac Symp Biocomput (2008), pp. 489-500. by R. W. Lusk, M. B. Eisen posted to affinity binding_site transcription_factor variation yeast by dpollard to the group EisenLab on 2008-02-01 06:19:09 as along with 3 people and 1 group lusk maximilianh caseybrown cis-regulatory-evolution
	Alignment Uncertainty and Genomic Analysis [My Copy] Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476. by Karen M. Wong, Marc A. Suchard, John P. Huelsenbeck posted to alignment alignment_accuracy by dpollard to the group EisenLab on 2008-02-01 06:16:51 as along with 33 people and 1 group Jporci operon walshtp darian ptrobajo friendpine skembel druvus treangen bpb aprasad dayjm pradiptaray tny djkt cjeans zwang lisa1 cactus biomcgary lilou dandaman gjuggler renatomilani mclarenv youdon bpcusack guhjy jdelcampo adacier gracio timflutre jfr microbiology_nijmegen
	The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. [My Copy] Pac Symp Biocomput (2008), pp. 25-36. by S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow posted to accuracy alignment alignment_accuracy method multiple_alignment phylogeny reconstruction by dpollard to the group EisenLab on 2008-02-01 06:14:52 as along with 2 people sriesenfeld treangen
	Multiple RTK pathways downregulate Groucho-mediated repression in Drosophila embryogenesis. [My Copy] Development (23 January 2008) by Einat Cinnamon, Aharon Helman, Rachel Ben-Haroush Schyr, Amir Orian, Gerardo Jiménez, Ze'ev Paroush posted to post_transcriptional_modification repression by dpollard to the group EisenLab on 2008-02-01 06:09:59 as
	Delimiting the conserved features of hunchback function for the trunk organization of insects. [My Copy] Development (23 January 2008) by Henrique Marques-Souza, Manuel Aranda, Diethard Tautz posted to drosophila expression_pattern gene_function_evolution insects pattern targets transcription_factor tribolium by dpollard to the group EisenLab on 2008-02-01 06:06:54 as
	Evigan: A Hidden Variable Model for Integrating Gene Evidence for Eukaryotic Gene Prediction. [My Copy] Bioinformatics (10 January 2008) by Qian Liu, Aaron J J. Mackey, David S S. Roos, Fernando C N C. Pereira posted to combiners comparative gene_prediction genome_annotation by stajich to the group EisenLab on 2008-01-13 21:12:18 as along with 7 people and 1 group bourby azazello GustavoLacerda druvus mingzhi gongScience alexl Mycology
	Fungal CSL transcription factors [My Copy] BMC Genomics, Vol. 8 (13 July 2007), 233. by Martin Prevorovsky, Frantisek Puta, Petr Folk posted to fungal notch transcription_factor by stajich to the group EisenLab on 2008-01-11 19:44:32 as along with 1 person and 1 group GustavoLacerda Mycology
	Contrasting the efficacy of selection on the X and autosomes in Drosophila. [My Copy] Molecular biology and evolution, Vol. 25, No. 2. (1 February 2008), pp. 454-467. by Nadia D. Singh, Amanda M. Larracuente, Andrew G. Clark posted to drosophila selection x_vs_autosomes by dpollard to the group EisenLab on 2008-01-11 18:03:53 as along with 1 person daveGerrard
	CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction [My Copy] Genome Biology, Vol. 8, No. 12. (20 December 2007), R269. by Samuel Gross, Chuong Do, Marina Sirota, Serafim Batzoglou posted to comparative_genomics gene_prediction by stajich to the group EisenLab on 2007-12-23 21:48:05 as along with 5 people and 1 group seb1 talponer dakelley GustavoLacerda renatomilani Mycology
	The Making of a Fly: The Genetics of Animal Design [My Copy] (15 April 1992) by Peter A. Lawrence posted to no-tag by indigoviolet to the group EisenLab on 2007-12-15 03:00:50 as
	WebLogo: a sequence logo generator. [My Copy] Genome research, Vol. 14, No. 6. (1 June 2004), pp. 1188-1190. by Gavin E. Crooks, Gary Hon, John-Marc M. Chandonia, Steven E. Brenner posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 15:10:46 as along with 16 people and 1 group saunders daforerog ramonvidal gwallau ivankel dsmueller GustavoLacerda rpetrenko calderonv hplatero dfgreen Mehlhorn analogAI xiaobeizhao sobolevnrm yevishere baker-group
	Sequence logos: a new way to display consensus sequences. [My Copy] Nucleic acids research, Vol. 18, No. 20. (25 October 1990), pp. 6097-6100. by T. D. Schneider, R. M. Stephens posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 15:08:00 as along with 8 people mgomes GustavoLacerda stubrown calderonv hplatero analogAI yevishere austin
	An overview of the structures of protein-DNA complexes [My Copy] Genome Biology, Vol. 1, No. 1. (2000) by Nicholas M. Luscombe, Susan E. Austin, Helen M. Berman, Janet M. Thornton posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:49:58 as along with 5 people agustinarce svozil kaarsinogen medic0747 emptyhb
	Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. [My Copy] Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1747-1749. by C. M. Bergman, J. W. Carlson, S. E. Celniker posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:40:40 as along with 1 person and 1 group yas T_lab
	GOstat: find statistically overrepresented Gene Ontologies within a group of genes [My Copy] Bioinformatics, Vol. 20, No. 9. (12 June 2004), pp. 1464-1465. by Tim Beissbarth, Terence P. Speed posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:40:11 as along with 9 people jperkins vkwn leechuck Yanno miguel RMGraze jdiggans yevishere ellakat
	Gene Ontology: tool for the unification of biology [My Copy] Nature Genetics, Vol. 25, No. 1. (01 May 2000), pp. 25-29. by Michael Ashburner, Catherine A. Ball, Judith A. Blake, et al.David Botstein, Heather Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan T. Eppig, Midori A. Harris, David P. Hill, Laurie Issel-Tarver, Andrew Kasarskis, Suzanna Lewis, John C. Matese, Joel E. Richardson, Martin Ringwald, Gerald M. Rubin, Gavin Sherlock posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:35:50 as along with 78 people and 7 groups josepe krapnik suizan sanchezbuelna Jporci artaban421 mtaschuk niallhaslam Zephyrus nicklynch mauriceccy pmendes jperkins timhubbard ipark-kaist jeremymiller vkwn MarcoAlvarez humburg mqbphcw3 kiekyon karinlag ocs marti robert85 allysonlister daforerog chasmand lawraga jorisslob bertelsen mshossain ajbattle paszkows coela fbristow kshameer anthropomorphism nolodie dagmar Robinder verdicchio raistrick vertikalist aalibes miguel dragonrez lfriedl chad_davis yas balajis benny dullhunk nirfriedman fisherp caporaso helliontroy zlu gurkanbebek djkt massivemayhem incovoma leechuck aconesa sgoetz javamint bootsy PunkRock natstreet naegele CitoJam pablomendes carlk marck dgront roys rvosa fongenae 8_01 BTS-PT-AS-CS kdl Bioinformatics T_lab biomedical-nlp FAB-lab
	Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. [My Copy] Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 36-44. by K. Tamura, S. Subramanian, S. Kumar posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:32:29 as along with 3 people jlncdr lizbiogen isimpson
	Gene Recognition Via Spliced Sequence Alignment [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 17. (1996), pp. 9061-9066. by Mikhail S. Gelfand, Andrey A. Mironov, Pavel A. Pevzner posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:20:24 as
	TRANSFAC: a database on transcription factors and their DNA binding sites [My Copy] Nucl. Acids Res., Vol. 24, No. 1. (1 January 1996), pp. 238-241. by E. Wingender, P. Dietze, H. Karas, R. Knuppel posted to database by indigoviolet to the group EisenLab on 2007-12-12 14:09:36 as along with 4 people tonamswish Mehlhorn ea dquest
	Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase [My Copy] Science, Vol. 249, No. 4968. (3 August 1990), pp. 505-510. by C. Tuerk, L. Gold posted to no-tag by indigoviolet to the group EisenLab on 2007-12-12 14:09:06 as along with 3 people and 2 groups absterga malcook jonathanjacobs SIMR bioinformatics Molecular Biology
	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 algorithm motif by indigoviolet to the group EisenLab on 2007-12-12 14:01:38 as along with 8 people megraw tonamswish wowalz yylin tuck dquest lusk chad_davis
	A computational genomics approach to the identification of gene networks [My Copy] Nucl. Acids Res., Vol. 25, No. 18. (15 September 1997), pp. 3594-3604. by A. Wagner posted to motif by indigoviolet to the group EisenLab on 2007-12-12 11:05:07 as
	A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. [My Copy] Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739. by B. T. Naughton, E. Fratkin, S. Batzoglou, D. L. Brutlag posted to motif by indigoviolet to the group EisenLab on 2007-12-12 11:00:03 as along with 4 people nklee yevishere xili03 GustavoLacerda
	Combining evidence using p-values: application to sequence homology searches. [My Copy] Bioinformatics, Vol. 14, No. 1. (1998), pp. 48-54. by T. L. Bailey, M. Gribskov posted to algorithm by indigoviolet to the group EisenLab on 2007-12-12 10:57:32 as along with 3 people bshkspr pansapiens sconlan
	Methods and statistics for combining motif match scores. [My Copy] J Comput Biol, Vol. 5, No. 2. (1998), pp. 211-221. by T. L. Bailey, M. Gribskov posted to motif by indigoviolet to the group EisenLab on 2007-12-12 10:56:53 as
	Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. [My Copy] BMC Bioinformatics, Vol. 4 (22 December 2003) by A. G. Nazina, D. A. Papatsenko posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:21:45 as
	Detection of cis -element clusters in higher eukaryotic DNA [My Copy] Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 878-889. by Martin C. Frith, Ulla Hansen, Zhiping Weng posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:15:36 as along with 2 people and 1 group maximilianh daveGerrard BergmanLab
	Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences [My Copy] Nucl. Acids Res., Vol. 30, No. 14. (15 July 2002), pp. 3214-3224. by Martin C. Frith, John L. Spouge, Ulla Hansen, Zhiping Weng posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:15:32 as along with 1 person xili03
	JASPAR: an open-access database for eukaryotic transcription factor binding profiles [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D91-94. by Albin Sandelin, Wynand Alkema, Par Engstrom, Wyeth W. Wasserman, Boris Lenhard posted to database motif by indigoviolet to the group EisenLab on 2007-12-12 09:14:43 as along with 5 people and 1 group antonkratz aalibes jguinney nklee heliopais Motif Discovery
	ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1032-1034. by Dmitri Papatsenko posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:12:26 as along with 2 people bsamal guhjy
	Cluster-Buster: finding dense clusters of motifs in DNA sequences [My Copy] Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3666-3668. by Martin C. Frith, Michael C. Li, Zhiping Weng posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:10:10 as along with 3 people Dulce isimpson nklee
	Decoding human regulatory circuits. [My Copy] Genome Res, Vol. 14, No. 10A. (October 2004), pp. 1967-1974. by W. Thompson, M. J. Palumbo, W. W. Wasserman, J. S. Liu, C. E. Lawrence posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 09:09:40 as along with 1 person Mehlhorn
	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 algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 08:37:53 as along with 2 people tuck lusk
	Modulefinder: a tool for computational discovery of cis regulatory modules. [My Copy] Pac Symp Biocomput (2005), pp. 519-530. by A. A. Philippakis, F. S. He, M. L. Bulyk posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 07:50:58 as along with 2 people wowalz ccr
	Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by O. Johansson, W. Alkema, W. W. Wasserman, J. Lagergren posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 07:47:27 as along with 2 people xili03 isimpson
	MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by V. D. Marinescu, I. S. Kohane, A. Riva posted to algorithm motif by indigoviolet to the group EisenLab on 2007-12-12 05:44:21 as
	CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by R. Sharan, I. Ovcharenko, A. Ben-Hur, R. M. Karp posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 05:41:45 as along with 1 person dquest
	Identification of regulatory regions which confer muscle-specific gene expression [My Copy] Journal of Molecular Biology, Vol. 278, No. 1. (24 April 1998), pp. 167-181. by Wyeth W. Wasserman, James W. Fickett posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-12 05:40:08 as along with 2 people gpalidwor isimpson
	Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. [My Copy] Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2738-2750. by Y. H. Grad, F. P. Roth, M. S. Halfon, G. M. Church posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-11 10:22:44 as along with 1 person maximilianh
	Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models [My Copy] Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2031-2037. by Wendy S. Wong, Rasmus Nielsen posted to algorithm enhancer-prediction by indigoviolet to the group EisenLab on 2007-12-11 05:05:47 as along with 2 people cabbagezs csdhwang
	Distinguishing protein-coding and noncoding genes in the human genome [My Copy] Proceedings of the National Academy of Sciences In Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19428-19433. by Michele Clamp, Ben Fry, Mike Kamal, et al.Xiaohui Xie, James Cuff, Michael F. Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S. Lander posted to annotation comparative_genomics gene_finding genome_annotation human noncoding orf by stajich to the group EisenLab on 2007-12-09 07:19:20 as along with 18 people and 2 groups bpcusack antonkratz jo_davies tmmurali rvosa balicea sebastien_vigneau giovanni neils cjeans cabbagezs maximilianh oelemento gjuggler slroberd renatomilani gracio Ema FAB-lab Mycology

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