Deep learning on genome sequence to identify epistatic effects in complex diseases

基因组序列深度学习可识别复杂疾病的上位效应

• 批准号: 20K15773
• 负责人: Koido Masaru
• 金额: $ 2.66万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Early-Career Scientists
• 财政年份: 2020
• 资助国家: 日本
• 起止时间: 2020-04-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-20K15773/
• 关键词: ディープラーニング; 機械学習; 遺伝子発現制御; エピスタシス; ゲノム解析

项目成果

Stroke genetics informs drug discovery and risk prediction across ancestries.

• DOI: 10.1038/s41586-022-05165-3
• 发表时间: 2022-11
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Mishra, Aniket;Malik, Rainer;Hachiya, Tsuyoshi;Jurgenson, Tuuli;Namba, Shinichi;Posner, Daniel C.;Kamanu, Frederick K.;Koido, Masaru;Le Grand, Quentin;Shi, Mingyang;He, Yunye;Georgakis, Marios K.;Caro, Ilana;Krebs, Kristi;Liaw, Yi-Ching;Vaura, Felix C.;Lin, Kuang;Winsvold, Bendik Slagsvold;Srinivasasainagendra, Vinodh;Parodi, Livia;Bae, Hee-Joon;Chauhan, Ganesh;Chong, Michael R.;Tomppo, Liisa;Akinyemi, Rufus;Roshchupkin, Gennady V.;Habib, Naomi;Jee, Yon Ho;Thomassen, Jesper Qvist;Abedi, Vida;Carcel-Marquez, Jara;Nygaard, Marianne;Leonard, Hampton L.;Yang, Chaojie;Yonova-Doing, Ekaterina;Knol, Maria J.;Lewis, Adam J.;Judy, Renae L.;Ago, Tetsuro;Amouyel, Philippe;Armstrong, Nicole D.;Bakker, Mark K.;Bartz, Traci M.;Bennett, David A.;Bis, Joshua C.;Bordes, Constance;Borte, Sigrid;Cain, Anael;Ridker, Paul M.;Cho, Kelly;Chen, Zhengming;Cruchaga, Carlos;Cole, John W.;de Jager, Phil L.;de Cid, Rafael;Endres, Matthias;Ferreira, Leslie E.;Geerlings, Mirjam I.;Gasca, Natalie C.;Gudnason, Vilmundur;Hata, Jun;He, Jing;Heath, Alicia K.;Ho, Yuk-Lam;Havulinna, Aki S.;Hopewell, Jemma C.;Hyacinth, Hyacinth I.;Inouye, Michael;Jacob, Mina A.;Jeon, Christina E.;Jern, Christina;Kamouchi, Masahiro;Keene, Keith L.;Kitazono, Takanari;Kittner, Steven J.;Konuma, Takahiro;Kumar, Amit;Lacaze, Paul;Launer, Lenore J.;Lee, Keon-Joo;Lepik, Kaido;Li, Jiang;Li, Liming;Manichaikul, Ani;Markus, Hugh S.;Marston, Nicholas A.;Meitinger, Thomas;Mitchell, Braxton D.;Montellano, Felipe A.;Morisaki, Takayuki;Mosley, Thomas H.;Nalls, Mike A.;Nordestgaard, Borge G.;O'Donnell, Martin J.;Okada, Yukinori;Onland-Moret, N. Charlotte;Ovbiagele, Bruce;Peters, Annette;Psaty, Bruce M.;Rich, Stephen S.;Rosand, Jonathan;Sabatine, Marc S.;Sacco, Ralph L.;Saleheen, Danish;Sandset, Else Charlotte;Salomaa, Veikko;Sargurupremraj, Muralidharan;Sasaki, Makoto;Satizabal, Claudia L.;Schmidt, Carsten O.;Shimizu, Atsushi;Smith, Nicholas L.;Sloane, Kelly L.;Sutoh, Yoichi;Sun, Yan V.;Tanno, Kozo;Tiedt, Steffen;Tatlisumak, Turgut;Torres-Aguila, Nuria P.;Tiwari, Hemant K.;Tregouet, David-Alexandre;Trompet, Stella;Tuladhar, Anil Man;Tybjaerg-Hansen, Anne;van Vugt, Marion;Vibo, Riina;Verma, Shefali S.;Wiggins, Kerri L.;Wennberg, Patrik;Woo, Daniel;Wilson, Peter W. F.;Xu, Huichun;Yang, Qiong;Yoon, Kyungheon;Millwood, Iona Y.;Gieger, Christian;Ninomiya, Toshiharu;Grabe, Hans J.;Jukema, J. Wouter;Rissanen, Ina L.;Strbian, Daniel;Kim, Young Jin;Chen, Pei-Hsin;Mayerhofer, Ernst;Howson, Joanna M. M.;Irvin, Marguerite R.;Adams, Hieab;Wassertheil-Smoller, Sylvia;Christensen, Kaare;Ikram, Mohammad A.;Rundek, Tatjana;Worrall, Bradford B.;Lathrop, G. Mark;Riaz, Moeen;Simonsick, Eleanor M.;Korv, Janika;Franca, Paulo H. C.;Zand, Ramin;Prasad, Kameshwar;Frikke-Schmidt, Ruth;de Leeuw, Frank-Erik;Liman, Thomas;Haeusler, Karl Georg;Ruigrok, Ynte M.;Heuschmann, Peter Ulrich;Longstreth, W. T.;Jung, Keum Ji;Bastarache, Lisa;Pare, Guillaume;Damrauer, Scott M.;Chasman, Daniel I.;Rotter, Jerome I.;Anderson, Christopher D.;Zwart, John-Anker;Niiranen, Teemu J.;Fornage, Myriam;Liaw, Yung-Po;Seshadri, Sudha;Fernandez-Cadenas, Israel;Walters, Robin G.;Ruff, Christian T.;Owolabi, Mayowa O.;Huffman, Jennifer E.;Milani, Lili;Kamatani, Yoichiro;Dichgans, Martin;Debette, Stephanie;Lee, Jin-Moo;Cheng, Yu-Ching;Meschia, James F.;Chen, Wei Min;Sale, Michele M.;Zonderman, Alan B.;Evans, Michele K.;Wilson, James G.;Correa, Adolfo;Traylor, Matthew;Lewis, Cathryn M.;Reiner, Alexander;Haessler, Jeffrey;Langefeld, Carl D.;Gottesman, Rebecca F.;Yaffe, Kristine;Liu, Yong Mei;Kooperberg, Charles;Lange, Leslie A.;Furie, Karen L.;Arnett, Donna K.;Benavente, Oscar R.;Grewal, Raji P.;Peddareddygari, Leema Reddy;Hveem, Kristian;Lindstrom, Sara;Wang, Lu;Smith, Erin N.;Gordon, William;Vlieg, Astrid van Hylckama;de Andrade, Mariza;Brody, Jennifer A.;Pattee, Jack W.;Brumpton, Ben M.;Suchon, Pierre;Chen, Ming-Huei;Frazer, Kelly A.;Turman, Constance;Germain, Marine;MacDonald, James;Braekkan, Sigrid K.;Armasu, Sebastian M.;Pankratz, Nathan;Jackson, Rebecca D.;Nielsen, Jonas B.;Giulianin, Franco;Puurunen, Marja K.;Ibrahim, Manal;Heckbert, Susan R.;Bammler, Theo K.;McCauley, Bryan M.;Taylor, Kent D.;Pankow, James S.;Reiner, Alexander P.;Gabrielsen, Maiken E.;Deleuze, Jean-Francois;O'Donnell, Chris J.;Kim, Jihye;McKnight, Barbara;Kraft, Peter;Hansen, John-Bjarne;Rosendaal, Frits R.;Heit, John A.;Tang, Weihong;Morange, Pierre-Emmanuel;Johnson, Andrew D.;Kabrhel, Christopher;van Dijk, Ewoud J.;Koudstaal, Peter J.;Luijckx, Gert-Jan;Nederkoorn, Paul J.;van Oostenbrugge, Robert J.;Visser, Marieke C.;Wermer, Marieke J. H.;Kappelle, L. Jaap;Esko, Tonu;Metspalu, Andres;Magi, Reedik;Nelis, Mari;Levi, Christopher R.;Maguire, Jane;Jimenez-Conde, Jordi;Sharma, Pankaj;Sudlow, Cathie L. M.;Rannikmae, Kristiina;Schmidt, Reinhold;Slowik, Agnieszka;Pera, Joanna;Thijs, Vincent N. S.;Lindgren, Arne G.;Ilinca, Andreea;Melander, Olle;Engstrom, Gunnar;Rexrode, Kathryn M.;Rothwell, Peter M.;Stanne, Tara M.;Johnson, Julie A.;Danesh, John;Butterworth, Adam S.;Heitsch, Laura;Boncoraglio, Giorgio B.;Kubo, Michiaki;Pezzini, Alessandro;Rolfs, Arndt;Giese, Anne-Katrin;Weir, David;Ross, Owen A.;Lemmons, Robin;Soderholm, Martin;Cushman, Mary;Jood, Katarina;McDonough, Caitrin W.;Bell, Steven;Linkohr, Birgit;Lee, Tsong-Hai;Putaala, Jukka;Lopez, Oscar L.;Carty, Cara L.;Jian, Xueqiu;Schminke, Ulf;Cullell, Natalia;Delgado, Pilar;Ibanez, Laura;Krupinski, Jerzy;Lioutas, Vasileios;Matsuda, Koichi;Montaner, Joan;Muino, Elena;Roquer, Jaume;Sarnowski, Chloe;Sattar, Naveed;Sibolt, Gerli;Teumer, Alexander;Rutten-Jacobs, Loes;Kanai, Masahiro;Gretarsdottir, Solveig;Rost, Natalia S.;Yusuf, Salim;Almgren, Peter;Ay, Hakan;Bevan, Steve;Brown, Robert D., Jr.;Carrera, Caty;Buring, Julie E.;Chen, Wei-Min;Cotlarciuc, Ioana;de Bakker, Paul I. W.;DeStefano, Anita L.;den Hoed, Marcel;Duan, Qing;Engelter, Stefan T.;Falcone, Guido J.;Gustafsson, Stefan;Hassan, Ahamad;Holliday, Elizabeth G.;Howard, George;Hsu, Fang-Chi;Ingelsson, Erik;Harris, Tamara B.;Kissela, Brett M.;Kleindorfer, Dawn O.;Langenberg, Claudia;Leys, Didier;Lin, Wei-Yu;Lorentzen, Erik;Magnusson, Patrik K.;McArdle, Patrick F.;Pulit, Sara L.;Rice, Kenneth;Sakaue, Saori;Sapkota, Bishwa R.;Tanislav, Christian;Thorleifsson, Gudmar;Thorsteinsdottir, Unnur;Tzourio, Christophe;van Duijn, Cornelia M.;Walters, Matthew;Wareham, Nicholas J.;Amin, Najaf;Aparicio, Hugo J.;Attia, John;Beiser, Alexa S.;Berr, Claudine;Bustamante, Mariana;Caso, Valeria;Choi, Seung Hoan;Chowhan, Ayesha;Dartigues, Jean-Francois;Delavaran, Hossein;Dorr, Marcus;Ford, Ian;Gurpreet, Wander S.;Hamsten, Anders;Hozawa, Atsushi;Ingelsson, Martin;Iwasaki, Motoki;Kaffashian, Sara;Kalra, Lalit;Kjartansson, Olafur;Kloss, Manja;Labovitz, Daniel L.;Laurie, Cathy C.;Li, Linxin;Lind, Lars;Lindgren, Cecilia M.;Makoto, Hirata;Minegishi, Naoko;Morris, Andrew P.;Mueller-Nurasyid, Martina;Norrving, Bo;Ogishima, Soichi;Parati, Eugenio A.;Pedersen, Nancy L.;Perola, Markus;Jousilahti, Pekka;Pileggi, Silvana;Rabionet, Raquel;Riba-Llena, Iolanda;Ribases, Marta;Romero, Jose R.;Rudd, Anthony G.;Sarin, Antti-Pekka;Sarju, Ralhan;Satoh, Mamoru;Sawada, Norie;Sigurdsson, Asgeir;Smith, Albert;Stine, O. Colin;Stott, David J.;Strauch, Konstantin;Takai, Takako;Tanaka, Hideo;Touze, Emmanuel;Tsugane, Shoichiro;Uitterlinden, Andre G.;Valdimarsson, Einar M.;van der Lee, Sven J.;Wakai, Kenji;Williams, Stephen R.;Wolfe, Charles D. A.;Wong, Quenna;Yamaji, Taiki;Sanghera, Dharambir K.;Stefansson, Kari;Martinez-Majander, Nicolas;Sobue, Kenji;Soriano-Tarraga, Carolina;Volzke, Henry;Akpa, Onoja;Sarfo, Fred S.;Akpalu, Albert;Obiako, Reginald;Wahab, Kolawole;Osaigbovo, Godwin;Owolabi, Lukman;Komolafe, Morenikeji;Jenkins, Carolyn;Arulogun, Oyedunni;Ogbole, Godwin;Adeoye, Abiodun M.;Akinyemi, Joshua;Agunloye, Atinuke;Fakunle, Adekunle G.;Uvere, Ezinne;Olalere, Abimbola;Adebajo, Olayinka J.;Chen, Junshi;Clarke, Robert;Collins, Rory;Guo, Yu;Wang, Chen;Lv, Jun;Peto, Richard;Chen, Yiping;Fairhurst-Hunter, Zammy;Hill, Michael;Pozarickij, Alfred;Schmidt, Dan;Stevens, Becky;Turnbull, Iain;Yu, Canqing;Nagai, Akiko;Murakami, Yoishinori;Shiroma, Eric J.;Sigurdsson, Sigurdur;Ghanbari, Mohsen;Boerwinkle, Eric;Fongang, Bernard;Wang, Ruiqi;Ikram, Mohammad K.;Volker, Uwe;de Laat, Karlijn F.;van Norden, Anouk G. W.;de Kort, Paul L.;Vermeer, Sarah E.;Brouwers, Paul J. A. M.;Gons, Rob A. R.;den Heijer, Tom;van Dijk, Gert W.;van Rooij, Frank G. W.;Aamodt, Anne H.;Skogholt, Anne H.;Willer, Cristen J.;Heuch, Ingrid;Hagen, Knut;Fritsche, Lars G.;Pedersen, Linda M.;Ellekjaer, Hanne;Zhou, Wei;Martinsen, Amy E.;Kristoffersen, Espen S.;Thomas, Laurent F.;Kleinschnitz, Christoph;Frantz, Stefan;Ungethum, Kathrin;Gallego-Fabrega, Cristina;Lledos, Miquel;Llucia-Carol, Laia;Sobrino, Tomas;Campos, Francisco;Castillo, Jose;Freijo, Marimar;Arenillas, Juan Francisco;Obach, Victor;Alvarez-Sabin, Jose;Molina, Carlos A.;Ribo, Marc;Munoz-Narbona, Lucia;Lopez-Cancio, Elena;Millan, Monica;Diaz-Navarro, Rosa;Vives-Bauza, Cristofol;Serrano-Heras, Gemma;Segura, Tomas;Dhar, Rajat;Delgado-Mederos, Raquel;Prats-Sanchez, Luis;Camps-Renom, Pol;Blay, Natalia;Sumoy, Lauro;Marti-Fabregas, Joan;Schnohr, Peter;Jensen, Gorm B.;Benn, Marianne;Afzal, Shoaib;Kamstrup, Pia R.;van Setten, Jessica;van der Laan, Sander W.;Vonk, Jet M. J.;Kim, Bong-Jo;Curtze, Sami;Tiainen, Marjaana;Kinnunen, Janne;Menon, Vilas;Sung, Yun Ju;Yang, Chengran;Saillour-Glenisson, Florence;Gravel, Simon
• 通讯作者: Gravel, Simon

Predicting cell-type-specific non-coding RNA transcription from genome sequence

• DOI: 10.1101/2020.03.29.011205
• 发表时间: 2020-03
• 期刊: bioRxiv
• 作者: Masaru Koido;C. Hon;S. Koyama;H. Kawaji;Y. Murakawa;K. Ishigaki;K. Ito;J. Sese;Y. Kamatani;Piero Carninci;C. Terao

遺伝的リスクを生物学的に解釈するゲノム・オミックス・ヒト細胞モデルの統合解析

基因组、组学和人类细胞模型的综合分析，从生物学角度解释遗传风险

• 发表时间: 2022
• 作者: Kamikawa R;Mochizuki T;Sakamoto M;Tanizawa Y;Nakayama T;Onuma R;Cenci U;Moog D;Speak S;Sarkozi K;Toseland A;van Oosterhout C;Oyama K;Kato M;Kume K;Kayama M;Azuma T;Ishii K;Miyashita H;Henrissat B;Lombard V;Win J;Kamoun S;Kashiyama Y;Mayama S;Miyagishima S;小井土大
• 通讯作者: 小井土大

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元WET研究者によるオミクス統合解析手法の開発

前WET研究员开发的整合组学分析方法

• 发表时间: 2022
• 作者: 田中冴;荒川和晴;小井土大
• 通讯作者: 小井土大