• The bio.tools registry of software tools and data resources for the life sciences 

      Ison, Jon; Ienasescu, Hans-Ioan; Chmura, Piotr; Rydza, Emil; Ménager, Hervé; Kalaš, Matúš; Schwämmle, Veit; Grüning, Björn A.; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Svobodová Vařeková, Radka; Raček, Tomáš; Vondrášek, Jiří; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; et al., +18 authors (total 37) (Peer reviewed; Journal article, 2019-08-12)
      Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise ...
    • Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation 

      Lommer, Markus; Specht, Michael; Roy, Alexandra-Sophie; Kraemer, Lars; Andreson, Reidar; Gutowska, Magdalena A.; Wolf, Juliane; Bergner, Sonja V.; Schilhabel, Markus B.; Klostermeier, Ulrich C.; Beiko, Robert G.; Rosenstiel, Philip; Hippler, Michael; LaRoche, Julie (Peer reviewed; Journal article, 2012-07-26)
      Background: Biogeochemical elemental cycling is driven by primary production of biomass via phototrophic phytoplankton growth, with 40% of marine productivity being assigned to diatoms. Phytoplankton growth is widely limited ...
    • Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis 

      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 Michael; 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. (Journal article; Peer reviewed, 2022)
      Background Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding ...
    • Massively parallel sequencing identifies a previously unrecognized X-linked disorder resulting in lethality in male infants owing to amino-terminal acetyltransferase deficiency 

      Rope, Alan F.; Wang, Kai; Evjenth, Rune; Xing, Jinchuan; Johnston, Jennifer J.; Swensen, Jeffrey J.; Johnson, W. E.; Moore, Barry; Huff, Chad D.; Bird, Lynne M.; Carey, John C.; Opitz, John M.; Stevens, Cathy A.; Schank, Christa; Fain, Heidi D.; Robison, Reid; Dalley, Brian; Chin, Steven; South, Sarah T.; Pysher, Theodore J.; Jorde, Lynn B.; Hakonarson, Hakon; Lillehaug, Johan; Biesecker, Leslie G.; Yandell, Mark; Arnesen, Thomas; Lyon, Gholson J. (Conference poster, 2011-09-19)
    • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes 

      Kikuta, Hiroshi; Fredman, David; Rinkwitz, Silke; Lenhard, Boris; Becker, Thomas S. (Journal article; Peer reviewed, 2007-10-31)
      A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around ...
    • Susceptibility to hormone-mediated cancer is reflected by different tick rates of the epithelial and general epigenetic clock 

      Barrett, James E.; Herzog, Chiara; Kim, Yoo-Na; Bartlett, Thomas E.; Jones, Allison; Evans, Iona; Cibula, David; Zikan, Michal; Bjørge, Line; Harbeck, Nadia; Colombo, Nicoletta; Howell, Sacha J.; Rådestad, Angelique Flöter; Gemzell-Danielsson, Kristina; Widschwendter, Martin (Journal article; Peer reviewed, 2022)
      Background A variety of epigenetic clocks utilizing DNA methylation changes have been developed; these clocks are either tissue-independent or designed to predict chronological age based on blood or saliva samples. Whether ...
    • Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes 

      Dong, Xianjun; Fredman, David; Lenhard, Boris (Journal article; Peer reviewed, 2009-08-21)
      Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into ...
    • Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis 

      Sasakura, Yasunori; Oogai, Yuichi; Matsuoka, Terumi; Satoh, Nori; Awazu, Satoko (Journal article; Peer reviewed, 2007-10-31)
      Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis, is discussed. A Tc1/mariner superfamily transposon, Minos, has excision and transposition activities in Ciona. Minos enables ...