WanderingAengus's library 36 articles Export

	How the Dorsal gradient works: Insights from postgenome technologies [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20072-20076. by Joung-Woo Hong, David A. Hendrix, Dmitri Papatsenko, Michael S. Levine posted to dorsal drosophila regulation by WanderingAengus on 2009-02-26 01:07:20 as along with 2 people emptyhb kshundyak
	ChIP-seq accurately predicts tissue-specific activity of enhancers [My Copy] Nature, Vol. 457, No. 7231. (12 February 2009), pp. 854-858. by Axel Visel, Matthew J. Blow, Zirong Li, et al.Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin, Len A. Pennacchio posted to chip-seq deep-seq mouse p300 regulation tfbs by WanderingAengus on 2009-02-26 01:04:56 as along with 22 people and 2 groups tonamswish ewilban1 samanthacooper ashkelon13 isimpson gdb dnewburger jochenG bertelsen oelemento rpatward cajunsushi absterga provero cassj anphony dpollard caseybrown biomcgary xingxu idonaldson djkt RockmanLab cis-regulatory-evolution
	Long non-coding RNAs: insights into functions. [My Copy] Nature reviews. Genetics, Vol. 10, No. 3. (3 March 2009), pp. 155-159. by T. R. Mercer, M. E. Dinger, J. S. Mattick posted to nc-rnas review by WanderingAengus on 2009-02-18 15:30:17 as along with 9 people daforerog guhjy galka8_diploma lp2 psique reyez svozil rdowell dchughes
	PASS: a program to align short sequences [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 967-968. by Davide Campagna, Alessandro Albiero, Alessandra Bilardi, et al.Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, Giorgio Valle posted to comp-bio deep-seq short-read-alignment by WanderingAengus on 2009-02-13 20:09:49 as along with 17 people and 1 group seb1 bozdagd adijr heliopais darian maren n00c nuin skembel cassj Neeperando helminth_lab rschulz guhjy natstreet druvus renatomilani iSEEM
	Nucleosome positioning and gene regulation: advances through genomics [My Copy] Nature Reviews Genetics, Vol. 10, No. 3. (01 March 2009), pp. 161-172. by Cizhong Jiang, B. Franklin Pugh posted to chromatin-structure nucleosomes regulation by WanderingAengus on 2009-02-13 20:06:45 as along with 13 people and 1 group tonamswish hagechouchin443 humburg talponer fenghezi inesdesantiago rpatward timflutre nilsbecker siebert aalibes idonaldson provero cube_and_beyond
	Putting chromatin immunoprecipitation into context. [My Copy] Journal of cellular biochemistry, Vol. 107, No. 1. (1 May 2009), pp. 19-29. by Vincent Zecchini, Ian G. Mills posted to chip-chip chromatin-structure regulation tfbs by WanderingAengus on 2009-02-13 20:03:42 as along with 2 people rdowell guhjy
	Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals [My Copy] Nature, Vol. 458, No. 7235. (01 February 2009), pp. 223-227. by Mitchell Guttman, Ido Amit, Manuel Garber, et al.Courtney French, Michael F. Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W. Carey, John P. Cassady, Moran N. Cabili, Rudolf Jaenisch, Tarjei S. Mikkelsen, Tyler Jacks, Nir Hacohen, Bradley E. Bernstein, Manolis Kellis, Aviv Regev, John L. Rinn, Eric S. Lander posted to deep-seq es-lander histone-marks nc-rnas stem stem-cell by WanderingAengus on 2009-02-10 15:44:16 as along with 28 people and 2 groups jwfoley rsaito greg mkiyer gdb YukaH galka8_diploma antonkratz bertelsen natstreet fenghezi TRHvidsten megraw tonamswish biomcgary inesdesantiago djkt samgj dchughes admash neils absterga cisevol jm12 daforerog bpcusack ericsuh mhamada Chinnaiyan Lab JLab
	A Primer on Regression Methods for Decoding cis-Regulatory Logic [My Copy] PLoS Comput Biol, Vol. 5, No. 1. (30 January 2009), e1000269. by Debopriya Das, Matteo Pellegrini, Joe W. Gray posted to machine-learning motifs regression regulation tfbs by WanderingAengus on 2009-02-05 20:03:22 as along with 12 people Zephyrus orzenil daforerog TRHvidsten jfr rdiaz natstreet druvus Borelli rdowell dolchan xinhe2
	Differential chromatin marking of introns and expressed exons by H3K36me3. [My Copy] Nature genetics (1 February 2009) by Paulina Kolasinska-Zwierz, Thomas Down, Isabel Latorre, Tao Liu, X Shirley S. Liu, Julie Ahringer posted to c-elegans deep-seq histone-marks by WanderingAengus on 2009-02-05 19:57:19 as along with 8 people and 1 group dpollard bpcusack inesdesantiago absterga fenghezi Dulcinea dchughes djkt RockmanLab
	Latent dirichlet allocation [My Copy] J. Mach. Learn. Res., Vol. 3 (2003), pp. 993-1022. by David M. Blei, Andrew Y. Ng, Michael I. Jordan posted to lda machine-learning mi-jordan topics by WanderingAengus on 2009-01-29 20:56:55 as along with 14 people and 1 group abellogin eddymier psj ChenxingYang bsilverthorn weiweiguo galyardt briordan ldietz Phanix leinine whym lillejul adamsi L3S
	Unsupervised learning of finite mixture models [My Copy] Pattern Analysis and Machine Intelligence, IEEE Transactions on, Vol. 24, No. 3. (2002), pp. 381-396. by M. A. F. Figueiredo, A. K. Jain posted to ak-jain em machine-learning mixture-models by WanderingAengus on 2009-01-29 16:59:46 as along with 7 people and 2 groups zhaomin jessopher alexr balicea shilad edmundo59 nklee Autoregulation GroupLens
	Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. [My Copy] BMC genomics, Vol. 10 (21 January 2009), 37. by Philippe Lefrançois, Ghia M. Euskirchen, Raymond K. Auerbach, et al.Joel Rozowsky, Theodore Gibson, Christopher M. Yellman, Mark Gerstein, Michael Snyder posted to chip-seq deep-seq multiplexing by WanderingAengus on 2009-01-27 17:10:37 as along with 5 people Vincent_Rouilly guhjy lusk emptyhb abizar
	A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology [My Copy] BMC Genomics, Vol. 9, No. Suppl 2. (2008), S23. by Weixing Feng, Yunlong Liu, Jiejun Wu, Kenneth Nephew, Tim Huang, Lang Li posted to chip-seq comp-bio deep-seq by WanderingAengus on 2009-01-24 21:52:03 as along with 2 people tonamswish ewilban1
	Modeling ChIP Sequencing In Silico with Applications [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (22 August 2008), e1000158. by Zhengdong D. Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang, Mark Gerstein posted to chip-seq comp-bio deep-seq peak-finder by WanderingAengus on 2009-01-24 21:50:03 as along with 10 people ewilban1 cassj rschulz inesdesantiago aramesh2 djkt kengg Stew gdb caseybrown
	Design and analysis of ChIP-seq experiments for DNA-binding proteins. [My Copy] Nature biotechnology, Vol. 26, No. 12. (16 December 2008), pp. 1351-1359. by Peter V. Kharchenko, Michael Y. Tolstorukov, Peter J. Park posted to chip-seq comp-bio deep-seq peak-finder by WanderingAengus on 2009-01-24 21:44:30 as along with 18 people and 2 groups stubrown guhjy gdb tonamswish ewilban1 coela ekotelnikova jfr floatingpoint idonaldson inesdesantiago vplagnol xwbcn fpattyn mutagenic kengg rschulz ghattem KCL & UCL Bioinformatics SIMR bioinformatics
	Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 523. by David Nix, Samir Courdy, Kenneth Boucher posted to chip-seq comp-bio deep-seq peak-finder by WanderingAengus on 2009-01-24 21:44:10 as along with 9 people and 2 groups darian gdb slv23 inesdesantiago ewilban1 floatingpoint magusina ghattem caseybrown Bioinformatics - CRUK SIMR bioinformatics
	Model-based Analysis of ChIP-Seq (MACS) [My Copy] Genome Biology, Vol. 9, No. 9. (2008), R137. by Yong Zhang, Tao Liu, Clifford Meyer, et al.Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, X. Shirley Liu posted to chip-seq deep-seq peak-finder xs-liu by WanderingAengus on 2009-01-24 21:39:39 as along with 23 people and 2 groups Vincent_Rouilly darian stubrown mkiyer humburg cassj floatingpoint bryankr jfr rschulz mcm polivares gdb ghattem yadadi djkt stajich mdperry fpattyn bcondon idonaldson caseybrown kengg SIMR bioinformatics Mycology
	Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data [My Copy] Nature Methods, Vol. 5, No. 9. (17 August 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 chip-seq deep-seq peak-finder by WanderingAengus on 2009-01-24 21:36:57 as along with 19 people and 1 group jwfoley ewilban1 nklee bertelsen stajich smiddha clearbluespring polivares ptrobajo mdperry idonaldson gdb megraw kengg alhufton guhjy kjglennie bryankr maximilianh Mycology
	FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology [My Copy] Bioinformatics, Vol. 24, No. 15. (1 August 2008), pp. 1729-1730. by Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew Bainbridge, Steven J. M. Jones posted to chip-seq deep-seq peak-finder by WanderingAengus on 2009-01-24 21:36:37 as along with 18 people and 2 groups darian n00c polivares idonaldson tonamswish ewilban1 humburg Thaverkamp natstreet druvus stajich cassj rschulz jfr sconlan reyez guhjy vega Bioinformatics Mycology
	The genome landscape of ERalpha- and ERbeta-binding DNA regions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 7. (19 February 2008), pp. 2604-2609. by Y. Liu, H. Gao, T. T. Marstrand, et al.A. Ström, E. Valen, A. Sandelin, J. A. Gustafsson, K. Dahlman-Wright posted to chip-chip comp-bio estrogen-receptor nuclear-receptors by WanderingAengus on 2009-01-22 15:20:50 as along with 1 person and 1 group Zephyrus R.E.A.D
	Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. [My Copy] Nature cell biology (11 January 2009) by Bo Feng, Jianming Jiang, Petra Kraus, et al.Jia-Hui H. Ng, Jian-Chien Dominic C. Heng, Yun-Shen S. Chan, Lai-Ping P. Yaw, Weiwei Zhang, Yuin-Han H. Loh, Jianyong Han, Vinsensius B B. Vega, Valere Cacheux-Rataboul, Bing Lim, Thomas Lufkin, Huck-Hui H. Ng posted to chip-seq esrrb reprogramming stem-cell by WanderingAengus on 2009-01-21 04:49:02 as
	A Sympotic Achilles, Horace Epode 13 [My Copy] The American Journal of Philology, Vol. 113, No. 3. (1992), pp. 413-433. by Michele Lowrie posted to achilles classics horace by WanderingAengus on 2009-01-16 02:04:19 as
	Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation [My Copy] Cell Stem Cell, Vol. 4, No. 1. (09 January 2009), pp. 80-93. by K. Cui, C. Zang, T. Roh, et al.D. Schones, R. Childs, W. Peng, K. Zhao posted to comp-bio deep-seq histone-marks keji-zhao regulation by WanderingAengus on 2009-01-14 18:25:23 as along with 2 people tonamswish inesdesantiago
	A model for transmission of the H3K27me3 epigenetic mark [My Copy] Nature Cell Biology, Vol. 10, No. 11. (19 October 2008), pp. 1291-1300. by Klaus H. Hansen, Adrian P. Bracken, Diego Pasini, et al.Nikolaj Dietrich, Simmi S. Gehani, Astrid Monrad, Juri Rappsilber, Mads Lerdrup, Kristian Helin posted to epigenetics histone-marks polycomb by WanderingAengus on 2009-01-12 20:19:43 as along with 1 person inesdesantiago
	Evolution of Regulatory Sequences in 12 Drosophila Species [My Copy] PLoS Genet, Vol. 5, No. 1. (January 2009), e1000330. by Jaebum Kim, Xin He, Saurabh Sinha posted to comp-bio evolution motifs regulation tfbs by WanderingAengus on 2009-01-11 18:14:01 as along with 12 people and 3 groups daveGerrard kevinemamy dpollard caseybrown druvus JustinCrocker cisevol cajunsushi djkt emptyhb cabbagesofdoom Stew RockmanLab BergmanLab cis-regulatory-evolution
	Prediction of regulatory elements in mammalian genomes using chromatin signatures [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 547. by Kyoung J. Won, Iouri Chepelev, Bing Ren, Wei Wang posted to comp-bio histone-marks regulation tfbs by WanderingAengus on 2009-01-11 18:08:46 as along with 4 people and 1 group tonamswish abizar polivares taguchi JLab
	Sequence-dependent nucleosome positioning. [My Copy] Journal of molecular biology, Vol. 386, No. 5. (13 March 2009), pp. 1411-1422. by Ho-Ryun R. Chung, Martin Vingron posted to motifs nucleosomes by WanderingAengus on 2009-01-11 18:07:52 as along with 2 people RyuOgawa hagechouchin443
	Decoding the epigenetic language of neuronal plasticity. [My Copy] Neuron, Vol. 60, No. 6. (26 December 2008), pp. 961-974. by E. Borrelli, E. J. Nestler, C. D. Allis, P. Sassone-Corsi posted to histone-marks neuron by WanderingAengus on 2009-01-11 18:06:33 as
	PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. [My Copy] Nature biotechnology, Vol. 27, No. 1. (04 January 2009), pp. 66-75. by Joel Rozowsky, Ghia Euskirchen, Raymond K. Auerbach, et al.Zhengdong D. Zhang, Theodore Gibson, Robert Bjornson, Nicholas Carriero, Michael Snyder, Mark B. Gerstein posted to chip-seq comp-bio deep-seq peak-finder by WanderingAengus on 2009-01-11 18:04:42 as along with 17 people and 1 group fpattyn gdb huali ewilban1 fenghezi smiddha jfr bertelsen JeremyZucker cassj inesdesantiago dakelley ghattem abizar polivares idonaldson guhjy SIMR bioinformatics
	Quantifying the evolutionary dynamics of language [My Copy] Nature, Vol. 449, No. 7163. (11 October 2007), pp. 713-716. by Erez Lieberman, Jean-Baptiste Michel, Joe Jackson, Tina Tang, Martin A. Nowak posted to evolution language linguistics by WanderingAengus on 2009-01-11 18:03:32 as along with 18 people and 2 groups halukbingol sen_cheng anphony voiklis garyfeng baronka junwang4 briordan alexsteer Koh ngdelamo rcrane cactus qwermish heliopais julianjonker S_Ray soramame_0518 Soslab Semantic networks in translation
	Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. [My Copy] Genome research, Vol. 16, No. 10. (October 2006), pp. 1299-1309. by Josée Dostie, Todd A. Richmond, Ramy A. Arnaout, et al.Rebecca R. Selzer, William L. Lee, Tracey A. Honan, Eric D. Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum, Roland D. Green, Job Dekker posted to 5c chromatin-structure by WanderingAengus on 2009-01-11 18:02:38 as along with 5 people TorstenWaldminghaus idonaldson polivares elzodw mdimon
	Gene Regulation in the Third Dimension [My Copy] Science, Vol. 319, No. 5871. (28 March 2008), pp. 1793-1794. by Job Dekker posted to chromatin-structure regulation by WanderingAengus on 2009-01-11 18:01:57 as along with 11 people and 3 groups operon AbnerCYH ealloza biomcgary sunhwan dlobo lambda Haze emptyhb inesdesantiago ArtemPankin TranscriptionalRegulationWithThermodynamicModels GEB Khavkin's lab
	Long-range chromosomal interactions and gene regulation. [My Copy] Molecular bioSystems, Vol. 4, No. 11. (November 2008), pp. 1046-1057. by Adriana Miele, Job Dekker posted to chromatin-structure histone-marks regulation by WanderingAengus on 2009-01-11 17:59:22 as along with 1 person Annab
	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 chromatin-structure comp-bio deep-seq histone-marks tfbs by WanderingAengus on 2009-01-11 17:54:26 as along with 7 people vingron akundaje inesdesantiago polivares lptolik xili03 maximilianh
	The DNA-encoded nucleosome organization of a eukaryotic genome. [My Copy] Nature, Vol. 458, No. 7236. (19 March 2009), pp. 362-366. by Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, et al.Andrea J. Gossett, Desiree Tillo, Yair Field, Emily M. LeProust, Timothy R. Hughes, Jason D. Lieb, Jonathan Widom, Eran Segal posted to motifs nucleosomes regulation by WanderingAengus on 2009-01-10 17:30:02 as along with 10 people and 1 group clearbluespring suizifish inesdesantiago gdb kshundyak absterga rschulz skoch3 dchughes maximilianh Koch_Lab
	Prediction of regulatory elements in mammalian genomes using chromatin signatures [My Copy] BMC Bioinformatics, Vol. 9 (Dec 2008) by Kyoung J. Won, Iouri Chepelev, Bing Ren, Wei Wang posted to histone-marks regulation by WanderingAengus on 2009-01-10 17:21:20 as

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deep-seq	15
regulation	12
chip-seq	11
comp-bio	11
histone-marks	9
peak-finder	7
chromatin-structure	6
tfbs	6
motifs	4
machine-learning	3
nucleosomes	3
chip-chip	2
evolution	2
nc-rnas	2
stem-cell	2
5c	1
achilles	1
ak-jain	1
c-elegans	1
classics	1
dorsal	1
drosophila	1
em	1
epigenetics	1
es-lander	1
esrrb	1
estrogen-receptor	1
horace	1
keji-zhao	1
language	1
lda	1
linguistics	1
mi-jordan	1
mixture-models	1
mouse	1
multiplexing	1
neuron	1
nuclear-receptors	1
p300	1
polycomb	1
regression	1
reprogramming	1
review	1
short-read-alignment	1
stem	1
topics	1
xs-liu	1

WanderingAengus's library 36 articles Export

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