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Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
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References

Adams, D. C., and M. L. Collyer. 2017. Multivariate phylogenetic comparative methods: Evaluations, comparisons, and recommendations. Systematic Biology 67(1):14–31.

Adams, M. D., S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne, P. G. Amanatides, S. E. Scherer, P. W. Li, R. A. Hoskins, R. F. Galle, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287(5461):2185–2195.

Aguet, F., A. N. Barbeira, R. Bonazzola, A. Brown, S. E. Castel, B. Jo, S. Kasela, S. KimHellmuth, Y. Liang, M. Oliva, P. E. Parsana, E. Flynn, L. Fresard, E. R. Gaamzon, A. R. Hamel, Y. He, F. Hormozdiari, P. Mohammadi, M. Muñoz-Aguirre, Y. Park, A. Saha, A. V. Segrć, B. J. Strober, X. Wen, V. Wucher, S. Das, D. Garrido-Martín, N. R. Gay, R. E. Handsaker, P. J. Hoffman, S. Kashin, A. Kwong, X. Li, D. MacArthur, J. M. Rouhana, M. Stephens, E. Todres, A. Viñuela, G. Wang, Y. Zou, C. D. Brown, N. Cox, E. Dermitzakis, B. E. Engelhardt, G. Getz, R. Guigo, S. B. Montgomery, B. E. Stranger, H. K. Im, A. Battle, K. G. Ardlie, and T. Lappalainen. 2019. The GTEx Consortium atlas of genetic regulatory effects across human tissues. bioRxiv 787903.

Albuisson, J., B. Isidor, M. Giraud, O. Pichon, T. Marsaud, A. David, C. Le Caignec, and S. Bezieau. 2011. Identification of two novel mutations in SHH long-range regulator associated with familial pre-axial polydactyly. Clinical Genetics 79(4):371–377.

Anderson, G. R., P. S. Winter, K. H. Lin, D. P. Nussbaum, M. Cakir, E. M. Stein, R. S. Soderquist, L. Crawford, J. C. Leeds, R. Newcomb, P. Stepp, C. Yip, S. E. Wardell, J. P. Tingley, M. Ali, M. Xu, M. Ryan, S. J. McCall, A. J. McRee, C. M. Counter, C. J. Der, and K. C. Wood. 2017. A landscape of therapeutic cooperativity in KRAS mutant cancers reveals principles for controlling tumor evolution. Cell Reports 20(4):999–1015.

Anderson, S. N., M. C. Stitzer, A. B. Brohammer, P. Zhou, J. M. Noshay, C. H. O’Connor, C. D. Hirsch, J. Ross-Ibarra, C. N. Hirsch, and N. M. Springer. 2019. Transposable elements contribute to dynamic genome content in maize. The Plant Journal 100(5):1052–1065.

Benfey, P. N., P. J. Linstead, K. Roberts, J. W. Schiefelbein, M. T. Hauser, and R. A. Aeschbacher. 1993. Root development in Arabidopsis: Four mutants with dramatically altered root morphogenesis. Development 119(1):57–70.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Bernstein, M. R., S. Zdraljevic, E. C. Andersen, and M. V. Rockman. 2019. Tightly linked antagonistic-effect loci underlie polygenic phenotypic variation in C. elegans. Evolution Letters 3(5):462–473.

Bielecki, P., S. J. Riesenfeld, M. S. Kowalczyk, M. C. Amezcua Vesely, L. Kroehling, P. Yaghoubi, D. Dionne, A. Jarret, H. R. Steach, H. M. McGee, C. B. M. Porter, P. Licona-Limon, W. Bailis, R. P. Jackson, N. Gagliani, R. M. Locksley, A. Regev, and R. A. Flavell. 2018. Skin inflammation driven by differentiation of quiescent tissue-resident ILCs into a spectrum of pathogenic effectors. bioRxiv 461228.

Blatti, C., III, A. Emad, M. J. Berry, L. Gatzke, M. Epstein, D. Lanier, P. Rizal, J. Ge, X. Liao, O. Sobh, M. Lambert, C. S. Post, J. Xiao, P. Groves, A. T. Epstein, X. Chen, S. Srinivasan, E. Lehnert, K. R. Kalari, L. Wang, R. M. Weinshilboum, J. S. Song, C. V. Jongeneel, J. Han, U. Ravaioli, N. Sobh, C. B. Bushell, and S. Sinha. 2020. Knowledge-guided analysis of “omics” data using the KnowEnG cloud platform. PLOS Biology 18(1):e3000583.

Bloom, J. S., J. Boocock, S. Treusch, M. J. Sadhu, L. Day, H. Oates-Barker, and L. Kruglyak. 2019. Rare variants contribute disproportionately to quantitative trait variation in yeast. eLife 8:e49212.

Blumberg, A., Y. Zhao, Y.-F. Huang, N. Dukler, E. J. Rice, K. Krumholz, C. G. Danko, and A. Siepel. 2019. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. bioRxiv 690644.

Bolnick, D. I., R. D. H. Barrett, K. B. Oke, D. J. Rennison, and Y. E. Stuart. 2018. (non)parallel evolution. Annual Review of Ecology, Evolution, and Systematics 49(1):303–330.

Brady, S. M., D. A. Orlando, J.-Y. Lee, J. Y. Wang, J. Koch, J. R. Dinneny, D. Mace, U. Ohler, and P. N. Benfey. 2007. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318(5851):801–806.

C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282(5396):2012–2018.

Chapman, P. B., A. Hauschild, C. Robert, J. B. Haanen, P. Ascierto, J. Larkin, R. Dummer, C. Garbe, A. Testori, M. Maio, D. Hogg, P. Lorigan, C. Lebbe, T. Jouary, D. Schadendorf, A. Ribas, S. J. O’Day, J. A. Sosman, J. M. Kirkwood, A. M. M. Eggermont, B. Dreno, K. Nolop, J. Li, B. Nelson, J. Hou, R. J. Lee, K. T. Flaherty, and G. A. McArthur. 2011. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. New England Journal of Medicine 364(26):2507–2516.

Chen, Q., J. He, C. Ma, D. Yu, and L. Kang. 2015. Syntaxin 1A modulates the sexual maturity rate and progeny egg size related to phase changes in locusts. Insect Biochemistry and Molecular Biology 56:1–8.

Chick, J. M., S. C. Munger, P. Simecek, E. L. Huttlin, K. Choi, D. M. Gatti, N. Raghupathy, K. L. Svenson, G. A. Churchill, and S. P. Gygi. 2016. Defining the consequences of genetic variation on a proteome-wide scale. Nature 534(7608):500–505.

Chinwalla, A. T., L. L. Cook, K. D. Delehaunty, G. A. Fewell, L. A. Fulton, R. S. Fulton, T. A. Graves, L. W. Hillier, E. R. Mardis, J. D. McPherson, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–562.

Chu, T., E. J. Rice, G. T. Booth, H. H. Salamanca, Z. Wang, L. J. Core, S. L. Longo, R. J. Corona, L. S. Chin, J. T. Lis, H. Kwak, and C. G. Danko. 2018. Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nature Genetics 50(11):1553–1564.

Cleary, B., L. Cong, A. Cheung, E. S. Lander, and A. Regev. 2017. Efficient generation of transcriptomic profiles by random composite measurements. Cell 171(6):1424–1436.

Cooley, A. M., L. Shefner, W. N. McLaughlin, E. E. Stewart, and P. J. Wittkopp. 2012. The ontogeny of color: Developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evolution & Development 14(4):317–325.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Coolon, J. D., C. J. McManus, K. R. Stevenson, B. R. Graveley, and P. J. Wittkopp. 2014. Tempo and mode of regulatory evolution in Drosophila. Genome Research 24:797–808.

Cox, A. D., S. W. Fesik, A. C. Kimmelman, J. Luo, and C. J. Der. 2014. Drugging the undruggable RAS: Mission possible? Nature Reviews Drug Discovery 13(11):828–851.

Crow, J. F. 1997. Birth defects, Jimson weeds and bell curves. Genetics 147(1):1–6.

Cruz-Ramírez, A., S. Díaz-Triviño, I. Blilou, V. A. Grieneisen, R. Sozzani, C. Zamioudis, P. Miskolczi, J. Nieuwland, R. Benjamins, P. Dhonukshe, J. Caballero-Pérez, B. Horvath, Y. Long, A. P. Mähönen, H. Zhang, J. Xu, J. A. H. Murray, P. N. Benfey, L. Bako, A. F. M. Marée, and B. Scheres. 2012. A bistable circuit involving SCARECROWRETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell 150(5):1002–1015.

Cui, H., M. P. Levesque, T. Vernoux, J. W. Jung, A. J. Paquette, K. L. Gallagher, J. Y. Wang, I. Blilou, B. Scheres, and P. N. Benfey. 2007. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 316(5823):421–425.

de Bakker, M. A. G., D. A. Fowler, K. den Oude, E. M. Dondorp, M. C. G. Navas, J. O. Horbanczuk, J.-Y. Sire, D. Szczerbi ska, and M. K. Richardson. 2013. Digit loss in archosaur evolution and the interplay between selection and constraints. Nature 500(7463):445–448.

de Boer, C. G., E. D. Vaishnav, R. Sadeh, E. L. Abeyta, N. Friedman, and A. Regev. 2020. Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. Nature Biotechnology 38(1):56–65.

Denyer, T., X. Ma, S. Klesen, E. Scacchi, K. Nieselt, and M. C. P. Timmermans. 2019. Spatiotemporal developmental trajectories in the Arabidopsis root revealed using high-throughput single-cell RNA sequencing. Developmental Cell 48(6):840–852.

Di Laurenzio, L., J. Wysocka-Diller, J. E. Malamy, L. Pysh, Y. Helariutta, G. Freshour, M. G. Hahn, K. A. Feldmann, and P. N. Benfey. 1996. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86(3):423–433.

Dinneny, J. R., T. A. Long, J. Y. Wang, J. W. Jung, D. Mace, S. Pointer, C. Barron, S. M. Brady, J. Schiefelbein, and P. N. Benfey. 2008. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320(5878):942–945.

Dixit, A., O. Parnas, B. Li, J. Chen, C. P. Fulco, L. Jerby-Arnon, N. D. Marjanovic, D. Dionne, T. Burks, R. Raychowdhury, B. Adamson, T. M. Norman, E. S. Lander, J. S. Weissman, N. Friedman, and A. Regev. 2016. Perturb-seq: Dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167(7):1853–1866.

Donaldson, Z. R., and L. J. Young. 2013. The relative contribution of proximal 5′ flanking sequence and microsatellite variation on brain vasopressin 1a receptor (Avpr1a) gene expression and behavior. PLOS Genetics 9(8):e1003729.

Donaldson, Z. R., S.-H. Yang, A. W. S. Chan, and L. J. Young. 2009. Production of germline transgenic prairie voles (Microtus ochrogaster) using lentiviral vectors. Biology of Reproduction 81(6):1189–1195.

Duveau, F., W. Toubiana, and P. J. Wittkopp. 2017. Fitness effects of cis-regulatory variants in the Saccharomyces cerevisiae TDH3 promoter. Molecular Biology and Evolution 34(11):2908–2912.

Duveau, F., A. Hodgins-Davis, B. P. H. Metzger, B. Yang, S. Tryban, E. A. Walker, T. Lybrook, and P. J. Wittkopp. 2018. Fitness effects of altering gene expression noise in Saccharomyces cerevisiae. eLife 7:e37272.

Emad, A., J. Cairns, K. R. Kalari, L. Wang, and S. Sinha. 2017. Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance. Genome Biology 18(1):153.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Everett, L. J., W. Huang, S. Zhou, M. A. Carbone, R. F. Lyman, G. H. Arya, M. S. Geisz, J. Ma, F. Morgante, G. St. Armour, L. Turlapati, R. R. H. Anholt, and T. F. C. Mackay. 2020. Gene expression networks in the Drosophila genetic reference panel. Genome Research 30(3):485–496.

Farley, E. K., K. M. Olson, W. Zhang, A. J. Brandt, D. S. Rokhsar, and M. S. Levine. 2015. Suboptimization of developmental enhancers. Science 350(6258):325–328.

Fisher, R. A. 1918. The correlation between relatives on the supposition of Mendelian inheritance. Transactions of the Royal Society of Edinburgh 52(2):399–433.

Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269(5223):496–512.

Franke, M., D. M. Ibrahim, G. Andrey, W. Schwarzer, V. Heinrich, R. Schöpflin, K. Kraft, R. Kempfer, I. Jerkovi , W.-L. Chan, M. Spielmann, B. Timmermann, L. Wittler, I. Kurth, P. Cambiaso, O. Zuffardi, G. Houge, L. Lambie, F. Brancati, A. Pombo, M. Vingron, F. Spitz, and S. Mundlos. 2016. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 538(7624):265–269.

Fujiwara, T., M. Sanada, T. Kofuji, and K. Akagawa. 2016. Unusual social behavior in HPC-1/syntaxin1A knockout mice is caused by disruption of the oxytocinergic neural system. Journal of Neurochemistry 138(1):117–123.

Function. 2000. 2000: A focus on function. Nature Genetics 25:243–244.

Graf, U., E. A. Casanova, and P. Cinelli. 2011. The role of the leukemia inhibitory factor (LIF)—pathway in derivation and maintenance of murine pluripotent stem cells. Genes (Basel) 2(1):280–297.

Greenway, R., N. Barts, C. Henpita, A. P. Brown, L. A. Rodriguez, C. M. Rodríguez Peña, S. Arndt, G. Y. Lau, M. P. Murphy, L. Wu, D. Lin, J. H. Shaw, J. L. Kelley, and M. Tobler. 2020. Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments. bioRxiv 2020.02.24.959916.

GTEx (Genotype-Tissue Expression) Consortium. 2017. Genetic effects on gene expression across human tissues. Nature 550(7675):204–213.

Hammock, E. A. D., and L. J. Young. 2005. Microsatellite instability generates diversity in brain and sociobehavioral traits. Science 308(5728):1630–1634.

Helariutta, Y., H. Fukaki, J. Wysocka-Diller, K. Nakajima, J. Jung, G. Sena, M.-T. Hauser, and P. N. Benfey. 2000. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101(5):555–567.

Hodge, R. D., J. A. Miller, M. Novotny, B. E. Kalmbach, J. T. Ting, T. E. Bakken, B. D. Aevermann, E. R. Barkan, M. L. Berkowitz-Cerasano, C. Cobbs, F. Diez-Fuertes, S.-L. Ding, J. McCorrison, N. J. Schork, S. I. Shehata, K. A. Smith, S. M. Sunkin, D. N. Tran, P. Venepally, A. M. Yanny, F. J. Steemers, J. W. Phillips, A. Bernard, C. Koch, R. S. Lasken, R. H. Scheuermann, and E. S. Lein. 2020. Transcriptomic evidence that von economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons. Nature Communications 11(1):1172.

Hu, Z., T. B. Sackton, S. V. Edwards, and J. S. Liu. 2019. Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Molecular Biology and Evolution 36(5):1086–1100.

Huang, W., A. Massouras, Y. Inoue, J. Peiffer, M. Ràmia, A. M. Tarone, L. Turlapati, T. Zichner, D. Zhu, R. F. Lyman, M. M. Magwire, K. Blankenburg, M. A. Carbone, K. Chang, L. L. Ellis, S. Fernandez, Y. Han, G. Highnam, C. E. Hjelmen, J. R. Jack, M. Javaid, J. Jayaseelan, D. Kalra, S. Lee, L. Lewis, M. Munidasa, F. Ongeri, S. Patel, L. Perales, A. Perez, L. Pu, S. M. Rollmann, R. Ruth, N. Saada, C. Warner, A. Williams, Y.-Q. Wu, A. Yamamoto, Y. Zhang, Y. Zhu, R. R. H. Anholt, J. O. Korbel, D. Mittelman, D. M. Muzny, R. A. Gibbs, A. Barbadilla, J. S. Johnston, E. A. Stone, S. Richards, B. Deplancke, and T. F. C. Mackay. 2014. Natural variation in genome architecture among 205 Drosophila melanogaster genetic reference panel lines. Genome Research 24(7):1193–1208.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Huang, W., T. Campbell, M. A. Carbone, W. E. Jones, D. Unselt, R. R. H. Anholt, and T. F. C. Mackay. 2020. Context-dependent genetic architecture of Drosophila life span. PLOS Biology 18(3):e3000645.

International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431(7011):931–945.

Janes, D. E., C. Chapus, Y. Gondo, D. F. Clayton, S. Sinha, C. A. Blatti, C. L. Organ, M. K. Fujita, B. N. Balakrishnan, and S. V. Edwards. 2011. Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome Biology and Evolution 3:102–113.

Janssens, D. H., S. J. Wu, J. F. Sarthy, M. P. Meers, C. H. Myers, J. M. Olson, K. Ahmad, and S. Henikoff. 2018. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. Epigenetics & Chromatin 11(1):74.

Jean-Baptiste, K., J. L. McFaline-Figueroa, C. M. Alexandre, M. W. Dorrity, L. Saunders, K. L. Bubb, C. Trapnell, S. Fields, C. Queitsch, and J. T. Cuperus. 2019. Dynamics of gene expression in single root cells of Arabidopsis thaliana. The Plant Cell 31(5):993.

Jin, X., S. K. Simmons, A. X. Guo, A. S. Shetty, M. Ko, L. Nguyen, E. Robinson, P. Oyler, N. Curry, G. Deangeli, S. Lodato, J. Z. Levin, A. Regev, F. Zhang, and P. Arlotta. 2019. In vivo Perturb-seq reveals neuronal and glial abnormalities associated with autism risk genes. bioRxiv 791525.

John, A. V., L. L. Sramkoski, E. A. Walker, A. M. Cooley, and P. J. Wittkopp. 2016. Sensitivity of allelic divergence to genomic position: Lessons from the Drosophila tan gene. G3: Genes Genomes Genetics 6(9):2955–2962.

Jones, F. C., M. G. Grabherr, Y. F. Chan, P. Russell, E. Mauceli, J. Johnson, R. Swofford, M. Pirun, M. C. Zody, S. White, E. Birney, S. Searle, J. Schmutz, J. Grimwood, M. C. Dickson, R. M. Myers, C. T. Miller, B. R. Summers, A. K. Knecht, S. D. Brady, H. Zhang, A. A. Pollen, T. Howes, C. Amemiya, J. Baldwin, T. Bloom, D. B. Jaffe, R. Nicol, J. Wilkinson, Broad Institute Genome Sequencing Platform and Whole Genome Assembly Team, E. S. Lander, F. Di Palma, K. Lindblad-Toh, and D. M. Kingsley. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484(7392):55–61.

Kalay, G., and P. J. Wittkopp. 2010. Nomadic enhancers: Tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLOS Genetics 6(11):e1001222.

Kalay, G., J. Lachowiec, U. Rosas, M. R. Dome, and P. J. Wittkopp. 2019. Redundant and cryptic enhancer activities of the Drosophila yellow gene. Genetics 212(1):343–360.

Kapheim, K. M., H. Pan, C. Li, S. L. Salzberg, D. Puiu, T. Magoc, H. M. Robertson, M. E. Hudson, A. Venkat, B. J. Fischman, A. Hernandez, M. Yandell, D. Ence, C. Holt, G. D. Yocum, W. P. Kemp, J. Bosch, R. M. Waterhouse, E. M. Zdobnov, E. Stolle, F. B. Kraus, S. Helbing, R. F. A. Moritz, K. M. Glastad, B. G. Hunt, M. A. D. Goodisman, F. Hauser, C. J. P. Grimmelikhuijzen, D. G. Pinheiro, F. M. F. Nunes, M. P. M. Soares, É. D. Tanaka, Z. L. P. Simões, K. Hartfelder, J. D. Evans, S. M. Barribeau, R. M. Johnson, J. H. Massey, B. R. Southey, M. Hasselmann, D. Hamacher, M. Biewer, C. F. Kent, A. Zayed, C. Blatti, S. Sinha, J. S. Johnston, S. J. Hanrahan, S. D. Kocher, J. Wang, G. E. Robinson, and G. Zhang. 2015. Genomic signatures of evolutionary transitions from solitary to group living. Science 348(6239):1139–1143.

Kaya-Okur, H. S., S. J. Wu, C. A. Codomo, E. S. Pledger, T. D. Bryson, J. G. Henikoff, K. Ahmad, and S. Henikoff. 2019. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature Communications 10(1):1930.

Kelley, J. L., L. Arias-Rodriguez, D. Patacsil Martin, M.-C. Yee, C. D. Bustamante, and M. Tobler. 2016. Mechanisms underlying adaptation to life in hydrogen sulfide–rich environments. Molecular Biology and Evolution 33(6):1419–1434.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Kerwin, R. E., and A. L. Sweigart. 2020. Rampant misexpression in a Mimulus (monkeyflower) introgression line caused by hybrid sterility, not regulatory divergence. Molecular Biology and Evolution 37(7):2084–2098.

King, M. C., and A. C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188(4184):107–116.

Kocher, S. D., R. Mallarino, B. E. R. Rubin, D. W. Yu, H. E. Hoekstra, and N. E. Pierce. 2018. The genetic basis of a social polymorphism in halictid bees. Nature Communications 9(1):4338.

Kolata, G. 2013. Mice fall short as test subjects for some of humans’ deadly ills. The New York Times, February 11.

Krogh, A. 1929. The progress of physiology. Science 70(1809):200–204.

Lamb, A. M., E. A. Walker, and P. J. Wittkopp. 2017. Tools and strategies for scarless allele replacement in Drosophila using CRISPR/Cas9. Fly 11(1):53–64.

Li, X., A. Battle, K. J. Karczewski, Z. Zappala, D. A. Knowles, K. S. Smith, K. R. Kukurba, E. Wu, N. Simon, and S. B. Montgomery. 2014. Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. American Journal of Human Genetics 95(3):245–256.

Li, X., Y. Kim, E. K. Tsang, J. R. Davis, F. N. Damani, C. Chiang, G. T. Hess, Z. Zappala, B. J. Strober, A. J. Scott, A. Li, A. Ganna, M. C. Bassik, J. D. Merker, GTEx Consortium, I. M. Hall, A. Battle, and S. B. Montgomery. 2017. The impact of rare variation on gene expression across tissues. Nature 550(7675):239–243.

Lim, M. M., Z. Wang, D. E. Olazábal, X. Ren, E. F. Terwilliger, and L. J. Young. 2004. Enhanced partner preference in a promiscuous species by manipulating the expression of a single gene. Nature 429(6993):754–757.

Liu, L., L. Yu, and S. V. Edwards. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology 10(1):302.

Lupiáñez, D. G., K. Kraft, V. Heinrich, P. Krawitz, F. Brancati, E. Klopocki, D. Horn, H. Kayserili, J. M. Opitz, R. Laxova, F. Santos-Simarro, B. Gilbert-Dussardier, L. Wittler, M. Borschiwer, S. A. Haas, M. Osterwalder, M. Franke, B. Timmermann, J. Hecht, M. Spielmann, A. Visel, and S. Mundlos. 2015. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161(5):1012–1025.

Mackay, T. F. C., S. Richards, E. A. Stone, A. Barbadilla, J. F. Ayroles, D. Zhu, S. Casillas, Y. Han, M. M. Magwire, J. M. Cridland, M. F. Richardson, R. R. H. Anholt, M. Barrón, C. Bess, K. P. Blankenburg, M. A. Carbone, D. Castellano, L. Chaboub, L. Duncan, Z. Harris, M. Javaid, J. C. Jayaseelan, S. N. Jhangiani, K. W. Jordan, F. Lara, F. Lawrence, S. L. Lee, P. Librado, R. S. Linheiro, R. F. Lyman, A. J. Mackey, M. Munidasa, D. M. Muzny, L. Nazareth, I. Newsham, L. Perales, L.-L. Pu, C. Qu, M. Ràmia, J. G. Reid, S. M. Rollmann, J. Rozas, N. Saada, L. Turlapati, K. C. Worley, Y.-Q. Wu, A. Yamamoto, Y. Zhu, C. M. Bergman, K. R. Thornton, D. Mittelman, and R. A. Gibbs. 2012. The Drosophila melanogaster genetic reference panel. Nature 482(7384):173–178.

Martin, A., and V. Orgogozo. 2013. The loci of repeated evolution: A catalog of genetic hotspots of phenotypic variation. Evolution 67(5):1235–1250.

McClintock, B. 1950. The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences of the United States of America 36:344–355.

McManus, C. J., J. D. Coolon, M. O. Duff, J. Eipper-Mains, B. R. Graveley, and P. J. Wittkopp. 2010. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Research 20(6):816–825.

Metzger, B. P. H., and P. J. Wittkopp. 2019. Compensatory trans-regulatory alleles minimizing variation in TDH3 expression are common within Saccharomyces cerevisiae. Evolution Letters 3(5):448–461.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Metzger, B. P. H., D. C. Yuan, J. D. Gruber, F. Duveau, and P. J. Wittkopp. 2015. Selection on noise constrains variation in a eukaryotic promoter. Nature 521(7552):344–347.

Metzger, B. P. H., P. J. Wittkopp, and J. D. Coolon. 2017. Evolutionary dynamics of regulatory changes underlying gene expression divergence among Saccharomyces species. Genome Biology and Evolution 9(4):843–854.

Morin, M., E. C. Pierce, and R. J. Dutton. 2018. Changes in the genetic requirements for microbial interactions with increasing community complexity. eLife 7:e37072.

Munson, M. 2015. Synaptic-vesicle fusion: A need for speed. Nature Structural & Molecular Biology 22(7):509–511.

Nakajima, K., G. Sena, T. Nawy, and P. N. Benfey. 2001. Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413(6853):307–311.

Naqvi, S., A. K. Godfrey, J. F. Hughes, M. L. Goodheart, R. N. Mitchell, and D. C. Page. 2019. Conservation, acquisition, and functional impact of sex-biased gene expression in mammals. Science 365(6450):eaaw7317.

Nora, E. P., A. Goloborodko, A.-L. Valton, J. H. Gibcus, A. Uebersohn, N. Abdennur, J. Dekker, K. A. Mirny, and B. G. Bruneau. 2017. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169(5):930–944.

Passow, C. N., C. Henpita, J. H. Shaw, C. R. Quackenbush, W. C. Warren, M. Schartl, L. Arias-Rodriguez, J. L. Kelley, and M. Tobler. 2017. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Molecular Ecology 26(22):6384–6399.

Phelps, S. M., and L. J. Young. 2003. Extraordinary diversity in vasopressin (V1a) receptor distributions among wild prairie voles (Microtus ochrogaster): Patterns of variation and covariation. Journal of Comparative Neurology 466(4):564–576.

Plateaux-Quénu, C., L. Plateaux, and L. Packer. 2000. Population-typical behaviours are retained when eusocial and non-eusocial forms of Evylaeus albipes (f.) (Hymenoptera, Halictidae) are reared simultaneously in the laboratory. Insectes Sociaux 47(3):263–270.

Rawlik, K., O. Canela-Xandri, and A. Tenesa. 2016. Evidence for sex-specific genetic architectures across a spectrum of human complex traits. Genome Biology 17(1):166.

Ricci, W. A., Z. Lu, L. Ji, A. P. Marand, C. L. Ethridge, N. G. Murphy, J. M. Noshay, M. Galli, M. K. Mejía-Guerra, M. Colomé-Tatché, F. Johannes, M. J. Rowley, V. G. Corces, J. Zhai, M. J. Scanlon, E. S. Buckler, A. Gallavotti, N. M. Springer, R. J. Schmitz, and X. Zhang. 2019. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants 5(12):1237–1249.

Rodgers-Melnick, E., D. L. Vera, H. W. Bass, and E. S. Buckler. 2016. Open chromatin reveals the functional maize genome. Proceedings of the National Academy of Sciences of the United States of America 113(22):E3177–E3184.

Ryu, K. H., L. Huang, H. M. Kang, and J. Schiefelbein. 2019. Single-cell RNA sequencing resolves molecular relationships among individual plant cells. Plant Physiology 179(4):1444–1456.

Sackton, T. B., P. Grayson, A. Cloutier, Z. Hu, J. S. Liu, N. E. Wheeler, P. P. Gardner, J. A. Clarke, A. J. Baker, M. Clamp, and S. V. Edwards. 2019. Convergent regulatory evolution and loss of flight in paleognathous birds. Science 364(6435):74–78.

Sakurai, A., and P. S. Katz. 2017. Artificial synaptic rewiring demonstrates that distinct neural circuit configurations underlie homologous behaviors. Current Biology 27(12):1721–1734.

Sanjak, J. S., J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences of the United States of America 115(1):151–156.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Schwarzer, W., N. Abdennur, A. Goloborodko, A. Pekowska, G. Fudenberg, Y. Loe-Mie, N. A. Fonseca, W. Huber, C. H. Haering, L. Mirny, and F. Spitz. 2017. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551(7678):51–56.

Seok, J., H. S. Warren, A. G. Cuenca, M. N. Mindrinos, H. V. Baker, W. Xu, D. R. Richards, G. P. McDonald-Smith, H. Gao, L. Hennessy, C. C. Finnerty, C. M. López, S. Honari, E. E. Moore, J. P. Minei, J. Cuschieri, P. E. Bankey, J. L. Johnson, J. Sperry, A. B. Nathens, T. R. Billiar, M. A. West, M. G. Jeschke, M. B. Klein, R. L. Gamelli, N. S. Gibran, B. H. Brownstein, C. Miller-Graziano, S. E. Calvano, P. H. Mason, J. P. Cobb, L. G. Rahme, S. F. Lowry, R. V. Maier, L. L. Moldawer, D. N. Herndon, R. W. Davis, W. Xiao, and R. G. Tompkins. 2013. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proceedings of the National Academy of Sciences of the United States of America 110(9):3507–3512.

Shulse, C. N., B. J. Cole, D. Ciobanu, J. Lin, Y. Yoshinaga, M. Gouran, G. M. Turco, Y. Zhu, R. C. O’Malley, S. M. Brady, and D. E. Dickel. 2019. High-throughput single-cell transcriptome profiling of plant cell types. Cell Reports 27(7):2241–2247.

Sidorenko, J., I. Kassam, K. E. Kemper, J. Zeng, L. R. Lloyd-Jones, G. W. Montgomery, G. Gibson, A. Metspalu, T. Esko, J. Yang, A. F. McRae, and P. M. Visscher. 2019. The effect of X-linked dosage compensation on complex trait variation. Nature Communications 10(1):3009.

Skene, P. J., and S. Henikoff. 2017. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6:e21856.

Skene, P. J., J. G. Henikoff, and S. Henikoff. 2018. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nature Protocols 13(5):1006–1019.

Smillie, C. S., M. Biton, J. Ordovas-Montanes, K. M. Sullivan, G. Burgin, D. B. Graham, R. H. Herbst, N. Rogel, M. Slyper, J. Waldman, M. Sud, E. Andrews, G. Velonias, A. L. Haber, K. Jagadeesh, S. Vickovic, J. Yao, C. Stevens, D. Dionne, L. T. Nguyen, A.-C. Villani, M. Hofree, E. A. Creasey, H. Huang, O. Rozenblatt-Rosen, J. J. Garber, H. Khalili, A. N. Desch, M. J. Daly, A. N. Ananthakrishnan, A. K. Shalek, R. J. Xavier, and A. Regev. 2019. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178(3):714–730.

Sosman, J. A., K. B. Kim, L. Schuchter, R. Gonzalez, A. C. Pavlick, J. S. Weber, G. A. McArthur, T. E. Hutson, S. J. Moschos, K. T. Flaherty, P. Hersey, R. Kefford, D. Lawrence, I. Puzanov, K. D. Lewis, R. K. Amaravadi, B. Chmielowski, H. J. Lawrence, Y. Shyr, F. Ye, J. Li, K. B. Nolop, R. J. Lee, A. K. Joe, and A. Ribas. 2012. Survival in BRAF V600–mutant advanced melanoma treated with vemurafenib. New England Journal of Medicine 366(8):707–714.

Stoeckius, M., C. Hafemeister, W. Stephenson, B. Houck-Loomis, P. K. Chattopadhyay, H. Swerdlow, R. Satija, and P. Smibert. 2017. Simultaneous epitope and transcriptome measurement in single cells. Nature Methods 14(9):865–868.

Stuart, T., A. Butler, P. Hoffman, C. Hafemeister, E. Papalexi, W. M. Mauck, III, Y. Hao, M. Stoeckius, P. Smibert, and R. Satija. 2019. Comprehensive integration of single-cell data. Cell 177(7):1888–1902.

Sweigart, A. L., and L. E. Flagel. 2015. Evidence of natural selection acting on a polymorphic hybrid incompatibility locus in Mimulus. Genetics 199(2):543–554.

Sweigart, A. L., L. Fishman, and J. H. Willis. 2006. A simple genetic incompatibility causes hybrid male sterility in Mimulus. Genetics 172(4):2465–2479.

Symmons, O., V. V. Uslu, T. Tsujimura, S. Ruf, S. Nassari, W. Schwarzer, L. Ettwiller, and F. Spitz. 2014. Functional and topological characteristics of mammalian regulatory domains. Genome Research 24(3):390–400.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Tasic, B., Z. Yao, L. T. Graybuck, K. A. Smith, T. N. Nguyen, D. Bertagnolli, J. Goldy, E. Garren, M. N. Economo, S. Viswanathan, O. Penn, T. Bakken, V. Menon, J. Miller, O. Fong, K. E. Hirokawa, K. Lathia, C. Rimorin, M. Tieu, R. Larsen, T. Casper, E. Barkan, M. Kroll, S. Parry, M. V. Shapovalova, D. Hirschstein, J. Pendergraft, H. A. Sullivan, T. K. Kim, A. Szafer, N. Dee, P. Groblewski, I. Wickersham, A. Cetin, J. A. Harris, B. P. Levi, S. M. Sunkin, L. Madisen, T. L. Daigle, L. Looger, A. Bernard, J. Phillips, E. Lein, M. Hawrylycz, K. Svoboda, A. R. Jones, C. Koch, and H. Zeng. 2018. Shared and distinct transcriptomic cell types across neocortical areas. Nature 563(7729):72–78.

Tobler, M., I. Schlupp, K. U. Heubel, R. Riesch, F. J. G. de León, O. Giere, and M. Plath. 2006. Life on the edge: Hydrogen sulfide and the fish communities of a Mexican cave and surrounding waters. Extremophiles 10(6):577–585.

Tobler, M., J. L. Kelley, M. Plath, and R. Riesch. 2018. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Molecular Ecology 27(4):843–859.

Tsujimura, T., F. A. Klein, K. Langenfeld, J. Glaser, W. Huber, and F. Spitz. 2015. A discrete transition zone organizes the topological and regulatory autonomy of the adjacent TFAP2C and BMP7 genes. PLOS Genetics 11(1):e1004897.

Uslu, V. V., M. Petretich, S. Ruf, K. Langenfeld, N. A. Fonseca, J. C. Marioni, and F. Spitz. 2014. Long-range enhancers regulating MYC expression are required for normal facial morphogenesis. Nature Genetics 46(7):753–758.

Verta, J.-P., and F. C. Jones. 2019. Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. eLife 8:e43785.

Wagle, N., C. Emery, M. F. Berger, M. J. Davis, A. Sawyer, P. Pochanard, S. M. Kehoe, C. M. Johannessen, L. E. Macconaill, W. C. Hahn, M. Meyerson, and L. A. Garraway. 2011. Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling. Journal of Clinical Oncology 29(22):3085–3096.

Wang, X., W. E. Allen, M. A. Wright, E. L. Sylwestrak, N. Samusik, S. Vesuna, K. Evans, C. Liu, C. Ramakrishnan, J. Liu, G. P. Nolan, F.-A. Bava, and K. Deisseroth. 2018. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361(6400):eaat5691.

Wetmore, K. M., M. N. Price, R. J. Waters, J. S. Lamson, J. He, C. A. Hoover, M. J. Blow, J. Bristow, G. Butland, A. P. Arkin, and A. Deutschbauer. 2015. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. mBio 6(3):e00306–e00315.

Wittkopp, P. J., and G. Kalay. 2011. Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence. Nature Reviews Genetics 13(1):59–69.

Wittkopp, P. J., B. L. Williams, J. E. Selegue, and S. B. Carroll. 2003. Drosophila pigmentation evolution: Divergent genotypes underlying convergent phenotypes. Proceedings of the National Academy of Sciences of the United States of America 100(4):1808–1813.

Wittkopp, P. J., B. K. Haerum, and A. G. Clark. 2004. Evolutionary changes in cis and trans gene regulation. Nature 430(6995):85–88.

Wittkopp, P. J., B. K. Haerum, and A. G. Clark. 2008. Regulatory changes underlying expression differences within and between Drosophila species. Nature Genetics 40(3):346–350.

Wittkopp, P. J., E. E. Stewart, L. L. Arnold, A. H. Neidert, B. K. Haerum, E. M. Thompson, S. Akhras, G. Smith-Winberry, and L. Shefner. 2009. Intraspecific polymorphism to inter-specific divergence: Genetics of pigmentation in Drosophila. Science 326(5952):540–544.

Wolfe, B. E., J. E. Button, M. Santarelli, and R. J. Dutton. 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158(2):422–433.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
×

Young, R. S., Y. Kumar, W. A. Bickmore, and M. S. Taylor. 2017. Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers. Genome Biology 18(1):242.

Zhang, T.-Q., Z.-G. Xu, G.-D. Shang, and J.-W. Wang. 2019. A single-cell RNA sequencing profiles the developmental landscape of Arabidopsis root. Molecular Plant 12(5):648–660.

Zhou, S., T. G. Campbell, E. A. Stone, T. F. C. Mackay, and R. R. H. Anholt. 2012. Phenotypic plasticity of the Drosophila transcriptome. PLOS Genetics 8(3):e1002593.

Zuellig, M. P., and A. L. Sweigart. 2018. Gene duplicates cause hybrid lethality between sympatric species of Mimulus. PLOS Genetics 14(4):e1007130.

Suggested Citation:"References." National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25780.
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One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.

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