The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Autor: Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn, Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael, Ostrovsky, Alexander, Mahmoud, Alexandru, Lonie, Andrew, Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur, Desanto, Assunta, Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn, Langhorst, Bradley, Carr, Bridget, Raubenolt, Bryan, Hyde, Cameron, Bromhead, Catherine, Barnett, Christopher, Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel, Baker, Dannon, Bouvier, Dave, Clements, Dave, de Lima Morais, David, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth, Cuccuru, Gianmauro, Corguillé, Gildas Le, von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hotz, Hans-Rudolf, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru, Taylor, James, Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John, Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline, Tangaro, Marco Antonio, van den Beek, Marius, Čech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie, Crusoe, Michael, Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan, Moreno, Pablo, Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik, Gu, Qiang, Weber, Ralf, Lazarus, Ross, Vorderman, Ruben, Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon, Gladman, Simon, Leo, Simone, Mehta, Subina, Griffin, Timothy, Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay, Bacon, Wendi, de Koning, Willem, Maier, Wolfgang, Briggs, Peter

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, 2022, 50 (W1), pp.W345-W351. ⟨10.1093/nar/gkac247⟩
Afgan, E, Nekrutenko, A, Grüning, B A, Blankenberg, D, Goecks, J, Schatz, M C, Ostrovsky, A E, Mahmoud, A, Lonie, A J, Syme, A, Fouilloux, A, Bretaudeau, A, Nekrutenko, A, Kumar, A, Eschenlauer, A C, Desanto, A D, Guerler, A, Serrano-Solano, B, Batut, B, Grüning, B A, Langhorst, B W, Carr, B, Raubenolt, B A, Hyde, C J, Bromhead, C J, Barnett, C B, Royaux, C, Gallardo, C, Blankenberg, D, Fornika, D J, Baker, D, Bouvier, D, Clements, D, De Lima Morais, D A, Tabernero, D L, Lariviere, D, Nasr, E, Afgan, E, Zambelli, F, Heyl, F, Psomopoulos, F, Coppens, F, Price, G R, Cuccuru, G, Corguillé, G L, Von Kuster, G, Akbulut, G G, Rasche, H, Hans-Rudolf, H, Eguinoa, I, Makunin, I, Ranawaka, I J, Taylor, J P, Joshi, J, Hillman-Jackson, J, Chilton, J M, Kamali, K, Suderman, K, Poterlowicz, K, Yvan, L B, Lopez-Delisle, L, Sargent, L, Bassetti, M E, Tangaro, M A, Van Den Beek, M, Cech, M, Bernt, M, Fahrner, M, Tekman, M, Föll, M C, Schatz, M C, Crusoe, M R, Roncoroni, M, Kucher, N, Coraor, N, Stoler, N, Rhodes, N, Soranzo, N, Pinter, N, Goonasekera, N A, Moreno, P A, Videm, P, Melanie, P, Mandreoli, P, Jagtap, P D, Gu, Q, Weber, R J M, Lazarus, R, Vorderman, R H P, Hiltemann, S, Golitsynskiy, S, Garg, S, Bray, S A, Gladman, S L, Leo, S, Mehta, S P, Griffin, T J, Jalili, V, Yves, V, Wen, V, Nagampalli, V K, Bacon, W A, De Koning, W, Maier, W & Briggs, P J 2022, ' The Galaxy platform for accessible, reproducible and collaborative biomedical analyses : 2022 update ', Nucleic Acids Research, vol. 50, no. W1, pp. W345-W351 . https://doi.org/10.1093/nar/gkac247
Nucleic Acids Research, 50(W1), W345-W351. Oxford University Press

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c391994be394041f6d06e629a94d035a
https://hal.science/hal-04142105

Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations.

Autor: Ferreira‐Neto, José Ribamar Costa, de Araújo, Flávia Czekalski, de Oliveira Silva, Roberta Lane, de Melo, Natoniel Franklin, Pandolfi, Valesca, Frosi, Gabriella, de Lima Morais, David Anderson, da Silva, Manassés Daniel, Rivas, Rebeca, Santos, Mauro Guida, de Tarso Aidar, Saulo, Morgante, Carolina Vianna, Benko‐Iseppon, Ana Maria

Publikováno v: Physiologia Plantarum; Nov/Dec2022, Vol. 174 Issue 6, p1-22, 22p

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Importance of inositols and their derivatives in cowpea under root dehydration: An omics perspective.

Autor: Ferreira-Neto, José R. C., da Silva, Manassés D., Rodrigues, Fabiana A., Nepomuceno, Alexandre L., Pandolfi, Valesca, de Lima Morais, David A., Kido, Ederson A., Benko-Iseppon, Ana M.

Publikováno v: Physiologia Plantarum; Jun2021, Vol. 172 Issue 2, p441-462, 22p

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Autor: Hurst, Laurence D., Ghanbarian, Avazeh T., Forrest, Alistair R R, Huminiecki, Lukasz, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J L, Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Baker, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan, Swati Bhatt, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun ichi, Geijtenbeek, Teunis B., Gibson, Andrew, Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori, Mutsumi Katayama, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay, Alan sim, Manabe, Riichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao, Sayaka Sato, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada, Mariko Hatakeyama, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 't Hoen, Peter A C, Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Suzan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, Hayashizaki, Yoshihide

Publikováno v: PLoS Biology, Vol 13, Iss 12, p e1002315 (2015)
PLoS Biol, 13(12). Public Library of Science
PLoS Biology
PLoS Biology, 13(12). Public Library of Science
Hurst, L D, Ghanbarian, A T, Forrest, A R R, Huminiecki, L, Rehli, M, Kenneth Baillie, J, de Hoon, M J L, Haberle, V, Lassmann, T, Kulakovskiy, I V, Lizio, M, Itoh, M, Andersson, R, Mungall, C J, Meehan, T F, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, Y A, Plessy, C, Vitezic, M, Severin, J, Semple, C A, Ishizu, Y, Young, R S, Francescatto, M, Alam, I, Albanese, D, Altschuler, G M, Arakawa, T, Archer, J A C, Arner, P, Babina, M, Baker, S, Balwierz, P J, Beckhouse, A G, Pradhan, S B, Blake, J A, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Maxwell Burroughs, A, Califano, A, Cannistraci, C V, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, H C, Dalla, E, Davis, C A, Detmar, M, Diehl, A D, Dohi, T, Drabløs, F, Edge, A S B, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach-Carson, M C, Faulkner, G J, Favorov, A V, Fisher, M E, Frith, M C, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J I, Geijtenbeek, T B, Gibson, A, Gingeras, T, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, S, Ha, T J, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, M, Hitchens, K J, Ho Sui, S J, Hofmann, O M, Hoof, I, Hori, F, Huminiecki, L, Iida, K, Ikawa, T, Jankovic, B R, Jia, H, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori, M K, Kasianov, A S, Kasukawa, T, Katayama, S, Kato, S, Kawaguchi, S, Kawamoto, H, Kawamura, Y I, Kawashima, T, Kempfle, J S, Kenna, T J, Kere, J, Khachigian, L M, Kitamura, T, Peter Klinken, S, Knox, A J, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kwon, A T, Laros, J F J, Lee, W, Lennartsson, A, Li, K, Lilje, B, Lipovich, L, Mackay, A S, Manabe, R, Mar, J C, Marchand, B, Mathelier, A, Mejhert, N, Meynert, A, Mizuno, Y, de Lima Morais, D A, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, C L, Murata, M, Nagao, S S, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, van Nimwegen, E, Ninomiya, N, Nishiyori, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Ohmiya, H, Ohno, H, Ohshima, M, Okada, M H, Okazaki, Y, Orlando, V, Ovchinnikov, D A, Pain, A, Passier, R, Patrikakis, M, Persson, H, Piazza, S, Prendergast, J G D, Rackham, O J L, Ramilowski, J A, Rashid, M, Ravasi, T, Rizzu, P, Roncador, M, Roy, S, Rye, M B, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schneider, C, Schultes, E A, Schulze-Tanzil, G G, Schwegmann, A, Sengstag, T, Sheng, G, Shimoji, H, Shimoni, Y, Shin, J W, Simon, C, Sugiyama, D, Sugiyama, T, Suzuki, M, Suzuki, N, Swoboda, R K, 't Hoen, P A C, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, van de Wetering, M, van den Berg, L M, Verardo, R, Vijayan, D, Vorontsov, I E, Wasserman, W W, Watanabe, S, Wells, C A, Winteringham, L N, Wolvetang, E, Wood, E J, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, S, Zabierowski, S E, Zhang, P G, Zhao, X, Zucchelli, S, Summers, K M, Suzuki, H, Daub, C O, Kawai, J, Heutink, P, Hide, W, Freeman, T C, Lenhard, B, Bajic, V B, Taylor, M S, Makeev, V J, Sandelin, A G, Hume, D A, Carninci, P & Hayashizaki, Y 2015, ' The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome ', PLoS Biology, vol. 13, no. 12, e1002315 . https://doi.org/10.1371/journal.pbio.1002315
PLoS biology, vol 13, iss 12
PLoS biology, 13(12). Public Library of Science
PLOS Biology
Huminiecki, L 2015, ' The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome ', PLoS Biology, vol. 13, no. 12, e1002315 . https://doi.org/10.1371/journal.pbio.1002315
Hurst, L D, Ghanbarian, A T, Forrest, A R R & Huminiecki, L 2015, ' The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome ', PLoS Biology, vol. 13, no. 12, e1002315 . https://doi.org/10.1371/journal.pbio.1002315

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0d97964e110e6dd328c8b584f2af1a6
https://doaj.org/article/8d6344bf6fbc4759a3a76e15d573f39a