Towards a scientific blockchain framework for reproducible data analysis

Autor: Furlanello, C., De Domenico, M., Jurman, G., Bussola, N.

Publishing reproducible analyses is a long-standing and widespread challenge for the scientific community, funding bodies and publishers. Although a definitive solution is still elusive, the problem is recognized to affect all disciplines and lead to

Externí odkaz: http://arxiv.org/abs/1707.06552

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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Autor: Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L.

Publikováno v: Nature communications, vol 12, iss 1
Nature Communications
Nature Communications, 2021, 12, pp.1-18/3297. ⟨10.1038/s41467-021-23143-7⟩
Nature communications, 12(1):3297. Nature Publishing Group
Nature Communications, Nature Publishing Group, 2021, 12, pp.1-18. ⟨10.1038/s41467-021-23143-7⟩
Nature Communications, Vol 12, Iss 1, Pp 1-18 (2021)
Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, J A, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-Ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-Sueki, H, Frith, M C, Abugessaisa, I, Aitken, S, Aken, B L, Alam, I, Alam, T, Alasiri, R, Alhendi, A M N, Alinejad-Rokny, H, Alvarez, M J, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Bornholdt, J, Boyd, M, Chen, Y, Coskun, M, Dalby, M, Ienasescu, H, Jørgensen, M, Kaczkowski, B, Kere, J, Li, K, Lilje, B, Nepal, C, Nguyen, Q H, Nielsen, L K, Rennie, S, Sandelin, A, Valen, E, Vitezic, M, Vitting-Seerup, K & FANTOM Consortium 2021, ' Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network ', Nature Communications, vol. 12, 3297 . https://doi.org/10.1038/s41467-021-23143-7
Grapotte, Mathys; Saraswat, Manu; Bessière, Chloé; Menichelli, Christophe; Ramilowski, Jordan A; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Tagami, Michihira; Murata, Mitsuyoshi; Kojima-Ishiyama, Miki; Noma, Shohei; Noguchi, Shuhei; Kasukawa, Takeya; Hasegawa, Akira; Suzuki, Harukazu; Nishiyori-Sueki, Hiromi; Frith, Martin C; Chatelain, Clément; Carninci, Piero; ... (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature communications, 12(1), p. 3297. Nature Publishing Group 10.1038/s41467-021-23143-7
Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, J A, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-sueki, H, Frith, M, Abugessaisa, I, Aitken, S, Aken, B L, Alam, I, Alam, T, Alasiri, R, Alhendi, A M N, Alinejad-rokny, H, Alvarez, M J, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, A L, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, J K, Bajic, V B, Bajpai, A, Baker, S, Baldarelli, R M, Balic, A, Bansal, M, Batagov, A O, Batzoglou, S, Beckhouse, A G, Beltrami, A P, Beltrami, C A, Bertin, N, Bhattacharya, S, Bickel, P J, Blake, J A, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, J B, Bult, C J, Burroughs, A M, Burt, D W, Busch, A, Caglio, G, Califano, A, Cameron, C J, Cannistraci, C V, Carbone, A, Carlisle, A J, Carninci, P, Carter, K W, Cesselli, D, Chang, J, Chen, J C, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, E L, Coskun, M, Dalby, M, Dalla, E, Daub, C O, Davis, C A, De Hoon, M J L, De Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, A D, Dieterich, L C, Dimont, E, Djebali, S, Dohi, T, Dostie, J, Drablos, F, Edge, A S B, Edinger, M, Ehrlund, A, Ekwall, K, Elofsson, A, Endoh, M, Enomoto, H, Enomoto, S, Faghihi, M, Fagiolini, M, Farach-carson, M C, Faulkner, G J, Favorov, A, Fernandes, A M, Ferrai, C, Forrest, A R R, Forrester, L M, Forsberg, M, Fort, A, Francescatto, M, Freeman, T C, Frith, M, Fukuda, S, Funayama, M, Furlanello, C, Furuno, M, Furusawa, C, Gao, H, Gazova, I, Gebhard, C, Geier, F, Geijtenbeek, T B H, Ghosh, S, Ghosheh, Y, Gingeras, T R, Gojobori, T, Goldberg, T, Goldowitz, D, Gough, J, Greco, D, Gruber, A J, Guhl, S, Guigo, R, Guler, R, Gusev, O, Gustincich, S, Ha, T J, Haberle, V, Hale, P, Hallstrom, B M, Hamada, M, Handoko, L, Hara, M, Harbers, M, Harrow, J, Harshbarger, J, Hase, T, Hasegawa, A, Hashimoto, K, Hatano, T, Hattori, N, Hayashi, R, Hayashizaki, Y, Herlyn, M, Hettne, K, Heutink, P, Hide, W, Hitchens, K J, Sui, S H, ’t Hoen, P A C, Hon, C C, Hori, F, Horie, M, Horimoto, K, Horton, P, Hou, R, Huang, E, Huang, Y, Hugues, R, Hume, D, Ienasescu, H, Iida, K, Ikawa, T, Ikemura, T, Ikeo, K, Inoue, N, Ishizu, Y, Ito, Y, Itoh, M, Ivshina, A V, Jankovic, B R, Jenjaroenpun, P, Johnson, R, Jorgensen, M, Jorjani, H, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kajiyama, K, Kaliyaperumal, R, Kaminuma, E, Kanaya, T, Kaneda, H, Kapranov, P, Kasianov, A S, Kasukawa, T, Katayama, T, Kato, S, Kawaguchi, S, Kawai, J, Kawaji, H, Kawamoto, H, Kawamura, Y I, Kawasaki, S, Kawashima, T, Kempfle, J S, Kenna, T J, Kere, J, Khachigian, L, Kiryu, H, Kishima, M, Kitajima, H, Kitamura, T, Kitano, H, Klaric, E, Klepper, K, Klinken, S P, Kloppmann, E, Knox, A J, Kodama, Y, Kogo, Y, Kojima, M, Kojima, S, Komatsu, N, Komiyama, H, Kono, T, Koseki, H, Koyasu, S, Kratz, A, Kukalev, A, Kulakovskiy, I, Kundaje, A, Kunikata, H, Kuo, R, Kuo, T, Kuraku, S, Kuznetsov, V A, Kwon, T J, Larouche, M, Lassmann, T, Law, A, Le-cao, K, Lecellier, C, Lee, W, Lenhard, B, Lennartsson, A, Li, K, Li, R, Lilje, B, Lipovich, L, Lizio, M, Lopez, G, Magi, S, Mak, G K, Makeev, V, Manabe, R, Mandai, M, Mar, J, Maruyama, K, Maruyama, T, Mason, E, Mathelier, A, Matsuda, H, Medvedeva, Y A, Meehan, T F, Mejhert, N, Meynert, A, Mikami, N, Minoda, A, Miura, H, Miyagi, Y, Miyawaki, A, Mizuno, Y, Morikawa, H, Morimoto, M, Morioka, M, Morishita, S, Moro, K, Motakis, E, Motohashi, H, Mukarram, A K, Mummery, C L, Mungall, C J, Murakawa, Y, Muramatsu, M, Murata, M, Nagasaka, K, Nagase, T, Nakachi, Y, Nakahara, F, Nakai, K, Nakamura, K, Nakamura, Y, Nakamura, Y, Nakazawa, T, Nason, G P, Nepal, C, Nguyen, Q H, Nielsen, L K, Nishida, K, Nishiguchi, K M, Nishiyori, H, Nitta, K, Noguchi, S, Noma, S, Notredame, C, Ogishima, S, Ohkura, N, Ohno, H, Ohshima, M, Ohtsu, T, Okada, Y, Okada-hatakeyama, M, Okazaki, Y, Oksvold, P, Orlando, V, Ow, G S, Ozturk, M, Pachkov, M, Paparountas, T, Parihar, S P, Park, S, Pascarella, G, Passier, R, Persson, H, Philippens, I H, Piazza, S, Plessy, C, Pombo, A, Ponten, F, Poulain, S, Poulsen, T M, Pradhan, S, Prezioso, C, Pridans, C, Qin, X, Quackenbush, J, Rackham, O, Ramilowski, J, Ravasi, T, Rehli, M, Rennie, S, Rito, T, Rizzu, P, Robert, C, Roos, M, Rost, B, Roudnicky, F, Roy, R, Rye, M B, Sachenkova, O, Saetrom, P, Sai, H, Saiki, S, Saito, M, Saito, A, Sakaguchi, S, Sakai, M, Sakaue, S, Sakaue-sawano, A, Sandelin, A, Sano, H, Sasamoto, Y, Sato, H, Saxena, A, Saya, H, Schafferhans, A, Schmeier, S, Schmidl, C, Schmocker, D, Schneider, C, Schueler, M, Schultes, E A, Schulze-tanzil, G, Semple, C A, Seno, S, Seo, W, Sese, J, Severin, J, Sheng, G, Shi, J, Shimoni, Y, Shin, J W, Simonsanchez, J, Sivertsson, A, Sjostedt, E, Soderhall, C, Laurent, G S, Stoiber, M H, Sugiyama, D, Summers, K M, Suzuki, A M, Suzuki, H, Suzuki, K, Suzuki, M, Suzuki, N, Suzuki, T, Swanson, D J, Swoboda, R K, Tagami, M, Taguchi, A, Takahashi, H, Takahashi, M, Takamochi, K, Takeda, S, Takenaka, Y, Tam, K T, Tanaka, H, Tanaka, R, Tanaka, Y, Tang, D, Taniuchi, I, Tanzer, A, Tarui, H, Taylor, M S, Terada, A, Terao, Y, Testa, A C, Thomas, M, Thongjuea, S, Tomii, K, Triglia, E T, Toyoda, H, Tsang, H G, Tsujikawa, M, Uhlén, M, Valen, E, Van De Wetering, M, Van Nimwegen, E, Velmeshev, D, Verardo, R, Vitezic, M, Vitting-seerup, K, Von Feilitzen, K, Voolstra, C R, Vorontsov, I E, Wahlestedt, C, Wasserman, W W, Watanabe, K, Watanabe, S, Wells, C A, Winteringham, L N, Wolvetang, E, Yabukami, H, Yagi, K, Yamada, T, Yamaguchi, Y, Yamamoto, M, Yamamoto, Y, Yamamoto, Y, Yamanaka, Y, Yano, K, Yasuzawa, K, Yatsuka, Y, Yo, M, Yokokura, S, Yoneda, M, Yoshida, E, Yoshida, Y, Yoshihara, M, Young, R, Young, R S, Yu, N Y, Yumoto, N, Zabierowski, S E, Zhang, P G, Zucchelli, S, Zwahlen, M, Chatelain, C, Carninci, P, De Hoon, M J L, Wasserman, W W, Bréhélin, L & Lecellier, C 2021, ' Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network ', Nature Communications, vol. 12, no. 1 . https://doi.org/10.1038/s41467-021-23143-7
Nature Communications, Nature Publishing Group, 2021, 12 (1), ⟨10.1038/s41467-021-23143-7⟩
Nature Communications, 12 (1)

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::071cc9b35fa8ab5830f24ee8cb404eaf
https://pubmed.ncbi.nlm.nih.gov/35232988

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