Looking back at the first twenty years of genomics

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References

[1] Rheinbay,E., Parasuraman,P., Grimsby,J., Tiao,G., Engreitz,J. M., Kim,J., Lawrence,M. S., Taylor-Weiner,A., Rodriguez-Cuevas,S., Rosenberg,M. . ( 2017). Recurrent and functional regulatory mutations in breast cancer. Nature, 547 : 55– 60

[2] Venter,J. C., Adams,M. D., Myers,E. W., Li,P. W., Mural,R. J., Sutton,G. G., Smith,H. O., Yandell,M., Evans,C. A., Holt,R. A. . ( 2001). The sequence of the human genome. Science, 291 : 1304– 1351

[3] Waterston,R. H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J. F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P. . ( 2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420 : 520– 562

[4] NHGRIPress Release. “International Consortium Completes Human Genome Project”. Available from the website of NHGRI in NIH

[5] International,Human Genome Sequencing Consortium ( 2004). Finishing the euchromatic sequence of the human genome. Nature, 431 : 931– 945

[6] Gregory,S. G., Barlow,K. F., McLay,K. E., Kaul,R., Swarbreck,D., Dunham,A., Scott,C. E., Howe,K. L., Woodfine,K., Spencer,C. C. . ( 2006). The DNA sequence and biological annotation of human chromosome 1. Nature, 441 : 315– 321

[7] NurkS., KorenS., RhieA., RautiainenM., BzikadzeA. V., MikheenkoA., VollgerM. R., AltemoseN., UralskyL., GershmanA.,. ( 2021) The complete sequence of a human genome. bioRxiv, 2021.05.26.445798

[8] Miga,K. H., Koren,S., Rhie,A., Vollger,M. R., Gershman,A., Bzikadze,A., Brooks,S., Howe,E., Porubsky,D., Logsdon,G. A. . ( 2020). Telomere-to-telomere assembly of a complete human X chromosome. Nature, 585 : 79– 84

[9] Reardon,S. ( 2021). A complete human genome sequence is close: how scientists filled in the gaps. Nature, 594 : 158– 159

[10] Loos,R. J. ( 2020). 15 years of genome-wide association studies and no signs of slowing down. Nat. Commun., 11 : 5900

[11] SalzbergS.. ( 2018) Open questions: How many genes do we have? BMC Biol., 16, 94

[12] Tam,V., Patel,N., Turcotte,M., ( 2019). Benefits and limitations of genome-wide association studies. Nat. Rev. Genet., 20 : 467– 484

[13] Manolio,T. Collins,F. Cox,N. Goldstein,D. Hindorff,L. Hunter,D. McCarthy,M. Ramos,E. Cardon,L. Chakravarti,A. . ( 2009). Finding the missing heritability of complex diseases. Nature. 461, 747– 53

[14] Wood,A. R., Esko,T., Yang,J., Vedantam,S., Pers,T. H., Gustafsson,S., Chu,A. Y., Estrada,K., Luan,J., Kutalik,Z. . ( 2014). Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet., 46 : 1173– 1186

[15] Fuchsberger,C., Flannick,J., Teslovich,T. M., Mahajan,A., Agarwala,V., Gaulton,K. J., Ma,C., Fontanillas,P., Moutsianas,L., McCarthy,D. J. . ( 2016). The genetic architecture of type 2 diabetes. Nature, 536 : 41– 47

[16] GTEx,Consortium; Laboratory Data,Analysis & Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI . ( 2017). Genetic effects on gene expression across human tissues. Nature, 550 : 204– 213

[17] Platig,J., Castaldi,P. J., DeMeo,D. ( 2016). Bipartite community structure of eQTLs. PLOS Comput. Biol., 12 : e1005033

[18] Fagny,M., Paulson,J. N., Kuijjer,M. L., Sonawane,A. R., Chen,C. Y., Lopes-Ramos,C. M., Glass,K., Quackenbush,J. ( 2017). Exploring regulation in tissues with eQTL networks. Proc. Natl. Acad. Sci. USA, 114 : E7841– E7850

[19] Boyle,E. A., Li,Y. I. Pritchard,J. ( 2017). An expanded view of complex traits: from polygenic to omnigenic. Cell, 169 : 1177– 1186

[20] Langfelder,P. ( 2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9 : 559

[21] KuijjerM. L., FagnyM., MarinA., QuackenbushJ.. PUMA: PANDA using microRNA associations. ( 2019) bioRxiv, 2019.12.18.874065

[22] SonawaneA. R., DeMeoD. L., QuackenbushJ.. ( 2020) Constructing gene regulatory networks using epigenetic data. bioRxiv. 2020.10.19.345827

[23] Glass,K., Quackenbush,J., Spentzos,D., Haibe-Kains,B. Yuan,G. ( 2015). A network model for angiogenesis in ovarian cancer. BMC Bioinformatics, 16 : 115

[24] Lopes-Ramos,C. M., Paulson,J. N., Chen,C. Y., Kuijjer,M. L., Fagny,M., Platig,J., Sonawane,A. R., DeMeo,D. L., Quackenbush,J. ( 2017). Regulatory network changes between cell lines and their tissues of origin. BMC Genomics, 18 : 723

[25] Sonawane,A. R., Platig,J., Fagny,M., Chen,C. Y., Paulson,J. N., Lopes-Ramos,C. M., DeMeo,D. L., Quackenbush,J., Glass,K. Kuijjer,M. ( 2017). Understanding tissue-specific gene regulation. Cell Rep., 21 : 1077– 1088

[26] Lopes-Ramos,C. M., Chen,C. Y., Kuijjer,M. L., Paulson,J. N., Sonawane,A. R., Fagny,M., Platig,J., Glass,K., Quackenbush,J. DeMeo,D. ( 2020). Sex differences in gene expression and regulatory networks across 29 human tissues. Cell Rep., 31 : 107795

[27] Lopes-Ramos,C. M., Kuijjer,M. L., Ogino,S., Fuchs,C. S., DeMeo,D. L., Glass,K. ( 2018). Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism. Cancer Res., 78 : 5538– 5547

[28] Weighill,D., Ben Guebila,M., Glass,K., Platig,J., Yeh,J. J. ( 2021). Gene targeting in disease networks. Front. Genet., 12 : 649942

[29] Katsanis,N., Worley,K. C. Lupski,J. ( 2001). An evaluation of the draft human genome sequence. Nat. Genet., 29 : 88– 91

[30] SalzbergS. L., WhiteO., PetersonJ. EisenJ.. ( 2001) Microbial genes in the human genome: lateral transfer or gene loss? Science, 292, 1903– 1906

[31] Andersson,J. O., Doolittle,W. F. ( 2001). Genomics. Are there bugs in our genome? Science, 292 : 1848– 1850

[32] Stanhope,M. J., Lupas,A., Italia,M. J., Koretke,K. K., Volker,C. Brown,J. ( 2001). Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature, 411 : 940– 944

[33] Quackenbush,J. ( 2001). The power of public access: the Human Genome Project and the scientific process. Nat. Genet., 29 : 4– 6

[34] Brazma,A., Hingamp,P., Quackenbush,J., Sherlock,G., Spellman,P., Stoeckert,C., Aach,J., Ansorge,W., Ball,C. A., Causton,H. C. . ( 2001). Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet., 29 : 365– 371

[35] Ball,C. A., Brazma,A., Causton,H., Chervitz,S., Edgar,R., Hingamp,P., Matese,J. C., Parkinson,H., Quackenbush,J., Ringwald,M. . ( 2004). Submission of microarray data to public repositories. PLoS Biol., 2 : e317

[36] Ball,C., Brazma,A., Causton,H., Chervitz,S., Edgar,R., Hingamp,P., Matese,J. C., Parkinson,H., Quackenbush,J., Ringwald,M. . ( 2004). Standards for microarray data: an open letter. Environ. Health Perspect., 112 : A666– A667

[37] Ball,C. A., Sherlock,G., Parkinson,H., Rocca-Sera,P., Brooksbank,C., Causton,H. C., Cavalieri,D., Gaasterland,T., Hingamp,P., Holstege,F. . ( 2002). Standards for microarray data. Science, 298 : 539

[38] Ball,C. A., Sherlock,G., Parkinson,H., Rocca-Sera,P., Brooksbank,C., Causton,H. C., Cavalieri,D., Gaasterland,T., Hingamp,P., Holstege,F. . ( 2002). The underlying principles of scientific publication. Bioinformatics, 18 : 1409

[39] Kaiser, J. (2015) Potti found guilty of research misconduct. Available from the website of Science

[40] Instituteof Medicine; Board on Health Care Services; Board on Health Sciences Policy; Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials. ( 2012) Evolution of Translational Omics: Lessons Learned and the Path Forward. Micheel, C. M., Nass, S. J. and Omenn, G. S., (Eds.). Washington, DC: The National Academies Press

[41] Barretina,J., Caponigro,G., Stransky,N., Venkatesan,K., Margolin,A. A., Kim,S., Wilson,C. J., Kryukov,G. V., Sonkin,D. . ( 2012). The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature, 483 : 603– 607

[42] Garnett,M. J., Edelman,E. J., Heidorn,S. J., Greenman,C. D., Dastur,A., Lau,K. W., Greninger,P., Thompson,I. R., Luo,X., Soares,J. . ( 2012). Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature, 483 : 570– 575

[43] Haibe-Kains,B., El-Hachem,N., Birkbak,N. J., Jin,A. C., Beck,A. H., Aerts,H. J. ( 2013). Inconsistency in large pharmacogenomic studies. Nature, 504 : 389– 393

[44] Cancer,Cell Line Encyclopedia Consortium Genomics,of Drug Sensitivity in Cancer Consortium ( 2015). Pharmacogenomic agreement between two cancer cell line data sets. Nature, 528 : 84– 87

[45] McKinney,S. M., Sieniek,M., Godbole,V., Godwin,J., Antropova,N., Ashrafian,H., Back,T., Chesus,M., Corrado,G. S., Darzi,A. . ( 2020). International evaluation of an AI system for breast cancer screening. Nature, 577 : 89– 94

[46] Haibe-Kains,B., Adam,G. A., Hosny,A., Khodakarami,F., Shraddha,T., Kusko,R., Sansone,S. Tong,W., Wolfinger,R. D., Mason,C. E. . ( 2020). Transparency and reproducibility in artificial intelligence. Nature, 586 : E14– E16

[47] Pollack,J. R., Perou,C. M., Alizadeh,A. A., Eisen,M. B., Pergamenschikov,A., Williams,C. F., Jeffrey,S. S., Botstein,D. Brown,P. ( 1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23 : 41– 46

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