xianjun's library 48 articles Export

	Structure of an RNA Polymerase II-TFIIB Complex and the Transcription Initiation Mechanism [My Copy] Science (12 November 2009), science.1182015. by Xin Liu, David A. Bushnell, Dong Wang, Guillermo Calero, Roger D. Kornberg posted to no-tag by xianjun on 2009-11-13 15:03:20 as
	A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1647-1654. by Fred P. Davis, Sean R. Eddy posted to spatial_expression gene_expression_patterns by xianjun on 2009-11-03 14:39:37 as along with 3 people and 1 group mox ppgardne daforerog Journal picks
	Detection of non-neutral substitution rates on mammalian phylogenies [My Copy] Genome Research (26 October 2009) by Katherine Pollard, Melissa Hubisz, Adam Siepel posted to phylop phastcons by xianjun on 2009-10-29 00:48:39 as
	Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 257-263. by Ido Amit, Manuel Garber, Nicolas Chevrier, et al.Ana P. Leite, Yoni Donner, Thomas Eisenhaure, Mitchell Guttman, Jennifer K. Grenier, Weibo Li, Or Zuk, Lisa A. Schubert, Brian Birditt, Tal Shay, Alon Goren, Xiaolan Zhang, Zachary Smith, Raquel Deering, Rebecca C. McDonald, Moran Cabili, Bradley E. Bernstein, John L. Rinn, Alex Meissner, David E. Root, Nir Hacohen, Aviv Regev posted to rna_binding_proteins regulatory_networks by xianjun on 2009-10-28 13:51:41 as along with 9 people inesdesantiago leliavski TRHvidsten agonzale gbloeb roys ptrobajo natgoodman tmmurali
	Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 38. (22 September 2009), pp. 16327-16332. by Vydianathan Ravi, Kevin Lam, Boon-Hui Tay, Alice Tay, Sydney Brenner, Byrappa Venkatesh posted to regulatory_elements hox_clusters elephant_shark cnes by xianjun on 2009-10-28 13:41:58 as along with 1 person vravi77
	Darwinian alchemy: Human genes from noncoding DNA [My Copy] Genome Research, Vol. 19, No. 10. (October 2009), pp. 1693-1695. by Adam Siepel posted to no-tag by xianjun on 2009-10-20 10:45:59 as along with 4 people and 1 group owhitney gjuggler ppgardne inesdesantiago Journal picks
	An ensemble model of competitive multi-factor binding of the genome [My Copy] Genome Research, Vol. 19, No. 11. (31 November 2009), pp. 2101-2112. by Todd Wasson, Alexander J. Hartemink posted to transcription_factors cooperativity by xianjun on 2009-10-20 10:39:31 as along with 6 people djkt megraw vingron owhitney bpcusack natstreet
	Nucleosomes are well positioned in exons and carry characteristic histone modifications [My Copy] Genome Research, Vol. 19, No. 10. (18 October 2009), pp. 1732-1741. by Robin Andersson, Stefan Enroth, Alvaro Rada-Iglesias, Claes Wadelius, Jan Komorowski posted to internal_exons histone_modification exon_painting by xianjun on 2009-10-20 10:14:34 as along with 7 people owhitney lp2 megraw djkt fenghezi inesdesantiago cajunsushi
	Recent de novo origin of human protein-coding genes. [My Copy] Genome research, Vol. 19, No. 10. (2 October 2009), pp. 1752-1759. by David G. Knowles, Aoife McLysaght posted to noncoding_sequences evolutionary_innovation chronic_lymphocytic_leukemia by xianjun on 2009-10-20 10:05:53 as along with 9 people and 2 groups rshe psique gjuggler biomcgary megraw fenghezi avilella bpcusack djkt Journal picks Ensembl Compara citations
	Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays [My Copy] PLoS Genet, Vol. 1, No. 2. (26 August 2005), e29. by Sinnakaruppan Mathavan, Serene G. P. Lee, Alicia Mak, et al.Lance D. Miller, Karuturi R. Murthy, Kunde R. Govindarajan, Yan Tong, Yi L. Wu, Siew H. Lam, Henry Yang, Yijun Ruan, Vladimir Korzh, Zhiyuan Gong, Edison T. Liu, Thomas Lufkin posted to no-tag by xianjun on 2009-10-16 10:52:29 as
	LookSeq: A browser-based viewer for deep sequencing data [My Copy] Genome Research, Vol. 19, No. 11. (29 November 2009), pp. 2125-2132. by Heinrich M. Manske, Dominic P. Kwiatkowski posted to web_viewer deep_sequencing by xianjun on 2009-09-30 00:32:39 as along with 27 people and 2 groups hzoltan darian dakelley tonamswish inesdesantiago Thaverkamp idonaldson heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn katholt stubrown orzenil operon guhjy kongl stajich n00c torfinnnome nuin kshameer neils druvus natstreet BergmanLab Mycology
	The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands [My Copy] Genome Research, Vol. 19, No. 11. (17 November 2009), pp. 1974-1982. by Hideyuki Takeshima, Satoshi Yamashita, Taichi Shimazu, Tohru Niwa, Toshikazu Ushijima posted to rna_polymerase_ii histone_modifications expression_analysis dna_methylation by xianjun on 2009-09-30 00:29:51 as along with 3 people megraw owhitney djkt
	Predictable Dynamic Program of Timing of DNA Replication in Human Cells [My Copy] Genome Research (18 September 2009) by Romain Desprat, Danielle Thierry-Mieg, Nathalie Lailler, et al.Julien Lajugie, Carl Schildkraut, Jean Thierry-Mieg, Eric Bouhassira posted to no-tag by xianjun on 2009-09-23 18:02:58 as
	Transcriptional features of genomic regulatory blocks [My Copy] Genome Biology, Vol. 10, No. 4. (2009), R38. by Altuna Akalin, David Fredman, Erik Arner, et al.Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten Daub, Yoshihide Hayashizaki, Boris Lenhard posted to target_gene_expression grb by xianjun on 2009-09-21 15:02:56 as along with 3 people djkt JustinCrocker dolchan
	Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates [My Copy] J Hered, Vol. 100, No. 5. (1 September 2009), pp. 605-617. by Matthew W. Hahn posted to gene_duplication evolutionary_models by xianjun on 2009-09-18 12:25:43 as along with 2 people DrRichardBadge operon
	Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8333-8338. by Marie SÃ©mon, Kenneth H. Wolfe posted to subfunctionalization slow-evolving genome_duplication by xianjun on 2009-09-18 11:00:39 as
	Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner [My Copy] Science, Vol. 325, No. 5945. (4 September 2009), pp. 1246-1250. by Antigone S. Dimas, Samuel Deutsch, Barbara E. Stranger, et al.Stephen B. Montgomery, Christelle Borel, Homa Attar-Cohen, Catherine Ingle, Claude Beazley, Maria G. Arcelus, Magdalena Sekowska, Marilyne Gagnebin, James Nisbett, Panos Deloukas, Emmanouil T. Dermitzakis, Stylianos E. Antonarakis posted to single_nucleotide_polymorphisms functional_variants by xianjun on 2009-09-10 16:30:55 as along with 12 people vplagnol cajunsushi ajbattle kintoki TRHvidsten djkt fenghezi rdiaz humburg guhjy frohike SeaBird
	Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 28. (14 July 2009), pp. 11667-11672. by Ahmad M. Khalil, Mitchell Guttman, Maite Huarte, et al.Manuel Garber, Arjun Raj, Dianali Rivea Morales, Kelly Thomas, Aviva Presser, Bradley E. Bernstein, Alexander van Oudenaarden, Aviv Regev, Eric S. Lander, John L. Rinn posted to lincrna chromatin by xianjun on 2009-09-10 16:26:42 as along with 7 people and 1 group jwfoley inesdesantiago daforerog clearbluespring wsjames scjparker fenghezi Oxford Virology
	Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage [My Copy] Genome Biology, Vol. 7, No. 7. (19 July 2006), R56. by Remo Sanges, Eva Kalmar, Pamela Claudiani, Maria D'Amato, Ferenc Muller, Elia Stupka posted to cne_colinear by xianjun on 2009-09-06 15:11:54 as along with 2 people and 1 group JustinCrocker indigoviolet EisenLab
	Nucleosome deposition and DNA methylation at coding region boundaries [My Copy] Genome Biology, Vol. 10, No. 9. (1 September 2009), R89. by Jung Choi, Jae B. Bae, Jaemyun Lyu, Tae Y. Kim, Young J. Kim posted to transcription_initiation nucleosome methylation epigenetic_regulation by xianjun on 2009-09-04 11:25:25 as along with 4 people megraw djkt yogita Schmidtc
	Unstable tandem repeats in promoters confer transcriptional evolvability. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5931. (29 May 2009), pp. 1213-1216. by M. D. Vinces, M. Legendre, M. Caldara, M. Hagihara, K. J. Verstrepen posted to promoter_evolution by xianjun on 2009-08-27 11:26:21 as along with 14 people and 1 group absterga orzenil gjuggler bpcusack pkonings cisevol fenghezi cambray APRegier antonkratz JustinCrocker scjparker leliavski jjray cis-regulatory-evolution
	Long-range regulation is a major driving force in maintaining genome integrity [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (15 August 2009), 203. by Emmanuel Mongin, Ken Dewar, Mathieu Blanchette posted to long-range_regulation breakpoint by xianjun on 2009-08-27 11:09:43 as along with 6 people and 1 group daveGerrard mkotlyar maximilianh cisevol JustinCrocker MickElliot BergmanLab
	Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans [My Copy] Genome Biology, Vol. 10, No. 7. (2009), R75. by Vaishali Katju, James Farslow, Ulfar Bergthorsson posted to duplicate evolution by xianjun on 2009-07-17 13:30:47 as along with 2 people maren biomcgary
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted to alignment tree_building by xianjun on 2009-07-17 12:42:31 as along with 26 people and 4 groups gjuggler parnell kinestetika robertrentzsch gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky aprasad timflutre inquil TRHvidsten djkt fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	Uniting Alignments and Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1528-1529. by Ari Loytynoja, Nick Goldman posted to alignment tree_building by xianjun on 2009-07-17 12:40:46 as along with 2 people and 2 groups ArtemPankin ppgardne Khavkin's lab Journal picks
	Automated identification of conserved synteny after whole-genome duplication [My Copy] Genome Research, Vol. 19, No. 8. (22 August 2009), pp. 1497-1505. by Julian M. Catchen, John S. Conery, John H. Postlethwait posted to synteny by xianjun on 2009-05-27 15:28:40 as along with 4 people biomcgary djkt maximilianh natstreet
	Duplicate genes increase expression diversity in closely related species and allopolyploids. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (23 January 2009) by Misook Ha, Eun-Deok D. Kim, Z Jeffrey J. Chen posted to expression_divergence genome_duplication by xianjun on 2009-05-26 10:15:12 as along with 3 people maximilianh RamuAnandakrishnan bpcusack
	Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. [My Copy] Genome research (2 April 2009) by Denis M M. Larkin, Greg Pape, Ravikiran Donthu, Loretta Auvil, Michael Welge, Harris A A. Lewin posted to evolution synteny by xianjun on 2009-05-08 11:21:54 as along with 2 people davfre maximilianh
	Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression [My Copy] Genome Research, Vol. 19, No. 7. (23 July 2009), pp. 1184-1194. by Céline Morey, Clémence Kress, Wendy A. Bickmore posted to bystander gene_expression by xianjun on 2009-04-28 15:02:48 as along with 3 people brianb JustinCrocker idonaldson
	The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome [My Copy] Genome Research (1 January 2009) by Subhajyoti De, Sarah A. Teichmann, Madan M. Babu posted to evolution_of_transcription by xianjun on 2009-03-25 13:40:35 as along with 11 people and 1 group natstreet clearbluespring maximilianh djkt alweber jbhiatt cisevol inesdesantiago provero JustinCrocker medic0747 cis-regulatory-evolution
	Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites [My Copy] The EMBO Journal, Vol. aop, No. current. (11 December 2008) by Valerie Borde, Nicolas Robine, Waka Lin, Sandrine Bonfils, Vincent Geli, Alain Nicolas posted to chromatin h3k4me3 by xianjun on 2009-01-21 17:58:13 as along with 1 person inesdesantiago
	Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells [My Copy] Genome Biology, Vol. 9 (02 December 2008), R168. by Catia, John A. Stamatoyannopoulos posted to enhancer hcne regulation by xianjun on 2008-12-10 15:09:44 as along with 7 people and 3 groups xingxu djkt Zephyrus oelemento samgj maximilianh cisevol Roswell Cancer Crosstalk JLab BergmanLab
	Selective Constraints in Experimentally Defined Primate Regulatory Regions [My Copy] PLoS Genet, Vol. 4, No. 8. (2008), e1000157. by Daniel J. Gaffney, Ran Blekhman, Jacek Majewski posted to no-tag by xianjun on 2008-11-26 21:01:25 as along with 10 people and 2 groups daveGerrard madreach alhufton djkt bpcusack aprasad pradiptaray caseybrown maximilianh cisevol BergmanLab cis-regulatory-evolution
	Analysis of combinatorial cis-regulation in synthetic and genomic promoters [My Copy] Nature, Vol. 457, No. 7226. (23 November 2008), pp. 215-218. by Jason Gertz, Eric D. Siggia, Barak A. Cohen posted to promoter tfbs by xianjun on 2008-11-26 20:52:34 as along with 17 people and 4 groups Vincent_Rouilly pcarbo emptyhb TRHvidsten rpatward jbhiatt lusk maximilianh roys dpollard druvus sebastien_vigneau pengchy sandersl djkt siebert isimpson TranscriptionalRegulationWithThermodynamicModels RockmanLab cis-regulatory-evolution microbiology_nijmegen
	Where Do Introns Come From? [My Copy] PLoS Biology, Vol. 6, No. 11. (1 November 2008), e283. by Francesco Catania, Michael Lynch posted to evolution intron by xianjun on 2008-11-25 18:38:45 as along with 13 people and 3 groups azazello GustavoLacerda stajich myzhang andreasapostolides alipi Zephyrus natstreet druvus dchughes clearbluespring djkt barry Mycology R.E.A.D McCammon
	Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome [My Copy] PLoS Biology, Vol. 6, No. 11. (1 November 2008), e277. by Vanessa Cheung, Gordon Chua, Nizar N. Batada, et al.Christian R. Landry, Stephen W. Michnick, Timothy R. Hughes, Fred Winston posted to cryptic protmoter-in-coding-region transcript yeast by xianjun on 2008-11-25 18:36:10 as along with 4 people inesdesantiago djkt bpcusack caseybrown
	Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts [My Copy] PLoS Biology, Vol. 6, No. 11. (1 November 2008), e263. by Justin Crocker, Yoichiro Tamori, Albert Erives posted to crm drosophila evolution by xianjun on 2008-11-25 18:31:17 as along with 4 people JustinCrocker emptyhb caseybrown djkt
	Conserved noncoding sequences are selectively constrained and not mutation cold spots [My Copy] Nature Genetics, Vol. 38, No. 2. (25 December 2005), pp. 223-227. by Jared A. Drake, Christine Bird, James Nemesh, et al.Daryl J. Thomas, Christopher Newton-Cheh, Alexandre Reymond, Laurent Excoffier, Homa Attar, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis, Joel N. Hirschhorn posted to hnce snp by xianjun on 2008-11-23 22:14:20 as along with 8 people and 2 groups daforerog provero aprasad ccots ashandanj Stew cisevol bpcusack EisenLab cis-regulatory-evolution
	Genome-wide detection and characterization of positive selection in human populations [My Copy] Nature, Vol. 449, No. 7164. (18 October 2007), pp. 913-918. by Pardis C. Sabeti, Patrick Varilly, Ben Fry, et al.Jason Lohmueller, Elizabeth Hostetter, Chris Cotsapas, Xiaohui Xie, Elizabeth H. Byrne, Steven A. McCarroll, Rachelle Gaudet, Stephen F. Schaffner, Eric S. Lander posted to no-tag by xianjun on 2008-11-23 22:11:58 as along with 16 people and 1 group memerman daforerog marywaye Zephyrus ilyashl jdbowes renewang misonneh brian dchughes djkt ramensky hms ryanraaum iris42 jasonflannick R.E.A.D
	Fast-evolving non-coding sequences in the human genome [My Copy] Genome Biology, Vol. 8 (19 June 2007), R118. by Christine P. Bird, Barbara E. Stranger, Maureen Liu, et al.Daryl J. Thomas, Catherine E. Ingle, Claude Beazley, Webb Miller, Matthew E. Hurles, Emmanouil T. Dermitzakis posted to fast-evolving hcne by xianjun on 2008-11-23 21:41:40 as along with 8 people and 2 groups balicea sriesenfeld djkt Stew jlangdon cisevol iris42 bpcusack EisenLab cis-regulatory-evolution
	Chromatin: Chopping the ends [My Copy] Nat Rev Mol Cell Biol, Vol. 9, No. 12. (December 2008), pp. 921-921. by Francesca Cesari posted to chromatin by xianjun on 2008-11-21 14:08:09 as
	A shared enhancer controls a temporal switch between promoters during Drosophila primary sex determination [My Copy] Proceedings of the National Academy of Sciences (14 November 2008) by Alejandra N. González, Hong Lu, James W. Erickson posted to drosophila enhancer by xianjun on 2008-11-20 16:59:57 as
	Sequencing the nuclear genome of the extinct woolly mammoth [My Copy] Nature, Vol. 456, No. 7220. (20 November 2008), pp. 387-390. by Webb Miller, Daniela I. Drautz, Aakrosh Ratan, et al.Barbara Pusey, Ji Qi, Arthur M. Lesk, Lynn P. Tomsho, Michael D. Packard, Fangqing Zhao, Andrei Sher, Alexei Tikhonov, Brian Raney, Nick Patterson, Kerstin Lindblad-Toh, Eric S. Lander, James R. Knight, Gerard P. Irzyk, Karin M. Fredrikson, Timothy T. Harkins, Sharon Sheridan, Tom Pringle, Stephan C. Schuster posted to mammoth new-genome by xianjun on 2008-11-20 16:58:36 as along with 13 people aprasad kiekyon katanaT usagi-kirin operon reyez EsepBib treangen hpaces neils djkt jbhiatt caseybrown
	Low conservation of gene content in the : Drosophila: Y chromosome : Article : Nature [My Copy] posted to no-tag by xianjun on 2008-11-20 16:29:48 as
	Regulation of Estrogen Receptor-mediated Long Range Transcription via Evolutionarily Conserved Distal Response Elements. [My Copy] The Journal of biological chemistry, Vol. 283, No. 47. (21 November 2008), pp. 32977-32988. by Y. F. Pan, K. D. Wansa, M. H. Liu, et al.B. Zhao, S. Z. Hong, P. Y. Tan, K. S. Lim, G. Bourque, E. T. Liu, E. Cheung posted to enhancer nucleosome tfbs by xianjun on 2008-11-20 15:45:16 as
	Identification and characterization of new long conserved noncoding sequences in vertebrates. [My Copy] Mammalian genome : official journal of the International Mammalian Genome Society (18 November 2008) by Yoshiyuki Sakuraba, Toru Kimura, Hiroshi Masuya, et al.Hideki Noguchi, Hideki Sezutsu, K R. Takahasi, Atsushi Toyoda, Ryutaro Fukumura, Takuya Murata, Yoshiyuki Sakaki, Masayuki Yamamura, Shigeharu Wakana, Tetsuo Noda, Toshihiko Shiroishi, Yoichi Gondo posted to lcns by xianjun on 2008-11-20 15:04:00 as along with 3 people operon treangen maximilianh
	Chromatin structure analyses identify miRNA promoters — Genes & Development [My Copy] posted to mirna nucleosome promoter by xianjun on 2008-11-20 14:20:58 as
	Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters [My Copy] BMC Evolutionary Biology, Vol. 8 (19 September 2008), 254. by Gorel Sundstrom, Tomas A. Larsson, Dan Larhammar posted to evolution hox synteny by xianjun on 2008-11-07 14:12:25 as

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evolution	5
chromatin	3
enhancer	3
nucleosome	3
synteny	3
alignment	2
drosophila	2
genome_duplication	2
hcne	2
promoter	2
tfbs	2
tree_building	2
breakpoint	1
bystander	1
chronic_lymphocytic_leukemia	1
cne_colinear	1
cnes	1
cooperativity	1
crm	1
cryptic	1
deep_sequencing	1
dna_methylation	1
duplicate	1
elephant_shark	1
epigenetic_regulation	1
evolutionary_innovation	1
evolutionary_models	1
evolution_of_transcription	1
exon_painting	1
expression_analysis	1
expression_divergence	1
fast-evolving	1
functional_variants	1
gene_duplication	1
gene_expression	1
gene_expression_patterns	1
grb	1
h3k4me3	1
histone_modification	1
histone_modifications	1
hnce	1
hox	1
hox_clusters	1
internal_exons	1
intron	1
lcns	1
lincrna	1
long-range_regulation	1
mammoth	1
methylation	1
mirna	1
new-genome	1
noncoding_sequences	1
phastcons	1
phylop	1
promoter_evolution	1
protmoter-in-coding-region	1
regulation	1
regulatory_elements	1
regulatory_networks	1
rna_binding_proteins	1
rna_polymerase_ii	1
single_nucleotide_polymorphisms	1
slow-evolving	1
snp	1
spatial_expression	1
subfunctionalization	1
target_gene_expression	1
transcript	1
transcription_factors	1
transcription_initiation	1
web_viewer	1
yeast	1

xianjun's library 48 articles Export

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