MBGLab--Papers-Master
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labidPMIDtitlecitationpreprintsubjectwebsiteYearfootnotewebsite2coreTool
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moat29121169MOAT: Efficient Detection of Highly Mutated Regions with the Mutations Overburdening Annotations Tool.Lochovsky L, Zhang J, Gerstein M. <i>Bioinformatics.</i> 2017 Nov 7.http://files.gersteinlab.org/public-docs/2017/11.14/moat_preprint.pdfcancer,coretools,resourceshttp://moat.gersteinlab.org2017
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JEME288695922017
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ALoFT288518731kgphase3,1000genomes,coretoolshttp://aloft.gersteinlab.org2017
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MrTadFinder28742097encode, HiChttps://github.com/gersteinlab/MrTADfinder2017
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28680106286801062017
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retrodup286620761kgphase3,1000genomes,svhttp://retrodup.gersteinlab.org2017
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brcanv28658210http://archive.gersteinlab.org/papers/e-print/brcanv/nature23085.pdfcancer2017
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28562279285622792017
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28463398284633982017
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ensemble283912062017
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28381614283816142017
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gbsuppl28381262epublishing2017(Internal lab ID gbsuppl)
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HiC-spector28369339http://biorxiv.org/content/early/2016/11/21/088922resources,3dgenome,interactions,coretools,encode,mininghttp://github.com/gersteinlab/HiC_spector2017
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prcc28358873cancer2017
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28350988283509882017
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28289238282892382017
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28235832282358322017
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intensification27939289resourceshttp://intensification.gersteinlab.org2016
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frustration279152902016
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dreiss27760135cmptxn,modencode,expression,mininghttp://dreiss.gersteinlab.org2016
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frankenfoodsOpinion: GMOs Are Not “Frankenfoods”D Greenbaum, M Gerstein (2016). <i>The Scientist</i> (30 Aug). http://www.the-scientist.com/?articles.view/articleNo/46908/title/Opinion--GMOs-Are-Not--Frankenfoods-/2016
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27519564275195642016
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27510566275105662016
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27255613272556132016
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27125642271256422016
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27123852271238522016
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27112789271127892016
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27076901270769012016
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alleledb27089393http://archive.gersteinlab.org/papers/e-print/alleledb/ncomms11101.pdfcoretools,resources,1kgphase3http://alleledb.gersteinlab.org2016
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stress27066750http://archive.gersteinlab.org/papers/e-print/stress/1-s2.0-S0969212616000861-main.pdfmotions,coretools,resources,studenthttp://stress.molmovdb.org2016
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netessay27047991http://archive.gersteinlab.org/papers/e-print/netessay/PIIS2405471216300448.pdfreview,networks2016
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gpm0mgWho Owns Your DNA?D Greenbaum, M Gerstein (2016). <i>Cell</i> 165:257-258.http://archive.gersteinlab.org/papers/e-print/gpm0mg/1-s2.0-S0092867416303300-main.pdfreview,bookreviewhttp://www.cell.com/cell/fulltext/S0092-8674(16)30330-02016
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27015116270151162016
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costseq2270091002016
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encodeauthors27005445epublishing,student2016
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privaseq26828419http://archive.gersteinlab.org/papers/e-print/privaseq/nmeth.3746.pdfprivacy,besthttp://privaseq.gersteinlab.org2016
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nrgnccan26781813http://archive.gersteinlab.org/papers/e-print/nrgnccan/nrg.2015.17.pdf2016
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26657727266577272016
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group_fhimKnowledge Based Factorized High Order Sparse Learning ModelsS Purushotham, MR Min, CJ Kuo, M Gerstein (2015). <i>NIPS</i> Workshop on Machine Learning in Computational Biology.http://archive.gersteinlab.org/papers/e-print/group_fhim/Group_FHIM.pdf2015
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26544944265449442015
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cosbdeep266587412015
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psychencode26605881http://psychencode.org2015
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deeper0mgIlluminating the Genome's Dark MatterD Greenbaum, M Gerstein (2015). <i>Cell</i> 163:1047-1048.http://archive.gersteinlab.org/public-docs/2015/11.21/deeper0mg-reprint-PIIS0092867415014750.pdfreview,bookreviewhttp://info.gersteinlab.org/Illuminating_the_Genome2015
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kirp265361692015
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1000gphase326432245A global reference for human genetic variation.1000 Genomes Project Consortium (2015). <i>Nature</i> 526:68-74.1000genomes,1kgphase3http://1000genomes.org2015
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1000sv264322461000genomes,sv,1kgphase3http://1000genomes.org2015
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26412485264124852015
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somaticseq263812352015
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26340425263404252015
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larva26304545cancer,coretools,resourceshttp://larva.gersteinlab.org2015
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peptide26206306cs-dml,mining2015
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2618619126186191FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum DisordersJ Mariani, G Coppola, P Zhang, A Abyzov, L Provini, L Tomasini, M Amenduni, A Szekely, D Palejev, M Wilson, M Gerstein, EL Grigorenko, K Chawarska, KA Pelphrey, JR Howe, FM Vaccarino. (2015) <i>Cell</i> Jul 16;162(2):375-90.2015
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phase1bkpt260282661000genomes,sv,student,1kgphase3http://sv.gersteinlab.org/phase1bkpts/2015
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innovators0mgThe computer connectionD Greenbaum, M Gerstein (2015). <i>Science</i> 347: 956.review,cs,bookreviewhttp://www.sciencemag.org/content/347/6225/956.1.full2015
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metasv25861968svhttp://bioinform.github.io/metasv2015
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loregic25884877encode,coretools,resources,mininghttps://github.com/gersteinlab/Loregic2015
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hinet25880651encode,mininghttp://www.gersteinlab.org/proj/hinet2015
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elshbm_1Ensemble Learning Based Sparse High-Order Boltzmann Machine for Unsupervised Feature Interaction IdentificationMR Min, X Ning, Y Qi, C Cheng, A Bonner, M Gerstein (2014). <i>NIPS</i> Workshop on Machine Learning in Computational Biology.http://archive.gersteinlab.org/papers/e-print/elshbm_1/ELSHBM.pdf2014
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aistats14Interpretable Sparse High-Order Boltzmann MachinesMR Min, X Ning, C Cheng, M Gerstein (2014). <i>JMLR</i> W&CP 33:614-622 (AISTATS 2014).http://archive.gersteinlab.org/papers/e-print/aistats14/Min_AISTATS14.pdf2014
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varsim255248952014-summary2014
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neuroprotrev25349915brainspan,2014-summary2014
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music25292436encode,expression,2014-summary,coretools,resources,mininghttp://music.gersteinlab.org2014
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funseq225273974cancer,2014-summary,coretools,resources,studenthttp://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-summary,resources,mininghttp://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-summaryhttp://github.com/gersteinlab/OrthoClust2014
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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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mlcb13Interpretable Sparse High-Order Boltzmann Machines for Transcription Factor Interaction IdentificationMR Min, X Ning, C Cheng, M Gerstein (2013). <i>NIPS</i> Workshop on Machine Learning in Computational Biology.http://archive.gersteinlab.org/papers/e-print/mlcb13/MLCB_June2013.pdfmining2013
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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-revs,bookreviewhttp://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://archive.gersteinlab.org/papers/e-print/funseq/1235587.full.pdf1000genomes,cancer,resources,fav0214,2013-summary,grant-lof,best,best2014,2014-summary,coretools,studenthttp://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/Proceed-with-Caution--The-Scientist--helaoped.pdfprivacyhttp://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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2345079423450794expt-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,resources,netessaylab,best2014,studenthttp://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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