@article{bib1, author = {Altman, DG and Royston, P}, journal = {BMJ}, year = {2006}, title = {The cost of dichotomising continuous variables}, volume = {332}, } @article{bib2, author = {Biggs, R and Macmillan, RL}, journal = {Journal of Clinical Pathology}, year = {1948}, pages = {288--291}, title = {The error of the red cell count}, volume = {1}, } @article{bib3, author = {Blum, D and Hao, H and McCarthy, M and {Reproducibility Project: Cancer Biology}}, journal = {eLife}, year = {2015}, title = {Registered report: Transcriptional amplification in tumor cells with elevated c-{Myc}}, volume = {4}, } @article{bib4, author = {Cohen, J}, journal = {Applied Psychological Measurement}, year = {1983}, pages = {249--253}, title = {The cost of dichotomization}, volume = {7}, } @article{bib5, author = {Duffy, DJ and Krstic, A and Halasz, M and Schwarzl, T and Fey, D and Iljin, K and Mehta, JP and Killick, K and Whilde, J and Turriziani, B and Haapa-Paananen, S and Fey, V and Fischer, M and Westermann, F and Henrich, K-O and Bannert, S and Higgins, DG and Kolch, W}, journal = {Oncotarget}, year = {2015}, pages = {43182--43201}, title = {Integrative omics reveals {MYCN} as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma}, volume = {6}, } @article{bib6, author = {Errington, TM and Iorns, E and Gunn, W and Tan, FE and Lomax, J and Nosek, BA}, journal = {eLife}, year = {2014}, title = {An open investigation of the reproducibility of cancer biology research}, volume = {3}, } @article{bib7, author = {Fagnocchi, L and Cherubini, A and Hatsuda, H and Fasciani, A and Mazzoleni, S and Poli, V and Berno, V and Rossi, RL and Reinbold, R and Endele, M and Schroeder, T and Rocchigiani, M and Szkar\l{}at, {\. Z} and Oliviero, S and Dalton, S and Zippo, A}, journal = {Nature Communications}, year = {2016}, title = {A {Myc}-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity}, volume = {7}, } @article{bib8, author = {Gelman, A and Stern, H}, journal = {The American Statistician}, year = {2006}, pages = {328--331}, title = {The difference between ``significant'' and ``not significant'' is not itself statistically significant}, volume = {60}, } @article{bib9, author = {Hart, JR and Roberts, TC and Weinberg, MS and Morris, KV and Vogt, PK}, journal = {Oncotarget}, year = {2014}, pages = {12543--12554}, title = {MYC regulates the non-coding transcriptome}, volume = {5}, } @article{bib10, author = {Hartgerink, CHJ}, year = {2017}, title = {Composing reproducible manuscripts using {R} {Markdown}}, howpublished = {https://elifesciences.org/labs/cad57bcf/composing-reproducible-manuscripts-using-r-markdown}, } @article{bib11, author = {Hiorns, LR and Bradshaw, TD and Skelton, LA and Yu, Q and Kelland, LR and Leyland-Jones, B}, journal = {British Journal of Cancer}, year = {2004}, pages = {476--482}, title = {Variation in {RNA} expression and genomic {DNA} content acquired during cell culture}, volume = {90}, } @article{bib12, author = {Hsu, TY and Simon, LM and Neill, NJ and Marcotte, R and Sayad, A and Bland, CS and Echeverria, GV and Sun, T and Kurley, SJ and Tyagi, S and Karlin, KL and Dominguez-Vida{\~ n}a, R and Hartman, JD and Renwick, A and Scorsone, K and Bernardi, RJ and Skinner, SO and Jain, A and Orellana, M and Lagisetti, C and Golding, I and Jung, SY and Neilson, JR and Zhang, XH and Cooper, TA and Webb, TR and Neel, BG and Shaw, CA and Westbrook, TF}, journal = {Nature}, year = {2015}, pages = {384--388}, title = {The spliceosome is a therapeutic vulnerability in {MYC}-driven cancer}, volume = {525}, } @article{bib13, author = {Hughes, P and Marshall, D and Reid, Y and Parkes, H and Gelber, C}, journal = {over-passaged cell lines: how much more data do we need? BioTechniques}, year = {2007}, pages = {575--586}, title = {The costs of using unauthenticated}, volume = {43}, } @article{bib14, author = {Kleensang, A and Vantangoli, MM and Odwin-DaCosta, S and Andersen, ME and Boekelheide, K and Bouhifd, M and Fornace, AJ and Li, HH and Livi, CB and Madnick, S and Maertens, A and Rosenberg, M and Yager, JD and Zhaog, L and Hartung, T}, journal = {Scientific Reports}, year = {2016}, title = {Genetic variability in a frozen batch of {MCF}-7 cells invisible in routine authentication affecting cell function}, volume = {6}, } @article{bib15, author = {Leek, JT and Scharpf, RB and Bravo, HC and Simcha, D and Langmead, B and Johnson, WE and Geman, D and Baggerly, K and Irizarry, RA}, journal = {Nature Reviews Genetics}, year = {2010}, pages = {733--739}, title = {Tackling the widespread and critical impact of batch effects in high-throughput data}, volume = {11}, } @article{bib16, author = {Lewis, LM and Edwards, MC and Meyers, ZR and Talbot, CC and Hao, H and Blum, D and Iorns, E and Tsui, R and Denis, A and Perfito, N and Errington, TM}, journal = {Open Science Framework}, year = {2017}, title = {Study 48: Replication of {Lin} et al., 2012 ({Cell})}, } @article{bib17, author = {Lin, CY and Lov{\' e}n, J and Rahl, PB and Paranal, RM and Burge, CB and Bradner, JE and Lee, TI and Young, RA}, journal = {Cell}, year = {2012}, pages = {56--67}, title = {Transcriptional amplification in tumor cells with elevated c-{Myc}}, volume = {151}, } @article{bib18, author = {Lorenzin, F and Benary, U and Baluapuri, A and Walz, S and Jung, LA and von Eyss, B and Kisker, C and Wolf, J and Eilers, M and Wolf, E}, journal = {eLife}, year = {2016}, title = {Different promoter affinities account for specificity in {MYC}-dependent gene regulation}, volume = {5}, } @article{bib19, author = {Nie, Z and Hu, G and Wei, G and Cui, K and Yamane, A and Resch, W and Wang, R and Green, DR and Tessarollo, L and Casellas, R and Zhao, K and Levens, D}, journal = {Cell}, year = {2012}, pages = {68--79}, title = {c-{Myc} is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells}, volume = {151}, } @article{bib20, author = {Nielson, L and Smyth, G and Greenfield, P}, journal = {Biotechnology Progress}, year = {1991}, pages = {560--563}, title = {Hemacytometer {Cell} {Count} {Distributions}: Implications of {Non}-{Poisson} {Behavior}}, volume = {7}, } @article{bib21, author = {Nieuwenhuis, S and Forstmann, BU and Wagenmakers, EJ}, journal = {Nature Neuroscience}, year = {2011}, pages = {1105--1107}, title = {Erroneous analyses of interactions in neuroscience: a problem of significance}, volume = {14}, } @article{bib22, author = {Padovan-Merhar, O and Nair, GP and Biaesch, AG and Mayer, A and Scarfone, S and Foley, SW and Wu, AR and Churchman, LS and Singh, A and Raj, A}, journal = {Molecular Cell}, year = {2015}, pages = {339--352}, title = {Single mammalian cells compensate for differences in cellular volume and {DNA} copy number through independent global transcriptional mechanisms}, volume = {58}, } @article{bib23, author = {Pajic, A and Spitkovsky, D and Christoph, B and Kempkes, B and Schuhmacher, M and Staege, MS and Brielmeier, M and Ellwart, J and Kohlhuber, F and Bornkamm, GW and Polack, A and Eick, D}, journal = {International Journal of Cancer}, year = {2000}, pages = {787--793}, title = {Cell cycle activation by c-myc in a burkitt lymphoma model cell line}, volume = {87}, } @article{bib24, author = {Pratt, JW}, journal = {Journal of the American Statistical Association}, year = {1959}, pages = {655--667}, title = {Remarks on zeros and ties in the wilcoxon signed rank procedures}, volume = {54}, } @article{bib25, author = {{R Core Team}}, year = {2017}, title = {R: A language and environment for statistical computing}, } @article{bib26, author = {Sab{\` o}, A and Amati, B}, journal = {Cold Spring Harbor Perspectives in Medicine}, year = {2014}, title = {Genome recognition by {MYC}}, volume = {4}, } @article{bib27, author = {Sab{\` o}, A and Kress, TR and Pelizzola, M and de Pretis, S and Gorski, MM and Tesi, A and Morelli, MJ and Bora, P and Doni, M and Verrecchia, A and Tonelli, C and Fag{\` a}, G and Bianchi, V and Ronchi, A and Low, D and M{\" u}ller, H and Guccione, E and Campaner, S and Amati, B}, journal = {Nature}, year = {2014}, pages = {488--492}, title = {Selective transcriptional regulation by {Myc} in cellular growth control and lymphomagenesis}, volume = {511}, } @article{bib28, author = {Schlosser, I and H{\" o}lzel, M and Hoffmann, R and Burtscher, H and Kohlhuber, F and Schuhmacher, M and Chapman, R and Weidle, UH and Eick, D}, journal = {Oncogene}, year = {2005}, pages = {520--524}, title = {Dissection of transcriptional programmes in response to serum and c-{Myc} in a human {B}-cell line}, volume = {24}, } @article{bib29, author = {Schneider, CA and Rasband, WS and Eliceiri, KW}, journal = {Nature Methods}, year = {2012}, pages = {671--675}, title = {NIH {Image} to {ImageJ}: 25 years of image analysis}, volume = {9}, } @article{bib30, author = {Schuhmacher, M and Staege, MS and Pajic, A and Polack, A and Weidle, UH and Bornkamm, GW and Eick, D and Kohlhuber, F}, journal = {Current Biology}, year = {1999}, pages = {1255--1258}, title = {Control of cell growth by c-{Myc} in the absence of cell division}, volume = {9}, } @article{bib31, author = {Silberzahn, R and Uhlmann, EL and Martin, DP and Anselmi, P and Aust, F and Awtrey, EC and Bahn{\' i}k, {\v S} and Bai, F and Bannard, C and Bonnier, E and Carlsson, R and Cheung, F and Christensen, G and Clay, R and Craig, MA and Dalla Rosa, A and Dam, L and Evans, MH and Cervantes, F and Fong, N and Gamez-Djokic, M and Glenz, A and Gordon-McKeon, S and Heaton, T and Eriksson, KH and Heene, M and Hofelich Mohr, A and H{\" o}gden, F and Hui, K and Johannesson, M and Kalodimos, J and Kaszubowski, E and Kennedy, DM and Lei, R and Lindsay, TA and Liverani, S and Madan, CR and Molden, DC and Molleman, E and Morey, RD and Mulder, LB and Nijstad, BA and Pope, B and Pope, NG and Prenoveau, JM and Rink, F and Robusto, E and Roderique, H and Sandberg, A and Schlueter, E and Sch{\" o}nbrodt, FD and Sherman, MF and Sommer, SA and Sotak, KL and Spain, SM and Sp{\" o}rlein, C and Stafford, T and Stefanutti, L and T{\" a}uber, S and Ullrich, J and Vianello, M and Wagenmakers, E-J and Witkowiak, M and Yoon, S and Nosek, BA}, journal = {PsyArXiv}, year = {2017}, title = {Many analysts, one dataset: Making transparent how variations in analytical choices affect results}, howpublished = {https://psyarxiv.com/qkwst/}, } @article{bib32, author = {Trakhtenberg, EF and Pho, N and Holton, KM and Chittenden, TW and Goldberg, JL and Dong, L}, journal = {Scientific Reports}, year = {2016}, pages = {32249}, title = {Cell types differ in global coordination of splicing and proportion of highly expressed genes}, volume = {6}, } @article{bib33, author = {Valentine, JC and Biglan, A and Boruch, RF and Castro, FG and Collins, LM and Flay, BR and Kellam, S and Mo{\' s}cicki, EK and Schinke, SP}, journal = {Prevention Science}, year = {2011}, pages = {103--117}, title = {Replication in prevention science}, volume = {12}, } @article{bib34, author = {Viechtbauer, W}, journal = {Journal of Statistical Software}, year = {2010}, pages = {1--48}, title = {Conducting {Meta}-{Analyses} in {R} with the metafor {Package}}, volume = {36}, } @article{bib35, author = {Walz, S and Lorenzin, F and Morton, J and Wiese, KE and von Eyss, B and Herold, S and Rycak, L and Dumay-Odelot, H and Karim, S and Bartkuhn, M and Roels, F and W{\" u}stefeld, T and Fischer, M and Teichmann, M and Zender, L and Wei, CL and Sansom, O and Wolf, E and Eilers, M}, journal = {Nature}, year = {2014}, pages = {483--487}, title = {Activation and repression by oncogenic {MYC} shape tumour-specific gene expression profiles}, volume = {511}, }