Add papers

papers.tsv

@@ -0,0 +1,289 @@
+paper	doi
+Aeby2020decapping 	https://doi.org/10.1038/s41556-020-0558-0
+Agarwal2021kdm1a 	https://doi.org/10.1101/gr.234559.118
+Aho2019displacement 	https://doi.org/10.1016/j.celrep.2019.02.047
+Akulenko2018transcriptional 	https://doi.org/10.1261/rna.062851.117
+Alexander2019imprinted 	
+Alhusini2017genomewide 	https://doi.org/10.1038/s41598-017-07062-6
+Allen2014global 	https://doi.org/10.7554/eLife.02200
+Anderson2020defining 	https://doi.org/10.1093/bioinformatics/btaa011
+Andersson2014nuclear 	https://doi.org/10.1038/ncomms6336
+Andrade2015dna 	https://doi.org/10.1093/nar/gkv148
+Andrysik2017identification 	https://doi.org/10.1101/gr.220533.117
+Aoi2020nelf 	https://doi.org/10.1016/j.molcel.2020.02.014
+Aprile-garcia2019nascent 	https://doi.org/10.1038/s41594-018-0182-x
+Ba2020ctcf 	https://doi.org/10.1038/s41586-020-2578-0
+Bahat2019targeting 	https://doi.org/10.1016/j.molcel.2019.08.024
+Barbieri2020rapid 	https://doi.org/10.1016/j.celrep.2020.108373
+Barucci2020small 	https://doi.org/10.1038/s41556-020-0462-7
+Beckedorff2020human 	https://doi.org/10.1016/j.celrep.2020.107917
+Bi2020enhancer 	https://doi.org/10.1038/s41556-020-0514-z
+Birkenheuer2018herpes 	https://doi.org/10.1128/JVI.02184-17
+Birkenheuer2020rna 	https://doi.org/10.1128/JVI.02035-19
+Blumberg2021characterizing 	https://doi.org/10.1186/s12915-021-00949-x
+Boija2017cbp 	https://doi.org/10.1016/j.molcel.2017.09.031
+Bonelt2019precocious 	https://doi.org/10.15252/embj.2018100010
+Booth2016divergence 	https://doi.org/10.1101/gr.204578.116
+Booth2018cdk9 	https://doi.org/10.1038/s41467-018-03006-4
+Bouvyliivrand2017analysis 	https://doi.org/10.1093/nar/gkx680
+Boxer2020mecp2 	https://doi.org/10.1016/j.molcel.2019.10.032
+Busslinger2017cohesin 	https://doi.org/10.1038/nature22063
+Cardamone2018mitochondrial 	https://doi.org/10.1016/j.molcel.2018.01.037
+Cecere2013zfp1 	https://doi.org/10.1016/j.molcel.2013.06.002
+Cecere2014global 	https://doi.org/10.1038/nsmb.2801
+Chen2014gene 	https://doi.org/10.1101/gad.250449.114
+Chen2015paf1 	https://doi.org/10.1016/j.cell.2015.07.042
+Chen2016cutoff 	https://doi.org/10.1016/j.molcel.2016.05.010
+Chen2017rchip 	https://doi.org/10.1016/j.molcel.2017.10.008
+Chen2018augmented 	https://doi.org/10.1016/j.molcel.2017.12.029
+Chen2018rna 	https://doi.org/10.1038/s41422-018-0076-9
+Chivu2020unpublished 	
+Chu2018chromatin 	https://doi.org/10.1038/s41588-018-0244-3
+Compagno2017phosphatidylinositol 	https://doi.org/10.1038/nature21406
+Core2008nascent 	https://doi.org/10.1126/science.1162228
+Core2012defining 	https://doi.org/10.1016/j.celrep.2012.08.034
+Core2014analysis 	https://doi.org/10.1038/ng.3142
+Cosby2021recurrent 	https://doi.org/10.1126/science.abc6405
+Cuartero2020control 	https://doi.org/10.1038/s41590-018-0184-1
+Czimmerer2018transcription 	https://doi.org/10.1016/j.immuni.2017.12.010
+Dai2020loop 	https://doi.org/10.1038/s41586-020-03121-7
+Daniel2018nuclear 	https://doi.org/10.1016/j.immuni.2018.09.005
+Danko2013signaling 	https://doi.org/10.1016/j.molcel.2013.02.015
+Danko2015identification 	https://doi.org/10.1038/nmeth.3329
+Danko2018dynamic 	https://doi.org/10.1038/s41559-017-0447-5
+Delgado-benito2018chromatin 	https://doi.org/10.1016/j.molcel.2018.08.042
+Dorighi2017mll3 	https://doi.org/10.1016/j.molcel.2017.04.018
+Douillet2020uncoupling 	https://doi.org/10.1038/s41588-020-0618-1
+Duarte2016transcription 	https://doi.org/10.1101/gad.284430.116
+Dukler2017nascent 	https://doi.org/10.1101/gr.222935.117
+Duttke2015human 	https://doi.org/10.1016/j.molcel.2014.12.029
+Duttke2017unpublished 	
+Elkon2015myc 	https://doi.org/10.15252/embr.201540717
+Elrod2019integrator 	https://doi.org/10.1016/j.molcel.2019.10.034
+Emmett2017histone 	https://doi.org/10.1038/nature22819
+Engreitz2016local 	https://doi.org/10.1038/nature20149
+Erhard2015nascent 	https://doi.org/10.1534/genetics.115.174714
+Escoubet-lozach2011mechanisms 	https://doi.org/10.1371/journal.pgen.1002401
+Esousa2019kinetics 	https://doi.org/10.1101/gr.245027.118
+Estaras2015smad 	https://doi.org/10.1016/j.molcel.2015.04.001
+Etchegaray2019histone 	https://doi.org/10.1016/j.molcel.2019.06.034
+Fan2020drb 	https://doi.org/10.1126/sciadv.aaz5041
+Fang2014circadian 	https://doi.org/10.1016/j.cell.2014.10.022
+Fant2020tfiid 	https://doi.org/10.1016/j.molcel.2020.03.008
+Fei2018ndf 	https://doi.org/10.1101/gad.313973.118
+Fleischer2017dna 	https://doi.org/10.1038/s41467-017-00510-x
+Flynn20167skbaf 	https://doi.org/10.1038/nsmb.3176
+Fong2014pre 	https://doi.org/10.1101/gad.252106.114
+Fong2017rna 	https://doi.org/10.1016/j.molcel.2017.04.016
+Fonseca2019diverse 	https://doi.org/10.1038/s41467-018-08236-0
+Franco2015tnfalpha 	https://doi.org/10.1016/j.molcel.2015.02.001
+Franco2018enhancer 	https://doi.org/10.1101/gr.226019.117
+Fuda2012fcp1 	https://doi.org/10.1128/MCB.00247-12
+Fuda2015gaga 	https://doi.org/10.1371/journal.pgen.1005108
+Galbraith2013hif1a 	https://doi.org/10.1016/j.cell.2013.04.048
+Gally2020gain 	https://doi.org/10.1172/jci.insight.144294
+Gao2017thyroid 	https://doi.org/10.1073/pnas.1711058114
+Gao2018jmjd6 	https://doi.org/10.1016/j.molcel.2018.03.006
+Gardini2014integrator 	https://doi.org/10.1016/j.molcel.2014.08.004
+Gibson2016chemical 	https://doi.org/10.1126/science.aaf7865
+Godfrey2017mll 	https://doi.org/10.1016/j.exphem.2016.11.003
+Guan2018diet 	https://doi.org/10.1016/j.cell.2018.06.031
+Hah2011rapid 	https://doi.org/10.1016/j.cell.2011.03.042
+Hah2013enhancer 	https://doi.org/10.1101/gr.152306.112
+Hah2015inflammation 	https://doi.org/10.1073/pnas.1424028112
+Harman2021invivo 	https://doi.org/10.1073/pnas.1918062118
+Heinaniemi2016transcription 	https://doi.org/10.7554/eLife.13087
+Heinz2013effect 	https://doi.org/10.1038/nature12615
+Herold2019recruitment 	https://doi.org/10.1038/s41586-019-1030-9
+Hetzel2016nascent 	https://doi.org/10.1073/pnas.1603217113
+Hong2017dissociation 	https://doi.org/10.1038/nm.4245
+Horibata2018erpositive 	https://doi.org/10.1371/journal.pone.0194023
+Hou2019paf1c 	https://doi.org/10.1073/pnas.1904324116
+Hu2012dicer 	https://doi.org/10.1038/nsmb.2400
+Huang2020integrator 	https://doi.org/10.1016/j.molcel.2020.08.016
+Ikegami2020phosphorylated 	https://doi.org/10.1016/j.devcel.2020.02.011
+Illingworth2016polycomb 	https://doi.org/10.7554/eLife.14926
+Incarnato2017vivo 	https://doi.org/10.1093/nar/gkx617
+Jaeger2020selective 	https://doi.org/10.1038/s41588-020-0635-0
+Jager2016nuclear 	https://doi.org/10.1074/jbc.M116.719120
+Ji2011transcriptional 	https://doi.org/10.1038/msb.2011.69
+Ji2013sr 	https://doi.org/10.1016/j.cell.2013.04.028
+Jiang2018multi 	https://doi.org/10.1038/s41598-018-24039-1
+Jin2013high 	https://doi.org/10.1038/nature12644
+Jin2014chem 	https://doi.org/10.1073/pnas.1404303111
+Johnson2017biotin 	https://doi.org/10.1038/nm.4406
+Johnston2020nascent 	https://doi.org/10.1016/j.gene.2020.144758
+Jones2023unpublished 	
+Jonkers2014genome 	https://doi.org/10.7554/eLife.02407
+Judd2020unpublished 	
+Judd2021pioneer 	https://doi.org/10.1101/gad.341768.120
+Kaikkonen2013remodeling 	https://doi.org/10.1016/j.molcel.2013.07.010
+Kaikkonen2014control 	https://doi.org/10.1093/nar/gku1036
+Kaikkonen2017genome 	https://doi.org/10.1161/CIRCGENETICS.117.001702
+Kantidakis2016mutation 	https://doi.org/10.1101/gad.275453.115
+Kelly2020unpublished 	
+Khodor2011nascent 	https://doi.org/10.1101/gad.178962.111
+Kim2018pluripotency 	https://doi.org/10.1038/s41586-018-0048-8
+Kloetgen2020three 	https://doi.org/10.1038/s41588-020-0602-9
+Komarov2020epigenetic 	https://doi.org/10.3390/cells9040922
+Korkmaz2019crispr 	https://doi.org/10.1093/nar/gkz675
+Kourtis2018oncogenic 	https://doi.org/10.1038/s41591-018-0105-8
+Kriaucionis2019unpublished 	
+Kristjansdottir2020population 	https://doi.org/10.1038/s41467-020-19829-z
+Kruesi2013condensin 	https://doi.org/10.7554/eLife.00808
+Kuosmanen2018nrf2 	https://doi.org/10.1093/nar/gkx1155
+Kwak2013precise 	https://doi.org/10.1126/science.1229386
+Kwon2017locus 	https://doi.org/10.1038/ncomms15315
+Lai2020directed 	https://doi.org/10.1016/j.molcel.2019.12.029
+Laitem2015cdk9 	https://doi.org/10.1038/nsmb.3000
+Lam2013rev 	https://doi.org/10.1038/nature12209
+Larschan2011x 	https://doi.org/10.1038/nature09757
+Le2013mapping 	https://doi.org/10.1371/journal.pone.0071355
+Leroy2019ledgf 	https://doi.org/10.1126/sciadv.aay3068
+Leveille2015genome 	https://doi.org/10.1038/ncomms7520
+Li2013functional 	https://doi.org/10.1038/nature12210
+Li2013ncor 	https://doi.org/10.1016/j.cell.2013.08.054
+Li2015condensin 	https://doi.org/10.1016/j.molcel.2015.06.002
+Li2017grid 	https://doi.org/10.1038/nbt.3968
+Li2018lncrna 	https://doi.org/10.1093/nar/gky087
+Li2020human 	https://doi.org/10.1371/journal.ppat.1008402
+Li2020signalosome 	https://doi.org/10.1161/CIRCULATIONAHA.119.044805
+Li2021comprehensive 	https://doi.org/10.1186/s13059-021-02272-8
+Liang2018targeting 	https://doi.org/10.1016/j.cell.2018.09.027
+Lin2012global 	https://doi.org/10.1038/ni.2432
+Link2018analysis 	https://doi.org/10.1016/j.cell.2018.04.018
+Linnakuosmanen2020nrf2 	https://doi.org/10.1093/cvr/cvaa219
+Liu2013brd4 	https://doi.org/10.1016/j.cell.2013.10.056
+Liu2014enhancer 	https://doi.org/10.1016/j.cell.2014.08.027
+Liu2017dynamic 	https://doi.org/10.1182/bloodadvances.2017008383
+Liu2017identification 	https://doi.org/10.1093/nar/gkx318
+Liu2017transcriptional 	https://doi.org/10.1073/pnas.1617636114
+Liu2018arabidopsis 	https://doi.org/10.1016/j.devcel.2017.12.002
+Liu2018rna-directed 	https://doi.org/10.1038/s41477-017-0100-y
+Liu2020immediate 	https://doi.org/10.1111/jipb.12990
+Liu2021transcription 	https://doi.org/10.1038/s41588-021-00798-y
+Lloret-llinares2018rna 	https://doi.org/10.1093/nar/gky817
+Lozano2018rna 	
+Lu2017nascent 	https://doi.org/10.1093/nar/gkx464
+Luo2014dynamic 	https://doi.org/10.1186/1471-2164-15-155
+Ma2020super 	https://doi.org/10.1016/j.celrep.2020.107532
+Magnuson2015identifying 	https://doi.org/10.1038/srep17978
+Mahat2016mammalian 	https://doi.org/10.1016/j.molcel.2016.02.025
+Malinen2017crosstalk 	https://doi.org/10.1093/nar/gkw855
+Marazzi2012suppression 	https://doi.org/10.1038/nature10892
+Mayer2015native 	https://doi.org/10.1016/j.cell.2015.03.010
+Mckinlay2011genome 	https://doi.org/10.1534/g3.111.000810
+Meng2014convergent 	https://doi.org/10.1016/j.cell.2014.11.014
+Meyerswallen2017xx 	https://doi.org/10.1371/journal.pone.0186331
+Miller2015senataxin 	https://doi.org/10.1038/ni.3132
+Min2011regulating 	https://doi.org/10.1101/gad.2005511
+Mohn2014rhino 	https://doi.org/10.1016/j.cell.2014.04.031
+Moreau2018transcriptional 	https://doi.org/10.3389/fcvm.2018.00159
+Mukai2020chromatin 	https://doi.org/10.1186/s12917-020-02395-3
+Murakami2017dynamic 	https://doi.org/10.1101/gad.302182.117
+Nair2019phase 	https://doi.org/10.1038/s41594-019-0190-5
+Nelson2018ppar 	https://doi.org/10.1101/gad.312355.118
+Ngoc2017human 	https://doi.org/10.1101/gad.293837.116
+Nguyen2020dichotomous 	https://doi.org/10.1038/s41586-020-2576-2
+Nilson2017oxidative 	https://doi.org/10.1093/nar/gkx724
+Niskanen2015global 	https://doi.org/10.1186/s13059-015-0717-y
+Niskanen2018endothelial 	https://doi.org/10.1093/nar/gkx1214
+Nojima2015mammalian 	https://doi.org/10.1016/j.cell.2015.03.027
+Oh2021enhancer 	https://doi.org/10.1038/s41586-021-03577-1
+Oittinen2017polycomb 	https://doi.org/10.1002/stem.2479
+Orioli2016human 	https://doi.org/10.1101/gr.201400.115
+Parida2019nucleotide 	https://doi.org/10.1128/mBio.02047-18
+Parikh2018critical 	https://doi.org/10.1074/jbc.AC118.003264
+Park2020global 	https://doi.org/10.1073/pnas.1922216117
+Parua2018cdk9-pp1 	https://doi.org/10.1038/s41586-018-0214-z
+Patel2020robust 	https://doi.org/10.1093/nar/gkaa687
+Perreault2019epigenetic 	https://doi.org/10.1038/sdata.2019.33
+Phanstiel2017static 	https://doi.org/10.1016/j.molcel.2017.08.006
+Puc2015ligand 	https://doi.org/10.1016/j.cell.2014.12.023
+Rahnamoun2017mutant 	https://doi.org/10.1038/s41467-017-01117-y
+Rao2017cohesin 	https://doi.org/10.1016/j.cell.2017.09.026
+Rozhkov2013multiple 	https://doi.org/10.1101/gad.209767.112
+Salony2016akt 	https://doi.org/10.1158/1535-7163.MCT-15-0414
+Santoriello2020rna 	https://doi.org/10.1038/s41556-020-0493-0
+Saponaro2014recql5 	https://doi.org/10.1016/j.cell.2014.03.048
+Sasse2019nascent 	https://doi.org/10.1101/gr.248187.119
+Sathyan2019improved 	https://doi.org/10.1101/gad.328237.119
+Saunders2013extensive 	https://doi.org/10.1101/gad.215459.113
+Schaaf2013genome 	https://doi.org/10.1371/journal.pgen.1003382
+Schaukowitch2017intrinsic 	https://doi.org/10.1016/j.celrep.2017.01.033
+Schick2021acute 	https://doi.org/10.1038/s41588-021-00777-3
+Schoeberl2012biased 	https://doi.org/10.1101/gad.196493.112
+Sen2019histone 	https://doi.org/10.1016/j.molcel.2019.01.021
+Sendinc2019pcif1 	https://doi.org/10.1016/j.molcel.2019.05.030
+Shamie2020unpublished 	
+Sheridan2019widespread 	https://doi.org/10.1016/j.molcel.2018.10.031
+Sienski2012transcriptional 	https://doi.org/10.1016/j.cell.2012.10.040
+Sigova2013divergent 	https://doi.org/10.1073/pnas.1221904110
+Sigova2015transcription 	https://doi.org/10.1126/science.aad3346
+Skowronskakrawczyk2014required 	https://doi.org/10.1038/nature13573
+Slobodin2017transcription 	https://doi.org/10.1016/j.cell.2017.03.031
+Smith2021peppro 	https://doi.org/10.1186/s13059-021-02349-4
+Soccio2015genetic 	https://doi.org/10.1016/j.cell.2015.06.025
+Steinparzer2019transcriptional 	https://doi.org/10.1016/j.molcel.2019.07.034
+Stender2017structural 	https://doi.org/10.1016/j.molcel.2017.02.008
+Stengel2019histone 	https://doi.org/10.1093/nar/gkz816
+Stengel2020definition 	https://doi.org/10.1016/j.molcel.2020.12.005
+Step2014antidiabetic 	https://doi.org/10.1101/gad.237628.114
+Strikoudis2016regulation 	https://doi.org/10.1038/ncb3424
+Sumida2018ultra 	https://doi.org/https://doi.org/10.1101/286583
+Sun2017enhancer 	
+Takahashi2020role 	https://doi.org/10.1038/s41467-020-14849-1
+Tan2016stress 	https://doi.org/10.1016/j.molcel.2016.03.013
+Tan2018dismissal 	https://doi.org/10.1016/j.molcel.2018.07.039
+Tastemel2017transcription 	https://doi.org/10.1016/j.scr.2017.11.012
+Telese2015lrp8 	https://doi.org/10.1016/j.neuron.2015.03.033
+Tena2020induction 	https://doi.org/10.1073/pnas.1922299117
+Teppo2016genome 	https://doi.org/10.1101/gr.193649.115
+Thomas2019interaction 	https://doi.org/10.1073/pnas.1910391116
+Tome2018single 	https://doi.org/10.1038/s41588-018-0234-5
+Toropainen2016global 	https://doi.org/10.1038/srep33510
+Trizzino2018tumor 	https://doi.org/10.1016/j.celrep.2018.05.097
+Ueberschar2019ben 	https://doi.org/10.1038/s41467-019-13558-8
+Vaid2020release 	https://doi.org/10.1093/nar/gkaa234
+Veloso2013genome-wide 	https://doi.org/10.1371/journal.pone.0078190
+Vian2018energetics 	https://doi.org/10.1016/j.cell.2018.03.072
+Vihervaara2017transcriptional 	https://doi.org/10.1038/s41467-017-00151-0
+Vihervaara2021stress 	https://doi.org/10.1016/j.molcel.2021.03.007
+Viiri2019extensive 	https://doi.org/10.1038/s41598-019-39215-0
+Wan2020h2bg53d 	https://doi.org/10.1038/s41392-020-00219-2
+Wang2011reprogramming 	https://doi.org/10.1038/nature10006
+Wang2014rna 	https://doi.org/10.1016/j.celrep.2014.01.037
+Wang2015epigenetic 	https://doi.org/10.1016/j.stem.2015.02.013
+Wang2015lsd1n 	https://doi.org/10.1038/nn.4069
+Wang2015molecular 	https://doi.org/10.1038/nature14482
+Wang2017cell 	https://doi.org/10.1084/jem.20161649
+Wang2018nascent 	https://doi.org/10.1186/s12864-018-5016-z
+Wang2019identification 	https://doi.org/10.1101/gr.238279.118
+Wang2020increased 	https://doi.org/10.1016/j.stem.2019.12.013
+Wang2020proapoptotic 	https://doi.org/10.1038/s41388-020-01435-4
+Wei2016long 	https://doi.org/10.1016/j.cell.2015.12.039
+Wei2016rbfox2 	https://doi.org/10.1016/j.molcel.2016.04.013
+Weissmiller2019inhibition 	https://doi.org/10.1038/s41467-019-10022-5
+Williams2015pausing 	https://doi.org/10.1016/j.molcel.2015.02.003
+Williamson2017uv 	https://doi.org/10.1016/j.cell.2017.01.019
+Woo2018ted 	https://doi.org/10.1016/j.celrep.2018.08.084
+Wu2017indentifying 	https://doi.org/10.1038/s41598-017-00176-x
+Xiao2019pervasive 	https://doi.org/10.1016/j.cell.2019.06.001
+Yang2013lncrna 	https://doi.org/10.1038/nature12451
+Yang2017glucocorticoid 	https://doi.org/10.1016/j.molcel.2017.03.019
+Yu2015panoramix 	https://doi.org/10.1126/science.aab0700
+Yu2020negative 	https://doi.org/10.1038/s41467-020-16209-5
+Zhang2015enhancer 	https://doi.org/10.1073/pnas.1424228112
+Zhang2016regulation 	https://doi.org/10.1038/srep21718
+Zhang2017hepatic 	https://doi.org/10.1101/gad.302323.117
+Zhang2018timing 	
+Zhang2019arerg 	https://doi.org/10.1101/gr.230243.117
+Zhang2019fundamental 	https://doi.org/10.1038/s41586-019-1723-0
+Zhang2020bcatenin 	https://doi.org/10.1126/sciadv.aba1593
+Zhang2021physiological 	https://doi.org/10.1073/pnas.2024392118
+Zhao2016high 	https://doi.org/10.1016/j.celrep.2016.07.032
+Zhao2019myod 	https://doi.org/10.1038/s41467-019-13598-0
+Zhu2017comprehensive 	https://doi.org/10.1101/gad.293910.116
+Zhu2018rna 	https://doi.org/10.1038/s41477-018-0280-0
+Zhu2019non 	https://doi.org/10.1016/j.molcel.2019.06.010
+Zhu2021calcium 	https://doi.org/10.1101/gad.343475.120