yevishere's watchlist [at least 200 articles] Export

Recent papers matching yevishere's watchlist criteria

	Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA [My Copy] Nature Immunology, Vol. 5, No. 8. (01 August 2004), pp. 768-774. by Julie Nardone, Dong U. Lee, K. Mark Ansel, Anjana Rao posted to review by nklee on 2009-11-18 23:56:24 as along with 5 people idonaldson ziquje moborg kianpeng Jporci
	Diversity and Complexity in DNA Recognition by Transcription Factors [My Copy] Science, Vol. 324, No. 5935. (26 June 2009), pp. 1720-1723. by Gwenael Badis, Michael F. Berger, Anthony A. Philippakis, et al.Shaheynoor Talukder, Andrew R. Gehrke, Savina A. Jaeger, Esther T. Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen, Hanna Kuznetsov, Chi-Fong Wang, David Coburn, Daniel E. Newburger, Quaid Morris, Timothy R. Hughes, Martha L. Bulyk posted to no-tag by nklee on 2009-11-18 04:56:23 as along with 22 people and 1 group sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts dpollard siebert JustinCrocker burak aalibes dipenps roys emptyhb tmmurali RockmanLab
	Distinguishing direct versus indirect transcription factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted to no-tag by nklee on 2009-11-18 04:54:37 as along with 11 people oannes djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder [My Copy] DNA Res, Vol. 16, No. 5. (1 October 2009), pp. 261-273. by Alexei A. Sharov, Minoru S. H. Ko posted to no-tag by nklee on 2009-11-18 04:54:01 as along with 3 people and 2 groups sebastien_vigneau operon polivares CTCF BergmanLab
	Connecting protein structure with predictions of regulatory sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7068-7073. by Alexandre V. Morozov, Eric D. Siggia posted to protein-dna interaction by nklee on 2009-11-13 06:23:47 as along with 7 people and 2 groups vingron maximilianh ana aalibes kaarsinogen johncumbers lusk structural_bioinformatics Bioinformatics
	Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential [My Copy] Nucl. Acids Res., Vol. 33, No. 2. (26 January 2005), pp. 546-558. by Zhijie Liu, Fenglou Mao, Jun-tao Guo, et al.Bo Yan, Peng Wang, Youxing Qu, Ying Xu posted to no-tag by nklee on 2009-11-13 05:20:09 as along with 2 people and 1 group kaarsinogen oannes Regulomics_UCHSC
	Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources [My Copy] PLoS ONE, Vol. 3, No. 3. (26 March 2008), e1820. by Harri Lähdesmäki, Alistair G. Rust, Ilya Shmulevich posted to multiple features by nklee on 2009-10-25 22:38:18 as along with 4 people and 1 group isimpson dolchan druvus guhjy Jarman Lab
	Estimates of the effect of natural selection on protein coding content [My Copy] Mol Biol Evol (8 October 2009), msp232. by Von B. Yap, Helen Lindsay, Simon Easteal, Gavin Huttley posted to selection protein evolution by medic0747 on 2009-10-09 08:37:18 as
	Comparative context analysis of codon pairs on an ORFeome scale [My Copy] Genome Biology, Vol. 6, No. 3. (2005), R28. by Gabriela Moura, Miguel Pinheiro, Raquel Silva, et al.Isabel Miranda, Vera Afreixo, Gaspar Dias, Adelaide Freitas, Jose Oliveira, Manuel Santos posted to codon by medic0747 on 2009-10-09 08:36:58 as
	Genomic DNA k-mer spectra: models and modalities [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R108. by Benny Chor, David Horn, Yaron Levy, Nick Goldman, Tim Massingham posted to dna by medic0747 on 2009-10-08 12:31:44 as along with 3 people and 1 group djkt TRHvidsten gjuggler iSEEM
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3191-3193. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted to motif chip by nklee on 2009-10-08 10:06:32 as along with 3 people idonaldson farhat maximilianh
	Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization [My Copy] Genome Biology, Vol. 6, No. 11. (2005), R96. by Francis Gibbons, Markus Proft, Kevin Struhl, Frederick Roth posted to no-tag by nklee on 2009-10-03 03:54:58 as along with 3 people and 1 group humburg oelemento blobbybirdman Myxo group
	Insights from genomic profiling of transcription factors [My Copy] Nature Reviews Genetics, Vol. 10, No. 9. (11 August 2009), pp. 605-616. by Peggy J. Farnham posted to review by nklee on 2009-09-09 05:25:02 as along with 17 people and 2 groups heliopais inesdesantiago fenghezi samanthacooper fpattyn druvus frohike stubrown qayub megraw TRHvidsten mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean Journal picks Chinnaiyan Lab
	A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (28 March 2008), e1000044. by Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph posted to no-tag by nklee on 2009-08-05 08:21:56 as along with 3 people roys xili03 eskay
	Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites [My Copy] PLoS ONE, Vol. 3, No. 2. (20 February 2008), e1623. by Troels T. Marstrand, Jes Frellsen, Ida Moltke, et al.Martin Thiim, Eivind Valen, Dorota Retelska, Anders Krogh posted to benchmark kmer overrepresentation by nklee on 2009-08-05 07:57:48 as along with 3 people natstreet druvus heliopais
	Finding regulatory elements and regulatory motifs: a general probabilistic framework [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 6. (2007), S4. by Erik van Nimwegen posted to statistic by nklee on 2009-07-21 04:43:05 as along with 2 people shigepong maximilianh
	Evolutionary computation for discovery of composite transcription factor binding sites [My Copy] Nucl. Acids Res., Vol. 36, No. 21. (1 December 2008), e142. by Gary B. Fogel, V. William Porto, Gabor Varga, et al.Ernst R. Dow, Andrew M. Craven, David M. Powers, Harry B. Harlow, Eric W. Su, Jude E. Onyia, Chen Su posted to algorithm genetic by nklee on 2009-07-21 04:40:07 as along with 5 people wowalz lptolik idonaldson davfre maximilianh
	A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes [My Copy] BMC Genomics, Vol. 9, No. 1. (31 October 2008), 517. by Stefan Kurtz, Apurva Narechania, Joshua Stein, Doreen Ware posted to no-tag by nklee on 2009-07-06 08:29:51 as along with 5 people skembel timflutre malcook operon treangen
	Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W247-252. by Federico Zambelli, Graziano Pesole, Giulio Pavesi posted to over-representation by nklee on 2009-07-03 02:50:26 as along with 5 people druvus natstreet idonaldson nuin isimpson
	Estimating the posterior probability that genome-wide association findings are true or false [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1807-1813. by Jozsef Bukszar, Joseph L. McClay, Edwin J. C. G. van den Oord posted to no-tag by nklee on 2009-07-03 02:50:01 as along with 3 people zufar djkt guhjy
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted to chip-chip by nklee on 2009-07-03 02:47:49 as along with 12 people and 1 group jfr tonamswish rdiaz fpattyn jcbarret guhjy hendrik85 inesdesantiago polivares ewilban1 idonaldson humburg Journal picks
	SPACER: identification of cis-regulatory elements with non-contiguous critical residues [My Copy] Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031. by Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. Deziel, Robert H. Gross posted to no-tag by nklee on 2009-07-02 02:46:43 as along with 3 people maximilianh wenhan csdhwang
	Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 13. (1 July 2009), pp. 1617-1624. by Dennis J. Hazelett, Daniel L. Lakeland, Joseph B. Weiss posted to no-tag by nklee on 2009-06-26 02:28:08 as along with 4 people and 2 groups guhjy TRHvidsten nuin cisevol cis-regulatory-evolution BergmanLab
	Computational methods for the detection of cis-regulatory modules [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 509-524. by Peter Van Loo, Peter Marynen posted to cis module regulatory survey by nklee on 2009-06-26 02:21:14 as along with 5 people and 1 group reyez idonaldson kshameer cisevol druvus BergmanLab
	Towards accurate human promoter recognition: a review of currently used sequence features and classification methods [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 498-508. by Jia Zeng, Shanfeng Zhu, Hong Yan posted to survey by nklee on 2009-06-26 02:19:53 as along with 1 person reyez
	PQS: a protein quaternary structure file server. [My Copy] Trends Biochem Sci, Vol. 23, No. 9. (September 1998), pp. 358-361. by K. Henrick, J. M. Thornton posted to protein quaternary server structure by medic0747 on 2009-06-17 19:43:54 as along with 3 people kgutwin bicko chad_davis
	MIPS: analysis and annotation of proteins from whole genomes. [My Copy] Nucleic Acids Res, Vol. 32 Database issue (1 January 2004) by H. W. Mewes, C. Amid, R. Arnold, et al.D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, A. Ruepp posted to database interaction protein-protein by medic0747 on 2009-06-17 19:41:01 as along with 3 people and 2 groups irenas lfriedl chad_davis dbk-lab kdl
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to force-field simulation by medic0747 on 2009-06-17 14:36:53 as along with 8 people and 1 group rodrigofaccioli mmuecke flbarroso jrperillaj xavierprat saravan sobolevnrm dimka baker-group
	The GROMOS software for biomolecular simulation: GROMOS05 [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (2005), pp. 1719-1751. by Markus Christen, Philippe H. Hünenberger, Dirk Bakowies, et al.Riccardo Baron, Roland Bürgi, Daan P. Geerke, Tim N. Heinz, Mika A. Kastenholz, Vincent Kräutler, Chris Oostenbrink, Christine Peter, Daniel Trzesniak, Wilfred F. van Gunsteren posted to force-field simulation by medic0747 on 2009-06-17 14:33:51 as
	ProTherm, version 2.0: thermodynamic database for proteins and mutants [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 283-285. by Michael M. Gromiha, Jianghong An, Hidetoshi Kono, et al.Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, Akinori Sarai posted to mutants protein stability thermodynamics by medic0747 on 2009-06-17 13:16:42 as
	Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis [My Copy] Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2002-2009. by Majid Masso, Iosif I. Vaisman posted to learning machine protein stability by medic0747 on 2009-06-17 12:05:56 as along with 4 people phoenixzxl zwang kluck afon
	Prediction of protein stability changes for single-site mutations using support vector machines. [My Copy] Proteins, Vol. 62, No. 4. (21 December 2005), pp. 1125-1132. by Jianlin Cheng, Arlo Randall, Pierre Baldi posted to learning machine protein stability svm by medic0747 on 2009-06-17 11:52:19 as along with 3 people bicko massivemayhem gisle
	I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. [My Copy] Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005) by E. Capriotti, P. Fariselli, R. Casadio posted to learning machine protein stability svm by medic0747 on 2009-06-17 11:51:13 as along with 1 person gisle
	Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction [My Copy] Protein Science, Vol. 11, No. 11. (2002), pp. 2714-2726. by Hongyi Zhou, Yaoqi Zhou posted to protein stability by medic0747 on 2009-06-17 11:49:14 as
	Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. [My Copy] J Mol Biol, Vol. 307, No. 3. (30 March 2001), pp. 929-938. by J. Park, M. Lappe, S. A. Teichmann posted to interaction protein-protein by medic0747 on 2009-06-15 15:16:35 as along with 5 people and 2 groups chad_davis ronkeliz ana tjimenez cjeans structural_bioinformatics Bioinformatics
	Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect [My Copy] Protein Science, Vol. 6, No. 1. (1997), pp. 53-64. by Chung-Jung Tsai, Shuo L. Lin, Haim J. Wolfson, Ruth Nussinov posted to analysis interface protein-protein by medic0747 on 2009-06-15 14:31:12 as
	Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis. [My Copy] Proteins, Vol. 77, No. 1. (October 2009), pp. 84-96. by Julia R. Forman, Catherine L. Worth, G. Richard Bickerton, Tim G. Eisen, Tom L. Blundell posted to correlation disease mutation protein by medic0747 on 2009-06-09 16:04:11 as along with 2 people and 1 group AliC bicko Orengo Group Journal Picks
	Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. [My Copy] Protein Sci, Vol. 13, No. 7. (July 2004), pp. 1865-1874. by V. A. Ilyin, A. Abyzov, C. M. Leslin posted to alignment protein structure by medic0747 on 2009-06-09 13:33:17 as along with 3 people and 2 groups reyez ana analogAI structural_bioinformatics Bioinformatics
	TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method [My Copy] Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D317-D321. by Leslin, M. Chesley, Abyzov, Alexej, Ilyin, A. Valentin posted to alignment database protein structural by medic0747 on 2009-06-09 12:47:31 as
	The ENZYME database in 2000 [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 304-305. by Amos Bairoch posted to database enzyme protein by medic0747 on 2009-06-09 12:44:38 as along with 4 people incovoma shung carlk grottenolm
	A New Algorithm For The Alignment Of Multiple Protein Structures Using Monte Carlo Optimization [My Copy] Pac. Symp. Biocomput, Vol. 6 (2001), pp. 275-286. by C. Guda, E. D. Scheeff, P. E. Bourne, I. N. Shindyalov posted to algorithm alignment multiple protein structure by medic0747 on 2009-06-09 12:31:40 as
	DMAPS: a database of multiple alignments for protein structures. [My Copy] Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006) by C. Guda, L. R. Pal, I. N. Shindyalov posted to alignment multiple protein structure by medic0747 on 2009-06-09 12:29:18 as
	Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. [My Copy] Protein Eng, Vol. 11, No. 9. (September 1998), pp. 739-747. by I. N. Shindyalov, P. E. Bourne posted to alignment protein structure by medic0747 on 2009-06-09 12:25:50 as along with 11 people and 2 groups sebk reyez pjcite nigham jwm analogAI dgront rabio siebertm Inchoate sim82 Radiation_Damage Stressosome
	DBAli: a database of protein structure alignments. [My Copy] Bioinformatics, Vol. 17, No. 8. (August 2001), pp. 746-747. by M. A. Martí-Renom, V. A. Ilyin, A. Sali posted to alignment database protein structure by medic0747 on 2009-06-09 11:55:13 as along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
	T-Coffee: A novel method for fast and accurate multiple sequence alignment. [My Copy] Journal of molecular biology, Vol. 302, No. 1. (8 September 2000), pp. 205-217. by C. Notredame, D. G. Higgins, J. Heringa posted to alignment multiple protein sequence by medic0747 on 2009-06-09 11:51:23 as along with 17 people and 1 group bratwurst viktor21614 tomjad robert laurabailey BioNica sebk miguel dayjm indigoviolet ffranca treangen Haggan siebertm adijr marti newton1234 EisenLab
	Protein structure comparison using SAP. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 143 (2000), pp. 19-32. by W. R. Taylor posted to comparison protein structure by medic0747 on 2009-06-09 11:48:23 as
	S4: structure-based sequence alignments of SCOP superfamilies [My Copy] Nucleic Acids Research, Vol. 33, No. Supplement 1. (1 January 2005), D219. by James Casbon, Mansoor A. S. Saqi posted to alignment database protein structure by medic0747 on 2009-06-09 11:39:08 as
	A systematic comparison of protein structure classifications: SCOP, CATH and FSSP [My Copy] Structure, Vol. 7, No. 9. (15 September 1999), pp. 1099-1112. by Caroline Hadley, David T. Jones posted to classification protein structure by medic0747 on 2009-06-09 11:33:11 as along with 1 person yuslinaz
	PROCHECK: a program to check the stereochemical quality of protein structures [My Copy] Journal of Applied Crystallography, Vol. 26, No. 2. (Apr 1993), pp. 283-291. by R. A. Laskowski, M. W. Macarthur, D. S. Moss, J. M. Thornton posted to evaluation protein structure by medic0747 on 2009-06-08 16:03:59 as
	Recognition of errors in three-dimensional structures of proteins. [My Copy] Proteins, Vol. 17, No. 4. (December 1993), pp. 355-362. by M. J. Sippl posted to evaluation protein structure by medic0747 on 2009-06-08 16:00:54 as along with 2 people j3xucite hmk

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hnf4	195
targets	158
s1a	126
pbm	18
mining	16
motifs	14
diabetes	10
tools	10
microarray	9
review	9
motif	8
expression	7
chipchip	6
analysis	5
interactions	4
labeling	4
pancreas	4
affymetrix	3
dutp	3
ligands	3
mapping	3
nuclear	3
receptor	3
toxicology	3
drugs	2
phosphorylation	2
aging	1
bileacids	1
cellcycle	1
cells	1
circadian	1
coactivator	1
differentiation	1
dna	1
encode	1
enrichment	1
er	1
expresion	1
fasting	1
fattyacid	1
filtering	1
genomics	1
hnf4gamma	1
interaction	1
intestine	1
isoforms	1
kidney	1
knockout	1
lentivirus	1
modulation	1
motf	1
mutant	1
mutatant	1
myc	1
odom	1
prediction	1
pwm	1
qpcr	1
stem	1
taf1	1
tool	1
tss	1
young	1

yevishere's watchlist [at least 200 articles] Export

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