maximilianh's Top Recommendations

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	Regulatory motif discovery using a population clustering evolutionary algorithm. [My Copy] IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414. by M. A. Lones, A. M. Tyrrell posted by 7 people Dulce wowalz nklee idonaldson xili03 csdhwang isimpson
	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 by 6 people druvus natstreet idonaldson nklee nuin isimpson
	Systematic functional characterization of cis-regulatory motifs in human core promoters [My Copy] Genome Research, Vol. 18, No. 3. (6 March 2008), pp. 477-488. by Saurabh Sinha, Adam S. Adler, Yair Field, Howard Y. Chang, Eran Segal posted by 9 people ptrobajo heliopais ealloza lp2 cabbagezs idonaldson emptyhb gracio isimpson
	An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance [My Copy] BMC Bioinformatics, Vol. 9 (07 February 2008), 89. by Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira posted by 4 people wowalz idonaldson xili03 isimpson
	Predicting expression patterns from regulatory sequence in Drosophila segmentation [My Copy] Nature, Vol. 451, No. 7178. (02 January 2008), pp. 535-540. by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul posted by 22 people TRHvidsten BergmanLab daveGerrard koller TranscriptionalRegulationWithThermodynamicModels dlmace ptrobajo isimpson dakelley tmmurali eckart_bindewald djkt bootsy biomcgary idonaldson roys emptyhb pkharchenko meiklej jrest tresch siebert
	Discovering Motifs in Ranked Lists of DNA Sequences [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39. by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini posted by 7 people eckart_bindewald zwang GeeSharpMinor ppark idonaldson hpaces isimpson
	MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs [My Copy] BMC Bioinformatics, Vol. 8 (22 March 2007), 100. by Mamoru Kato, Tatsuhiko Tsunoda posted by 5 people cwbrown nklee EisenLab idonaldson isimpson
	An introduction to ROC analysis [My Copy] Pattern Recogn. Lett. In ROC Analysis in Pattern Recognition, Vol. 27, No. 8. (June 2006), pp. 861-874. by Tom Fawcett posted by 42 people singhsh TLVincent module qluo q_w_e_r_t_y makrehchi Borelli mthomure sbarthelme jjrodriguez cen4ik jmetzen MosesCheckley ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo Bioinformatics Crypto VT_DLRL Randomness LIVIA tgyork idonaldson BergmanLab napvasconcelos cdeane haiyeong AbnerCYH isimpson guhjy nherveg
	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 by 20 people heliopais inesdesantiago fenghezi nklee samanthacooper fpattyn druvus frohike stubrown Journal picks qayub megraw TRHvidsten Chinnaiyan Lab mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean
	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 by 7 people reyez idonaldson kshameer nklee BergmanLab cisevol druvus
	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 by 14 people jfr tonamswish rdiaz fpattyn Journal picks jcbarret guhjy hendrik85 inesdesantiago nklee polivares ewilban1 idonaldson humburg
	MotifMap: a human genome-wide map of candidate regulatory motif sites [My Copy] Bioinformatics, Vol. 25, No. 2. (15 January 2009), pp. 167-174. by Xiaohui Xie, Paul Rigor, Pierre Baldi posted by 12 people jakebiesinger kmdaily guhjy wowalz ilyashl jfr abizar heliopais nklee idonaldson nuin djkt
	Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing [My Copy] Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), pp. 4549-4564. by Elizabeth D. Wederell, Mikhail Bilenky, Rebecca Cullum, et al.Nina Thiessen, Melis Dagpinar, Allen Delaney, Richard Varhol, Yongjun Zhao, Thomas Zeng, Bridget Bernier, Matthew Ingham, Martin Hirst, Gordon Robertson, Marco A. Marra, Steven Jones, Pamela A. Hoodless posted by 1 person idonaldson
	Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. [My Copy] Nucleic acids research, Vol. 36, No. 16. (6 September 2008), pp. 5221-5231. by R. Jothi, S. Cuddapah, A. Barski, K. Cui, K. Zhao posted by 11 people tonamswish talponer ewilban1 polivares guhjy mcm Eroslavochka inesdesantiago mdperry sebastien_vigneau idonaldson
	Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets [My Copy] Genome Research, Vol. 18, No. 3. (7 March 2008), pp. 393-403. by David S. Johnson, Wei Li, D. Benjamin Gordon, et al.Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S. Carroll, Myles Brown, Paul Flicek, Christoph M. Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J. Farnham, Philipp Kapranov, David A. Nix, Thomas R. Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland D. Green, Jun S. Song, Scott A. Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D. Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C. Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P. Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M. Myers, Jason D. Lieb, X. Shirley Liu posted by 15 people fenghezi jfr kengg djkt xiaobeizhao cabbagezs idonaldson BergmanLab caseybrown magusina lp2 stajich Mycology gracio gdb
	Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi [My Copy] Genome Res. (5 November 2007), gr.6531807. by Michael J. Cornell, Intikhab Alam, Darren M. Soanes, et al.Han M. Wong, Cornelia Hedeler, Norman W. Paton, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver posted by 8 people stajich grahamc GustavoLacerda nklee idonaldson Mycology seitentaisei alanrw
	Clustering of main orthologs for multiple genomes. [My Copy] Comput Syst Bioinformatics Conf, Vol. 6 (2007), pp. 195-201. by Z. Fu, T. Jiang posted by 2 people operon idonaldson
	Identifying tissue-selective transcription factor binding sites in vertebrate promoters. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 5. (1 February 2005), pp. 1560-1565. by A. D. Smith, P. Sumazin, M. Q. Zhang posted by 3 people raylim heliopais idonaldson
	Finding functional sequence elements by multiple local alignment [My Copy] Nucl. Acids Res., Vol. 32, No. 1. (2 January 2004), pp. 189-200. by Martin C. Frith, Ulla Hansen, John L. Spouge, Zhiping Weng posted by 8 people wyatt111 idonaldson wowalz treangen dquest kengg nklee Plantandetc
	Benchmarking tools for the alignment of functional noncoding DNA. [My Copy] BMC Bioinformatics, Vol. 5 (21 January 2004) by D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, M. B. Eisen posted by 8 people cap1 indigoviolet lilou adijr EisenLab idonaldson gjuggler nklee
	An improved map of conserved regulatory sites for Saccharomyces cerevisiae [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (7 March 2006), 113. by Kenzie Macisaac, Ting Wang, D. Benjamin Gordon, David Gifford, Gary Stormo, Ernest Fraenkel posted by 10 people roys idonaldson tuck eckart_bindewald cconboy raiyar lusk nklee barwil kristallreiner
	Discovery of regulatory elements in vertebrates through comparative genomics [My Copy] Nature Biotechnology, Vol. 23, No. 10. (06 October 2005), pp. 1249-1256. by Amol Prakash, Martin Tompa posted by 7 people idonaldson aprasad indigoviolet dchughes EisenLab G4ID Genetics-of-Gambling
	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 by 6 people nklee idonaldson ziquje moborg kianpeng Jporci
	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 by 26 people hzoltan tonamswish ewilban1 samanthacooper ashkelon13 isimpson gdb dnewburger jochenG bertelsen oelemento rpatward cajunsushi WanderingAengus absterga provero cassj anphony RockmanLab cis-regulatory-evolution dpollard caseybrown biomcgary xingxu idonaldson djkt
	Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. [My Copy] Nature protocols, Vol. 3, No. 10. (18 September 2008), pp. 1578-1588. by Jean-Valery V. Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques van Helden posted by 9 people kshameer isimpson heliopais druvus fhsantanna BergmanLab polivares idonaldson natstreet
	An integrated software system for analyzing ChIP-chip and ChIP-seq data. [My Copy] Nature biotechnology, Vol. 26, No. 11. (02 November 2008), pp. 1293-1300. by Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, Wing H. Wong posted by 28 people hzoltan Neuroblastoma fpattyn stubrown isimpson SIMR bioinformatics huali tonamswish ewilban1 sebastien_vigneau jfr kmdaily cassj bryankr malcook rschulz mcm behindtherabbit psique renatomilani polivares guhjy inesdesantiago pengchy kengg BenosLab bais idonaldson
	Inferring the role of transcription factors in regulatory networks [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (06 May 2008), 228. by Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel posted by 7 people dolchan guhjy idonaldson renatomilani heliopais maralena isimpson
	Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes [My Copy] Genome Biology, Vol. 9 (15 February 2008), R34. by Par G. Engstrom, David Fredman, Boris Lenhard posted by 6 people brant natstreet heliopais idonaldson boudinot isimpson
	Model-based deconvolution of genome-wide DNA binding. [My Copy] Bioinformatics (1 December 2007) by David J J. Reiss, Marc T T. Facciotti, Nitin S S. Baliga posted by 6 people djkt idonaldson yevishere guhjy vega isimpson
	JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D102-106. by Jan C. Bryne, Eivind Valen, Man-Hung E. Tang, et al.Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin posted by 8 people isimpson natstreet druvus guhjy dullhunk idonaldson sci91078 jfr
	Statistical power of phylo-HMM for evolutionarily conserved element detection [My Copy] BMC Bioinformatics, Vol. 8 (05 October 2007), 374. by Xiaodan Fan, Jun Zhu, Eric E. Schadt, Jun S. Liu posted by 4 people idonaldson BergmanLab pradiptaray isimpson
	Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. [My Copy] Algorithms for molecular biology : AMB, Vol. 2 (10 October 2007), 13. by V. Boeva, J. Clément, M. Régnier, M. A. Roytberg, V. J. Makeev posted by 5 people wowalz beete idonaldson guos isimpson
	A Primer on Learning in Bayesian Networks for Computational Biology [My Copy] PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e129. by Chris J. Needham, James R. Bradford, Andrew J. Bulpitt, David R. Westhead posted by 16 people sameersoi Sonix guhjy brian jfr balicea grahamc zwang bertelsen cabbagezs groepl Bioinformatics ppark idonaldson BergmanLab isimpson
	Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 898-909. by Ghia M. Euskirchen, Joel S. Rozowsky, Chia-Lin Wei, et al.Wah H. Lee, Zhengdong D. Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B. Gerstein, Yijun Ruan, Michael Snyder posted by 11 people kengg jtaylor ghattem epigenetics Bioinformatics Plantandetc blobbybirdman UH - Computational Biology idonaldson BergmanLab isimpson
	MATLIGN: a motif clustering, comparison and matching tool [My Copy] BMC Bioinformatics, Vol. 8 (08 June 2007), 189. by Matti Kankainen, Ari Loytynoja posted by 5 people idonaldson BergmanLab smbe2008 isimpson xili03
	How does DNA sequence motif discovery work? [My Copy] Nature Biotechnology, Vol. 24, No. 8., pp. 959-961. by Patrik D'Haeseleer posted by 11 people Dulce wowalz cambray bryankr okarsligil Evangelia antonkratz Bioinformatics xi03 idonaldson isimpson
	The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. [My Copy] Nature genetics, Vol. 38, No. 4. (05 April 2006), pp. 431-440. by Yuin-Han H. Loh, Qiang Wu, Joon-Lin L. Chew, et al.Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Y. Wong, Ken W. Sung, Charlie W. Lee, Xiao-Dong D. Zhao, Kuo-Ping P. Chiu, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin L. Wei, Yijun Ruan, Bing Lim, Huck-Hui H. Ng posted by 12 people isimpson inesdesantiago tonamswish guhjy cmmorel gpalidwor brixtonmc vega eukfn mikaelhuss idonaldson tdmckee
	PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. [My Copy] PLoS computational biology, Vol. 1, No. 7. (December 2005) by Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen posted by 21 people farhat wowalz aprasad cajunsushi treangen druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou structural_bioinformatics Bioinformatics EBI-regulation idonaldson yevishere isimpson
	CoMoDis: composite motif discovery in mammalian genomes. [My Copy] Nucleic Acids Res, Vol. 35, No. 1. (2007) by I. J. Donaldson, B. Göttgens posted by 3 people Bioinformatics idonaldson csdhwang
	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 by 24 people nklee sconlan isimpson jbhiatt daforerog absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts RockmanLab dpollard siebert JustinCrocker burak aalibes dipenps roys emptyhb tmmurali
	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 by 6 people nklee Jarman Lab isimpson dolchan druvus guhjy
	Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i41-49. by Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial posted by 6 people chad_davis isimpson druvus nklee sconlan nuin
	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 by 5 people Dulce isimpson nklee indigoviolet EisenLab
	Evolution of genes and genomes on the Drosophila phylogeny [My Copy] Nature, Vol. 450, No. 7167. (08 November 2007), pp. 203-218. posted by 42 people biomcgary nuttpo daveGerrard Anachff GustavoLacerda mqbphcw3 rpetrenko gwallau chica jlncdr aprasad gjuggler lizbiogen jbsaltz druvus pradiptaray pengchy operon tmmurali indigoviolet djkt timflutre stajich zwang Garamonfok lp2 Bioinformatics EisenLab CharlesM hpaces caseybrown emptyhb urgi Mycology noor PetrovLab isimpson balicea cisevol BergmanLab Drosophila-Genetics-Genomics-2008 hdopazo
	Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster [My Copy] PLoS Comput Biol, Vol. 3, No. 1. (19 January 2007), e7. by Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard posted by 13 people daveGerrard ychromosome timhubbard lusk wowalz indigoviolet dpollard dquest SeungjoonOh nklee EisenLab emptyhb isimpson
	MEME: discovering and analyzing DNA and protein sequence motifs [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W369-373. by Timothy L. Bailey, Nadya Williams, Chris Misleh, Wilfred W. Li posted by 9 people stharward wowalz coldmeadow yevishere pansapiens nklee bryankr dquest isimpson
	Applied bioinformatics for the identification of regulatory elements. [My Copy] Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287. by W. W. Wasserman, A. Sandelin posted by 27 people wowalz yas icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen Stew nklee structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling jdiezperezj ArtemPankin mariakmejia isimpson
	DBD: a transcription factor prediction database. [My Copy] Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) by S. K. Kummerfeld, S. A. Teichmann posted by 8 people isimpson troels_marstrand gpalidwor nickluscombe nklee EBI-regulation mariakmejia natstreet
	Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. [My Copy] Nucleic Acids Res, Vol. 33, No. 7. (2005), pp. 2290-2301. by N. I. Gershenzon, G. D. Stormo, I. P. Ioshikhes posted by 2 people Kiarostami csdhwang
	Advances in the Discovery of cis-Regulatory Elements [My Copy] Current Bioinformatics, Vol. 1, No. 3. (August 2006), pp. 321-336. by Pan, Youlian posted by 5 people wowalz druvus natstreet nklee csdhwang
	MOODS: fast search for position weight matrix matches in DNA sequences [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3181-3182. by Janne Korhonen, Petri Martinmaki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen posted by 5 people idonaldson Journal picks ppgardne farhat djkt
	Structural and dynamic changes of the serum response element and the core domain of serum response factor induced by their association [My Copy] Biochemical and Biophysical Research Communications (10 November 2009) by Josef Štěpánek, Kopecký Jr, Alberto Mezzetti, et al.Pierre-Yves Turpin, Denise Paulin, Bernard Alpert, Christian Zentz posted by 1 person idonaldson
	Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data [My Copy] Nucl. Acids Res. (11 November 2009), gkp1012. by Kimberly R. Blahnik, Lei Dou, Henriette O'Geen, et al.Timothy McPhillips, Xiaoqin Xu, Alina R. Cao, Sushma Iyengar, Charles M. Nicolet, Bertram Ludascher, Ian Korf, Peggy J. Farnham posted by 1 person idonaldson
	JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles [My Copy] Nucl. Acids Res. (11 November 2009), gkp950. by Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, et al.David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin posted by 2 people idonaldson daforerog
	BFAST: An Alignment Tool for Large Scale Genome Resequencing [My Copy] PLoS ONE, Vol. 4, No. 11. (11 November 2009), e7767. by Nils Homer, Barry Merriman, Stanley F. Nelson posted by 6 people n00c friendpine zwang druvus torfinnnome idonaldson
	Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression [My Copy] Genome Research (3 November 2009) by Yong Cheng, Weisheng Wu, Swathi Ashok Kumar, et al.Duonan Yu, Wulan Deng, Tamara Tripic, David C. King, Kuan-Bei Chen, Ying Zhang, Daniela Drautz, Belinda Giardine, Stephan C. Schuster, Webb Miller, Francesca Chiaromonte, Yu Zhang, Gerd A. Blobel, Mitchell J. Weiss, Ross C. Hardison posted by 1 person idonaldson
	A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays [My Copy] BMC Genomics, Vol. 10, No. 1. (27 October 2009), 497. by Danette Hartzell, Nathan Trinklein, Jacqui Mendez, et al.Nancy Murphy, Shelley Aldred, Keith Wood, Marjeta Urh posted by 1 person idonaldson
	G-compass: A web-based comparative genome browser between human and other vertebrate genomes [My Copy] Bioinformatics (21 October 2009), btp594. by Yoshihiro Kawahara, Ryuichi Sakate, Akihiro Matsuya, et al.Katsuhiko Murakami, Yoshiharu Sato, Hao Zhang, Takashi Gojobori, Takeshi Itoh, Tadashi Imanishi posted by 5 people idonaldson kshameer operon neils druvus
	HIGH-RESOLUTION NUCLEOSOME MAPPING REVEALS TRANSCRIPTION-DEPENDENT PROMOTER PACKAGING. [My Copy] Genome research (21 October 2009) by Assaf Weiner, Amanda Hughes, Moran Yassour, Oliver Rando, Nir Friedman posted by 3 people Epigenetics sebastien_vigneau idonaldson
	Windshield splatter analysis with the Galaxy metagenomic pipeline [My Copy] Genome Research, Vol. 19, No. 11. (9 November 2009), pp. 2144-2153. by Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, et al.Guruprasad Ananda, Wen-Yu Chung, James Taylor, Anton Nekrutenko posted by 11 people jmeppley seb1 microbiology_nijmegen Katje iSEEM djkt operon neils idonaldson jgill kshameer
	A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R109. by Cizhong Jiang, B. Franklin Pugh posted by 4 people idonaldson venancio aalibes lp2
	Phosphorylation of the Human MicroRNA-Generating Complex Mediates MAPK/Erk Signaling [My Copy] Cell, Vol. 139, No. 1. (02 October 2009), pp. 112-122. by Zain Paroo, Xuecheng Ye, She Chen, Qinghua Liu posted by 5 people idonaldson microRNA heliopais gbloeb valeriehilgers
	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG) [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2863-2864. by Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. De La Vega posted by 4 people seb1 idonaldson n00c druvus
	BayesPeak: Bayesian analysis of ChIP-seq data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 299. by Christiana Spyrou, Rory Stark, Andy Lynch, Simon Tavare posted by 16 people Vincent_Rouilly Bioinformatics tonamswish dswan fenghezi inesdesantiago idonaldson JLab BergmanLab polivares mkiyer druvus Mycology stajich humburg rschulz
	Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation [My Copy] Brief Funct Genomic Proteomic, Vol. 8, No. 4. (1 July 2009), pp. 297-309. by Robert-Jan Theo Sijtse Palstra posted by 1 person idonaldson
	The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. [My Copy] Blood, Vol. 113, No. 22. (28 May 2009), pp. 5456-5465. by Nicola K. Wilson, Diego Miranda-Saavedra, Sarah Kinston, et al.Nicolas Bonadies, Samuel D. Foster, Fernando Calero-Nieto, Mark A. Dawson, Ian J. Donaldson, Stephanie Dumon, Jonathan Frampton, Rekin's Janky, Xiao-Hong H. Sun, Sarah A. Teichmann, Andrew J. Bannister, Berthold Göttgens posted by 1 person idonaldson
	ID1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signaling. [My Copy] Blood, Vol. 114, No. 9. (27 August 2009), pp. 1820-1830. by Andrew D. Wood, Edwin Chen, Ian J. Donaldson, et al.Shilpa Hattangadi, Karly A. Burke, Mark A. Dawson, Diego Miranda-Saavedra, Harvey F. Lodish, Anthony R. Green, Berthold Göttgens posted by 1 person idonaldson
	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 by 30 people hzoltan dchughes RyuOgawa heliopais giovenko inesdesantiago pradiptaray dakelley clearbluespring akundaje rdiaz kimorley leliavski humburg reyez Journal picks qayub fenghezi tonamswish Orengo Group Journal Picks robertrentzsch JLab BergmanLab polivares idonaldson rschulz CTCF Chromatin cvaldes danmaclean
	TagDust--a program to eliminate artifacts from next generation sequencing data [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2839-2840. by Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub posted by 21 people hzoltan chvlyl operon kshameer djkt rtogawa seb1 idonaldson nuin debasis jgill GeeSharpMinor Journal picks sotacam torfinnnome walshtp heliopais jandot n00c rschulz druvus
	Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2739-2740. by Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden posted by 5 people druvus inesdesantiago idonaldson natstreet sebastien_vigneau
	Updates to the RMAP short-read mapping software [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2841-2842. by Andrew D. Smith, Wen-Yu Chung, Emily Hodges, et al.Jude Kendall, Greg Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang posted by 10 people seb1 darian natstreet djkt rtogawa idonaldson heliopais Journal picks n00c druvus
	From gene expression to gene regulatory networks in Arabidopsis thaliana [My Copy] BMC Systems Biology, Vol. 3, No. 1. (3 September 2009), 85. by Chris Needham, Iain Manfield, Andrew Bulpitt, Philip Gilmartin, David Westhead posted by 10 people idonaldson pengchy Borelli ptrobajo danmaclean TRHvidsten rmk barriot natstreet druvus
	Dissecting Nucleosome Free Regions by a Segmental Semi-Markov Model [My Copy] PLoS ONE, Vol. 4, No. 3. (6 March 2009), e4721. by Wei Sun, Wei Xie, Feng Xu, Michael Grunstein, Ker-Chau Li posted by 3 people BergmanLab cisevol idonaldson
	Chromatin poises miRNA- and protein-coding genes for expression. [My Copy] Genome research, Vol. 19, No. 10. (27 October 2009), pp. 1742-1751. by Artem Barski, Raja Jothi, Suresh Cuddapah, et al.Kairong Cui, Tae-Young Y. Roh, Dustin E. Schones, Keji Zhao posted by 12 people tonamswish microRNA heliopais samgj polivares megraw inesdesantiago Neuroblastoma fpattyn djkt fenghezi idonaldson
	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 by 30 people hzoltan darian dakelley tonamswish inesdesantiago Thaverkamp BergmanLab idonaldson heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn xianjun katholt stubrown orzenil operon guhjy kongl Mycology stajich n00c torfinnnome nuin kshameer neils druvus natstreet
	Statistical detection of cooperative transcription factors with similarity adjustment. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2103-2109. by Utz J. Pape, Holger Klein, Martin Vingron posted by 3 people idonaldson TRHvidsten djkt
	The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2730-2731. by John W. Nicol, Gregg A. Helt, Steven G. Blanchard, Archana Raja, Ann E. Loraine posted by 13 people Bioinformatics Core Service jforment ronbun_2009au dokky inesdesantiago daforerog torfinnnome idonaldson pkonings sebastien_vigneau guhjy natstreet druvus
	Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD[trade] system [My Copy] Nat Meth, Vol. 6, No. 4. (April 2009) by Anjali Shah posted by 1 person idonaldson
	RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2615-2616. by Nicole Cloonan, Qinying Xu, Geoffrey J. Faulkner, et al.Darrin F. Taylor, Dave T. P. Tang, Gabriel Kolle, Sean M. Grimmond posted by 16 people hzoltan idonaldson cthachuk ethanmj cassj GeeSharpMinor Journal picks sbmontgomery shyamsg natstreet dswan druvus samgj n00c guhjy GustavoLacerda
	Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. [My Copy] Nucleic acids research, Vol. 37, No. 12. (1 July 2009), e85. by A. Ameur, A. Rada-Iglesias, J. Komorowski, C. Wadelius posted by 3 people guhjy idonaldson Journal picks
	ViTraM: visualization of transcriptional modules. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2450-2451. by Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, Kathleen Marchal posted by 5 people idonaldson natstreet TRHvidsten guhjy frohike
	JBrowse: A next-generation genome browser [My Copy] Genome Research, Vol. 19, No. 9. (1 September 2009), pp. 1630-1638. by Mitchell E. Skinner, Andrew V. Uzilov, Lincoln D. Stein, Christopher J. Mungall, Ian H. Holmes posted by 31 people hzoltan darian mkiyer daforerog n00c torfinnnome fenghezi djkt WXuan Zephyrus idonaldson pkonings inesdesantiago jcbarret jamselem aprasad urgi polivares cassj guhjy giovanni druvus natstreet fpattyn BergmanLab cisevol danmaclean Journal picks timhubbard operon neils
	Managing and analyzing next-generation sequence data. [My Copy] PLoS computational biology, Vol. 5, No. 6. (26 June 2009), e1000369. by Brent G. Richter, David P. Sexton posted by 45 people Geknitics cthachuk hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor idonaldson darian daveGerrard tharris Yanno inesdesantiago jcaddy agbiotec humburg Zephyrus daforerog stubrown GustavoLacerda torfinnnome natstreet BergmanLab polivares orzenil kongl guhjy druvus n00c leemond31 nuin operon jasontsai jmeppley rdiaz michaelbarton Bioinformatics dswan reyez kshameer TRHvidsten djkt Journal picks ppgardne
	Comparison of comparative genomic hybridization technologies across microarray platforms. [My Copy] Journal of biomolecular techniques : JBT, Vol. 20, No. 2. (April 2009), pp. 135-151. by Susan D. Hester, Laura Reid, Norma Nowak, et al.Wendell D. Jones, Joel S. Parker, Kevin Knudtson, William Ward, Jay Tiesman, Nancy D. Denslow posted by 3 people shikin rdiaz idonaldson
	Extracting transcription factor targets from ChIP-Seq data [My Copy] Nucl. Acids Res., Vol. 37, No. 17. (1 September 2009), e113. by Geetu Tuteja, Peter White, Jonathan Schug, Klaus H. Kaestner posted by 19 people hzoltan Vincent_Rouilly mfgreen ewilban1 idonaldson guhjy Chinnaiyan Lab mkiyer rschulz fenghezi clearbluespring thegoose robeirne inesdesantiago SIMR bioinformatics malcook BergmanLab polivares Journal picks
	Text-based over-representation analysis of microarray gene lists with annotation bias. [My Copy] Nucleic acids research, Vol. 37, No. 11. (1 June 2009), e79. by H. S. Leong, D. Kipling posted by 4 people Orengo Group Journal Picks davidalee rdiaz idonaldson
	Circos: An information aesthetic for comparative genomics [My Copy] Genome Research, Vol. 19, No. 9. (18 September 2009), pp. 1639-1645. by Martin Krzywinski, Jacqueline Schein, Ä°nanã§ Birol, et al.Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones, Marco A. Marra posted by 12 people jmanning2k djkt rdiaz pkonings natstreet chrisamiller aprasad BergmanLab cisevol nuin idonaldson kshameer
	The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. [My Copy] Genome research, Vol. 19, No. 7. (4 July 2009), pp. 1316-1323. by Kim D. Pruitt, Jennifer Harrow, Rachel A. Harte, et al.Craig Wallin, Mark Diekhans, Donna R. Maglott, Steve Searle, Catherine M. Farrell, Jane E. Loveland, Barbara J. Ruef, Elizabeth Hart, Marie-Marthe M. Suner, Melissa J. Landrum, Bronwen Aken, Sarah Ayling, Robert Baertsch, Julio Fernandez-Banet, Joshua L. Cherry, Val Curwen, Michael Dicuccio, Manolis Kellis, Jennifer Lee, Michael F. Lin, Michael Schuster, Andrew Shkeda, Clara Amid, Garth Brown, Oksana Dukhanina, Adam Frankish, Jennifer Hart, Bonnie L. Maidak, Jonathan Mudge, Michael R. Murphy, Terence Murphy, Jeena Rajan, Bhanu Rajput, Lillian D. Riddick, Catherine Snow, Charles Steward, David Webb, Janet A. Weber, Laurens Wilming, Wenyu Wu, Ewan Birney, David Haussler, Tim Hubbard, James Ostell, Richard Durbin, David Lipman posted by 6 people ptrobajo megraw timhubbard idonaldson Journal picks ppgardne
	Identifying regulatory elements in eukaryotic genomes [My Copy] Brief Funct Genomic Proteomic, Vol. 8, No. 4. (1 July 2009), pp. 215-230. by Leelavati Narlikar, Ivan Ovcharenko posted by 5 people daveGerrard Journal picks ppgardne natstreet idonaldson
	The Sequence Alignment/Map format and SAMtools [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2078-2079. by Heng Li, Bob Handsaker, Alec Wysoker, et al.Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup posted by 30 people cthachuk hzoltan seb1 heliopais urgi idonaldson GustavoLacerda stubrown cassj kshameer ciax BergmanLab polivares carlosjavierna jandot katholt jmcq guhjy orzenil jasontsai operon farhat Journal picks AlexBateman chrisamiller nuin n00c natstreet sandfire druvus
	SOAP2: an improved ultrafast tool for short read alignment [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1966-1967. by Ruiqiang Li, Chang Yu, Yingrui Li, et al.Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang posted by 33 people hzoltan agbiotec torfinnnome natstreet cthachuk Bioinformatics Core Service jforment GustavoLacerda adijr bozdagd stubrown BergmanLab polivares guhjy Orengo Group Journal Picks ollieredfernwork operon cassj adamjamesreid Bioinformatics - CRUK Stew jamselem Bioinformatics dswan Journal picks idonaldson TRHvidsten humburg djkt farhat n00c jmeppley druvus
	Fewer permutations, more accurate P-values [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i161-168. by Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich posted by 12 people heliopais jfr rdiaz Ayest farhat Journal picks AlexBateman bmajoros idonaldson TRHvidsten djkt sameersoi
	NTAP: for NimbleGen tiling array ChIP-chip data analysis [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1838-1840. by Kun He, Xueyong Li, Junli Zhou, Xing-Wang Deng, Hongyu Zhao, Jingchu Luo posted by 5 people ashishanand Bioinformatics dswan idonaldson rschulz
	Fast and accurate short read alignment with Burrows-Wheeler transform. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1754-1760. by Heng Li, Richard Durbin posted by 38 people lianping hzoltan cthachuk maren bozdagd adijr heliopais jmanning2k GustavoLacerda stubrown jessopher guhjy katholt mkiyer jmcq idonaldson michaelbarton BergmanLab polivares darian orzenil cassj inesdesantiago TRHvidsten djkt operon SIMR bioinformatics ghattem n00c Bioinformatics danmaclean Journal picks ppgardne nuin rschulz natstreet druvus humburg
	An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome [My Copy] PLoS ONE, Vol. 4, No. 5. (12 May 2009), e5501. by Kyoung-Jae Won, Saurabh Agarwal, Li Shen, Robert Shoemaker, Bing Ren, Wei Wang posted by 5 people tonamswish guhjy idonaldson BergmanLab cisevol
	How to map billions of short reads onto genomes [My Copy] Nature Biotechnology, Vol. 27, No. 5. (01 May 2009), pp. 455-457. by Cole Trapnell, Steven L. Salzberg posted by 34 people cthachuk hzoltan tonamswish heliopais giovenko Bioinformatics jfr torfinnnome daforerog jonilaserson Chinnaiyan Lab mkiyer Annab darian BergmanLab polivares SIMR bioinformatics ghattem kiekyon n00c GeeSharpMinor guhjy nuin reyez orzenil Thaverkamp natstreet druvus fenghezi Bioinformatics - CRUK Stew inesdesantiago idonaldson neils
	FDR made easy in differential feature discovery and correlation analyses [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1461-1462. by Xuefeng B. Ling, Harvey Cohen, Joseph Jin, Irwin Lau, James Schilling posted by 8 people heliopais jfr rdiaz fishtank brianb nuin idonaldson guhjy
	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 by 4 people brianb JustinCrocker xianjun idonaldson
	MapView: visualization of short reads alignment on a desktop computer [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. 1554-1555. by Hua Bao, Hui Guo, Jinwei Wang, Renchao Zhou, Xuemei Lu, Suhua Shi posted by 11 people seb1 guhjy jmeppley dakelley n00c idonaldson Bioinformatics dswan operon natstreet druvus
	WebGBrowse--a web server for GBrowse. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. 1550-1551. by Ram Podicheti, Rajesh Gollapudi, Qunfeng Dong posted by 9 people guhjy idonaldson Bioinformatics dswan nuin operon orzenil natstreet druvus