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4. The molecular taxonomy and evolution of the guinea pig

Author

Li, W. -H., Hide, W.A., Zharkikh, A., Ma, D.-P., and Graur, D.

Subjects
Guinea pigs -- Genetic aspects, Amino acid sequence -- Analysis, Molecular structure -- Research, Zoology -- Identification and classification, Biological sciences
Abstract

A study was done on the molecular taxonomy and evolution of the guinea pig. Results have shown that caviomorph and myomorph lineages have evolved faster than the human lineage and as such it is possible that the guinea pig may not be a rodent or that many guinea pig genes have evolved at exceptionally high rates with a pattern of evolution that is highly unusual. The genetic distances between the caviomorph and the myomorphs suggest the possibility of classifying caviomorphs in a separate ordinal status.

Published
1992

6. Finding the missing honey bee genes: lessons learned from a genome upgrade

Author

Elsik, C. G., Worley, K. C., Bennett, A. K., Beye, M., Camara, F., Childers, C. P., de Graaf, D. C., Debyser, G., Deng, J., Devreese, B., Elhaik, E., Evans, J. D., Foster, L. J., Graur, D., Guigo, R., Hoff, K. J., Holder, M. E., Hudson, M. E., Hunt, G. J., Jiang, H., Joshi, V., Khetani, R. S., Kosarev, P., Kovar, C. L., Ma, J., Maleszka, R., Moritz, R. F. A., Munoz-Torres, M. C., Murphy, T. D., Muzny, D. M., Newsham, I. F., Reese, J. T., Robertson, H. M., Robinson, G. E., Rueppell, O., Solovyev, V., Stanke, M., Stolle, E., Tsuruda, J. M., Van Vaerenbergh, M., Waterhouse, R. M., Weaver, D. B., Whitfield, C. W., Wu, Y., Zdobnov, E. M., Zhang, L., Zhu, D., Gibbs, R. A., Teams, H. G. S. C. P., and Consor, H. B. G. S.

Subjects
fungi
Abstract

Background\ud The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.\ud \ud Results\ud Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.\ud \ud Conclusions\ud Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Published
2014

7. Abstracts of papers presented at

Author

Or, R., Fishler, G., Kehat, M., Chen, CH., Klein, Z., Dunkelblum, E., Gothilf, S., Muszkat, LEA, Melamed-madjar, VENEZIA, Yathom, SHOSHANA, Halperin, J., Mendel, Z., Bonneh, O., Saphir, NITZA, Golan, Y., Madar, Z., Moore, I., Snir, R., Harpaz, I., Mazor, MICHAL, Becker, D., Kimmel, T., Cyjon, R., Cosse, A., Wysoki, M., Hefetz, A., Graur, D., La-france, DALIA, Shani, A., Ravid, U., Ideses, RUT, Soroker, VICTORIA, Rafaeli, ADA, Nevo, E., Heth, G., Beiles, A., and Auffray, J. C.

Published
1987
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8. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

Author

Werren, J. H., Richards, S., Desjardins, C. A., Niehuis, O., Gadau, J., Colbourne, J. K., Beukeboom, L. W., Desplan, C., Elsik, C. G., Grimmelikhuijzen, C. J., Kitts, P., Lynch, J. A., Murphy, T., Oliveira, D. C., Smith, C. D., van de Zande, L., Worley, K. C., Zdobnov, E. M., Aerts, M., Albert, S., Anaya, V. H., Anzola, J. M., Barchuk, A. R., Behura, S. K., Bera, A. N., Berenbaum, M. R., Bertossa, R. C., Bitondi, M. M., Bordenstein, S. R., Bork, P., Bornberg-Bauer, E., Brunain, M., Cazzamali, G., Chaboub, L., Chacko, J., Chavez, D., Childers, C. P., Choi, J. H., Clark, M. E., Claudianos, C., Clinton, R. A., Cree, A. G., Cristino, A. S., Dang, P. M., Darby, A. C., de Graaf, D. C., Devreese, B., Dinh, H. H., Edwards, R., Elango, N., Elhaik, E., Ermolaeva, O., Evans, J. D., Foret, S., Fowler, G. R., Gerlach, D., Gibson, J. D., Gilbert, D. G., Graur, D., Gr�nder, S., Hagen, D. E., Han, Y., Hauser, F., Hultmark, D., Hunter, H. C., Hurst, G. D., Jhangian, S. N., Jiang, H., Johnson, R. M., Jones, A. K., Junier, T., Kadowaki, T., Kamping, A., Kapustin, Y., Kechavarzi, B., Kim, J., Kiryutin, B., Koevoets, T., Kovar, C. L., Kriventseva, E. V., Kucharski, R., Lee, H., Lee, S. L., Lees, K., Lewis, L. R., Loehlin, D. W., Logsdon, J. M., Lopez, J. A., Lozado, R. J., Maglott, D., Maleszka, R., Mayampurath, A., Mazur, D. J., McClure, M. A., Moore, A. D., Morgan, M. B., Muller, J., Munoz-Torres, M. C., Muzny, D. M., Nazareth, L. V., Neupert, S., Nguyen, N. B., Nunes, F. M., Oakeshott, J. G., Okwuonu, G. O., Pannebakker, B. A., Pejaver, V. R., Peng, Z., Pratt, S. C., Predel, R., Pu, L. L., Ranson, H., Raychoudhury, R., Rechtsteiner, A., Reese, J. T., Reid, J. G., Riddle, M., Robertson, H. M., Romero-Severson, J., Rosenberg, M., Sackton, T. B., Sattelle, D. B., Schl�ns, H., Schmitt, T., Schneider, M., Sch�ler, A., Schurko, A. M., Shuker, D. M., Sims, Z. L., Sinha, S., Smith, Z., Solovyev, V., Souvorov, A., Springauf, A., Stafflinger, E., Stage, D. E., Stanke, M., Tanaka, Y., Telschow, A., Trent, C., Vattathil, S., Verhulst, E. C., Viljakainen, L., Wanner, K. W., Waterhouse, R. M., Whitfield, J. B., Wilkes, T. E., Williamson, M., Willis, J. H., Wolschin, F., Wyder, S., Yamada, Takuji, Yi, S. V., Zecher, C. N., Zhang, L., Gibbs, R. A., Group, Nasonia Genome Working, Zdobnov, Evgeny, Gerlach, Daniel, Junier, Thomas, Muller, Jean, Beukeboom lab, and Van de Zande lab

Subjects
0106 biological sciences, Male, Wasp Venoms/chemistry/toxicity, Insecta, Insect Viruses/genetics, PARASITOLOGIA, VITRIPENNIS, Wasps, Genome, Insect, HYMENOPTERA, Wasp Venoms, Genes, Insect, 01 natural sciences, Genome, Nasonia vitripennis, HONEYBEE, PTEROMALIDAE, Wasps/ genetics/physiology, Arthropods/parasitology, Pteromalidae, DNA METHYLATION, ddc:616, Recombination, Genetic, 0303 health sciences, Multidisciplinary, biology, Ecology, WASP NASONIA, Biological Evolution, 3. Good health, Insects, DROSOPHILA, APIS-MELLIFERA, Insect Proteins, Wolbachia, Female, Wolbachia/genetics, Nasonia, GENES, Gene Transfer, Horizontal, Evolution, Genetic Speciation, Molecular Sequence Data, Quantitative Trait Loci, Insect Viruses, Quantitative trait locus, 010603 evolutionary biology, Article, Host-Parasite Interactions, 03 medical and health sciences, Genetic model, Animals, Life Science, Arthropods, 030304 developmental biology, fungi, Genetic Variation, Sequence Analysis, DNA, DNA Methylation, biology.organism_classification, SOCIAL INSECTS, Insects/genetics, Evolutionary biology, DNA Transposable Elements, Insect Proteins/genetics/metabolism
Abstract

Parasitoid Wasp Genomes Parasitoid wasps, which prey on and reproduce in host insect species, play important roles in plant herbivore interactions, and may provide valuable tools in the biological control of pest species. The Nasonia Genome Working Group (p. 343 ; see the news story by Pennisi ) presents the genome of three very closely related species: Nasonia vitripennis, N. giraulti , and N. longicornis . The findings document rapid evolution between a host and endosymbiont that can cause nuclear-cytoplasmic incompatibilities that may affect speciation.

Published
2010

9. The genome of the model beetle and pest tribolium castaneum

Author

Richards, S, Gibbs, RA, Weinstock, GM, Brown, SJ, Denell, R, Beeman, RW, Gibbs, R, Bucher, G, Friedrich, M, Grimmelikhuijzen, CJ, Klingler, M, Lorenzen, M, Roth, S, Schröder, R, Tautz, D, Zdobnov, EM, Muzny, D, Attaway, T, Bell, S, Buhay, CJ, Chandrabose, MN, Chavez, D, Clerk-Blankenburg, KP, Cree, A, Dao, M, Davis, C, Chacko, J, Dinh, H, Dugan-Rocha, S, Fowler, G, Garner, TT, Garnes, J, Gnirke, A, Hawes, A, Hernandez, J, Hines, S, Holder, M, Hume, J, Jhangiani, SN, Joshi, V, Khan, ZM, Jackson, L, Kovar, C, Kowis, A, Lee, S, Lewis, LR, Margolis, J, Morgan, M, Nazareth, LV, Nguyen, N, Okwuonu, G, Parker, D, Ruiz, SJ, Santibanez, J, Savard, J, Scherer, SE, Schneider, B, Sodergren, E, Vattahil, S, Villasana, D, White, CS, Wright, R, Park, Y, Lord, J, Oppert, B, Brown, S, Wang, L, Weinstock, G, Liu, Y, Worley, K, Elsik, CG, Reese, JT, Elhaik, E, Landan, G, Graur, D, Arensburger, P, Atkinson, P, Beidler, J, Demuth, JP, Drury, DW, Du, YZ, Fujiwara, H, Maselli, V, Osanai, M, Robertson, HM, Tu, Z, Wang, JJ, Wang, S, Song, H, Zhang, L, Werner, D, Stanke, M, Morgenstern, B, Solovyev, V, Kosarev, P, Brown, G, Chen, HC, Ermolaeva, O, Hlavina, W, Kapustin, Y, Kiryutin, B, Kitts, P, Maglott, D, Pruitt, K, Sapojnikov, V, Souvorov, A, Mackey, AJ, Waterhouse, RM, Wyder, S, Kriventseva, EV, Kadowaki, T, Bork, P, Aranda, M, Bao, R, Beermann, A, Berns, N, Bolognesi, R, Bonneton, F, Bopp, D, Butts, T, Chaumot, A, Denell, RE, Ferrier, DE, Gordon, CM, Jindra, M, Lan, Q, Lattorff, HM, Laudet, V, von Levetsow, C, Liu, Z, Lutz, R, Lynch, JA, da Fonseca, RN, Posnien, N, Reuter, R, Schinko, JB, Schmitt, C, Schoppmeier, M, Shippy, TD, Simonnet, F, Marques-Souza, H, Tomoyasu, Y, Trauner, J, Van der Zee, M, Vervoort, M, Wittkopp, N, Wimmer, EA, Yang, X, Jones, AK, Sattelle, DB, Ebert, PR, Nelson, D, Scott, JG, Muthukrishnan, S, Kramer, KJ, Arakane, Y, Zhu, Q, Hogenkamp, D, Dixit, R, Jiang, H, Zou, Z, Marshall, J, Elpidina, E, Vinokurov, K, Oppert, C, Evans, J, Lu, Z, Zhao, P, Sumathipala, N, Altincicek, B, Vilcinskas, A, Williams, M, Hultmark, D, Hetru, C, Hauser, F, Cazzamali, G, Williamson, M, Li, B, Tanaka, Y, Predel, R, Neupert, S, Schachtner, J, Verleyen, P, Raible, F, Walden, KK, Angeli, S, Forêt, S, Schuetz, S, Maleszka, R, Miller, SC, Grossmann, D, MDC Library, and Zdobnov, Evgeny

Subjects
0106 biological sciences, Repetitive Sequences, Nucleic Acid/genetics, Insecticides, Proteome, Genome, Insect, Cytochrome P-450 Enzyme System/genetics, Genes, Insect, Insect, Receptors, Odorant, 01 natural sciences, Genome, Receptors, G-Protein-Coupled, G-Protein-Coupled Receptors, Genome, Insect/ genetics, Oogenesis, Cytochrome P-450 Enzyme System, RNA interference, Odorant Receptors, Caenorhabditis elegans, Insect Genome, Phylogeny, media_common, Genetics, ddc:616, 0303 health sciences, Base Composition, Neurotransmitter Agents, Tribolium, Multidisciplinary, Neurotransmitter Agents/genetics, Receptors, Odorant/genetics, Vision, Ocular/genetics, Telomere, Insecticides/pharmacology, DNA Transposable Elements/genetics, Proteome/genetics, Genes, Insect/ genetics, Oogenesis/genetics, Taste, RNA Interference, Growth and Development, Drosophila melanogaster, animal structures, Nucleic Acid Repetitive Sequences, Taste/genetics, media_common.quotation_subject, 570 Life Sciences, Biology, 010603 evolutionary biology, 610 Medical Sciences, Medicine, 03 medical and health sciences, Humans, Insect Genes, Ocular Vision, Animals, Tribolium/classification/embryology/ genetics/physiology, Red flour beetle, Gene, Drosophila, Vision, Ocular, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, Growth and Development/genetics, Telomere/genetics, Body Patterning, fungi, biology.organism_classification, Body Patterning/genetics, Cardiovascular and Metabolic Diseases, DNA Transposable Elements, Receptors, G-Protein-Coupled/genetics
Abstract

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

Published
2008

10. Finding the missing honey bee genes: Lessons learned from a genome upgrade

Author

Elsik, CG, Worley, KC, Bennett, AK, Beye, M, Camara, F, Childers, CP, de Graaf, DC, Debyser, G, Deng, J, Devreese, B, Elhaik, E, Evans, JD, Foster, LJ, Graur, D, Guigo, R, Hoff, KJ, Holder, ME, Hudson, ME, Hunt, GJ, Jiang, H, Joshi, V, Khetani, RS, Kosarev, P, Kovar, CL, Ma, J, Maleszka, R, Moritz, RFA, Munoz-Torres, MC, Murphy, TD, Muzny, DM, Newsham, IF, Reese, JT, Robertson, HM, Robinson, GE, Rueppell, O, Solovyev, V, Stanke, M, Stolle, E, Tsuruda, JM, Vaerenbergh, MV, Waterhouse, RM, Weaver, DB, Whitfield, CW, Wu, Y, Zdobnov, EM, Zhang, L, Zhu, D, Gibbs, RA, Patil, S, Gubbala, S, Aqrawi, P, Arias, F, Bess, C, Blankenburg, KB, Brocchini, M, Buhay, C, Challis, D, Chang, K, Chen, D, Coleman, P, Drummond, J, English, A, Evani, U, Francisco, L, Fu, Q, Goodspeed, R, Haessly, TH, Hale, W, Han, H, Hu, Y, Jackson, L, Jakkamsetti, A, Jayaseelan, JC, Kakkar, N, Kalra, D, Kandadi, H, Lee, S, Li, H, Liu, Y, Macmil, S, Mandapat, CM, Mata, R, Mathew, T, Matskevitch, T, Munidasa, M, Nagaswamy, U, Najjar, R, Nguyen, N, Niu, J, Opheim, D, Palculict, T, Paul, S, Pellon, M, Perales, L, Pham, C, Pham, P, Pu, LL, Qi, S, Qu, J, Ren, Y, Elsik, CG, Worley, KC, Bennett, AK, Beye, M, Camara, F, Childers, CP, de Graaf, DC, Debyser, G, Deng, J, Devreese, B, Elhaik, E, Evans, JD, Foster, LJ, Graur, D, Guigo, R, Hoff, KJ, Holder, ME, Hudson, ME, Hunt, GJ, Jiang, H, Joshi, V, Khetani, RS, Kosarev, P, Kovar, CL, Ma, J, Maleszka, R, Moritz, RFA, Munoz-Torres, MC, Murphy, TD, Muzny, DM, Newsham, IF, Reese, JT, Robertson, HM, Robinson, GE, Rueppell, O, Solovyev, V, Stanke, M, Stolle, E, Tsuruda, JM, Vaerenbergh, MV, Waterhouse, RM, Weaver, DB, Whitfield, CW, Wu, Y, Zdobnov, EM, Zhang, L, Zhu, D, Gibbs, RA, Patil, S, Gubbala, S, Aqrawi, P, Arias, F, Bess, C, Blankenburg, KB, Brocchini, M, Buhay, C, Challis, D, Chang, K, Chen, D, Coleman, P, Drummond, J, English, A, Evani, U, Francisco, L, Fu, Q, Goodspeed, R, Haessly, TH, Hale, W, Han, H, Hu, Y, Jackson, L, Jakkamsetti, A, Jayaseelan, JC, Kakkar, N, Kalra, D, Kandadi, H, Lee, S, Li, H, Liu, Y, Macmil, S, Mandapat, CM, Mata, R, Mathew, T, Matskevitch, T, Munidasa, M, Nagaswamy, U, Najjar, R, Nguyen, N, Niu, J, Opheim, D, Palculict, T, Paul, S, Pellon, M, Perales, L, Pham, C, Pham, P, Pu, LL, Qi, S, Qu, J, and Ren, Y

Abstract

Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination. © 2014 Elsik et al.; licensee BioMed Central Ltd.

Published
2014

11. Neutral evolution of robustness in Drosophila microRNA precursors

Author

Price, N, Cartwright, R A, Sabath, N, Graur, D, Azevedo, R B R, Price, N, Cartwright, R A, Sabath, N, Graur, D, and Azevedo, R B R

Abstract

Mutational robustness describes the extent to which a phenotype remains unchanged in the face of mutations. Theory predicts that the strength of direct selection for mutational robustness is at most the magnitude of the rate of deleterious mutation. As far as nucleic acid sequences are concerned, only long sequences in organisms with high deleterious mutation rates and large population sizes are expected to evolve mutational robustness. Surprisingly, recent studies have concluded that molecules that meet none of these conditions--the microRNA precursors (pre-miRNAs) of multicellular eukaryotes--show signs of selection for mutational and/or environmental robustness. To resolve the apparent disagreement between theory and these studies, we have reconstructed the evolutionary history of Drosophila pre-miRNAs and compared the robustness of each sequence to that of its reconstructed ancestor. In addition, we "replayed the tape" of pre-miRNA evolution via simulation under different evolutionary assumptions and compared these alternative histories with the actual one. We found that Drosophila pre-miRNAs have evolved under strong purifying selection against changes in secondary structure. Contrary to earlier claims, there is no evidence that these RNAs have been shaped by either direct or congruent selection for any kind of robustness. Instead, the high robustness of Drosophila pre-miRNAs appears to be mostly intrinsic and likely a consequence of selection for functional structures.

Published
2011

20. Human genome meeting 2016

Author

Srivastava, A., Wang, Y., Huang, R., Skinner, C., Thompson, T., Pollard, L., Wood, T., Luo, F., Stevenson, R., Polimanti, R., Gelernter, J., Lin, X., Lim, I., Wu, Y., Teh, A., Chen, L., Aris, I., Soh, S., Tint, M., MacIsaac, J., Yap, F., Kwek, K., Saw, S., Kobor, M., Meaney, M., Godfrey, K., Chong, Y., Holbrook, J., Lee, Y., Gluckman, P., Karnani, N., Kapoor, A., Lee, D., Chakravarti, A., Maercker, C., Graf, F., Boutros, M., Stamoulis, G., Santoni, F., Makrythanasis, P., Letourneau, A., Guipponi, M., Panousis, N., Garieri, M., Ribaux, P., Falconnet, E., Borel, C., Antonarakis, S., Kumar, S., Curran, J., Blangero, J., Chatterjee, S., Kapoor, A., Akiyama, J., Auer, D., Berrios, C., Pennacchio, L., Chakravarti, A., Donti, T., Cappuccio, G., Miller, M., Atwal, P., Kennedy, A., Cardon, A., Bacino, C., Emrick, L., Hertecant, J., Baumer, F., Porter, B., Bainbridge, M., Bonnen, P., Graham, B., Sutton, R., Sun, Q., Elsea, S., Hu, Z., Wang, P., Zhu, Y., Zhao, J., Xiong, M., Bennett, David, Hidalgo-Miranda, A., Romero-Cordoba, S., Rodriguez-Cuevas, S., Rebollar-Vega, R., Tagliabue, E., Iorio, M., D’Ippolito, E., Baroni, S., Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itoh, M., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A., Semple, C., Rosenthal, E., Shirts, B., Amendola, L., Gallego, C., Horike-Pyne, M., Burt, A., Robertson, P., Beyers, P., Nefcy, C., Veenstra, D., Hisama, F., Bennett, R., Dorschner, M., Nickerson, D., Smith, J., Patterson, K., Crosslin, D., Nassir, R., Zubair, N., Harrison, T., Peters, U., Jarvik, G., Menghi, F., Inaki, K., Woo, X., Kumar, P., Grzeda, K., Malhotra, A., Kim, H., Ucar, D., Shreckengast, P., Karuturi, K., Keck, J., Chuang, J., Liu, E., Ji, B., Tyler, A., Ananda, G., Carter, G., Nikbakht, H., Montagne, M., Zeinieh, M., Harutyunyan, A., Mcconechy, M., Jabado, N., Lavigne, P., Majewski, J., Goldstein, J., Overman, M., Varadhachary, G., Shroff, R., Wolff, R., Javle, M., Futreal, A., Fogelman, D., Bravo, L., Fajardo, W., Gomez, H., Castaneda, C., Rolfo, C., Pinto, J., Akdemir, K., Chin, L., Futreal, A., Patterson, S., Statz, C., Mockus, S., Nikolaev, S., Bonilla, X., Parmentier, L., King, B., Bezrukov, F., Kaya, G., Zoete, V., Seplyarskiy, V., Sharpe, H., McKee, T., Letourneau, A., Ribaux, P., Popadin, K., Basset-Seguin, N., Chaabene, R., Santoni, F., Andrianova, M., Guipponi, M., Garieri, M., Verdan, C., Grosdemange, K., Sumara, O., Eilers, M., Aifantis, I., Michielin, O., de Sauvage, F., Antonarakis, S., Likhitrattanapisal, S., Lincoln, S., Kurian, A., Desmond, A., Yang, S., Kobayashi, Y., Ford, J., Ellisen, L., Peters, T., Alvarez, K., Hollingsworth, E., Lopez-Terrada, D., Hastie, A., Dzakula, Z., Pang, A., Lam, E., Anantharaman, T., Saghbini, M., Cao, H., Gonzaga-Jauregui, C., Ma, L., King, A., Rosenzweig, E., Krishnan, U., Reid, J., Overton, J., Dewey, F., Chung, W., Small, K., DeLuca, A., Cremers, F., Lewis, R., Puech, V., Bakall, B., Silva-Garcia, R., Rohrschneider, K., Leys, M., Shaya, F., Stone, E., Sobreira, N., Schiettecatte, F., Ling, H., Pugh, E., Witmer, D., Hetrick, K., Zhang, P., Doheny, K., Valle, D., Hamosh, A., Jhangiani, S., Akdemir, Z., Bainbridge, M., Charng, W., Wiszniewski, W., Gambin, T., Karaca, E., Bayram, Y., Eldomery, M., Posey, J., Doddapaneni, H., Hu, J., Sutton, V., Muzny, D., Boerwinkle, E., Valle, D., Lupski, J., Gibbs, R., Shekar, S., Salerno, W., English, A., Mangubat, A., Bruestle, J., Thorogood, A., Knoppers, B., Takahashi, H., Nitta, K., Kozhuharova, A., Suzuki, A., Sharma, H., Cotella, D., Santoro, C., Zucchelli, S., Gustincich, S., Carninci, P., Mulvihill, J., Baynam, G., Gahl, W., Groft, S., Kosaki, K., Lasko, P., Melegh, B., Taruscio, D., Ghosh, R., Plon, S., Scherer, S., Qin, X., Sanghvi, R., Walker, K., Chiang, T., Muzny, D., Wang, L., Black, J., Boerwinkle, E., Weinshilboum, R., Gibbs, R., Karpinets, T., Calderone, T., Wani, K., Yu, X., Creasy, C., Haymaker, C., Forget, M., Nanda, V., Roszik, J., Wargo, J., Haydu, L., Song, X., Lazar, A., Gershenwald, J., Davies, M., Bernatchez, C., Zhang, J., Futreal, A., Woodman, S., Chesler, E., Reynolds, T., Bubier, J., Phillips, C., Langston, M., Baker, E., Xiong, M., Ma, L., Lin, N., Amos, C., Lin, N., Wang, P., Zhu, Y., Zhao, J., Calhoun, V., Xiong, M., Dobretsberger, O., Egger, M., Leimgruber, F., Sadedin, S., Oshlack, A., Antonio, V., Ono, N., Ahmed, Z., Bolisetty, M., Zeeshan, S., Anguiano, E., Ucar, D., Sarkar, A., Nandineni, M., Zeng, C., Shao, J., Cao, H., Hastie, A., Pang, A., Lam, E., Liang, T., Pham, K., Saghbini, M., Dzakula, Z., Chee-Wei, Y., Dongsheng, L., Lai-Ping, W., Lian, D., Hee, R., Yunus, Y., Aghakhanian, F., Mokhtar, S., Lok-Yung, C., Bhak, J., Phipps, M., Shuhua, X., Yik-Ying, T., Kumar, V., Boon-Peng, H., Campbell, I., Young, M., James, P., Rain, M., Mohammad, G., Kukreti, R., Pasha, Q., Akilzhanova, A., Guelly, C., Abilova, Z., Rakhimova, S., Akhmetova, A., Kairov, U., Trajanoski, S., Zhumadilov, Z., Bekbossynova, M., Schumacher, C., Sandhu, S., Harkins, T., Makarov, V., Doddapaneni, H., Glenn, R., Momin, Z., Dilrukshi, B., Chao, H., Meng, Q., Gudenkauf, B., Kshitij, R., Jayaseelan, J., Nessner, C., Lee, S., Blankenberg, K., Lewis, L., Hu, J., Han, Y., Dinh, H., Jireh, S., Walker, K., Boerwinkle, E., Muzny, D., Gibbs, R., Hu, J., Walker, K., Buhay, C., Liu, X., Wang, Q., Sanghvi, R., Doddapaneni, H., Ding, Y., Veeraraghavan, N., Yang, Y., Boerwinkle, E., Beaudet, A., Eng, C., Muzny, D., Gibbs, R., Worley, K., Liu, Y., Hughes, D., Murali, S., Harris, R., English, A., Qin, X., Hampton, O., Larsen, P., Beck, C., Han, Y., Wang, M., Doddapaneni, H., Kovar, C., Salerno, W., Yoder, A., Richards, S., Rogers, J., Lupski, J., Muzny, D., Gibbs, R., Meng, Q., Bainbridge, M., Wang, M., Doddapaneni, H., Han, Y., Muzny, D., Gibbs, R., Harris, R., Raveenedran, M., Xue, C., Dahdouli, M., Cox, L., Fan, G., Ferguson, B., Hovarth, J., Johnson, Z., Kanthaswamy, S., Kubisch, M., Platt, M., Smith, D., Vallender, E., Wiseman, R., Liu, X., Below, J., Muzny, D., Gibbs, R., Yu, F., Rogers, J., Lin, J., Zhang, Y., Ouyang, Z., Moore, A., Wang, Z., Hofmann, J., Purdue, M., Stolzenberg-Solomon, R., Weinstein, S., Albanes, D., Liu, C., Cheng, W., Lin, T., Lan, Q., Rothman, N., Berndt, S., Chen, E., Bahrami, H., Khoshzaban, A., Keshal, S., Bahrami, H., Khoshzaban, A., Keshal, S., Alharbi, K., Zhalbinova, M., Akilzhanova, A., Rakhimova, S., Bekbosynova, M., Myrzakhmetova, S., Matar, M., Mili, N., Molinari, R., Ma, Y., Guerrier, S., Elhawary, N., Tayeb, M., Bogari, N., Qotb, N., McClymont, S., Hook, P., Goff, L., McCallion, A., Kong, Y., Charette, J., Hicks, W., Naggert, J., Zhao, L., Nishina, P., Edrees, B., Athar, M., Al-Allaf, F., Taher, M., Khan, W., Bouazzaoui, A., Harbi, N., Safar, R., Al-Edressi, H., Anazi, A., Altayeb, N., Ahmed, M., Alansary, K., Abduljaleel, Z., Kratz, A., Beguin, P., Poulain, S., Kaneko, M., Takahiko, C., Matsunaga, A., Kato, S., Suzuki, A., Bertin, N., Lassmann, T., Vigot, R., Carninci, P., Plessy, C., Launey, T., Graur, D., Lee, D., Kapoor, A., Chakravarti, A., Friis-Nielsen, J., Izarzugaza, J., Brunak, S., Chakraborty, A., Basak, J., Mukhopadhyay, A., Soibam, B., Das, D., Biswas, N., Das, S., Sarkar, S., Maitra, A., Panda, C., Majumder, P., Morsy, H., Gaballah, A., Samir, M., Shamseya, M., Mahrous, H., Ghazal, A., Arafat, W., Hashish, M., Gruber, J., Jaeger, N., Snyder, M., Patel, K., Bowman, S., Davis, T., Kraushaar, D., Emerman, A., Russello, S., Henig, N., Hendrickson, C., Zhang, K., Rodriguez-Dorantes, M., Cruz-Hernandez, C., Garcia-Tobilla, C., Solorzano-Rosales, S., Jäger, N., Chen, J., Haile, R., Hitchins, M., Brooks, J., Snyder, M., Jiménez-Morales, S., Ramírez, M., Nuñez, J., Bekker, V., Leal, Y., Jiménez, E., Medina, A., Hidalgo, A., Mejía, J., Halytskiy, V., Naggert, J., Collin, G., DeMauro, K., Hanusek, R., Nishina, P., Belhassa, K., Belhassan, K., Bouguenouch, L., Samri, I., Sayel, H., moufid, FZ., El Bouchikhi, I., Trhanint, S., Hamdaoui, H., Elotmani, I., Khtiri, I., Kettani, O., Quibibo, L., Ahagoud, M., Abbassi, M., Ouldim, K., Marusin, A., Kornetov, A., Swarovskaya, M., Vagaiceva, K., Stepanov, V., De La Paz, E., Sy, R., Nevado, J., Reganit, P., Santos, L., Magno, J., Punzalan, F., Ona, D., Llanes, E., Santos-Cortes, R., Tiongco, R., Aherrera, J., Abrahan, L., Pagauitan-Alan, P., Morelli, K., Domire, J., Pyne, N., Harper, S., Burgess, R., Zhalbinova, M., Akilzhanova, A., Rakhimova, S., Bekbosynova, M., Myrzakhmetova, S., Gari, M., Dallol, A., Alsehli, H., Gari, A., Gari, M., Abuzenadah, A., Thomas, M., Sukhai, M., Garg, S., Misyura, M., Zhang, T., Schuh, A., Stockley, T., Kamel-Reid, S., Sherry, S., Xiao, C., Slotta, D., Rodarmer, K., Feolo, M., Kimelman, M., Godynskiy, G., O’Sullivan, C., Yaschenko, E., Xiao, C., Yaschenko, E., Sherry, S., Rangel-Escareño, C., Rueda-Zarate, H., Tayubi, I., Mohammed, R., Ahmed, I., Ahmed, T., Seth, S., Amin, S., Song, X., Mao, X., Sun, H., Verhaak, R., Futreal, A., Zhang, J., Whiite, S., Chiang, T., English, A., Farek, J., Kahn, Z., Salerno, W., Veeraraghavan, N., Boerwinkle, E., Gibbs, R., Kasukawa, T., Lizio, M., Harshbarger, J., Hisashi, S., Severin, J., Imad, A., Sahin, S., Freeman, T., Baillie, K., Sandelin, A., Carninci, P., Forrest, A., Kawaji, H., Salerno, W., English, A., Shekar, S., Mangubat, A., Bruestle, J., Boerwinkle, E., Gibbs, R., Salem, A., Ali, M., Ibrahim, A., Ibrahim, M., Barrera, H., Garza, L., Torres, J., Barajas, V., Ulloa-Aguirre, A., Kershenobich, D., Mortaji, Shahroj, Guizar, Pedro, Loera, Eliezer, Moreno, Karen, De León, Adriana, Monsiváis, Daniela, Gómez, Jackeline, Cardiel, Raquel, Fernandez-Lopez, J., Bonifaz-Peña, V., Rangel-Escareño, C., Hidalgo-Miranda, A., Contreras, A., Polfus, L., Wang, X., Philip, V., Carter, G., Abuzenadah, A., Gari, M., Turki, R., Dallol, A., Uyar, A., Kaygun, A., Zaman, S., Marquez, E., George, J., Ucar, D., Hendrickson, C., Emerman, A., Kraushaar, D., Bowman, S., Henig, N., Davis, T., Russello, S., Patel, K., Starr, D., Baird, M., Kirkpatrick, B., Sheets, K., Nitsche, R., Prieto-Lafuente, L., Landrum, M., Lee, J., Rubinstein, W., Maglott, D., Thavanati, P., de Dios, A., Hernandez, R., Aldrate, M., Mejia, M., Kanala, K., Abduljaleel, Z., Khan, W., Al-Allaf, F., Athar, M., Taher, M., Shahzad, N., Bouazzaoui, A., Huber, E., Dan, A., Al-Allaf, F., Herr, W., Sprotte, G., Köstler, J., Hiergeist, A., Gessner, A., Andreesen, R., Holler, E., Al-Allaf, F., Alashwal, A., Abduljaleel, Z., Taher, M., Bouazzaoui, A., Abalkhail, H., Al-Allaf, A., Bamardadh, R., Athar, M., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Al-allaf, F., Mohiuddin, M., Zainularifeen, A., Mohammed, A., Abalkhail, H., Owaidah, T., and Bouazzaoui, A.

Abstract

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3rd7mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLRgene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Published
2016
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26. PROCEEDINGS OF THE THIRTY-NINTH MEETING OF THE ZOOLOGICAL SOCIETY OF ISRAEL.

Author

Graur, D.

Subjects
*ZOOLOGY, *SPERM competition, *SERRANIDAE, *GENE expression, GASTROPODA anatomy
Abstract

Presents abstracts of several studies presented at the 39th meeting of the Zoological Society of Israel held at the Tel Aviv University on December 1, 2002. "Variation in Aggregation Behavior and Anatomy Resulting From Differences in Degree of Sperm Competition in Groupers (Epinephelinae, Serranidae)," by A. Aronov and M. Goren; "Establishment of the Lessepsian Migrant Cellana Rota (Gastropoda) in the Mediterranean Sea and Its Demographic Effects on the Local Species Patella Caerulea," by I. Atad, T. Feldstein, A. Abelson and O. Mokady; "Unique Expression of the sPer1 Gene in Nocturnal Blind Subterranean Mole Rats," by A. Avivi, H. Oster, A. Joel, U. Albrecht and E. Nevo.

Published
2003
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29. Is the guinea-pig a rodent?

Author

Graur, D. and Hide, W.A.

Subjects
*ANIMALS
Abstract

Infers the taxonomic position of the guinea-pig. Analyzes the phylogeny of protein sequence data from the caviomorphs, myomorphs, the primates, the artiodactyls and some outgroup species such as marsupials, birds, or toads.

Published
1991
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30. Molecular evidence for the inclusion of cetaceans within the order Artiodactyla.

Author

Graur, D and Higgins, D G

Abstract

The transition in the cetaceans from terrestrial life to a fully aquatic existence is one of the most enduring evolutionary mysteries. Resolving the phylogenetic relationships between Cetacea and the other orders of eutherian mammals may provide us with important clues to the origin of whales and may help us date the evolutionary transition to aquatic life. Previous paleontological and molecular evidence has indicated that cetaceans and artiodactyls constitute a natural clade within subclass Eutheria. Our present phylogenetic analyses of protein and mitochondrial DNA sequence data indicate that cetaceans are not only intimately related to the artiodactyls; they are in fact deeply nested within the artiodactyl phylogenetic tree; i.e., they are more closely related to the members of one suborder of artiodactyls, the Ruminantia, than either ruminants or cetaceans are to members of the other two artiodactyl suborders: Suiformes and Tylopoda. On the basis of the rate of evolution of mitochondrial DNA sequences and using paleontological reference dates for calibration, we estimate that the whale lineage has branched off a protoruminant lineage < 50 Mya. By implication, the cetacean transition to aquatic life is inferred to be a relatively recent evolutionary event.

Published
1994
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31. An unusual histone H4 gene from Tilapia niloticaexhibiting characteristics of both a replication-dependent histone and a basal-expression histone: evolutionary considerations

Author

Englander, E., Moav, B., Tabachnik, M., Shuali, Y., and Graur, D.

Abstract

The nucleotide sequence of a histone H4 gene from the fish Tilapia niloticawas determined. The deduced amino acid sequence is identical to that of H4 from the trout, Salmo gairdnerii. The 3′ untranslated region of the Tilapiagene exhibits a unique combination of structural features each of which is usually associated with either a replication-dependent histone or a basal-expression histone, but not with both. The direction of nucleotide substitutions in the Tilapiaand Salmolineages was inferred. The Tilapiagene was found to evolve faster and to exhibit a more biased pattern of substitution and codon usage than its Salmohomologue. This combination of features cannot be explained by either mutation or purifying selection. The rapid embryonic development of Tilapiaprompts us to suggest that the molecular evolution of the histone H4 gene is driven by fixation of advantageous synonymous mutations.

Published
1993
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33. Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer.

Author

Landan, G, Cohen, G, Aharonowitz, Y, Shuali, Y, Graur, D, and Shiffman, D

Abstract

The isopenicillin N synthase genes from three fungal species, three Gram-positive species, and one Gram-negative bacterial species share an unusually high sequence similarity. A phylogenetic analysis was carried out to determine which type of evolutionary scenario best accounts for this similarity. The most plausible scenario is one in which a horizontal gene-transfer event, from the prokaryotes to the eukaryotes, occurred at a time close to the divergence between the Gram-positive and the Gram-negative bacteria.

Published
1990
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34. Human genome meeting 2016

Author

Srivastava, A. K., Wang, Y., Huang, R., Skinner, C., Thompson, T., Pollard, L., Wood, T., Luo, F., Stevenson, R., Polimanti, R., Gelernter, J., Lin, X., Lim, I. Y., Wu, Y., Teh, A. L., Chen, L., Aris, I. M., Soh, S. E., Tint, M. T., MacIsaac, J. L., Yap, F., Kwek, K., Saw, S. M., Kobor, M. S., Meaney, M. J., Godfrey, K. M., Chong, Y. S., Holbrook, J. D., Lee, Y. S., Gluckman, P. D., Karnani, N., Kapoor, A., Lee, D., Chakravarti, A., Maercker, C., Graf, F., Boutros, M., Stamoulis, G., Santoni, F., Makrythanasis, P., Letourneau, A., Guipponi, M., Panousis, N., Garieri, M., Ribaux, P., Falconnet, E., Borel, C., Antonarakis, S. E., Kumar, S., Curran, J., Blangero, J., Chatterjee, S., Akiyama, J., Auer, D., Berrios, C., Pennacchio, L., Donti, T. R., Cappuccio, G., Miller, M., Atwal, P., Kennedy, A., Cardon, A., Bacino, C., Emrick, L., Hertecant, J., Baumer, F., Porter, B., Bainbridge, M., Bonnen, P., Graham, B., Sutton, R., Sun, Q., Elsea, S., Hu, Z., Wang, P., Zhu, Y., Zhao, J., Xiong, M., Bennett, David A., Hidalgo-Miranda, A., Romero-Cordoba, S., Rodriguez-Cuevas, S., Rebollar-Vega, R., Tagliabue, E., Iorio, M., D’Ippolito, E., Baroni, S., Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itoh, M., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Semple, C. A., Rosenthal, E. A., Shirts, B., Amendola, L., Gallego, C., Horike-Pyne, M., Burt, A., Robertson, P., Beyers, P., Nefcy, C., Veenstra, D., Hisama, F., Bennett, R., Dorschner, M., Nickerson, D., Smith, J., Patterson, K., Crosslin, D., Nassir, R., Zubair, N., Harrison, T., Peters, U., Jarvik, G., Menghi, F., Inaki, K., Woo, X., Kumar, P., Grzeda, K., Malhotra, A., Kim, H., Ucar, D., Shreckengast, P., Karuturi, K., Keck, J., Chuang, J., Liu, E. T., Ji, B., Tyler, A., Ananda, G., Carter, G., Nikbakht, H., Montagne, M., Zeinieh, M., Harutyunyan, A., Mcconechy, M., Jabado, N., Lavigne, P., Majewski, J., Goldstein, J. B., Overman, M., Varadhachary, G., Shroff, R., Wolff, R., Javle, M., Futreal, A., Fogelman, D., Bravo, L., Fajardo, W., Gomez, H., Castaneda, C., Rolfo, C., Pinto, J. A., Akdemir, K. C., Chin, L., Patterson, S., Statz, C., Mockus, S., Nikolaev, S. N., Bonilla, X. I., Parmentier, L., King, B., Bezrukov, F., Kaya, G., Zoete, V., Seplyarskiy, V., Sharpe, H., McKee, T., Popadin, K., Basset-Seguin, N., Chaabene, R. Ben, Andrianova, M., Verdan, C., Grosdemange, K., Sumara, O., Eilers, M., Aifantis, I., Michielin, O., de Sauvage, F., Antonarakis, S., Likhitrattanapisal, S., Lincoln, S., Kurian, A., Desmond, A., Yang, S., Kobayashi, Y., Ford, J., Ellisen, L., Peters, T. L., Alvarez, K. R., Hollingsworth, E. F., Lopez-Terrada, D. H., Hastie, A., Dzakula, Z., Pang, A. W., Lam, E. T., Anantharaman, T., Saghbini, M., Cao, H., Gonzaga-Jauregui, C., Ma, L., King, A., Rosenzweig, E. Berman, Krishnan, U., Reid, J. G., Overton, J. D., Dewey, F., Chung, W. K., Small, K., DeLuca, A., Cremers, F., Lewis, R. A., Puech, V., Bakall, B., Silva-Garcia, R., Rohrschneider, K., Leys, M., Shaya, F. S., Stone, E., Sobreira, N. L., Schiettecatte, F., Ling, H., Pugh, E., Witmer, D., Hetrick, K., Zhang, P., Doheny, K., Valle, D., Hamosh, A., Jhangiani, S. N., Akdemir, Z. Coban, Bainbridge, M. N., Charng, W., Wiszniewski, W., Gambin, T., Karaca, E., Bayram, Y., Eldomery, M. K., Posey, J., Doddapaneni, H., Hu, J., Sutton, V. R., Muzny, D. M., Boerwinkle, E. A., Lupski, J. R., Gibbs, R. A., Shekar, S., Salerno, W., English, A., Mangubat, A., Bruestle, J., Thorogood, A., Knoppers, B. M., Takahashi, H., Nitta, K. R., Kozhuharova, A., Suzuki, A. M., Sharma, H., Cotella, D., Santoro, C., Zucchelli, S., Gustincich, S., Mulvihill, J. J., Baynam, G., Gahl, W., Groft, S. C., Kosaki, K., Lasko, P., Melegh, B., Taruscio, D., Ghosh, R., Plon, S., Scherer, S., Qin, X., Sanghvi, R., Walker, K., Chiang, T., Muzny, D., Wang, L., Black, J., Boerwinkle, E., Weinshilboum, R., Gibbs, R., Karpinets, T., Calderone, T., Wani, K., Yu, X., Creasy, C., Haymaker, C., Forget, M., Nanda, V., Roszik, J., Wargo, J., Haydu, L., Song, X., Lazar, A., Gershenwald, J., Davies, M., Bernatchez, C., Zhang, J., Woodman, S., Chesler, E. J., Reynolds, T., Bubier, J. A., Phillips, C., Langston, M. A., Baker, E. J., Lin, N., Amos, C., Calhoun, V., Dobretsberger, O., Egger, M., Leimgruber, F., Sadedin, S., Oshlack, A., Antonio, V. A. A., Ono, N., Ahmed, Z., Bolisetty, M., Zeeshan, S., Anguiano, E., Sarkar, A., Nandineni, M. R., Zeng, C., Shao, J., Liang, T., Pham, K., Chee-Wei, Y., Dongsheng, L., Lai-Ping, W., Lian, D., Hee, R. O. Twee, Yunus, Y., Aghakhanian, F., Mokhtar, S. S., Lok-Yung, C. V., Bhak, J., Phipps, M., Shuhua, X., Yik-Ying, T., Kumar, V., Boon-Peng, H., Campbell, I., Young, M. -A., James, P., Rain, M., Mohammad, G., Kukreti, R., Pasha, Q., Akilzhanova, A. R., Guelly, C., Abilova, Z., Rakhimova, S., Akhmetova, A., Kairov, U., Trajanoski, S., Zhumadilov, Z., Bekbossynova, M., Schumacher, C., Sandhu, S., Harkins, T., Makarov, V., Glenn, R., Momin, Z., Dilrukshi, B., Chao, H., Meng, Q., Gudenkauf, B., Kshitij, R., Jayaseelan, J., Nessner, C., Lee, S., Blankenberg, K., Lewis, L., Han, Y., Dinh, H., Jireh, S., Buhay, C., Liu, X., Wang, Q., Ding, Y., Veeraraghavan, N., Yang, Y., Beaudet, A. L., Eng, C. M., Worley, K. C. C., Liu, Y., Hughes, D. S. T., Murali, S. C., Harris, R. A., English, A. C., Hampton, O. A., Larsen, P., Beck, C., Wang, M., Kovar, C. L., Salerno, W. J., Yoder, A., Richards, S., Rogers, J., Raveenedran, M., Xue, C., Dahdouli, M., Cox, L., Fan, G., Ferguson, B., Hovarth, J., Johnson, Z., Kanthaswamy, S., Kubisch, M., Platt, M., Smith, D., Vallender, E., Wiseman, R., Below, J., Yu, F., Lin, J., Zhang, Y., Ouyang, Z., Moore, A., Wang, Z., Hofmann, J., Purdue, M., Stolzenberg-Solomon, R., Weinstein, S., Albanes, D., Liu, C. S., Cheng, W. L., Lin, T. T., Lan, Q., Rothman, N., Berndt, S., Chen, E. S., Bahrami, H., Khoshzaban, A., Keshal, S. Heidari, Alharbi, K. K. R., Zhalbinova, M., Akilzhanova, A., Bekbosynova, M., Myrzakhmetova, S., Matar, M., Mili, N., Molinari, R., Ma, Y., Guerrier, S., Elhawary, N., Tayeb, M., Bogari, N., Qotb, N., McClymont, S. A., Hook, P. W., Goff, L. A., McCallion, A., Kong, Y., Charette, J. R., Hicks, W. L., Naggert, J. K., Zhao, L., Nishina, P. M., Edrees, B. M., Athar, M., Al-Allaf, F. A., Taher, M. M., Khan, W., Bouazzaoui, A., Harbi, N. A., Safar, R., Al-Edressi, H., Anazi, A., Altayeb, N., Ahmed, M. A., Alansary, K., Abduljaleel, Z., Kratz, A., Beguin, P., Poulain, S., Kaneko, M., Takahiko, C., Matsunaga, A., Kato, S., Bertin, N., Vigot, R., Plessy, C., Launey, T., Graur, D., Friis-Nielsen, J., Izarzugaza, J. M., Brunak, S., Chakraborty, A., Basak, J., Mukhopadhyay, A., Soibam, B. S., Das, D., Biswas, N., Das, S., Sarkar, S., Maitra, A., Panda, C., Majumder, P., Morsy, H., Gaballah, A., Samir, M., Shamseya, M., Mahrous, H., Ghazal, A., Arafat, W., Hashish, M., Gruber, J. J., Jaeger, N., Snyder, M., Patel, K., Bowman, S., Davis, T., Kraushaar, D., Emerman, A., Russello, S., Henig, N., Hendrickson, C., Zhang, K., Rodriguez-Dorantes, M., Cruz-Hernandez, C. D., Garcia-Tobilla, C. D. P., Solorzano-Rosales, S., Jäger, N., Chen, J., Haile, R., Hitchins, M., Brooks, J. D., Jiménez-Morales, S., Ramírez, M., Nuñez, J., Bekker, V., Leal, Y., Jiménez, E., Medina, A., Hidalgo, A., Mejía, J., Halytskiy, V., Naggert, J., Collin, G. B., DeMauro, K., Hanusek, R., Belhassa, K., Belhassan, K., Bouguenouch, L., Samri, I., Sayel, H., moufid, FZ., El Bouchikhi, I., Trhanint, S., Hamdaoui, H., Elotmani, I., Khtiri, I., Kettani, O., Quibibo, L., Ahagoud, M., Abbassi, M., Ouldim, K., Marusin, A. V., Kornetov, A. N., Swarovskaya, M., Vagaiceva, K., Stepanov, V., De La Paz, E. M. Cutiongco, Sy, R., Nevado, J., Reganit, P., Santos, L., Magno, J. D., Punzalan, F. E., Ona, D., Llanes, E., Santos-Cortes, R. L., Tiongco, R., Aherrera, J., Abrahan, L., Pagauitan-Alan, P., Morelli, K. H., Domire, J. S., Pyne, N., Harper, S., Burgess, R., Gari, M. A., Dallol, A., Alsehli, H., Gari, A., Gari, M., Abuzenadah, A., Thomas, M., Sukhai, M., Garg, S., Misyura, M., Zhang, T., Schuh, A., Stockley, T., Kamel-Reid, S., Sherry, S., Xiao, C., Slotta, D., Rodarmer, K., Feolo, M., Kimelman, M., Godynskiy, G., O’Sullivan, C., Yaschenko, E., Rangel-Escareño, C., Rueda-Zarate, H., Tayubi, I. A., Mohammed, R., Ahmed, I., Ahmed, T., Seth, S., Amin, S., Mao, X., Sun, H., Verhaak, R. G., Whiite, S. J., Farek, J., Kahn, Z., Kasukawa, T., Lizio, M., Harshbarger, J., Hisashi, S., Severin, J., Imad, A., Sahin, S., Freeman, T. C., Baillie, K., Shekar, S. N., Salem, A. H., Ali, M., Ibrahim, A., Ibrahim, M., Barrera, H. A., Garza, L., Torres, J. A., Barajas, V., Ulloa-Aguirre, A., Kershenobich, D., Mortaji, Shahroj, Guizar, Pedro, Loera, Eliezer, Moreno, Karen, De León, Adriana, Monsiváis, Daniela, Gómez, Jackeline, Cardiel, Raquel, Fernandez-Lopez, J. C., Bonifaz-Peña, V., Contreras, A. V., Polfus, L., Wang, X., Philip, V., Abuzenadah, A. A., Turki, R., Uyar, A., Kaygun, A., Zaman, S., Marquez, E., George, J., Hendrickson, C. L., Starr, D. B., Baird, M., Kirkpatrick, B., Sheets, K., Nitsche, R., Prieto-Lafuente, L., Landrum, M., Lee, J., Rubinstein, W., Maglott, D., Thavanati, P. K. R., de Dios, A. Escoto, Hernandez, R. E. Navarro, Aldrate, M. E. Aguilar, Mejia, M. R. Ruiz, Kanala, K. R. R., Shahzad, N., Huber, E., Dan, A., Herr, W., Sprotte, G., Köstler, J., Hiergeist, A., Gessner, A., Andreesen, R., Holler, E., Al-Allaf, F., Alashwal, A., Taher, M., Abalkhail, H., Al-Allaf, A., Bamardadh, R., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Kobets, M. N., Al-allaf, F. A., Mohiuddin, M. T., Zainularifeen, A., Mohammed, A., and Owaidah, T.

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37. The multiple personalities of Watson and Crick strands

Author

Graur Dan and Cartwright Reed A

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.

Published
2011
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38. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve

Author

Josić Krešimir, Graur Dan, and Elhaik Eran

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as S = a2+ c2+t2+g2, where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than 1/3 for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius r = 1/ contains almost all points corresponding to various genomes, implying that S

Published
2010
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39. A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives

Author

Price Nicholas, Sabath Niv, and Graur Dan

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract The Israeli acute paralysis virus (IAPV) is a honeybee-infecting virus that was found to be associated with colony collapse disorder. The IAPV genome contains two genes encoding a structural and a nonstructural polyprotein. We applied a recently developed method for the estimation of selection in overlapping genes to detect purifying selection and, hence, functionality. We provide evolutionary evidence for the existence of a functional overlapping gene, which is translated in the +1 reading frame of the structural polyprotein gene. Conserved orthologs of this putative gene, which we provisionally call pog (predicted overlapping gene), were also found in the genomes of a monophyletic clade of dicistroviruses that includes IAPV, acute bee paralysis virus, Kashmir bee virus, and Solenopsis invicta (red imported fire ant) virus 1.

Published
2009
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40. Same-strand overlapping genes in bacteria: compositional determinants of phase bias

Author

Landan Giddy, Graur Dan, and Sabath Niv

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Same-strand overlapping genes may occur in frameshifts of one (phase 1) or two nucleotides (phase 2). In previous studies of bacterial genomes, long phase-1 overlaps were found to be more numerous than long phase-2 overlaps. This bias was explained by either genomic location or an unspecified selection advantage. Models that focused on the ability of the two genes to evolve independently did not predict this phase bias. Here, we propose that a purely compositional model explains the phase bias in a more parsimonious manner. Same-strand overlapping genes may arise through either a mutation at the termination codon of the upstream gene or a mutation at the initiation codon of the downstream gene. We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes. Results We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in the two phases. We show that the frequencies of start codons in each of the two phases, and, hence, the potential for the creation of overlapping genes, are determined by a universal amino-acid frequency and species-specific codon usage, leading to a correlation between long phase-1 overlaps and genomic GC content. Conclusion Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes. Reviewers This article was reviewed by Bill Martin, Itai Yanai, and Mikhail Gelfand.

Published
2008
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43. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author

Amro Hamdoun, Virginia Brockton, Huyen Dinh, Qiang Tu, Richard O. Hynes, Maria Ina Arnone, Wratko Hlavina, L. Courtney Smith, Mariano A. Loza, David R. Burgess, Matthew P. Hoffman, Florian Raible, Qiu Autumn Yuan, Geoffrey Okwuonu, Mark Y. Tong, Jennifer Hume, Donna Maglott, Manisha Goel, Olivier Fedrigo, Manuel L. Gonzalez-Garay, Celina E. Juliano, Judith Hernandez, Gary M. Wessel, William F. Marzluff, Audrey J. Majeske, Christian Gache, Louise Duloquin, Xingzhi Song, François Lapraz, Fowler J, Alexandre Souvorov, Jared V. Goldstone, Georgia Panopoulou, Sandra Hines, Kyle M. Judkins, Clay Davis, Christine G. Elsik, Paul Kitts, Mariano Loza-Coll, Greg Wray, Taku Hibino, Eric Röttinger, Allison M. Churcher, Annamaria Locascio, Arcady Mushegian, Masashi Kinukawa, Anna Reade, Katherine M. Buckley, I. R. Gibbons, Bert Gold, Aleksandar Milosavljevic, David Epel, Victor D. Vacquier, Ling Ling Pu, Vincenzo Cavalieri, Erin L. Allgood, Lan Zhang, Lynne V. Nazareth, Constantin N. Flytzanis, Ian Bosdet, Yi-Hsien Su, Zeev Pancer, Matthew L. Rowe, Robert C. Angerer, David R. McClay, William H. Klein, Rachel F. Gray, Julian L. Wong, Shunsuke Yaguchi, Robert Bellé, Aaron J. Mackey, Herath Jayantha Gunaratne, Karl Frederik Bergeron, Bruce P. Brandhorst, Greg Murray, Avis H. Cohen, Stephanie Bell, Kristin Tessmar-Raible, Ian K. Townley, Bertrand Cosson, Thomas D. Glenn, Jongmin Nam, Cynthia A. Bradham, Michael Dean, Joseph Chacko, Anthony J. Robertson, Margherita Branno, Valeria Matranga, K. James Durbin, Esther Miranda, Lili Chen, Eran Elhaik, Robert D. Burke, Rita A. Wright, Paola Oliveri, Sandra L. Lee, Gary W. Moy, Alexander E Primus, Shawn S. McCafferty, Cristina Calestani, David A. Garfield, Erica Sodergren, Karen Wilson, Joel Smith, Marco A. Marra, Cynthia Messier, Julia Morales, Kim D. Pruitt, Rachel Thorn, Rachel Gill, John S. Taylor, Mark E. Hahn, Victor Sapojnikov, Meredith Howard-Ashby, Lynne M. Angerer, Maurice R. Elphick, Kathy R. Foltz, Anne Marie Genevière, Justin T. Reese, Blanca E. Galindo, Kim C. Worley, Andrew Leone, Glen Humphrey, Kevin Berney, Olga Ermolaeva, George Miner, David P. Terwilliger, Elly Suk Hen Chow, Lora Lewis, Dan Graur, C. Titus Brown, Gerard Manning, Kevin J. Peterson, Angela Jolivet, Michele K. Anderson, Francesca Rizzo, Ekaterina Voronina, Thierry Lepage, Giorgio Matassi, Antonio Fernandez-Guerra, Mamoru Nomura, Charles A. Whittaker, James R.R. Whittle, James A. Coffman, George M. Weinstock, Mohammed M. Idris, Ashlan M. Musante, Sebastian D. Fugmann, Katherine D. Walton, Sorin Istrail, Shu-Yu Wu, Cerrissa Hamilton, Jonah Cool, Jacqueline E. Schein, Stacey M. Curry, Athula Wikramanayke, Seth Carbonneau, Blair J. Rossetti, Christopher E. Killian, Melissa J. Landrum, Amanda P. Rawson, Jenifer C. Croce, Ryan C. Range, Rahul Satija, John J. Stegeman, Yufeng Shen, Cavit Agca, Terry Gaasterland, Rocky Cheung, Takae Kiyama, Nikki Adams, Jonathan P. Rast, Robert Piotr Olinski, Andrew Cree, Mark Scally, Shuguang Liang, David A. Parker, Rebecca Thomason, Gretchen E. Hofmann, Michelle M. Roux, Ronghui Xu, Robert A. Obar, Enrique Arboleda, Odile Mulner-Lorillon, Shannon Dugan-Rocha, David J. Bottjer, Gabriele Amore, Manoj P. Samanta, Waraporn Tongprasit, Véronique Duboc, La Ronda Jackson, Fred H. Wilt, Viktor Stolc, Anna T. Neill, Michael Raisch, Pei Yun Lee, Jia L. Song, Margaret Morgan, Brian T. Livingston, Sofia Hussain, Zheng Wei, Bryan J. Cole, Tonya F. Severson, Victor V. Solovyev, Finn Hallböök, Donna M. Muzny, Christine A. Byrum, Albert J. Poustka, Xiuqian Mu, Andrew R. Jackson, Shin Heesun, Euan R. Brown, Nansheng Chen, Patrick Cormier, Ralph Haygood, Pedro Martinez, R. Andrew Cameron, D. Wang, Wendy S. Beane, Eric H. Davidson, Christie Kovar, Hemant Kelkar, Charles A. Ettensohn, Sham V. Nair, Robert L. Morris, Stefan C. Materna, Michael C. Thorndyke, Richard A. Gibbs, Dan O Mellott, Department of Physiology and Biophysics, Stony Brook University [The State University of New York] ( SBU ), Astronomy Unit ( AU ), Queen Mary University of London ( QMUL ), Urban and Industrial Air Quality Group, CSIRO Energy Technology, Commonwealth Scientific and Industrial Research Organisation Energy Technology ( CSIRO Energy Technology ), Commonwealth Scientific and Industrial Research Organisation, Center for Polymer Studies ( CPS ), Boston University [Boston] ( BU ), Physics Department [Boston] ( BU-Physics ), Max Planck Institute for Psycholinguistics, Max-Planck-Institut, Department of Biology [Norton], Wheaton College [Norton], Mathematical Institute [Oxford] ( MI ), University of Oxford [Oxford], Centre for the Analysis of Time Series ( CATS ), London School of Economics and Political Science ( LSE ), Thomas Jefferson National Accelerator Facility ( Jefferson Lab ), Thomas Jefferson National Accelerator Facility, Laboratoire d'Energétique et de Mécanique Théorique Appliquée ( LEMTA ), Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Evolution, Génomes et Spéciation ( LEGS ), Centre National de la Recherche Scientifique ( CNRS ), Department of Geology, University of Illinois at Urbana-Champaign [Urbana], Department of Electrical and Computer Engineering [Portland] ( ECE ), Portland State University [Portland] ( PSU ), Saint-Gobain Crystals [USA], SAINT-GOBAIN, Institute for Animal Health ( IAH ), Biotechnology and Biological Sciences Research Council, Center for Agricultural Resources Research, Chinese Academy of Sciences [Changchun Branch] ( CAS ), Ipsen Inc. [Milford] ( Ipsen ), IPSEN, Department of Physics [Berkeley], University of California [Berkeley], Institute for Climate and Atmospheric Science [Leeds] ( ICAS ), University of Leeds, Chung-Ang University ( CAU ), Chung-Ang University [Seoul], Antarctic Climate and Ecosystems Cooperative Research Center ( ACE-CRC ), Institute of Aerodynamics and Fluid Mechanics ( AER ), Technische Universität München [München] ( TUM ), Mer et santé ( MS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Imperial College London, Radio and Atmospheric Sciences Division, National Physical Laboratory [Teddington] ( NPL ), International Research Institute for Climate and Society ( IRI ), Earth Institute at Columbia University, Columbia University [New York]-Columbia University [New York], Soils Group, The Macaulay Institute, Department of Haematology, University of Cambridge [UK] ( CAM ), School of Biology and Biochemistry, Queen's University, Leslie Hill Institute for Plant Conservation ( PCU ), University of Cape Town, Institute for Microelectronics and Microsystems/ Istituto per la Microelettronica e Microsistemi ( IMM ), Consiglio Nazionale delle Ricerche ( CNR ), Laboratoire d'acoustique de l'université du Mans ( LAUM ), Le Mans Université ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Interactive Systems Labs ( ISL ), Carnegie Mellon University [Pittsburgh] ( CMU ), Dalian Institute of Chemical Physics ( DICP ), Architectures, Languages and Compilers to Harness the End of Moore Years ( ALCHEMY ), Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique ( Inria ), Clean Air Task Force ( CATF ), Clean Air Task Force, Space Physics Laboratory, Indian Space Research Organisation ( ISRO ), Centre d'études et de recherches appliquées à la gestion ( CERAG ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Microbiology and Immunology, College of Medicine and Health Sciences-Sultan Qaboos University, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), Department of Biostatistics, University of Michigan [Ann Arbor], Department of Radiation Oncology [Michigan] ( Radonc ), Department of Physics and Astronomy [Leicester], University of Leicester, Informatique, Biologie Intégrative et Systèmes Complexes ( IBISC ), Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut für Meteorologie und Klimaforschung ( IMK ), Karlsruher Institut für Technologie ( KIT ), Physics Department [UNB], University of New Brunswick ( UNB ), Laboratoire Parole et Langage ( LPL ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ), Institut des Sciences Chimiques de Rennes ( ISCR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Ecole Nationale Supérieure de Chimie de Rennes-Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Bioprojet, Laboratoire de Matériaux à Porosité Contrôlée ( LMPC ), Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique ( CNRS ), School of Information Engineering [USTB] ( SIE ), University of Science and Technology Beijing [Beijing] ( USTB ), Laboratory for Atmospheric and Space Physics [Boulder] ( LASP ), University of Colorado Boulder [Boulder], Department of Applied Mathematics [Sheffield], University of Sheffield [Sheffield], School of Mathematics and Statistics [Sheffield] ( SoMaS ), Laboratoire de Mécanique de Lille - FRE 3723 ( LML ), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Centre National de la Recherche Scientifique ( CNRS ), Computer Science Department [UCLA] ( CSD ), University of California at Los Angeles [Los Angeles] ( UCLA ), Développement et évolution ( DE ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie du Développement de Villefranche sur mer ( LBDV ), Laboratoire Pierre Aigrain ( LPA ), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris ( FRDPENS ), Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Mathematics and Statistics [Mac Gill], McGill University, Departamento de Botánica [Comahue], Universidad nacional del Comahue, Bioénergétique Cellulaire et Pathologique ( BECP ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Environnements et Paléoenvironnements OCéaniques ( EPOC ), Observatoire aquitain des sciences de l'univers ( OASU ), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratori Nazionali del Sud ( LNS ), National Institute for Nuclear Physics ( INFN ), Departament de Matemàtiques [Barcelona], Universitat Autònoma de Barcelona [Barcelona] ( UAB ), Max-Planck-Institut für Kohlenforschung (coal research), Institute of Oceanology [CAS] ( IOCAS ), National Chiao Tung University ( NCTU ), Department of Hydrology and Water Resources ( HWR ), University of Arizona, Centre for Educational Technology, Environment Department [York], University of York [York, UK], State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Peking University [Beijing], Department of Physics and Astronomy [Iowa City], University of Iowa [Iowa], NASA Ames Research Center ( ARC ), Department of Materials, Digital Language & Knowledge Contents Research Association ( DICORA ), Hankuk University of Foreign Studies, Department of Physics [Coventry], University of Warwick [Coventry], Space Science and Technology Department [Didcot] ( RAL Space ), STFC Rutherford Appleton Laboratory ( RAL ), Science and Technology Facilities Council ( STFC ) -Science and Technology Facilities Council ( STFC ), Institut de biologie et chimie des protéines [Lyon] ( IBCP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), H M Nautical Almanac Office [RAL] ( HMNAO ), Rutherford Appleton Laboratory, United Kingdom Met Office [Exeter], University College of London [London] ( UCL ), Department of Pathology and Laboratory Medicine [UCLA], University of California at Los Angeles [Los Angeles] ( UCLA ) -School of Medicine, School of Earth and Environmental Sciences [Seoul] ( SEES ), Seoul National University [Seoul], Department of Chemistry, Seoul Women's University, MicroMachines Centre ( MMC ), Nanyang Technological University [Singapour], Regroupement Québécois sur les Matériaux de Pointe ( RQMP ), École Polytechnique de Montréal ( EPM ) -Université de Sherbrooke [Sherbrooke]-McGill University-Université de Montréal-Fonds Québécois de Recherche sur la Nature et les Technologies ( FQRNT ), Département de Physique [Montréal], Université de Montréal, School of Earth and Environment [Leeds] ( SEE ), Centre for Ecology and Hydrology ( CEH ), Natural Environment Research Council ( NERC ), Norwegian Institute for Water Research ( NIVA ), Norwegian Institute for Water Research, Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Astronomy Unit [London] (AU), Queen Mary University of London (QMUL), Commonwealth Scientific and Industrial Research Organisation Energy Technology (CSIRO Energy Technology), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Department of Biochemistry and Molecular Biology [Houston], The University of Texas Medical School at Houston, Mathematical Institute [Oxford] (MI), University of Oxford, Centre for the Analysis of Time Series (CATS), London School of Economics and Political Science (LSE), Thomas Jefferson National Accelerator Facility (Jefferson Lab), Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA ), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), University of Illinois System-University of Illinois System, Department of Electrical and Computer Engineering [Portland] (ECE), Portland State University [Portland] (PSU), Saint-Gobain, Institute for Animal Health (IAH), Biotechnology and Biological Sciences Research Council (BBSRC), Chinese Academy of Sciences [Changchun Branch] (CAS), Ipsen Inc. [Milford] (Ipsen), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Chung-Ang University (CAU), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Institute of Aerodynamics and Fluid Mechanics (AER), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Mer et santé (MS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), National Physical Laboratory [Teddington] (NPL), International Research Institute for Climate and Society (IRI), Macaulay Institute, University of Cambridge [UK] (CAM), Queen's University [Kingston, Canada], Leslie Hill Institute for Plant Conservation (PCU), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Interactive Systems Labs (ISL), Carnegie Mellon University [Pittsburgh] (CMU), Dalian Institute of Chemical Physics (DICP), Architectures, Languages and Compilers to Harness the End of Moore Years (ALCHEMY), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Clean Air Task Force (CATF), Indian Space Research Organisation (ISRO), Centre d'études et de recherches appliquées à la gestion (CERAG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS), Sultan Qaboos University (SQU)-College of Medicine and Health Sciences [Baylor], Baylor University-Baylor University, European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Michigan System-University of Michigan System, Department of Radiation Oncology [Michigan] (Radonc), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute for Meteorology and Climate Research (IMK), Karlsruhe Institute of Technology (KIT), University of New Brunswick (UNB), Laboratoire Parole et Langage (LPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Matériaux à Porosité Contrôlée (LMPC), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), School of Information Engineering [USTB] (SIE), University of Science and Technology Beijing [Beijing] (USTB), Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], School of Mathematics and Statistics [Sheffield] (SoMaS), Laboratoire de Mécanique de Lille - FRE 3723 (LML), Université de Lille, Sciences et Technologies-Centrale Lille-Centre National de la Recherche Scientifique (CNRS), Computer Science Department [UCLA] (CSD), University of California [Los Angeles] (UCLA), Développement et évolution (DE), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Pierre Aigrain (LPA), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Statistics [Montréal], McGill University = Université McGill [Montréal, Canada], Departamento de Botánica [Bariloche], Centro Regional Universitario Bariloche [Bariloche] (CRUB), Universidad Nacional del Comahue [Neuquén] (UNCOMA)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), Bioénergétique Cellulaire et Pathologique (BECP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratori Nazionali del Sud (LNS), Istituto Nazionale di Fisica Nucleare (INFN), Departament de Matemàtiques [Barcelona] (UAB), Universitat Autònoma de Barcelona (UAB), Max-Planck-Institut für Kohlenforschung (Coal Research), Max-Planck-Gesellschaft, CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS), National Chiao Tung University (NCTU), Department of Hydrology and Water Resources (HWR), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), University of Iowa [Iowa City], NASA Ames Research Center (ARC), Digital Language & Knowledge Contents Research Association (DICORA), Space Science and Technology Department [Didcot] (RAL Space), STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC)-Science and Technology Facilities Council (STFC), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), H M Nautical Almanac Office [RAL] (HMNAO), University College of London [London] (UCL), University of California (UC)-University of California (UC)-School of Medicine, School of Earth and Environmental Sciences [Seoul] (SEES), Seoul National University [Seoul] (SNU), MicroMachines Centre (MMC), Regroupement Québécois sur les Matériaux de Pointe (RQMP), École Polytechnique de Montréal (EPM)-Université de Sherbrooke (UdeS)-McGill University = Université McGill [Montréal, Canada]-Université de Montréal (UdeM)-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal (UdeM), Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Norwegian Institute for Water Research (NIVA), SEA URCHIN GENOME SEQUENCING CONSORTIUM, SODERGREN E, WEINSTOCK GM, DAVIDSON EH, CAMERON RA, GIBBS RA, ANGERER RC, ANGERER LM, ARNONE MI, BURGESS DR, BURKE RD, COFFMAN JA, DEAN M, ELPHICK MR, ETTENSOHN CA, FOLTZ KR, HAMDOUN A, HYNES RO, KLEIN WH, MARZLUFF W, MCCLAY DR, MORRIS RL, MUSHEGIAN A, RAST JP, SMITH LC, THORNDYKE MC, VACQUIER VD, WESSEL GM, WRAY G, ZHANG L, ELSIK CG, ERMOLAEVA O, HLAVINA W, HOFMANN G, KITTS P, LANDRUM MJ, MACKEY AJ, MAGLOTT D, PANOPOULOU G, POUSTKA AJ, PRUITT K, SAPOJNIKOV V, SONG X, SOUVOROV A, SOLOVYEV V, WEI Z, WHITTAKER CA, WORLEY K, DURBIN KJ, SHEN Y, FEDRIGO O, GARFIELD D, HAYGOOD R, PRIMUS A, SATIJA R, SEVERSON T, GONZALEZ-GARAY ML, JACKSON AR, MILOSAVLJEVIC A, TONG M, KILLIAN CE, LIVINGSTON BT, WILT FH, ADAMS N, BELLE R, CARBONNEAU S, CHEUNG R, CORMIER P, COSSON B, CROCE J, FERNANDEZ-GUERRA A, GENEVIERE AM, GOEL M, KELKAR H, MORALES J, MULNER-LORILLON O, ROBERTSON AJ, GOLDSTONE JV, COLE B, EPEL D, GOLD B, HAHN ME, HOWARD-ASHBY M, SCALLY M, STEGEMAN JJ, ALLGOOD EL, COOL J, JUDKINS KM, MCCAFFERTY SS, MUSANTE AM, OBAR RA, RAWSON AP, ROSSETTI BJ, GIBBONS IR, HOFFMAN MP, LEONE A, ISTRAIL S, MATERNA SC, SAMANTA MP, STOLC V, TONGPRASIT W, TU Q, BERGERON KF, BRANDHORST BP, WHITTLE J, BERNEY K, BOTTJER DJ, CALESTANI C, PETERSON K, CHOW E, YUAN QA, ELHAIK E, GRAUR D, REESE JT, BOSDET I, HEESUN S, MARRA MA, SCHEIN J, ANDERSON MK, BROCKTON V, BUCKLEY KM, COHEN AH, FUGMANN SD, HIBINO T, LOZA-COLL M, MAJESKE AJ, MESSIER C, NAIR SV, PANCER Z, TERWILLIGER DP, AGCA C, ARBOLEDA E, CHEN N, CHURCHER AM, HALLBOOK F, HUMPHREY GW, IDRIS MM, KIYAMA T, LIANG S, MELLOTT D, MU X, MURRAY G, OLINSKI RP, RAIBLE F, ROWE M, TAYLOR JS, TESSMAR-RAIBLE K, WANG D, WILSON KH, YAGUCHI S, GAASTERLAND T, GALINDO BE, GUNARATNE HJ, JULIANO C, KINUKAWA M, MOY GW, NEILL AT, NOMURA M, RAISCH M, READE A, ROUX MM, SONG JL, SU YH, TOWNLEY IK, VORONINA E, WONG JL, AMORE G, BRANNO M, BROWN ER, CAVALIERI, V, DUBOC V, DULOQUIN L, FLYTZANIS C, GACHE C, LAPRAZ F, LEPAGE T, LOCASCIO A, MART, University of California-University of California, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), University of California-University of California-School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), University of Manchester Institute of Science and Technology (UMIST), Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Brookhaven National Laboratory [Upton, NY] (BNL), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE), Baylor College of Medicine (BCM), Baylor University, Laboratoire de Traitement de l'Information Medicale (LaTIM), Université européenne de Bretagne - European University of Brittany (UEB)-Université de Brest (UBO)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire de Modélisation et Simulation Multi Echelle (MSME), Université Paris-Est Marne-la-Vallée (UPEM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Instituto Andaluz de Geofísica y Prevención de Desastres Sísmicos [Granada] (IAGPDS), Universidad de Granada (UGR), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), University of New South Wales [Sydney] (UNSW), Celera Genomics (CRA), Celera Genomics, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma Tor Vergata [Roma], Unité de recherches forestières (BORDX PIERR UR ), Institut National de la Recherche Agronomique (INRA), Deptartment of Neuroscience, Uppsala University, State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch]-Chinese Academy of Sciences [Nanjing Branch], Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), Department of Physical and Environmental Sciences [Toronto], University of Toronto at Scarborough, inconnu temporaire UPEMLV, Inconnu, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Atmospheric Sciences [Seattle], University of Washington [Seattle], National Institute of Advanced Industrial Science and Technology (AIST), Department of Pharmacy, Università degli studi di Genova = University of Genoa (UniGe), Interdisciplinary Arts and Sciences Department, St. Vincent's Hospital, Sydney, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Electrical Engineering (DEE-POSTECH), Pohang University of Science and Technology (POSTECH), Centre Suisse d'Electronique et de Microtechnique SA [Neuchatel] (CSEM), Centre Suisse d'Electronique et Microtechnique SA (CSEM), Human Genome Sequencing Center [Houston] (HGSC), Brookhaven National Laboratory, Meteorological Service of Canada, 4905 Dufferin Street, Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Mines-Télécom [Paris] (IMT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Paris-Est Marne-la-Vallée (UPEM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Forestières, Department of Physical and Environmental Sciences, University of Toronto [Scarborough, Canada], National Institute for Nuclear Physics (INFN), University of Genoa (UNIGE), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Universidad de Granada = University of Granada (UGR), Laboratoire d'Energétique et de Mécanique Théorique Appliquée (LEMTA ), Technische Universität München [München] (TUM), Queen's University [Kingston], Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Grenoble Alpes (UGA), Institut für Meteorologie und Klimaforschung (IMK), Karlsruher Institut für Technologie (KIT), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille, Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universitat Autònoma de Barcelona [Barcelona] (UAB), École Polytechnique de Montréal (EPM)-Université de Sherbrooke [Sherbrooke]-Université de Montréal [Montréal]-McGill University-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal [Montréal], U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, MESH: Signal Transduction, MESH: Sequence Analysis, DNA, MESH : Transcription Factors, MESH : Calcification, Physiologic, Genome, MESH : Proteins, 0302 clinical medicine, MESH : Embryonic Development, MESH: Gene Expression Regulation, Developmental, Innate, MESH: Embryonic Development, Developmental, Nervous System Physiological Phenomena, MESH: Animals, MESH: Proteins, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Complement Activation, ComputingMilieux_MISCELLANEOUS, MESH: Evolution, Molecular, MESH : Strongylocentrotus purpuratus, Genetics, 0303 health sciences, MESH: Nervous System Physiological Phenomena, Multidisciplinary, biology, Medicine (all), MESH: Immunologic Factors, Gene Expression Regulation, Developmental, Genome project, MESH: Transcription Factors, MESH : Immunity, Innate, MESH : Complement Activation, MESH: Genes, Bacterial artificial chromosome (BAC)DeuterostomesStrongylocentrotus purpuratusVertebrate innovations, Echinoderm, MESH : Nervous System Physiological Phenomena, embryonic structures, MESH: Cell Adhesion Molecules, MESH : Genes, MESH: Immunity, Innate, Sequence Analysis, Signal Transduction, MESH: Computational Biology, Genome evolution, MESH: Complement Activation, Sequence analysis, Evolution, MESH: Strongylocentrotus purpuratus, MESH : Male, Embryonic Development, MESH : Immunologic Factors, Article, MESH: Calcification, Physiologic, Calcification, MESH : Cell Adhesion Molecules, Evolution, Molecular, 03 medical and health sciences, Calcification, Physiologic, Animals, Immunologic Factors, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Physiologic, Gene, Strongylocentrotus purpuratus, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH : Signal Transduction, Bacterial artificial chromosome, Immunity, Molecular, Computational Biology, Proteins, Cell Adhesion Molecules, Genes, Immunity, Innate, Transcription Factors, Sequence Analysis, DNA, DNA, biology.organism_classification, MESH: Male, Gene Expression Regulation, MESH : Animals, MESH : Gene Expression Regulation, Developmental, MESH : Genome, 030217 neurology & neurosurgery, MESH : Computational Biology, MESH : Sequence Analysis, DNA
Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus , a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Published
2006
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44. Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist.

Author

Graur D

Subjects
Algorithms, Animals, Base Composition, Brain, Humans, Mammals genetics, Genome, Human, Isochores
Abstract

The isochore theory, which was proposed more than 40 years ago, depicts the mammalian genome as a mosaic of long, homogeneous regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five compositionally distinct isochore families. The isochore theory, in all its reincarnations, has been repeatedly falsified in the literature, yet isochore proponents have persistently resurrected it by either redefining isochores or by proposing alternative means of testing the theory. Here, I deal with the latest attempt to salvage this seemingly immortal zombie-a sequence segmentation method called isoSegmenter, which was claimed to "identify" isochores while at the same time disregarding the main characteristic attribute of isochores-compositional homogeneity. I used a series of controlled, randomly generated simulated sequences as a benchmark to study the performance of isoSegmenter. The main advantage of using simulated sequences is that, unlike real data, the exact start and stop point of any isochore or homogeneous compositional domain is known. Based on three key performance metrics-sensitivity, precision, and Jaccard similarity index-isoSegmenter was found to be vastly inferior to isoPlotter, a segmentation algorithm with no user input. Moreover, isoSegmenter identified isochores where none exist and failed to identify compositionally homogeneous sequences that were shorter than 100-200 kb. Will this zillionth refutation of "isochores" ensure a final and permanent entombment of the isochore theory? This author is not holding his breath.

Published
2022
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46. On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn't.

Author

Elhaik E and Graur D

Subjects
Evolution, Molecular, Genetic Drift, Humans, Adaptation, Physiological, Algorithms, Artificial Intelligence, Genetics, Population, Genome, Human, Machine Learning, Selection, Genetic
Abstract

In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transformation was aided by a series of articles by Daniel Schrider and Andrew Kern. Within this series, a paper entitled "Soft sweeps are the dominant mode of adaptation in the human genome" (Schrider and Kern, Mol. Biol. Evolut . 2017 , 34 (8), 1863-1877) attracted a great deal of attention, in particular in conjunction with another paper (Kern and Hahn, Mol. Biol. Evolut . 2018 , 35 (6), 1366-1371), for purporting to discredit the Neutral Theory of Molecular Evolution (Kimura 1968). Here, we address an alleged novelty in Schrider and Kern's paper, i.e., the claim that their study involved an artificial intelligence technique called supervised machine learning (SML). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known empirically to be true. Curiously, Schrider and Kern did not possess a training dataset of genomic segments known a priori to have evolved either neutrally or through soft or hard selective sweeps. Thus, their claim of using SML is thoroughly and utterly misleading. In the absence of legitimate training datasets, Schrider and Kern used: (1) simulations that employ many manipulatable variables and (2) a system of data cherry-picking rivaling the worst excesses in the literature. These two factors, in addition to the lack of negative controls and the irreproducibility of their results due to incomplete methodological detail, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., S/HIC) should be taken with a huge shovel of salt.

Published
2021
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49. ProtParCon : A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements.

Author

Yuan F, Nguyen H, and Graur D

Subjects
Amino Acid Sequence, Evolution, Molecular, Phylogeny, Software, Computational Biology methods
Abstract

Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present ProtParCon , a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, ProtParCon implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. ProtParCon also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of ProtParCon , including scripts containing user tutorials, the full API reference and documentation are publicly and freely available under an open source MIT License via GitHub. The latest stable release is also available on PyPI (the Python Package Index).

Published
2019
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50. Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.

Author

Zheng Y, Graur D, and Azevedo RBR

Subjects
Amino Acid Sequence, Amino Acid Substitution, Animals, Genes, Mammals genetics, Phylogeny, Statistics, Nonparametric, Amino Acids genetics, Proteins chemistry, Proteins genetics, Selection, Genetic
Abstract

A low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is an indicator of functional constraint caused by purifying selection. Intuitively, the functional constraint would also be expected to prevent such a codon from being deleted. However, to the best of our knowledge, the correlation between the rates of deletion and substitution has never actually been estimated. Here, we use 8595 protein-coding region sequences from nine mammalian species to examine the relationship between deletion rate and dN/dS. We find significant positive correlations at the levels of both sites and genes. We compared our data against controls consisting of simulated coding sequences evolving along identical phylogenetic trees, where deletions occur independently of substitutions. A much weaker correlation was found in the corresponding simulated sequences, probably caused by alignment errors. In the real data, the correlations cannot be explained by alignment errors. Separate investigations on nonsynonymous (dN) and synonymous (dS) substitution rates indicate that the correlation is most likely due to a similarity in patterns of selection rather than in mutation rates.

Published
2018
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