akundaje's library 108 articles Export

	Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation [My Copy] BMC Genomics, Vol. 10, No. 1. (8 September 2009), 419. by Sergei Manakov, Seth Grant, Anton Enright posted to mrna microrna gene expression dataset by akundaje on 2009-09-28 09:22:33 as along with 3 people and 2 groups heliopais daforerog danmaclean microRNA Gene Regulation
	ChIP\|[ndash]\|seq: advantages and challenges of a maturing technology [My Copy] Nature Reviews Genetics, Vol. 10, No. 10. (08 September 2009), pp. 669-680. by Peter J. Park posted to review chipseq chip-seq by akundaje on 2009-09-27 03:22:00 as along with 22 people and 6 groups dchughes RyuOgawa heliopais giovenko inesdesantiago pradiptaray dakelley clearbluespring rdiaz kimorley leliavski humburg reyez qayub fenghezi tonamswish robertrentzsch polivares idonaldson rschulz cvaldes danmaclean Journal picks Orengo Group Journal Picks JLab BergmanLab CTCF Chromatin
	High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. [My Copy] Nucleic acids research, Vol. 37, No. 1. (1 January 2009), pp. 14-25. by Tom Whitington, Andrew C. Perkins, Timothy L. Bailey posted to tfbs integration encode chromatin by akundaje on 2009-09-22 22:18:17 as along with 7 people vingron inesdesantiago polivares lptolik WanderingAengus xili03 maximilianh
	Cytoplasmic functions of the tumour suppressor p53. [My Copy] Nature, Vol. 458, No. 7242. (30 April 2009), pp. 1127-1130. by Douglas R. Green, Guido Kroemer posted to cancer p53 review by akundaje on 2009-05-26 07:18:08 as along with 2 people guhjy rbweinbe
	Histone modifications at human enhancers reflect global cell-type-specific gene expression. [My Copy] Nature, Vol. 459, No. 7243. (7 May 2009), pp. 108-112. by Nathaniel D. Heintzman, Gary C. Hon, R. David Hawkins, et al.Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis, Bing Ren posted to dataset epigeneticsenhancers epigenomics histonemodification human by akundaje on 2009-05-26 07:01:35 as along with 14 people and 2 groups RyuOgawa inesdesantiago gdb djkt tonamswish t08681mn leliavski scjparker fenghezi TRHvidsten humburg frohike idonaldson sebastien_vigneau Epigenetics CTCF
	The structure and function of G-protein-coupled receptors [My Copy] Nature, Vol. 459, No. 7245. (20 May 2009), pp. 356-363. by Daniel M. Rosenbaum, Soren G. F. Rasmussen, Brian K. Kobilka posted to gpcr review signaling by akundaje on 2009-05-26 06:48:37 as along with 8 people diod guhjy viktor21614 agrossfield patricia xdeupi hsekiguc barry
	Genome-wide association studies: Detecting gene-gene interactions that underlie human diseases. [My Copy] Nature reviews. Genetics, Vol. 10, No. 6. (12 May 2009), pp. 392-404. by Heather J. Cordell posted to gwas review by akundaje on 2009-05-26 06:42:59 as along with 16 people and 3 groups rdiaz lwaldron PabloMarin misonneh kimorley ilyashl pkonings lp2 turnersd Zephyrus daforerog roys colmryan fenghezi jbhiatt guhjy Journal picks MGEL Reading Roswell Cancer Crosstalk
	Genome-wide association studies for complex traits: consensus, uncertainty and challenges [My Copy] Nature Reviews Genetics, Vol. 9, No. 5. (01 May 2008), pp. 356-369. by Mark I. McCarthy, Goncalo R. Abecasis, Lon R. Cardon, et al.David B. Goldstein, Julian Little, John P. A. Ioannidis, Joel N. Hirschhorn posted to gwas review by akundaje on 2009-05-26 06:42:10 as along with 19 people and 1 group roys PabloMarin ilyashl sameersoi rdiaz qfwills Zephyrus daforerog cheyloveday klo misonneh psique guhjy xingxu vplagnol echinotrix aconesa ptrobajo srp33 Roswell Cancer Crosstalk
	Detection of DNA structural motifs in functional genomic elements. [My Copy] Genome Res, Vol. 17, No. 6. (June 2007), pp. 940-946. by J. A. Greenbaum, S. C. Parker, T. D. Tullius posted to dna structure tfbs by akundaje on 2009-04-23 18:42:16 as along with 4 people and 1 group scjparker wowalz athma ghattem Bioinformatics
	Validating, augmenting and refining genome-wide association signals. [My Copy] Nature reviews. Genetics, Vol. 10, No. 5. (01 May 2009), pp. 318-329. by John P. Ioannidis, Gilles Thomas, Mark J. Daly posted to gwas review by akundaje on 2009-04-18 23:37:59 as along with 12 people rdiaz druvus PabloMarin buyske daforerog turnersd psique guhjy TRHvidsten roys jbhiatt lp2
	Linking DNA methylation and histone modification: patterns and paradigms [My Copy] Nature Reviews Genetics, Vol. 10, No. 5. (01 May 2009), pp. 295-304. by Howard Cedar, Yehudit Bergman posted to dna epigenomics histone-marks histonemodification methylation by akundaje on 2009-04-18 23:36:41 as along with 9 people aprickett rdiaz cvaldes inesdesantiago megraw guhjy songpku clearbluespring fenghezi
	Construction of a genome-scale structural map at single-nucleotide resolution [My Copy] Genome Research, Vol. 17, No. 6. (June 2007), pp. 947-953. by Jason A. Greenbaum, Bo Pang, Thomas D. Tullius posted to dna prediction structure by akundaje on 2009-04-18 22:33:32 as along with 5 people and 1 group aprasad antonkratz hagechouchin443 dnewburger ghattem Bioinformatics
	Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes [My Copy] Nat Rev Genet, Vol. 9, No. 4. (April 2008), pp. 303-313. by Elliott H. Margulies, Ewan Birney posted to comparative conservation review sequence by akundaje on 2009-04-18 20:02:05 as along with 7 people timflutre guhjy zwang mingzhi phoenixzxl ptrobajo natstreet
	Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome [My Copy] Science, Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. J. Parker, Loren Hansen, Hatice O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted to comparative conservation dna motif-discovery structure tfbs now by akundaje on 2009-04-18 19:58:46 as along with 38 people and 6 groups daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings athma absterga rpatward timflutre stajich bpcusack jbhiatt djkt dhlbh friendpine dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab EisenLab cis-regulatory-evolution
	The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain [My Copy] Science, Vol. 324, No. 5929. (15 May 2009), pp. 929-930. by Skirmantas Kriaucionis, Nathaniel Heintz posted to chromatin dna by akundaje on 2009-04-18 19:20:21 as along with 6 people and 1 group aprickett dkolk01 isimpson GeeSharpMinor rpatward rschulz Jarman Lab
	OSCAR: One-class SVM for Accurate Recognition of Cis-elements [My Copy] Bioinformatics (5 October 2007), pp. btm473-btm473. by Bo Jiang, Michael Zhang, Xuegong Zhang posted to cis-regulation file-import-09-04-15 tfbs tool by akundaje on 2009-04-15 09:21:11 as
	Assessing computational tools for the discovery of transcription factor binding sites [My Copy] Nature Biotechnology, Vol. 23, No. 1. (6 January 2005), pp. 144, 137-144, 137. by Martin Tompa, Nan Li, Timothy Bailey, et al.George Church, Bart De Moor, Eleazar Eskin, Alexander Favorov, Martin Frith, Yutao Fu, James Kent, Vsevolod Makeev, Andrei Mironov, William Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu posted to now analysis file-import-09-04-15 tfbs by akundaje on 2009-04-15 09:21:11 as
	Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks [My Copy] Nature, Vol. 456, No. 7218. (6 November 2008), pp. 125-129. by Daniel Zilberman, Devin Coleman-Derr, Tracy Ballinger, Steven Henikoff posted to epigentics file-import-09-04-15 methylation by akundaje on 2009-04-15 09:21:11 as
	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [My Copy] Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816. posted to file-import-09-04-15 by akundaje on 2009-04-15 09:21:11 as
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data [My Copy] Nat Meth, Vol. 5, No. 9. (2008), pp. 829-834. by Anton Valouev, David S. Johnson, Andreas Sundquist, et al.Catherine Medina, Elizabeth Anton, Serafim Batzoglou, Richard M. Myers, Arend Sidow posted to algorithm chipseq file-import-09-04-15 peakcaller software solexa by akundaje on 2009-04-15 09:21:11 as
	Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 59, 47-59, 47. by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, et al.Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale posted to file-import-09-04-15 prediction tfbs by akundaje on 2009-04-15 09:21:11 as
	Spectral methods in machine learning and new strategies for very large datasets [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 2. (13 January 2009), pp. 369-374. by Mohamed-Ali Belabbas, Patrick J. Wolfe posted to file-import-09-04-15 by akundaje on 2009-04-15 09:21:11 as
	Transcriptional regulatory code of a eukaryotic genome [My Copy] Nature, Vol. 431, No. 7004. (2004), pp. 104, 99-104, 99. by Christopher Harbison, Benjamin Gordon, Tong Lee, et al.Nicola Rinaldi, Kenzie Macisaac, Timothy Danford, Nancy Hannett, Jean-Bosco Tagne, David Reynolds, Jane Yoo, Ezra Jennings, Julia Zeitlinger, Dmitry Pokholok, Manolis Kellis, Alex Rolfe, Ken Takusagawa, Eric Lander, David Gifford, Ernest Fraenkel, Richard Young posted to file-import-09-04-15 over-representation promoter regulation tfbs by akundaje on 2009-04-15 09:21:10 as
	CUR matrix decompositions for improved data analysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 3. (20 January 2009), pp. 697-702. by Michael W. Mahoney, Petros Drineas posted to file-import-09-04-15 by akundaje on 2009-04-15 09:21:10 as
	Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics [My Copy] Genome Res., Vol. 14, No. 3. (1 March 2004), pp. 458, 451-458, 451. by Yueyi Liu, Shirley Liu, Liping Wei, Russ Altman, Serafim Batzoglou posted to file-import-09-04-15 gibbs tfbs by akundaje on 2009-04-15 09:21:10 as
	Discovery of novel transcription factor binding sites by statistical overrepresentation. [My Copy] Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5560, 5549-5560, 5549. by S. Sinha, M. Tompa posted to now file-import-09-04-15 tfbs by akundaje on 2009-04-15 09:21:10 as
	Extensive low-affinity transcriptional interactions in the yeast genome [My Copy] Genome Res., Vol. 16, No. 8. (2006), pp. 962-972. by Amos Tanay posted to file-import-09-04-15 by akundaje on 2009-04-15 09:21:10 as
	ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome [My Copy] PLoS Computational Biology, Vol. 4, No. 10. (October 2008), pp. e1000201-e1000201. by Gary Hon, Bing Ren, Wei Wang posted to artificial-intelligence chromatin chromatin-immunoprecipitation computational-biology enhancer-elements file-import-09-04-15 genetic genome hela-cells histones human humans models oligonucleotide-array-sequence-analysis post-translational promoter-regions protein-processing statistical transcription-initiation-site by akundaje on 2009-04-15 09:21:10 as
	ConSite: web-based prediction of regulatory elements using cross-species comparison. [My Copy] Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004) by A. Sandelin, W. W. Wasserman, B. Lenhard posted to conservation file-import-09-04-15 tfbs by akundaje on 2009-04-15 09:21:10 as
	A systems view of Drosophila segmentation [My Copy] Genome Biology, Vol. 9, No. 2. (2008), pp. 207-207. by Mike Levine posted to developmental-biology drosophila file-import-09-04-15 gene-regulation modeling segmentation systems-biology by akundaje on 2009-04-15 09:21:09 as
	Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors [My Copy] Nucl. Acids Res., Vol. 30, No. 5. (1 March 2002), pp. 1255-1261. by Martha L. Bulyk, Philip L. Johnson, George M. Church posted to now file-import-09-04-15 by akundaje on 2009-04-15 09:21:09 as
	A census of human transcription factors: function, expression and evolution [My Copy] Nat Rev Genet, Vol. 10, No. 4. (April 2009), pp. 263, 252-263, 252. by Juan Vaquerizas, Sarah Kummerfeld, Sarah Teichmann, Nicholas Luscombe posted to file-import-09-04-15 tfbs by akundaje on 2009-04-15 09:21:09 as
	Reliable prediction of regulator targets using 12 Drosophila genomes [My Copy] (1 December 2007) posted to now file-import-09-04-15 by akundaje on 2009-04-15 09:21:09 as
	Practical Strategies for Discovering Regulatory DNA Sequence Motifs [My Copy] PLoS Computational Biology, Vol. 2, No. 4. (1 April 2006), pp. e36-e36. by Kenzie Macisaac, Ernest Fraenkel posted to now binding dna factor file-import-09-04-15 motifs reulatory site tfbs transcription by akundaje on 2009-04-15 09:21:09 as
	Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data [My Copy] Nucl. Acids Res. (6 August 2008), pp. gkn488-gkn488. by Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, Keji Zhao posted to chipseq file-import-09-04-15 motif-discovery peakcaller sissrs solexa by akundaje on 2009-04-15 09:21:09 as
	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. (2005), pp. 402, 395-402, 395. by T. Vavouri, G. Elgar posted to now file-import-09-04-15 preditction tfbs by akundaje on 2009-04-15 09:21:09 as
	Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells [My Copy] Genome Research, Vol. 18, No. 8. (August 2008), pp. 1325-35. by Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng, Sheng Zhong posted to algorithms animals binding-sites cells cultured dna-binding-proteins embryonic-stem-cells enhancer-elements file-import-09-04-15 gene-expression-regulation genetic genomics hmgb-proteins humans kruppel-like-transcription-factors mice muscle-cells regulatory-elements soxb1-transcription-factors transcription-factors transcriptional by akundaje on 2009-04-15 09:21:09 as
	Prediction of regulatory elements in mammalian genomes using chromatin signatures [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Kyoung Won, Iouri Chepelev, Bing Ren, Wei Wang posted to comp-bio file-import-09-04-15 histone-marks regulation tfbs by akundaje on 2009-04-15 09:21:09 as
	Myc-binding-site recognition in the human genome is determined by chromatin context [My Copy] Nature Cell Biology, Vol. 8, No. 7. (July 2006), pp. 764-70. by Ernesto Guccione, Francesca Martinato, Giacomo Finocchiaro, et al.Lucilla Luzi, Laura Tizzoni, Valentina Dall' Olio, Giuseppe Zardo, Clara Nervi, Loris Bernard, Bruno Amati posted to now acetylation animals binding-sites cell-line cell-nucleus chromatin cluster-analysis dna file-import-09-04-15 gene-expression-profiling genetic genetic-markers genome histones human humans methylation oligonucleotide-array-sequence-analysis promoter-regions protein-binding proto-oncogene-proteins-c-myc rats transcription-factors by akundaje on 2009-04-15 09:21:08 as
	Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae [My Copy] Journal of molecular biology, Vol. 296, No. 5. (10 March 2000), pp. 1205-14. by J. D. Hughes, P. W. Estep, S. Tavazoie, G. M. Church posted to now algorithms base-sequence bias-epidemiology binding-sites calibration codon computational-biology databases factual file-import-09-04-15 fungal genes genome initiator multigene-family open-reading-frames reproducibility-of-results response-elements saccharomyces-cerevisiae sequence-alignment software transcription-factors by akundaje on 2009-04-15 09:21:08 as
	Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 25. (19 June 2007), pp. 10364-10369. by Marcus B. Smolka, Claudio P. Albuquerque, Sheng-Hong Chen, Huilin Zhou posted to dna-damage dna-repair file-import-09-04-15 signal-transduction yeast by akundaje on 2009-04-15 09:21:08 as
	A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast [My Copy] PLoS Comput Biol, Vol. 3, No. 11. (9 November 2007), pp. e215-e215. by Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink posted to now file-import-09-04-15 by akundaje on 2009-04-15 09:21:08 as
	Type S error rates for classical and Bayesian Single and multiple comparison procedures [My Copy] by Andrew Gelman posted to file-import-09-04-15 multiple-comparsison statistics by akundaje on 2009-04-15 09:21:08 as
	A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. [My Copy] Genome Res, Vol. 16, No. 3. (March 2006), pp. 413, 405-413, 405. by L. W. Chang, R. Nagarajan, J. A. Magee, J. Milbrandt, G. D. Stormo posted to now file-import-09-04-15 modules motif tfbs by akundaje on 2009-04-15 09:21:08 as
	Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation [My Copy] Molecular and Cellular Biology, Vol. 20, No. 24. (December 2000), pp. 9103-12. by D. Schübeler, M. C. Lorincz, D. M. Cimbora, et al.A. Telling, Y. Q. Feng, E. E. Bouhassira, M. Groudine posted to now acetylation animals artificial-gene-fusion blotting cell-line cell-nucleus chromatin dna dna-directed-rna-polymerases dna-methylation dna-replication enhancer-elements file-import-09-04-15 flow-cytometry gene-expression-regulation gene-targeting genes genetic histones humans integrases plasmids precipitin-tests promoter-regions reporter southern time-factors transgenes viral-proteins by akundaje on 2009-04-15 09:21:08 as
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. [My Copy] Nature methods, Vol. 5, No. 9. (2008), pp. 834, 829-834, 829. by A. Valouev, D. S. Johnson, A. Sundquist, et al.C. Medina, E. Anton, S. Batzoglou, R. M. Myers, A. Sidow posted to file-import-09-04-15 ontologyanalysis prediction tfbs by akundaje on 2009-04-15 09:21:08 as
	A generic motif discovery algorithm for sequential data [My Copy] Bioinformatics, Vol. 22, No. 1. (1 January 2006), pp. 28, 21-28, 21. by Kyle Jensen, Mark Styczynski, Isidore Rigoutsos, Gregory Stephanopoulos posted to discovery factor file-import-09-04-15 motif tfbs transcription by akundaje on 2009-04-15 09:21:08 as
	Protein-DNA binding specificity predictions with structural models. [My Copy] Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5798, 5781-5798, 5781. by A. V. Morozov, J. J. Havranek, D. Baker, E. D. Siggia posted to now file-import-09-04-15 tfbs by akundaje on 2009-04-15 09:21:08 as
	VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006) by J. Grau, I. Ben-Gal, S. Posch, I. Grosse posted to file-import-09-04-15 tfbs vobn vom by akundaje on 2009-04-15 09:21:07 as
	Informative priors based on transcription factor structural class improve de novo motif discovery [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. 392, e384-392, e384. by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander Hartemink posted to now file-import-09-04-15 motif-discovery structural tfbs by akundaje on 2009-04-15 09:21:07 as

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