Recherche

Zhang, Jasper Zhongyuan; Rios, Juan David; Pechlivanoglou, Tilemanchos; Yang, Alan; Zhang, Qiyue; Deris, Dimitrios; Cromwell, Ian; Pechlivanoglou, Petros — 2024 Supplementary Material 7: Fig. S7 Bland Alman plots illustrating the agreement between manual and automated digitization Test 3 PFS curve 1 and curve 2. https://creativecommons.org/licenses/by/4.0/legalcode

Taj, Billy; Adeolu, Mobolaji; Xiong, Xuejian; Ang, Jordan; Nursimulu, Nirvana; Parkinson, John — 2024 Additional file 12: Table S8. Computational performance statistics of MetaPro, HUMAnN3, and SAMSA2. This table reports the amount of processing time required for each run of the three pipelines.  MetaPro additionally exports the timing data of each stage independently. HUMAnN3’s pre-processing step is a separate stage using a separate tool called KneadData. SAMSA2 cleans the data in the pipeline, but it is integrated and does not export timing data. https://creativecommons.org/licenses/by/4.0/legalcode

Wu, Yinqiao; Zhang, Yuedong; Liu, Hang; Gao, Yun; Liu, Yuyan; Chen, Ling; Liu, Lu; Irwin, David M.; Hou, Chunhui; Zhou, Zhongyin; Zhang, Yaping — 2022 Additional file 5: Table S4. Characterization of a total of 2576 functional enhancers in the pig genome. https://creativecommons.org/licenses/by/4.0/legalcode

Kanoni, Stavroula; Graham, Sarah E.; Wang, Yuxuan; Surakka, Ida; Ramdas, Shweta; Zhu, Xiang; Clarke, Shoa L.; Bhatti, Konain Fatima; Vedantam, Sailaja; Winkler, Thomas W.; Locke, Adam E.; Marouli, Eirini; Zajac, Greg J. M.; Wu, Kuan-Han H.; Ntalla, Ioanna; Hui, Qin; Klarin, Derek; Hilliard, Austin T.; Wang, Zeyuan; Xue, Chao; Thorleifsson, Gudmar; Helgadottir, Anna; Gudbjartsson, Daniel F.; Holm, Hilma; Olafsson, Isleifur; Hwang, Mi Yeong; Han, Sohee; Akiyama, Masato; Sakaue, Saori; Terao, Chikashi; Kanai, Masahiro; Zhou, Wei; Brumpton, Ben M.; Rasheed, Humaira; Havulinna, Aki S.; Veturi, Yogasudha; Pacheco, Jennifer Allen; Rosenthal, Elisabeth A.; Lingren, Todd; Feng, QiPing; Kullo, Iftikhar J.; Narita, Akira; Takayama, Jun; Martin, Hilary C.; Hunt, Karen A.; Trivedi, Bhavi; Haessler, Jeffrey; Giulianini, Franco; Bradford, Yuki; Miller, Jason E.; Campbell, Archie; Lin, Kuang; Millwood, Iona Y.; Rasheed, Asif; Hindy, George; Faul, Jessica D.; Zhao, Wei; Weir, David R.; Turman, Constance; Huang, Hongyan; Graff, Mariaelisa; Choudhury, Ananyo; Sengupta, Dhriti; Mahajan, Anubha; Brown, Michael R.; Zhang, Weihua; Yu, Ketian; Schmidt, Ellen M.; Pandit, Anita; Gustafsson, Stefan; Yin, Xianyong; Luan, Jian’an; Zhao, Jing-Hua; Matsuda, Fumihiko; Jang, Hye-Mi; Yoon, Kyungheon; Medina-Gomez, Carolina; Pitsillides, Achilleas; Hottenga, Jouke Jan; Wood, Andrew R.; Ji, Yingji; Gao, Zishan; Haworth, Simon; Yousri, Noha A.; Mitchell, Ruth E.; Chai, Jin Fang; Aadahl, Mette; Bjerregaard, Anne A.; Yao, Jie; Manichaikul, Ani; Hwu, Chii-Min; Hung, Yi-Jen; Warren, Helen R.; Ramirez, Julia; Bork-Jensen, Jette; Kårhus, Line L.; Goel, Anuj; Sabater-Lleal, Maria; Noordam, Raymond; Mauro, Pala; Matteo, Floris; McDaid, Aaron F.; Marques-Vidal, Pedro; Wielscher, Matthias; Trompet, Stella; Sattar, Naveed; Møllehave, Line T.; Munz, Matthias; Zeng, Lingyao; Huang, Jianfeng; Yang, Bin; Poveda, Alaitz; Kurbasic, Azra; Lamina, Claudia; Forer, Lukas; Scholz, Markus; Galesloot, Tessel E.; Bradfield, Jonathan P.; Ruotsalainen, Sanni E.; Daw, EWarwick; Zmuda, Joseph M.; Mitchell, Jonathan S.; Fuchsberger, Christian; Christensen, Henry; Brody, Jennifer A.; Vazquez-Moreno, Miguel; Feitosa, Mary F.; Wojczynski, Mary K.; Wang, Zhe; Preuss, Michael H.; Mangino, Massimo; Christofidou, Paraskevi; Verweij, Niek; Benjamins, Jan W.; Engmann, Jorgen; Tsao, Noah L.; Verma, Anurag; Slieker, Roderick C.; Lo, Ken Sin; Zilhao, Nuno R.; Le, Phuong; Kleber, Marcus E.; Delgado, Graciela E.; Huo, Shaofeng; Ikeda, Daisuke D.; Iha, Hiroyuki; Yang, Jian; Liu, Jun; Demirkan, Ayşe; Leonard, Hampton L.; Marten, Jonathan; Frank, Mirjam; Schmidt, Börge; Smyth, Laura J.; Cañadas-Garre, Marisa; Wang, Chaolong; Nakatochi, Masahiro; Wong, Andrew; Hutri-Kähönen, Nina; Sim, Xueling; Xia, Rui; Huerta-Chagoya, Alicia; Fernandez-Lopez, Juan Carlos; Lyssenko, Valeriya; Nongmaithem, Suraj S.; Bayyana, Swati; Stringham, Heather M.; Irvin, Marguerite R.; Oldmeadow, Christopher; Kim, Han-Na; Ryu, Seungho; Timmers, Paul R. H. J.; Arbeeva, Liubov; Dorajoo, Rajkumar; Lange, Leslie A.; Prasad, Gauri; Lorés-Motta, Laura; Pauper, Marc; Long, Jirong; Li, Xiaohui; Theusch, Elizabeth; Takeuchi, Fumihiko; Spracklen, Cassandra N.; Loukola, Anu; Bollepalli, Sailalitha; Warner, Sophie C.; Wang, Ya Xing; Wei, Wen B.; Nutile, Teresa; Ruggiero, Daniela; Sung, Yun Ju; Chen, Shufeng; Liu, Fangchao; Yang, Jingyun; Kentistou, Katherine A.; Banas, Bernhard; Nardone, Giuseppe Giovanni; Meidtner, Karina; Bielak, Lawrence F.; Smith, Jennifer A.; Hebbar, Prashantha; Farmaki, Aliki-Eleni; Hofer, Edith; Lin, Maoxuan; Concas, Maria Pina; Vaccargiu, Simona; van der Most, Peter J.; Pitkänen, Niina; Cade, Brian E.; van der Laan, Sander W.; Chitrala, Kumaraswamy Naidu; Weiss, Stefan; Bentley, Amy R.; Doumatey, Ayo P.; Adeyemo, Adebowale A.; Lee, Jong Young; Petersen, Eva R. B.; Nielsen, Aneta A.; Choi, Hyeok Sun; Nethander, Maria; Freitag-Wolf, Sandra; Southam, Lorraine; Rayner, Nigel W.; Wang, Carol A.; Lin, Shih-Yi; Wang, Jun-Sing; Couture, Christian; Lyytikäinen, Leo-Pekka; Nikus, Kjell; Cuellar-Partida, Gabriel; Vestergaard, Henrik; Hidalgo, Bertha; Giannakopoulou, Olga; Cai, Qiuyin; Obura, Morgan O.; van Setten, Jessica; Li, Xiaoyin; Liang, Jingjing; Tang, Hua; Terzikhan, Natalie; Shin, Jae Hun; Jackson, Rebecca D.; Reiner, Alexander P.; Martin, Lisa Warsinger; Chen, Zhengming; Li, Liming; Kawaguchi, Takahisa; Thiery, Joachim; Bis, Joshua C.; Launer, Lenore J.; Li, Huaixing; Nalls, Mike A.; Raitakari, Olli T.; Ichihara, Sahoko; Wild, Sarah H.; Nelson, Christopher P.; Campbell, Harry; Jäger, Susanne; Nabika, Toru; Al-Mulla, Fahd; Niinikoski, Harri; Braund, Peter S.; Kolcic, Ivana; Kovacs, Peter; Giardoglou, Tota; Katsuya, Tomohiro; de Kleijn, Dominique; de Borst, Gert J.; Kim, Eung Kweon; Adams, Hieab H. H.; Ikram, M. Arfan; Zhu, Xiaofeng; Asselbergs, Folkert W.; Kraaijeveld, Adriaan O.; Beulens, Joline W. J.; Shu, Xiao-Ou; Rallidis, Loukianos S.; Pedersen, Oluf; Hansen, Torben; Mitchell, Paul; Hewitt, Alex W.; Kähönen, Mika; Pérusse, Louis; Bouchard, Claude; Tönjes, Anke; Chen, Yii-Der Ida; Pennell, Craig E.; Mori, Trevor A.; Lieb, Wolfgang; Franke, Andre; Ohlsson, Claes; Mellström, Dan; Cho, Yoon Shin; Lee, Hyejin; Yuan, Jian-Min; Koh, Woon-Puay; Rhee, Sang Youl; Woo, Jeong-Taek; Heid, Iris M.; Stark, Klaus J.; Zimmermann, Martina E.; Völzke, Henry; Homuth, Georg; Evans, Michele K.; Zonderman, Alan B.; Polasek, Ozren; Pasterkamp, Gerard; Hoefer, Imo E.; Redline, Susan; Pahkala, Katja; Oldehinkel, Albertine J.; Snieder, Harold; Biino, Ginevra; Schmidt, Reinhold; Schmidt, Helena; Bandinelli, Stefania; Dedoussis, George; Thanaraj, Thangavel Alphonse; Kardia, Sharon L. R.; Peyser, Patricia A.; Kato, Norihiro; Schulze, Matthias B.; Girotto, Giorgia; Böger, Carsten A.; Jung, Bettina; Joshi, Peter K.; Bennett, David A.; De Jager, Philip L.; Lu, Xiangfeng; Mamakou, Vasiliki; Brown, Morris; Caulfield, Mark J.; Munroe, Patricia B.; Guo, Xiuqing; Ciullo, Marina; Jonas, Jost B.; Samani, Nilesh J.; Kaprio, Jaakko; Pajukanta, Päivi; Tusié-Luna, Teresa; Aguilar-Salinas, Carlos A.; Adair, Linda S.; Bechayda, Sonny Augustin; de Silva, H. Janaka; Wickremasinghe, Ananda R.; Krauss, Ronald M.; Wu, Jer-Yuarn; Zheng, Wei; Hollander, Anneke Iden; Bharadwaj, Dwaipayan; Correa, Adolfo; Wilson, James G.; Lind, Lars; Heng, Chew-Kiat; Nelson, Amanda E.; Golightly, Yvonne M.; Wilson, James F.; Penninx, Brenda; Kim, Hyung-Lae; Attia, John; Scott, Rodney J.; Rao, D. C.; Arnett, Donna K.; Hunt, Steven C.; Walker, Mark; Koistinen, Heikki A.; Chandak, Giriraj R.; Mercader, Josep M.; Costanzo, Maria C.; Jang, Dongkeun; Burtt, Noël P.; Villalpando, Clicerio Gonzalez; Orozco, Lorena; Fornage, Myriam; Tai, EShyong; van Dam, Rob M.; Lehtimäki, Terho; Chaturvedi, Nish; Yokota, Mitsuhiro; Liu, Jianjun; Reilly, Dermot F.; McKnight, Amy Jayne; Kee, Frank; Jöckel, Karl-Heinz; McCarthy, Mark I.; Palmer, Colin N. A.; Vitart, Veronique; Hayward, Caroline; Simonsick, Eleanor; van Duijn, Cornelia M.; Jin, Zi-Bing; Qu, Jia; Hishigaki, Haretsugu; Lin, Xu; März, Winfried; Gudnason, Vilmundur; Tardif, Jean-Claude; Lettre, Guillaume; Hart, Leen M.‘t; Elders, Petra J. M.; Damrauer, Scott M.; Kumari, Meena; Kivimaki, Mika; van der Harst, Pim; Spector, Tim D.; Loos, Ruth J. F.; Province, Michael A.; Parra, Esteban J.; Cruz, Miguel; Psaty, Bruce M.; Brandslund, Ivan; Pramstaller, Peter P.; Rotimi, Charles N.; Christensen, Kaare; Ripatti, Samuli; Widén, Elisabeth; Hakonarson, Hakon; Grant, Struan F. A.; Kiemeney, Lambertus A. L. M.; de Graaf, Jacqueline; Loeffler, Markus; Kronenberg, Florian; Gu, Dongfeng; Erdmann, Jeanette; Schunkert, Heribert; Franks, Paul W.; Linneberg, Allan; Jukema, J. Wouter; Khera, Amit V.; Männikkö, Minna; Jarvelin, Marjo-Riitta; Kutalik, Zoltan; Francesco, Cucca; Mook-Kanamori, Dennis O.; van Dijk, Ko Willems; Watkins, Hugh; Strachan, David P.; Grarup, Niels; Sever, Peter; Poulter, Neil; Chuang, Lee-Ming; Rotter, Jerome I.; Dantoft, Thomas M.; Karpe, Fredrik; Neville, Matt J.; Timpson, Nicholas J.; Cheng, Ching-Yu; Wong, Tien-Yin; Khor, Chiea Chuen; Li, Hengtong; Sabanayagam, Charumathi; Peters, Annette; Gieger, Christian; Hattersley, Andrew T.; Pedersen, Nancy L.; Magnusson, Patrik K. E.; Boomsma, Dorret I.; Willemsen, Allegonda H. M.; Cupples, LAdrienne; van Meurs, Joyce B. J.; Ghanbari, Mohsen; Gordon-Larsen, Penny; Huang, Wei; Kim, Young Jin; Tabara, Yasuharu; Wareham, Nicholas J.; Langenberg, Claudia; Zeggini, Eleftheria; Kuusisto, Johanna; Laakso, Markku; Ingelsson, Erik; Abecasis, Goncalo; Chambers, John C.; Kooner, Jaspal S.; de Vries, Paul S.; Morrison, Alanna C.; Hazelhurst, Scott; Ramsay, Michèle; North, Kari E.; Daviglus, Martha; Kraft, Peter; Martin, Nicholas G.; Whitfield, John B.; Abbas, Shahid; Saleheen, Danish; Walters, Robin G.; Holmes, Michael V.; Black, Corri; Smith, Blair H.; Baras, Aris; Justice, Anne E.; Buring, Julie E.; Ridker, Paul M.; Chasman, Daniel I.; Kooperberg, Charles; Tamiya, Gen; Yamamoto, Masayuki; van Heel, David A.; Trembath, Richard C.; Wei, Wei-Qi; Jarvik, Gail P.; Namjou, Bahram; Hayes, M. Geoffrey; Ritchie, Marylyn D.; Jousilahti, Pekka; Salomaa, Veikko; Hveem, Kristian; Åsvold, Bjørn Olav; Kubo, Michiaki; Kamatani, Yoichiro; Okada, Yukinori; Murakami, Yoshinori; Kim, Bong-Jo; Thorsteinsdottir, Unnur; Stefansson, Kari; Zhang, Jifeng; Chen, YEugene; Ho, Yuk-Lam; Lynch, Julie A.; Rader, Daniel J.; Tsao, Philip S.; Chang, Kyong-Mi; Cho, Kelly; O’Donnell, Christopher J.; Gaziano, John M.; Wilson, Peter W. F.; Frayling, Timothy M.; Hirschhorn, Joel N.; Kathiresan, Sekar; Mohlke, Karen L.; Sun, Yan V.; Morris, Andrew P.; Boehnke, Michael; Brown, Christopher D.; Natarajan, Pradeep; Deloukas, Panos; Willer, Cristen J.; Assimes, Themistocles L.; Peloso, Gina M. — 2023 Additional file 30: Table S20. Colocalization results for the sex-specific loci. https://creativecommons.org/licenses/by/4.0/legalcode

Kanoni, Stavroula; Graham, Sarah E.; Wang, Yuxuan; Surakka, Ida; Ramdas, Shweta; Zhu, Xiang; Clarke, Shoa L.; Bhatti, Konain Fatima; Vedantam, Sailaja; Winkler, Thomas W.; Locke, Adam E.; Marouli, Eirini; Zajac, Greg J. M.; Wu, Kuan-Han H.; Ntalla, Ioanna; Hui, Qin; Klarin, Derek; Hilliard, Austin T.; Wang, Zeyuan; Xue, Chao; Thorleifsson, Gudmar; Helgadottir, Anna; Gudbjartsson, Daniel F.; Holm, Hilma; Olafsson, Isleifur; Hwang, Mi Yeong; Han, Sohee; Akiyama, Masato; Sakaue, Saori; Terao, Chikashi; Kanai, Masahiro; Zhou, Wei; Brumpton, Ben M.; Rasheed, Humaira; Havulinna, Aki S.; Veturi, Yogasudha; Pacheco, Jennifer Allen; Rosenthal, Elisabeth A.; Lingren, Todd; Feng, QiPing; Kullo, Iftikhar J.; Narita, Akira; Takayama, Jun; Martin, Hilary C.; Hunt, Karen A.; Trivedi, Bhavi; Haessler, Jeffrey; Giulianini, Franco; Bradford, Yuki; Miller, Jason E.; Campbell, Archie; Lin, Kuang; Millwood, Iona Y.; Rasheed, Asif; Hindy, George; Faul, Jessica D.; Zhao, Wei; Weir, David R.; Turman, Constance; Huang, Hongyan; Graff, Mariaelisa; Choudhury, Ananyo; Sengupta, Dhriti; Mahajan, Anubha; Brown, Michael R.; Zhang, Weihua; Yu, Ketian; Schmidt, Ellen M.; Pandit, Anita; Gustafsson, Stefan; Yin, Xianyong; Luan, Jian’an; Zhao, Jing-Hua; Matsuda, Fumihiko; Jang, Hye-Mi; Yoon, Kyungheon; Medina-Gomez, Carolina; Pitsillides, Achilleas; Hottenga, Jouke Jan; Wood, Andrew R.; Ji, Yingji; Gao, Zishan; Haworth, Simon; Yousri, Noha A.; Mitchell, Ruth E.; Chai, Jin Fang; Aadahl, Mette; Bjerregaard, Anne A.; Yao, Jie; Manichaikul, Ani; Hwu, Chii-Min; Hung, Yi-Jen; Warren, Helen R.; Ramirez, Julia; Bork-Jensen, Jette; Kårhus, Line L.; Goel, Anuj; Sabater-Lleal, Maria; Noordam, Raymond; Mauro, Pala; Matteo, Floris; McDaid, Aaron F.; Marques-Vidal, Pedro; Wielscher, Matthias; Trompet, Stella; Sattar, Naveed; Møllehave, Line T.; Munz, Matthias; Zeng, Lingyao; Huang, Jianfeng; Yang, Bin; Poveda, Alaitz; Kurbasic, Azra; Lamina, Claudia; Forer, Lukas; Scholz, Markus; Galesloot, Tessel E.; Bradfield, Jonathan P.; Ruotsalainen, Sanni E.; Daw, EWarwick; Zmuda, Joseph M.; Mitchell, Jonathan S.; Fuchsberger, Christian; Christensen, Henry; Brody, Jennifer A.; Vazquez-Moreno, Miguel; Feitosa, Mary F.; Wojczynski, Mary K.; Wang, Zhe; Preuss, Michael H.; Mangino, Massimo; Christofidou, Paraskevi; Verweij, Niek; Benjamins, Jan W.; Engmann, Jorgen; Tsao, Noah L.; Verma, Anurag; Slieker, Roderick C.; Lo, Ken Sin; Zilhao, Nuno R.; Le, Phuong; Kleber, Marcus E.; Delgado, Graciela E.; Huo, Shaofeng; Ikeda, Daisuke D.; Iha, Hiroyuki; Yang, Jian; Liu, Jun; Demirkan, Ayşe; Leonard, Hampton L.; Marten, Jonathan; Frank, Mirjam; Schmidt, Börge; Smyth, Laura J.; Cañadas-Garre, Marisa; Wang, Chaolong; Nakatochi, Masahiro; Wong, Andrew; Hutri-Kähönen, Nina; Sim, Xueling; Xia, Rui; Huerta-Chagoya, Alicia; Fernandez-Lopez, Juan Carlos; Lyssenko, Valeriya; Nongmaithem, Suraj S.; Bayyana, Swati; Stringham, Heather M.; Irvin, Marguerite R.; Oldmeadow, Christopher; Kim, Han-Na; Ryu, Seungho; Timmers, Paul R. H. J.; Arbeeva, Liubov; Dorajoo, Rajkumar; Lange, Leslie A.; Prasad, Gauri; Lorés-Motta, Laura; Pauper, Marc; Long, Jirong; Li, Xiaohui; Theusch, Elizabeth; Takeuchi, Fumihiko; Spracklen, Cassandra N.; Loukola, Anu; Bollepalli, Sailalitha; Warner, Sophie C.; Wang, Ya Xing; Wei, Wen B.; Nutile, Teresa; Ruggiero, Daniela; Sung, Yun Ju; Chen, Shufeng; Liu, Fangchao; Yang, Jingyun; Kentistou, Katherine A.; Banas, Bernhard; Nardone, Giuseppe Giovanni; Meidtner, Karina; Bielak, Lawrence F.; Smith, Jennifer A.; Hebbar, Prashantha; Farmaki, Aliki-Eleni; Hofer, Edith; Lin, Maoxuan; Concas, Maria Pina; Vaccargiu, Simona; van der Most, Peter J.; Pitkänen, Niina; Cade, Brian E.; van der Laan, Sander W.; Chitrala, Kumaraswamy Naidu; Weiss, Stefan; Bentley, Amy R.; Doumatey, Ayo P.; Adeyemo, Adebowale A.; Lee, Jong Young; Petersen, Eva R. B.; Nielsen, Aneta A.; Choi, Hyeok Sun; Nethander, Maria; Freitag-Wolf, Sandra; Southam, Lorraine; Rayner, Nigel W.; Wang, Carol A.; Lin, Shih-Yi; Wang, Jun-Sing; Couture, Christian; Lyytikäinen, Leo-Pekka; Nikus, Kjell; Cuellar-Partida, Gabriel; Vestergaard, Henrik; Hidalgo, Bertha; Giannakopoulou, Olga; Cai, Qiuyin; Obura, Morgan O.; van Setten, Jessica; Li, Xiaoyin; Liang, Jingjing; Tang, Hua; Terzikhan, Natalie; Shin, Jae Hun; Jackson, Rebecca D.; Reiner, Alexander P.; Martin, Lisa Warsinger; Chen, Zhengming; Li, Liming; Kawaguchi, Takahisa; Thiery, Joachim; Bis, Joshua C.; Launer, Lenore J.; Li, Huaixing; Nalls, Mike A.; Raitakari, Olli T.; Ichihara, Sahoko; Wild, Sarah H.; Nelson, Christopher P.; Campbell, Harry; Jäger, Susanne; Nabika, Toru; Al-Mulla, Fahd; Niinikoski, Harri; Braund, Peter S.; Kolcic, Ivana; Kovacs, Peter; Giardoglou, Tota; Katsuya, Tomohiro; de Kleijn, Dominique; de Borst, Gert J.; Kim, Eung Kweon; Adams, Hieab H. H.; Ikram, M. Arfan; Zhu, Xiaofeng; Asselbergs, Folkert W.; Kraaijeveld, Adriaan O.; Beulens, Joline W. J.; Shu, Xiao-Ou; Rallidis, Loukianos S.; Pedersen, Oluf; Hansen, Torben; Mitchell, Paul; Hewitt, Alex W.; Kähönen, Mika; Pérusse, Louis; Bouchard, Claude; Tönjes, Anke; Chen, Yii-Der Ida; Pennell, Craig E.; Mori, Trevor A.; Lieb, Wolfgang; Franke, Andre; Ohlsson, Claes; Mellström, Dan; Cho, Yoon Shin; Lee, Hyejin; Yuan, Jian-Min; Koh, Woon-Puay; Rhee, Sang Youl; Woo, Jeong-Taek; Heid, Iris M.; Stark, Klaus J.; Zimmermann, Martina E.; Völzke, Henry; Homuth, Georg; Evans, Michele K.; Zonderman, Alan B.; Polasek, Ozren; Pasterkamp, Gerard; Hoefer, Imo E.; Redline, Susan; Pahkala, Katja; Oldehinkel, Albertine J.; Snieder, Harold; Biino, Ginevra; Schmidt, Reinhold; Schmidt, Helena; Bandinelli, Stefania; Dedoussis, George; Thanaraj, Thangavel Alphonse; Kardia, Sharon L. R.; Peyser, Patricia A.; Kato, Norihiro; Schulze, Matthias B.; Girotto, Giorgia; Böger, Carsten A.; Jung, Bettina; Joshi, Peter K.; Bennett, David A.; De Jager, Philip L.; Lu, Xiangfeng; Mamakou, Vasiliki; Brown, Morris; Caulfield, Mark J.; Munroe, Patricia B.; Guo, Xiuqing; Ciullo, Marina; Jonas, Jost B.; Samani, Nilesh J.; Kaprio, Jaakko; Pajukanta, Päivi; Tusié-Luna, Teresa; Aguilar-Salinas, Carlos A.; Adair, Linda S.; Bechayda, Sonny Augustin; de Silva, H. Janaka; Wickremasinghe, Ananda R.; Krauss, Ronald M.; Wu, Jer-Yuarn; Zheng, Wei; Hollander, Anneke Iden; Bharadwaj, Dwaipayan; Correa, Adolfo; Wilson, James G.; Lind, Lars; Heng, Chew-Kiat; Nelson, Amanda E.; Golightly, Yvonne M.; Wilson, James F.; Penninx, Brenda; Kim, Hyung-Lae; Attia, John; Scott, Rodney J.; Rao, D. C.; Arnett, Donna K.; Hunt, Steven C.; Walker, Mark; Koistinen, Heikki A.; Chandak, Giriraj R.; Mercader, Josep M.; Costanzo, Maria C.; Jang, Dongkeun; Burtt, Noël P.; Villalpando, Clicerio Gonzalez; Orozco, Lorena; Fornage, Myriam; Tai, EShyong; van Dam, Rob M.; Lehtimäki, Terho; Chaturvedi, Nish; Yokota, Mitsuhiro; Liu, Jianjun; Reilly, Dermot F.; McKnight, Amy Jayne; Kee, Frank; Jöckel, Karl-Heinz; McCarthy, Mark I.; Palmer, Colin N. A.; Vitart, Veronique; Hayward, Caroline; Simonsick, Eleanor; van Duijn, Cornelia M.; Jin, Zi-Bing; Qu, Jia; Hishigaki, Haretsugu; Lin, Xu; März, Winfried; Gudnason, Vilmundur; Tardif, Jean-Claude; Lettre, Guillaume; Hart, Leen M.‘t; Elders, Petra J. M.; Damrauer, Scott M.; Kumari, Meena; Kivimaki, Mika; van der Harst, Pim; Spector, Tim D.; Loos, Ruth J. F.; Province, Michael A.; Parra, Esteban J.; Cruz, Miguel; Psaty, Bruce M.; Brandslund, Ivan; Pramstaller, Peter P.; Rotimi, Charles N.; Christensen, Kaare; Ripatti, Samuli; Widén, Elisabeth; Hakonarson, Hakon; Grant, Struan F. A.; Kiemeney, Lambertus A. L. M.; de Graaf, Jacqueline; Loeffler, Markus; Kronenberg, Florian; Gu, Dongfeng; Erdmann, Jeanette; Schunkert, Heribert; Franks, Paul W.; Linneberg, Allan; Jukema, J. Wouter; Khera, Amit V.; Männikkö, Minna; Jarvelin, Marjo-Riitta; Kutalik, Zoltan; Francesco, Cucca; Mook-Kanamori, Dennis O.; van Dijk, Ko Willems; Watkins, Hugh; Strachan, David P.; Grarup, Niels; Sever, Peter; Poulter, Neil; Chuang, Lee-Ming; Rotter, Jerome I.; Dantoft, Thomas M.; Karpe, Fredrik; Neville, Matt J.; Timpson, Nicholas J.; Cheng, Ching-Yu; Wong, Tien-Yin; Khor, Chiea Chuen; Li, Hengtong; Sabanayagam, Charumathi; Peters, Annette; Gieger, Christian; Hattersley, Andrew T.; Pedersen, Nancy L.; Magnusson, Patrik K. E.; Boomsma, Dorret I.; Willemsen, Allegonda H. M.; Cupples, LAdrienne; van Meurs, Joyce B. J.; Ghanbari, Mohsen; Gordon-Larsen, Penny; Huang, Wei; Kim, Young Jin; Tabara, Yasuharu; Wareham, Nicholas J.; Langenberg, Claudia; Zeggini, Eleftheria; Kuusisto, Johanna; Laakso, Markku; Ingelsson, Erik; Abecasis, Goncalo; Chambers, John C.; Kooner, Jaspal S.; de Vries, Paul S.; Morrison, Alanna C.; Hazelhurst, Scott; Ramsay, Michèle; North, Kari E.; Daviglus, Martha; Kraft, Peter; Martin, Nicholas G.; Whitfield, John B.; Abbas, Shahid; Saleheen, Danish; Walters, Robin G.; Holmes, Michael V.; Black, Corri; Smith, Blair H.; Baras, Aris; Justice, Anne E.; Buring, Julie E.; Ridker, Paul M.; Chasman, Daniel I.; Kooperberg, Charles; Tamiya, Gen; Yamamoto, Masayuki; van Heel, David A.; Trembath, Richard C.; Wei, Wei-Qi; Jarvik, Gail P.; Namjou, Bahram; Hayes, M. Geoffrey; Ritchie, Marylyn D.; Jousilahti, Pekka; Salomaa, Veikko; Hveem, Kristian; Åsvold, Bjørn Olav; Kubo, Michiaki; Kamatani, Yoichiro; Okada, Yukinori; Murakami, Yoshinori; Kim, Bong-Jo; Thorsteinsdottir, Unnur; Stefansson, Kari; Zhang, Jifeng; Chen, YEugene; Ho, Yuk-Lam; Lynch, Julie A.; Rader, Daniel J.; Tsao, Philip S.; Chang, Kyong-Mi; Cho, Kelly; O’Donnell, Christopher J.; Gaziano, John M.; Wilson, Peter W. F.; Frayling, Timothy M.; Hirschhorn, Joel N.; Kathiresan, Sekar; Mohlke, Karen L.; Sun, Yan V.; Morris, Andrew P.; Boehnke, Michael; Brown, Christopher D.; Natarajan, Pradeep; Deloukas, Panos; Willer, Cristen J.; Assimes, Themistocles L.; Peloso, Gina M. — 2023 Additional file 32: Table S21. Significant X chromosome results in the sex-combined and sex-stratified analysis and replication. https://creativecommons.org/licenses/by/4.0/legalcode

Kanoni, Stavroula; Graham, Sarah E.; Wang, Yuxuan; Surakka, Ida; Ramdas, Shweta; Zhu, Xiang; Clarke, Shoa L.; Bhatti, Konain Fatima; Vedantam, Sailaja; Winkler, Thomas W.; Locke, Adam E.; Marouli, Eirini; Zajac, Greg J. M.; Wu, Kuan-Han H.; Ntalla, Ioanna; Hui, Qin; Klarin, Derek; Hilliard, Austin T.; Wang, Zeyuan; Xue, Chao; Thorleifsson, Gudmar; Helgadottir, Anna; Gudbjartsson, Daniel F.; Holm, Hilma; Olafsson, Isleifur; Hwang, Mi Yeong; Han, Sohee; Akiyama, Masato; Sakaue, Saori; Terao, Chikashi; Kanai, Masahiro; Zhou, Wei; Brumpton, Ben M.; Rasheed, Humaira; Havulinna, Aki S.; Veturi, Yogasudha; Pacheco, Jennifer Allen; Rosenthal, Elisabeth A.; Lingren, Todd; Feng, QiPing; Kullo, Iftikhar J.; Narita, Akira; Takayama, Jun; Martin, Hilary C.; Hunt, Karen A.; Trivedi, Bhavi; Haessler, Jeffrey; Giulianini, Franco; Bradford, Yuki; Miller, Jason E.; Campbell, Archie; Lin, Kuang; Millwood, Iona Y.; Rasheed, Asif; Hindy, George; Faul, Jessica D.; Zhao, Wei; Weir, David R.; Turman, Constance; Huang, Hongyan; Graff, Mariaelisa; Choudhury, Ananyo; Sengupta, Dhriti; Mahajan, Anubha; Brown, Michael R.; Zhang, Weihua; Yu, Ketian; Schmidt, Ellen M.; Pandit, Anita; Gustafsson, Stefan; Yin, Xianyong; Luan, Jian’an; Zhao, Jing-Hua; Matsuda, Fumihiko; Jang, Hye-Mi; Yoon, Kyungheon; Medina-Gomez, Carolina; Pitsillides, Achilleas; Hottenga, Jouke Jan; Wood, Andrew R.; Ji, Yingji; Gao, Zishan; Haworth, Simon; Yousri, Noha A.; Mitchell, Ruth E.; Chai, Jin Fang; Aadahl, Mette; Bjerregaard, Anne A.; Yao, Jie; Manichaikul, Ani; Hwu, Chii-Min; Hung, Yi-Jen; Warren, Helen R.; Ramirez, Julia; Bork-Jensen, Jette; Kårhus, Line L.; Goel, Anuj; Sabater-Lleal, Maria; Noordam, Raymond; Mauro, Pala; Matteo, Floris; McDaid, Aaron F.; Marques-Vidal, Pedro; Wielscher, Matthias; Trompet, Stella; Sattar, Naveed; Møllehave, Line T.; Munz, Matthias; Zeng, Lingyao; Huang, Jianfeng; Yang, Bin; Poveda, Alaitz; Kurbasic, Azra; Lamina, Claudia; Forer, Lukas; Scholz, Markus; Galesloot, Tessel E.; Bradfield, Jonathan P.; Ruotsalainen, Sanni E.; Daw, EWarwick; Zmuda, Joseph M.; Mitchell, Jonathan S.; Fuchsberger, Christian; Christensen, Henry; Brody, Jennifer A.; Vazquez-Moreno, Miguel; Feitosa, Mary F.; Wojczynski, Mary K.; Wang, Zhe; Preuss, Michael H.; Mangino, Massimo; Christofidou, Paraskevi; Verweij, Niek; Benjamins, Jan W.; Engmann, Jorgen; Tsao, Noah L.; Verma, Anurag; Slieker, Roderick C.; Lo, Ken Sin; Zilhao, Nuno R.; Le, Phuong; Kleber, Marcus E.; Delgado, Graciela E.; Huo, Shaofeng; Ikeda, Daisuke D.; Iha, Hiroyuki; Yang, Jian; Liu, Jun; Demirkan, Ayşe; Leonard, Hampton L.; Marten, Jonathan; Frank, Mirjam; Schmidt, Börge; Smyth, Laura J.; Cañadas-Garre, Marisa; Wang, Chaolong; Nakatochi, Masahiro; Wong, Andrew; Hutri-Kähönen, Nina; Sim, Xueling; Xia, Rui; Huerta-Chagoya, Alicia; Fernandez-Lopez, Juan Carlos; Lyssenko, Valeriya; Nongmaithem, Suraj S.; Bayyana, Swati; Stringham, Heather M.; Irvin, Marguerite R.; Oldmeadow, Christopher; Kim, Han-Na; Ryu, Seungho; Timmers, Paul R. H. J.; Arbeeva, Liubov; Dorajoo, Rajkumar; Lange, Leslie A.; Prasad, Gauri; Lorés-Motta, Laura; Pauper, Marc; Long, Jirong; Li, Xiaohui; Theusch, Elizabeth; Takeuchi, Fumihiko; Spracklen, Cassandra N.; Loukola, Anu; Bollepalli, Sailalitha; Warner, Sophie C.; Wang, Ya Xing; Wei, Wen B.; Nutile, Teresa; Ruggiero, Daniela; Sung, Yun Ju; Chen, Shufeng; Liu, Fangchao; Yang, Jingyun; Kentistou, Katherine A.; Banas, Bernhard; Nardone, Giuseppe Giovanni; Meidtner, Karina; Bielak, Lawrence F.; Smith, Jennifer A.; Hebbar, Prashantha; Farmaki, Aliki-Eleni; Hofer, Edith; Lin, Maoxuan; Concas, Maria Pina; Vaccargiu, Simona; van der Most, Peter J.; Pitkänen, Niina; Cade, Brian E.; van der Laan, Sander W.; Chitrala, Kumaraswamy Naidu; Weiss, Stefan; Bentley, Amy R.; Doumatey, Ayo P.; Adeyemo, Adebowale A.; Lee, Jong Young; Petersen, Eva R. B.; Nielsen, Aneta A.; Choi, Hyeok Sun; Nethander, Maria; Freitag-Wolf, Sandra; Southam, Lorraine; Rayner, Nigel W.; Wang, Carol A.; Lin, Shih-Yi; Wang, Jun-Sing; Couture, Christian; Lyytikäinen, Leo-Pekka; Nikus, Kjell; Cuellar-Partida, Gabriel; Vestergaard, Henrik; Hidalgo, Bertha; Giannakopoulou, Olga; Cai, Qiuyin; Obura, Morgan O.; van Setten, Jessica; Li, Xiaoyin; Liang, Jingjing; Tang, Hua; Terzikhan, Natalie; Shin, Jae Hun; Jackson, Rebecca D.; Reiner, Alexander P.; Martin, Lisa Warsinger; Chen, Zhengming; Li, Liming; Kawaguchi, Takahisa; Thiery, Joachim; Bis, Joshua C.; Launer, Lenore J.; Li, Huaixing; Nalls, Mike A.; Raitakari, Olli T.; Ichihara, Sahoko; Wild, Sarah H.; Nelson, Christopher P.; Campbell, Harry; Jäger, Susanne; Nabika, Toru; Al-Mulla, Fahd; Niinikoski, Harri; Braund, Peter S.; Kolcic, Ivana; Kovacs, Peter; Giardoglou, Tota; Katsuya, Tomohiro; de Kleijn, Dominique; de Borst, Gert J.; Kim, Eung Kweon; Adams, Hieab H. H.; Ikram, M. Arfan; Zhu, Xiaofeng; Asselbergs, Folkert W.; Kraaijeveld, Adriaan O.; Beulens, Joline W. J.; Shu, Xiao-Ou; Rallidis, Loukianos S.; Pedersen, Oluf; Hansen, Torben; Mitchell, Paul; Hewitt, Alex W.; Kähönen, Mika; Pérusse, Louis; Bouchard, Claude; Tönjes, Anke; Chen, Yii-Der Ida; Pennell, Craig E.; Mori, Trevor A.; Lieb, Wolfgang; Franke, Andre; Ohlsson, Claes; Mellström, Dan; Cho, Yoon Shin; Lee, Hyejin; Yuan, Jian-Min; Koh, Woon-Puay; Rhee, Sang Youl; Woo, Jeong-Taek; Heid, Iris M.; Stark, Klaus J.; Zimmermann, Martina E.; Völzke, Henry; Homuth, Georg; Evans, Michele K.; Zonderman, Alan B.; Polasek, Ozren; Pasterkamp, Gerard; Hoefer, Imo E.; Redline, Susan; Pahkala, Katja; Oldehinkel, Albertine J.; Snieder, Harold; Biino, Ginevra; Schmidt, Reinhold; Schmidt, Helena; Bandinelli, Stefania; Dedoussis, George; Thanaraj, Thangavel Alphonse; Kardia, Sharon L. R.; Peyser, Patricia A.; Kato, Norihiro; Schulze, Matthias B.; Girotto, Giorgia; Böger, Carsten A.; Jung, Bettina; Joshi, Peter K.; Bennett, David A.; De Jager, Philip L.; Lu, Xiangfeng; Mamakou, Vasiliki; Brown, Morris; Caulfield, Mark J.; Munroe, Patricia B.; Guo, Xiuqing; Ciullo, Marina; Jonas, Jost B.; Samani, Nilesh J.; Kaprio, Jaakko; Pajukanta, Päivi; Tusié-Luna, Teresa; Aguilar-Salinas, Carlos A.; Adair, Linda S.; Bechayda, Sonny Augustin; de Silva, H. Janaka; Wickremasinghe, Ananda R.; Krauss, Ronald M.; Wu, Jer-Yuarn; Zheng, Wei; Hollander, Anneke Iden; Bharadwaj, Dwaipayan; Correa, Adolfo; Wilson, James G.; Lind, Lars; Heng, Chew-Kiat; Nelson, Amanda E.; Golightly, Yvonne M.; Wilson, James F.; Penninx, Brenda; Kim, Hyung-Lae; Attia, John; Scott, Rodney J.; Rao, D. C.; Arnett, Donna K.; Hunt, Steven C.; Walker, Mark; Koistinen, Heikki A.; Chandak, Giriraj R.; Mercader, Josep M.; Costanzo, Maria C.; Jang, Dongkeun; Burtt, Noël P.; Villalpando, Clicerio Gonzalez; Orozco, Lorena; Fornage, Myriam; Tai, EShyong; van Dam, Rob M.; Lehtimäki, Terho; Chaturvedi, Nish; Yokota, Mitsuhiro; Liu, Jianjun; Reilly, Dermot F.; McKnight, Amy Jayne; Kee, Frank; Jöckel, Karl-Heinz; McCarthy, Mark I.; Palmer, Colin N. A.; Vitart, Veronique; Hayward, Caroline; Simonsick, Eleanor; van Duijn, Cornelia M.; Jin, Zi-Bing; Qu, Jia; Hishigaki, Haretsugu; Lin, Xu; März, Winfried; Gudnason, Vilmundur; Tardif, Jean-Claude; Lettre, Guillaume; Hart, Leen M.‘t; Elders, Petra J. M.; Damrauer, Scott M.; Kumari, Meena; Kivimaki, Mika; van der Harst, Pim; Spector, Tim D.; Loos, Ruth J. F.; Province, Michael A.; Parra, Esteban J.; Cruz, Miguel; Psaty, Bruce M.; Brandslund, Ivan; Pramstaller, Peter P.; Rotimi, Charles N.; Christensen, Kaare; Ripatti, Samuli; Widén, Elisabeth; Hakonarson, Hakon; Grant, Struan F. A.; Kiemeney, Lambertus A. L. M.; de Graaf, Jacqueline; Loeffler, Markus; Kronenberg, Florian; Gu, Dongfeng; Erdmann, Jeanette; Schunkert, Heribert; Franks, Paul W.; Linneberg, Allan; Jukema, J. Wouter; Khera, Amit V.; Männikkö, Minna; Jarvelin, Marjo-Riitta; Kutalik, Zoltan; Francesco, Cucca; Mook-Kanamori, Dennis O.; van Dijk, Ko Willems; Watkins, Hugh; Strachan, David P.; Grarup, Niels; Sever, Peter; Poulter, Neil; Chuang, Lee-Ming; Rotter, Jerome I.; Dantoft, Thomas M.; Karpe, Fredrik; Neville, Matt J.; Timpson, Nicholas J.; Cheng, Ching-Yu; Wong, Tien-Yin; Khor, Chiea Chuen; Li, Hengtong; Sabanayagam, Charumathi; Peters, Annette; Gieger, Christian; Hattersley, Andrew T.; Pedersen, Nancy L.; Magnusson, Patrik K. E.; Boomsma, Dorret I.; Willemsen, Allegonda H. M.; Cupples, LAdrienne; van Meurs, Joyce B. J.; Ghanbari, Mohsen; Gordon-Larsen, Penny; Huang, Wei; Kim, Young Jin; Tabara, Yasuharu; Wareham, Nicholas J.; Langenberg, Claudia; Zeggini, Eleftheria; Kuusisto, Johanna; Laakso, Markku; Ingelsson, Erik; Abecasis, Goncalo; Chambers, John C.; Kooner, Jaspal S.; de Vries, Paul S.; Morrison, Alanna C.; Hazelhurst, Scott; Ramsay, Michèle; North, Kari E.; Daviglus, Martha; Kraft, Peter; Martin, Nicholas G.; Whitfield, John B.; Abbas, Shahid; Saleheen, Danish; Walters, Robin G.; Holmes, Michael V.; Black, Corri; Smith, Blair H.; Baras, Aris; Justice, Anne E.; Buring, Julie E.; Ridker, Paul M.; Chasman, Daniel I.; Kooperberg, Charles; Tamiya, Gen; Yamamoto, Masayuki; van Heel, David A.; Trembath, Richard C.; Wei, Wei-Qi; Jarvik, Gail P.; Namjou, Bahram; Hayes, M. Geoffrey; Ritchie, Marylyn D.; Jousilahti, Pekka; Salomaa, Veikko; Hveem, Kristian; Åsvold, Bjørn Olav; Kubo, Michiaki; Kamatani, Yoichiro; Okada, Yukinori; Murakami, Yoshinori; Kim, Bong-Jo; Thorsteinsdottir, Unnur; Stefansson, Kari; Zhang, Jifeng; Chen, YEugene; Ho, Yuk-Lam; Lynch, Julie A.; Rader, Daniel J.; Tsao, Philip S.; Chang, Kyong-Mi; Cho, Kelly; O’Donnell, Christopher J.; Gaziano, John M.; Wilson, Peter W. F.; Frayling, Timothy M.; Hirschhorn, Joel N.; Kathiresan, Sekar; Mohlke, Karen L.; Sun, Yan V.; Morris, Andrew P.; Boehnke, Michael; Brown, Christopher D.; Natarajan, Pradeep; Deloukas, Panos; Willer, Cristen J.; Assimes, Themistocles L.; Peloso, Gina M. — 2023 Additional file 18: Table S10. Lambda GC values across minor allele frequency bins for sex-specific meta-analyses. https://creativecommons.org/licenses/by/4.0/legalcode

Agarwal, Medha; Xu, Jason — 2023 The principle of majorization-minimization (MM) provides a general framework for eliciting effective algorithms to solve optimization problems. However, the resulting methods often suffer from slow convergence, especially in large-scale and high-dimensional data settings. This has motivated several acceleration schemes tailored for MM algorithms, but many existing approaches are either problem-specific, or rely on approximations and heuristics loosely inspired by the optimization literature. We propose a novel quasi-Newton method for accelerating any valid MM algorithm, cast as seeking a fixed point of the MM <i>algorithm map</i>. The method does not require specific information or computation from the objective function or its gradient, and enjoys a limited-memory variant amenable to efficient computation in high-dimensional settings. By rigorously connecting our approach to Broyden’s classical root-finding methods, we establish convergence guarantees and identify conditions for linear and super-linear convergence. These results are validated numerically and compared to peer methods in a thorough empirical study, showing that it achieves state-of-the-art performance across a diverse range of problems. https://creativecommons.org/licenses/by/4.0/legalcode

Bakhshinyan, David; Suk, Yujin; Kuhlman, Laura; Adile, Ashley A.; Ignatchenko, Vladimir; Custers, Stefan; Gwynne, William D.; Mackling, Andrew; Venugopal, Chitra; Kislinger, Thomas; Singh, Sheila K. — 2023 Supplementary Material 1: Fig. 1, related to Fig. 1 Glycocapture box blot (A) prior to and (B) after SUC2-normalization (yellow dot; NPVLAANSTQFRDPK peptide). (C) Hierarchical clustering heatmap based on Euclidean distance of differentially expressed proteins demonstrating close clustering of technical triplicates. (D) ITGA5 peptide tag intensity, (E)ITGA5 mRNA expression and (F) ITGB1 protein expression in Group 3 MB cells isolated at pre-determined timepoints through therapy. (G) Comparison of ITGA5 intensity to SUC2 demonstrating selective enrichment for ITGA5 in Group 3 MB through therapy. Bars represent mean of at least three technical replicates. *p ≤ 0.05, **p ≤ 0.001, ***p ≤ 0.0001, ****p ≤ 0.00001; unpaired t-test or one-way ANOVA with Sidak’s method for multiple comparisons. Fig. 2, related to Fig. 1. (A) A Venn diagram demonstrating the number of unique and overlapping surface proteins enriched at each stage of therapy when compared to their expression at engraftment and control timepoints. (B) A list of proteins used to generate the Venn diagram. R = post-radiation; RC = post-chemoradiotherapy; Re = relapse. Fig. 2, related to Fig. 2. In silico evaluation of ITGA5 in publicly available MB repository. (A) Kaplan-Meir curve demonstrating worse overall survival in patients (n = 288) with relative mRNA expression of ITGA5 over 4.6 (RMA- Normalized). (B) Transcriptional expression of ITGA5 of 632 patients across 12 MB subtypes described in Cavalli et al. and (C) based on age group affiliation. **p ≤ 0.001; one-way ANOVA with Dunnett’s method for multiple comparisons. Fig. 3, related to Fig. 3. Characterization and validation of ITGA5 KD. (A) mRNA expression of ITGA5 in HEK293FT cells post ITGA5 KD. (B) Microscopic images of HEK293FT cells post ITGA5 KD. Changes in (C)ITGA5 mRNA expression in reccurent Group 3 MB cells post ITGA5 KD. (D) Flow cytometric evaluation of changes in ITGA5 surface expression in HD-MB03-Re cells post ITGA5 KD. Bars represent mean of at least three technical replicates. *p ≤ 0.05, **p ≤ 0.001, ***p ≤ 0.0001, ****p ≤ 0.00001; unpaired t-test or one-way ANOVA with Sidak’s method for multiple comparisons. Fig. 4, related to Fig. 4. Selectivity characterization of dioscin in recurrent Group 3 MB cells and hNSCs. (A) Dose response curves and (B) corresponding IC50 concentrations and hill slopes of dioscin in hNSCs and three recurrent Group 3 MB lines. Points represent mean of three technical replicates, normalized to DMSO. Error bars represent standard error of the mean. IC50 and Hill slope values standardized to two decimal places. Fig. 5, related to Fig. 4. Expression of ITGA5 in healthy human tissue samples (A) ITGA5 protein levels as detected by whole cell proteomics in health tissues, reported by Wang et al. Protein intensity is reported as intensity-based absolute quantification (iBAQ) values, normalized using median centering across tissues. (B) ITGA5 protein expression as detected by antibody staining using the Human Proteome Atlas public repository. Staining strength corresponds to expression levels, including high (3), medium (2), low (1), and not detected (0). (C) mRNA expression of ITGA5 in various tissues according to Genotype-Tissue Expression (GTEx) dataset ( https://www.proteinatlas.org/ ); expressed in transcripts per million (TPM). https://creativecommons.org/licenses/by/4.0/legalcode

Xu, Fuqi; Juty, Nick; Goble, Carole; Jupp, Simon; Parkinson, Helen; Courtot, Mélanie — 2023 Additional file 2: Supplementary Table 2. Excluded RDA data maturity indicators. RDA indicators that are not mapped to FAIR Vocabulary Features. https://creativecommons.org/licenses/by/4.0/legalcode

Xu, Fuqi; Juty, Nick; Goble, Carole; Jupp, Simon; Parkinson, Helen; Courtot, Mélanie — 2023 Additional file 5: Supplementary Table 5. FAIR assessment results of ICD-11. Details of the FAIR assessment for International Classification of Diseases 11th Revision. https://creativecommons.org/licenses/by/4.0/legalcode

Chakraborty, Saptarshi; Xu, Jason — 2023 Convex clustering has recently garnered increasing interest due to its attractive theoretical and computational properties, but its merits become limited in the face of high-dimensional data. In such settings, pairwise affinity terms that rely on <i>k</i>-nearest neighbors become poorly specified and Euclidean measures of fit provide weaker discriminating power. To surmount these issues, we propose to modify the convex clustering objective so that feature weights are optimized jointly with the centroids. The resulting problem becomes biconvex, and as such remains well-behaved statistically and algorithmically. In particular, we derive a fast algorithm with closed form updates and convergence guarantees, and establish finite-sample bounds on its prediction error. Under interpretable regularity conditions, the error bound analysis implies consistency of the proposed estimator. Biconvex clustering performs feature selection throughout the clustering task: as the learned weights change the effective feature representation, pairwise affinities can be updated adaptively across iterations rather than precomputed within a dubious feature space. We validate the contributions on real and simulated data, showing that our method effectively addresses the challenges of dimensionality while reducing dependence on carefully tuned heuristics typical of existing approaches. Supplementary materials for this article are available online. https://creativecommons.org/licenses/by/4.0/legalcode

Xu, Fuqi; Juty, Nick; Goble, Carole; Jupp, Simon; Parkinson, Helen; Courtot, Mélanie — 2023 Additional file 3: Supplementary Table 3. FAIR assessment results of Gene ontology. Details of the FAIR assessment for Gene Ontology. https://creativecommons.org/licenses/by/4.0/legalcode

Bonsel, Joshua M.; Itiola, Ademola J.; Huberts, Anouk S.; Bonsel, Gouke J.; Penton, Hannah — 2024 Supplementary Material 3. https://creativecommons.org/licenses/by/4.0/legalcode

Ma, Zhiyao; Li, David Xinzheyang; Lan, Xiaoyi; Bubelenyi, Adam; Vyhlidal, Margaret; Kunze, Melanie; Sommerfeldt, Mark; Adesida, Adetola B. — 2024 Supplementary Table 1 https://creativecommons.org/licenses/by/4.0/legalcode

Ko, Haesu; Pasternak, J. Alex; Mulligan, Margaret K.; Hamonic, Glenn; Ramesh, Naresh; MacPhee, Daniel J.; Plastow, Graham S.; Harding, John C. S. — 2024 Additional file 4 https://creativecommons.org/licenses/by/4.0/legalcode

Lu, Chang; Cutumisu, Maria — 2022 Additional file 1. Supplementary Material. https://creativecommons.org/licenses/by/4.0/legalcode

Prado, Ivana Meyer; Abreu, Lucas Guimarães; Pordeus, Isabela Almeida; Amin, Maryam; Paiva, Saul Martins; Serra-Negra, Junia Maria — 2023 Abstract The aims of this study were to perform an exploratory analysis of probable awake (AB) and sleep bruxism (SB) prevalence using of different diagnosis criteria based on the International Consensus; evaluate the associations between self-report and clinical signs/symptoms in adolescents. Participated in this cross-sectional study 403 adolescents aged 12- to 19-years-old enrolled in public and private schools from Belo Horizonte, Brazil. Parents/caregivers answered a questionnaire about sociodemographic status and adolescents’ health status. Adolescents answered a questionnaire evaluating AB (e.g., grinding and clenching) and SB (e.g., grinding, bracing, and thrusting) activities and frequent headaches. A clinical examination was performed on adolescents to evaluate bruxism clinical signs/symptoms (pain upon palpation on masseter and temporal, linea alba, indentation on the tongue and attrition wear severity). Descriptive statistics and Pearson’s Qui-square test were performed (P≤0.05). Adolescents mean age was 14.3±1.5 years, and 58.1% were female. Self-report of SB was identified in 31% of participants and self-report of AB in 51.6%. Almost all adolescents (99%) presented at least one tooth with attrition wear (98.5% on enamel and 0.5% on dentin), with a mean number of 12.4±5.7 teeth. Depending on the diagnosis criteria, the prevalence of probable SB and AB varied from 0- 99% and 0.2- 99%, respectively. A high inconsistency was found for the prevalence of probable AB and SB in adolescents, which were influenced by the different clinical sings/symptoms used as diagnosis criteria. Frequent headaches and pain upon palpation on masseter and temporal muscle were associated to self-report of AB and SB among adolescents. https://creativecommons.org/licenses/by/4.0/legalcode

Watson, Andrea R.; Füssel, Jessika; Veseli, Iva; DeLongchamp, Johanna Zaal; Silva, Marisela; Trigodet, Florian; Lolans, Karen; Shaiber, Alon; Fogarty, Emily; Runde, Joseph M.; Quince, Christopher; Yu, Michael K.; Söylev, Arda; Morrison, Hilary G.; Lee, Sonny T. M.; Kao, Dina; Rubin, David T.; Jabri, Bana; Louie, Thomas; Eren, A. Murat — 2023 Additional file 5. Accession numbers of gut metagenomes from 17 countries. https://creativecommons.org/licenses/by/4.0/legalcode

Yang, Chen Xi; Sin, Don D.; Ng, Raymond T. — 2024 Additional file 2: Table S1. Marker genes used in SMART for deconvolution of the MK dataset. https://creativecommons.org/licenses/by/4.0/legalcode

Blackburn, Gwylim S.; Keeling, Christopher I.; Prunier, Julien; Keena, Melody A.; Béliveau, Catherine; Hamelin, Richard; Havill, Nathan P.; Hebert, Francois Olivier; Levesque, Roger C.; Cusson, Michel; Porth, Ilga — 2024 Additional file 2. https://creativecommons.org/licenses/by/4.0/legalcode