MBGLab--Papers-Master
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labidPMIDtitlecitationpreprintsubjectwebsiteYearfootnotewebsite2coreTool
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loregic25884877encodehttps://github.com/gersteinlab/Loregic2015
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hinet25880651encode2015
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varsim255248952014-summary2014
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neuroprotrev25349915brainspan,2014-summary2014
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music25292436
encode,expression,2014-summaryhttp://music.gersteinlab.org2014
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funseq225273974cancer,2014-summaryhttp://funseq2.gersteinlab.org2014
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cmpreg25164757encode,modencode,modencoderollout,2014-summaryhttp://encodeproject.org/comparative2014
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cmptxn25164755encode,modencode,modencoderollout,best,best2014,2014-summaryhttp://encodeproject.org/comparative2014
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cmppgene25157146encode,modencode,pseudogenes,best,best2014,2014-summaryhttp://psicube.pseudogene.org2014
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orthoclust25249401interactions,mining,modencoderollout,resources,RNA-seq,2014-summary2014
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24759409247594092014-summary2014
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encoderesponse24753594encode,2014-summary2014
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2469522924695229brainspan,2014-summary2014
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24374310243743102014-summary2014
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rgasp24185837Assessment of transcript reconstruction methods for RNA-seq.T Steijger, J F Abril, P G Engstrom, F Kokocinski, The RGASP Consortium,T J Hubbard, R Guigo, J Harrow, P Bertone (2013).<i> Nat Methods </i> 10:1177-84.2013
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sportsgeneDeep Inside Champions, Just Genes?D Greenbaum, J Chen, M Gerstein (2013). <i>Science</i> 342: 560.http://archive.gersteinlab.org/papers/e-print/sportsgene/sports_gene.pdfreview,opinion-review,best-revshttp://www.sciencemag.org/content/342/6158/560.abs2013
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funseq24092746Integrative annotation of variants from 1092 humans: application to cancer genomics.E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, L Lochovsky, J Chen, A Harmanci, J Das, A Abyzov, S Balasubramanian, K Beal, D Chakravarty, D Challis, Y Chen, D Clarke, L Clarke, F Cunningham, US Evani, P Flicek, R Fragoza, E Garrison, R Gibbs, ZH Gumus, J Herrero, N Kitabayashi, Y Kong, K Lage, V Liluashvili, SM Lipkin, DG MacArthur, G Marth, D Muzny, TH Pers, GR Ritchie, JA Rosenfeld, C Sisu, X Wei, M Wilson, Y Xue, F Yu, 1000 Genomes Project Consortium, ET Dermitzakis, H Yu, MA Rubin, C Tyler-Smith, M Gerstein (2013). <i>Science</i> 342: 1235587http://www.sciencemag.org/content/342/6154/1235587.full.pdf?keytype=ref&siteid=sci&ijkey=Z1OXCCRtLgCTA1000genomes,cancer,resources,fav0214,coretools,2013-summary,grant-lof,best,best2014,2014-summaryhttp://funseq.gersteinlab.org2013
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svpgene24026178Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.A Abyzov, R Iskow, O Gokcumen, DW Radke, S Balasubramanian, B Pei, L Habegger, The 1000 Genomes Project Consortium, C Lee, M Gerstein (2013). <i>Genome Res </i> 23:2042-52.http://archive.gersteinlab.org/papers/e-print/Retrodups/Retrodups_variation.fin5.pdfsv,pseudogenes,1000genomes,2013-summary2013
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helaopedProceed with CautionD Greenbaum, M Gerstein (2013). <i>The Scientist</i> 27:26 (1 Oct.) http://archive.gersteinlab.org/mark/out/log/2014/05.09/helaoped/privacyhttp://www.the-scientist.com/?articles.view/articleNo/37592/title/Proceed-with-Caution/2013
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ycc238952322013-summary2013
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2331176223311762review,sv2013
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2337537423375374expt-collab,cancer,cs-network2013
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23450794 23450794expt-collab,rnaseq2013
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2347840023478400The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.SB Montgomery, DL Goode, E Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter (2013). <i>Genome Res</i> 23: 749-61.expt-collab,variation,1000genomes2013
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2365151823651518otherpub,opinion-review2013
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MLGenomeAnnotation23731483http://archive.gersteinlab.org/papers/e-print/MLGenomeAnnotation/MLGenomeAnnotation_v19_cleaned.pdfopinion-review,mining,review,intro-cs,2013-summary2013
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netsnp23505346http://archive.gersteinlab.org/papers/e-print/netsnp/preprint.pdfinformatics-research-article,variants,interactions,intro-to-lab,2013-summaryhttp://archive.gersteinlab.org/proj/netsnp/2013
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2323373623233736expt-collab,cancer,expression2012
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ips23160490sv,informatics-research-article2012
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1000gphase123128226An integrated map of genetic variation from 1,092 human genomes.1000 Genomes Project Consortium (2012). <i>Nature</i> 491:56-651000genomes,informatics-research-article,variation,persgenomics,grant-lofhttp://1000genomes.org2012
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encodecomm22972285https://docs.google.com/document/pub?id=1heyk3HxGYbkqsVugg4MFU5Ykkb3s8wizaQkLyG0RyN8encoderollout,opinion-review,otherpub,mining,cs-dml,cs-network,intro-to-labhttp://www.nature.com/encode/2012
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encodemain22955616An integrated encyclopedia of DNA elements in the human genome.The ENCODE Project Consortium (2012). <i>Nature</i> 489: 57-74.encoderollout,mining,persgenomics,encode-nc,informatics-research-article,statmodelshttp://www.nature.com/encode/2012
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encodenets22955619encoderollout,fav0214,networks,regnet,mining,cs-dml,cs-network,encode-nc,best,informatics-research-article,intro-to-lab-old,intro-cs,coretools,resources,netessaylab,best2014http://encodenets.gersteinlab.org2012
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encoderna22955620encoderollout,transcription,rnaseq,expression,expt-collabhttp://www.nature.com/encode/2012
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gencode22955987encoderollout,expt-collab,persgenomicshttp://www.nature.com/encode/2012
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metatrack22950945encoderollout,mining,cs-dml,resources,informatics-research-article,intro-cs,transcriptionhttp://encodenets.gersteinlab.org/metatracks/2012
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tfmodel22955978encoderollout,statmodels,transcription,rnaseq,expression,mining,cs-dml,resources,almostbest,informatics-research-article,intro-to-labhttp://www.nature.com/encode/2012
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encodechipstd22955991encoderollout,expt-collab,modencode,reviewhttp://www.nature.com/encode/2012
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encodeprodpgenes22951037encoderollout,pseudogenes,almostbest,informatics-research-article,intro-to-labhttp://pseudogene.org/psidr2012
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2295036822950368encoderollout,expt-collab,expression,featureshttp://www.nature.com/encode/2012
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tcf722412390expt-collab,expression,interactions2012
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hugeseq22398614informatics-research-article,resources,variationhttp://hugeseq.hugolam.com/2012
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2242154622421546expt-collab,expression,persgenomics2012
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i0cfwhumprot22583803otherpub,opinion-review,persgenomics2012
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2262807522628075otherpub,opinion-review,persgenomics2012
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vat22743228informatics-research-article,intro-to-lab,intro-cs,resources,variation,coretools,grant-lofhttp://vat.gersteinlab.org/2012
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sports22762737http://archive.gersteinlab.org/papers/e-print/sports/preprint.pdfopinion-review,review2012
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c1322396667expt-collab,strgenhttp://asco.gersteinlab.org2012
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mikeome22424236expt-collab,persgenomics2012
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lof22344438A systematic survey of loss-of-function variants in human protein-coding genes.DG MacArthur, S Balasubramanian, A Frankish, N Huang, J Morris, K Walter, L Jostins, L Habegger, JK Pickrell, SB Montgomery, CA Albers, ZD Zhang, DF Conrad, G Lunter, H Zheng, Q Ayub, MA DePristo, E Banks, M Hu, RE Handsaker, JA Rosenfeld, M Fromer, M Jin, XJ Mu, E Khurana, K Ye, M Kay, GI Saunders, MM Suner, T Hunt, IH Barnes, C Amid, DR Carvalho-Silva, AH Bignell, C Snow, B Yngvadottir, S Bumpstead, DN Cooper, Y Xue, IG Romero, 1000 Genomes Project Consortium, J Wang, Y Li, RA Gibbs, SA McCarroll, ET Dermitzakis, JK Pritchard, JC Barrett, J Harrow, ME Hurles, MB Gerstein, C Tyler-Smith (2012). <i>Science</i> 335:823-8. 1000genomes,informatics-research-article,intro-to-lab-old,variation,grant-lof2012MG and CTS are co-senior authors.
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2226540422265404otherencodepapers,expt-collab,transcription,interactions2012
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2234308722343087informatics-research-article,intro-to-lab-old,strgen,cs-network,interactions2012
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iqseq22238592ngtools, resources,otherencodepapers,informatics-research-article,coretoolshttp://archive.gersteinlab.org/proj/rnaseq/IQSeq/2012
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2217899322178993expt-collab,ngtools,review2011
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pnasperspective22160691opinion-review,informatics-research-article,interactions2011
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genomicsandprivacy22144881Genomics and Privacy: Implications of the New Reality of Closed Data for the FieldD Greenbaum, A Sboner, X J Mu, M Gerstein (2011). <i>PLoS Comput Biol</i> 7: e1002278cs-other,privacy,best-revs,review,intro-to-lab,best2014,best2011
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sraclosure21418618bigdata, epublishing,otherpub2011
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2214047422140474sv,1000genomes,expt-collab,expression2011
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mirnet22125477networks,interactions,otherencodepapers,informatics-research-article,regnet,intro-to-labhttp://archive.gersteinlab.org/proj/mirnet/2011
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yeast-hm22060676encode,mining,informatics-research-article,transcription,statmodels2011
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ajobcloud22047125privacy,otherpub2011
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tip22039215http://archive.gersteinlab.org/mark/out/log/2011/11.24/tip/Bioinformatics-2011-Cheng-bioinformatics_btr552.pdfcs-dml,encode-nc,otherencodepapers,informatics-research-article,intro-cs2011
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confexplorer22032721motions,informatics-research-article2011
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sdr21835011informatics-research-article,strgen2011
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tfhm-mouse21926158encode,mining,almostbest,informatics-research-article,transcription,statmodels2011
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2188540421885404cancer,expt-collab2011
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dynasin21826754motions,interactions,resources,informatics-research-article,intro-to-lab,coretoolshttp://dynasin.molmovdb.org2011
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costseq21867570http://archive.gersteinlab.org/papers/e-print/costseq/preprint.pdfopinion-review,best-revs,review,best,best20142011
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AlleleSeq21811232variation, sv, resources, cegs,ngtools,encode-nc,1000genomes, otherencodepapers,best,informatics-research-article,intro-to-lab-old,coretools,best2014,2014-summaryhttp://alleleseq.gersteinlab.org2011
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sric21787423sv, resources, cegs,ngtools,CNVpre1KG,informatics-research-article2011
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pervasive-transcription21765801transcription,otherencodepapers,rnaseq,expt-collab2011
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infoflow21603617epublishing,cs-other,informatics-research-article,intro-cs2011
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ncvar21596777sv, cegs,ngtools,encode-nc,1000genomes,otherencodepapers,informatics-research-article,intro-to-lab-old,grant-lofhttp://info.gersteinlab.org/NCVAR2011
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ajobgwas21534147otherpub,opinion-review2011
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encode10121526222A user's guide to the encyclopedia of DNA elements (ENCODE).The ENCODE Project Consortium (2011). <i>PLoS Biol</i> 9: e1001046.encodecore,otherpub2011
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2146004021460040expt-collab,interactions2011
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crit21453526formalism,informatics-research-article,interrelate2011
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cisreg21430782encodecore,expt-collab,interactions2011
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2140820421408204otherencodepapers,expt-collab2011
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act21349863resources, cegs,ngtools,encode-nc, otherencodepapers,informatics-research-article,coretoolshttp://act.gersteinlab.org2011
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wavelets21338513otherencodepapers,otherpub,expression2011
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CNVnator21324876sv,resources, cegs,ngtools,1000genomes,informatics-research-article,intro-to-lab, coretools,almostbesthttp://sv.gersteinlab.org/cnvnator/2011
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worm_HM21324173modencode,encode-nc,informatics-research-article,expression,intro-to-lab,statmodelshttp://archive.gersteinlab.org/proj/chromodel2011
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cancergenome21307934expt-collab,cancer2011
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1kgv21293372sv,1000genomes,expt-collab,persgenomics2011EE Eichler, MB Gerstein, ME Hurles, C Lee, SA McCarroll, and JO Korbel are co-senior authors.
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rewiring21253555interactions,encode-nc,informatics-research-article,cs-network,netessaylab,almostbest2011
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age21233167persgenomics,sv, cegs,ngtools,CNVpre1KG,informatics-research-articlehttp://sv.gersteinlab.org/age2011
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refgeneset21205862pseudogenes,encode-nc,persgenomics,informatics-research-article,intro-to-lab-old,grant-lof2011
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2120483421204834review,opinion-review2011
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incrna21177971http://archive.gersteinlab.org/papers/e-print/incrna/preprint.pdfrnaseq, resources,ngtools,modencode,encode-nc,informatics-research-article,interrelatehttp://archive.gersteinlab.org/proj/incrna/2011
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2117796321177963expt-collab,transcription,interrelate2011
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rseqtools21134889resources, rnaseq, cegs,ngtools,encode-nc, privacy,otherencodepapers,almostbest,informatics-research-article,intro-to-lab,coretoolshttp://rseqtools.gersteinlab.org2011
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notetsfusions21036922expt-collab,rnaseq,cancer2011
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isproundtableReproducible Research: Addressing the need for data and code sharing in computational scienceYale Law School Roundtable on Data and Code Sharing (2010). <i>Computing in Science & Engineering</i> 12(5): 8-13 (Sept/Oct).epublishing,2010-summary,otherpub,privacyhttp://www.computer.org/portal/web/csdl/doi/10.1109/MCSE.2010.1132010
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wormawg21177976http://archive.gersteinlab.org/papers/e-print/wormawg/preprint.pdf2010-summary, modencode,encode-nc,fav0312,best,informatics-research-article,statmodels,best2014http://www.modencode.org/publications/integrative_worm_2010/2010
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hier-rewiring21045205http://archive.gersteinlab.org/papers/e-print/hier-rewiring/preprint.pdfinteractions,2010-summary,informatics-research-article,transcription,intro-to-labhttp://info.gersteinlab.org/Rewiring_hierarchy2010
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21035178210351782010-summary,expt-collab,interactions2010
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cnv-mcmc21034510persgenomics, formalism,2010-summary,cs-dml,informatics-research-article,intro-cs,sv2010
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1kgpilot20981092A map of human genome variation from population-scale sequencing1000 Genomes Project Consortium (2010). <i>Nature</i> 467:1061-73persgenomics,variation,2010-summary,1000genomes,informatics-research-article2010
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