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1. Inhibition of acyl-CoA binding protein (ACBP) by means of a GABAARγ2-derived peptide

Author

Anagnostopoulos, Gerasimos, Saavedra, Ester, Lambertucci, Flavia, Motiño, Omar, Dimitrov, Jordan, Roiz-Valle, David, Quesada, Victor, Alvarez-Valadez, Karla, Chen, Hui, Sauvat, Allan, Rong, Yan, Nogueira-Recalde, Uxía, Li, Sijing, Montégut, Léa, Djavaheri-Mergny, Mojgan, Castedo, Maria, Lopez-Otin, Carlos, Maiuri, Maria Chiara, Martins, Isabelle, and Kroemer, Guido

Published
2024
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2. An exact, unconditional, nuisance-agnostic test for contingency tables

Author

Araujo-Voces, Miguel and Quesada, Víctor

Subjects
Statistics - Methodology, Mathematics - Statistics Theory, 62H17 (Primary) 65Y15 (Secondary)
Abstract

Exact tests greatly improve the analysis of contingency tables when marginals are low. For instance, researchers often use Fisher's exact test, which is conditional, or Barnard's test, which is unconditional but needs to deal with a nuisance parameter. Here, we describe the m-test, an exact, unconditional test for the study of d x m binomial contingency tables. When comparing binomial trials, the m-test is related to Barnard's exact test. However, the nuisance parameter is integrated over all its possible values, instead of maximized or otherwise estimated. According to Monte Carlo simulations, this strategy yields a higher statistical power than other exact tests. We also provide a package to perform the m-test in R., Comment: 10 pages, 2 figures. Contains Supplementary Information with detailed proofs

Published
2021

5. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author

Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Published
2022
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6. Inhibition of acyl-CoA binding protein (ACBP) by means of a GABAARγ2-derived peptide.

Author

Anagnostopoulos, Gerasimos, Saavedra, Ester, Lambertucci, Flavia, Motiño, Omar, Dimitrov, Jordan, Roiz-Valle, David, Quesada, Victor, Alvarez-Valadez, Karla, Chen, Hui, Sauvat, Allan, Rong, Yan, Nogueira-Recalde, Uxía, Li, Sijing, Montégut, Léa, Djavaheri-Mergny, Mojgan, Castedo, Maria, Lopez-Otin, Carlos, Maiuri, Maria Chiara, Martins, Isabelle, and Kroemer, Guido

Published
2024
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11. Suppl Table 2 from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Author

Cortazar, Ana R., primary, Torrano, Veronica, primary, Martín-Martín, Natalia, primary, Caro-Maldonado, Alfredo, primary, Camacho, Laura, primary, Hermanova, Ivana, primary, Guruceaga, Elizabeth, primary, Lorenzo-Martín, Luis F., primary, Caloto, Ruben, primary, Gomis, Roger R., primary, Apaolaza, Iñigo, primary, Quesada, Victor, primary, Trka, Jan, primary, Gomez-Muñoz, Antonio, primary, Vincent, Silvestre, primary, Bustelo, Xose R., primary, Planes, Francisco J., primary, Aransay, Ana M., primary, and Carracedo, Arkaitz, primary

Published
2023
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12. Data from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Author

Cortazar, Ana R., primary, Torrano, Veronica, primary, Martín-Martín, Natalia, primary, Caro-Maldonado, Alfredo, primary, Camacho, Laura, primary, Hermanova, Ivana, primary, Guruceaga, Elizabeth, primary, Lorenzo-Martín, Luis F., primary, Caloto, Ruben, primary, Gomis, Roger R., primary, Apaolaza, Iñigo, primary, Quesada, Victor, primary, Trka, Jan, primary, Gomez-Muñoz, Antonio, primary, Vincent, Silvestre, primary, Bustelo, Xose R., primary, Planes, Francisco J., primary, Aransay, Ana M., primary, and Carracedo, Arkaitz, primary

Published
2023
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13. Supplementary Figure legends from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Author

Cortazar, Ana R., primary, Torrano, Veronica, primary, Martín-Martín, Natalia, primary, Caro-Maldonado, Alfredo, primary, Camacho, Laura, primary, Hermanova, Ivana, primary, Guruceaga, Elizabeth, primary, Lorenzo-Martín, Luis F., primary, Caloto, Ruben, primary, Gomis, Roger R., primary, Apaolaza, Iñigo, primary, Quesada, Victor, primary, Trka, Jan, primary, Gomez-Muñoz, Antonio, primary, Vincent, Silvestre, primary, Bustelo, Xose R., primary, Planes, Francisco J., primary, Aransay, Ana M., primary, and Carracedo, Arkaitz, primary

Published
2023
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14. Suppl Table 1 from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Author

Cortazar, Ana R., primary, Torrano, Veronica, primary, Martín-Martín, Natalia, primary, Caro-Maldonado, Alfredo, primary, Camacho, Laura, primary, Hermanova, Ivana, primary, Guruceaga, Elizabeth, primary, Lorenzo-Martín, Luis F., primary, Caloto, Ruben, primary, Gomis, Roger R., primary, Apaolaza, Iñigo, primary, Quesada, Victor, primary, Trka, Jan, primary, Gomez-Muñoz, Antonio, primary, Vincent, Silvestre, primary, Bustelo, Xose R., primary, Planes, Francisco J., primary, Aransay, Ana M., primary, and Carracedo, Arkaitz, primary

Published
2023
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15. Supplementary figures from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Author

Cortazar, Ana R., primary, Torrano, Veronica, primary, Martín-Martín, Natalia, primary, Caro-Maldonado, Alfredo, primary, Camacho, Laura, primary, Hermanova, Ivana, primary, Guruceaga, Elizabeth, primary, Lorenzo-Martín, Luis F., primary, Caloto, Ruben, primary, Gomis, Roger R., primary, Apaolaza, Iñigo, primary, Quesada, Victor, primary, Trka, Jan, primary, Gomez-Muñoz, Antonio, primary, Vincent, Silvestre, primary, Bustelo, Xose R., primary, Planes, Francisco J., primary, Aransay, Ana M., primary, and Carracedo, Arkaitz, primary

Published
2023
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19. Presentación

Author

Michelle Quesada Victor

Abstract

Presentamos el volumen 10, no.1 de la Revista REDpensar bajo el título “Condiciones humanas complejas y emotivas en el tránsito del Bicentenario”. Esta Revista es el resultado de un esfuerzo conjunto de varios autores, investigadores y docentes, que promueven desde su quehacer diario, la investigación social crítica, con investigaciones que están comprometidas de forma permanente con la transformación de las personas y la sociedad. La edición de este número de la Revista REDpensar, es un ejemplo de la diversidad investigativa nacional e internacional. Los artículos presentados en este número, han contado con un proceso riguroso de revisión y edición, con la participación de evaluadores externos y del Consejo Editorial, quienes con su amplio expertise, han dado el aval para estas publicaciones. Autores y autoras, han realizado un gran esfuerzo, que se ve reflejado en cada página de este número de REDpensar.

Published
2021
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23. Presentación

Author

Micheel Quesada Victor

Abstract

Presentamos el volumen 8 no.2 de la Revista REDpensar “Miradas investigativas: educación, aprendizaje e innovación en un mundo globalizado”. Esta Revista es el resultado de un proceso dinámico que se genera desde la Universidad De La Salle, la cual promueve una cultura de investigación crítica, comprometida de forma permanente con la transformación de las personas y la sociedad. En esta edición quedan plasmados espacios de investigación jurídicos, educativos, socioculturales y ambientales, que facilitan la producción de conocimiento en el proceso continuo y constante de aprendizaje. La Universidad De La Salle Costa Rica, a través de esta publicación nos invita a comprender sobre la importancia que tienen los procesos investigativos en la formación académica, profesional y personal.

Published
2020
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24. Comparative and demographic analysis of orang-utan genomes

Author

Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Valle, Giuliano Della, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Published
2011
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25. Cystatin D is a candidate tumor suppressor gene induced by vitamin D in human colon cancer cells

Author

Alvarez-Diaz, Silvia, Valle, Noelia, Garcia, Jose Miguel, Pena, Cristina, Freije, Jose M.P., Quesada, Victor, Astudillo, Aurora, Bonilla, Felix, Lopez-Otin, Carlos, and Munoz, Alberto

Subjects
Colon cancer -- Genetic aspects, Colon cancer -- Care and treatment, Colon cancer -- Research, Gene expression -- Research, Tumor suppressor genes -- Health aspects, Tumor suppressor genes -- Research, Alfacalcidol -- Health aspects, Alfacalcidol -- Chemical properties, Alfacalcidol -- Research, Calcifediol -- Health aspects, Calcifediol -- Chemical properties, Calcifediol -- Research, Vitamin D -- Health aspects, Vitamin D -- Chemical properties, Vitamin D -- Research
Abstract

The active vitamin D metabolite 1[alpha],25-dihydroxyvitamin [D.sub.3] [1[alpha],25[(OH).sub.2][D.sub.3] has wide but not fully understood antitumor activity. A previous transcriptomic analysis of 1[alpha],25[(OH).sub.2][D.sub.3] action on human colon cancer cells revealed cystatin D (CST5), which encodes an inhibitor of several cysteine proteases of the cathepsin family, as a candidate target gene. Here we report that 1[alpha],25[(OH).sub.2][D.sub.3] induced vitamin D receptor (VDR) binding to, and activation of, the CST5 promoter and increased CST5 RNA and protein levels in human colon cancer cells. In cells lacking endogenous cystatin D, ectopic cystatin D expression inhibited both proliferation in vitro and xenograft tumor growth in vivo. Furthermore, cystatin D inhibited migration and anchorage-independent growth, antagonized the Wnt/[beta]-catenin signaling pathway, and repressed c-MYC expression. Cystatin D repressed expression of the epithelial-mesenchymal transition inducers SNAI1, SNAI2, ZEB1, and ZEB2 and, conversely, induced E-cadherin and other adhesion proteins. CST5 knockdown using shRNA abrogated the antiproliferative effect of 1[alpha],25[(OH).sub.2][D.sub.3], attenuated E-cadherin expression, and increased c-MYC expression. In human colorectal tumors, expression of cystatin D correlated with expression of VDR and E-cadherin, and loss of cystatin D correlated with poor tumor differentiation. Based on these data, we propose that CST5 has tumor suppressor activity that may contribute to the antitumoral action of 1[alpha],25[(OH).sub.2][D.sub.3] in colon cancer., Introduction There is an increasing interest in the active vitamin D metabolite 1[alpha],25-dihydroxyvitamin [D.sub.3] [1[alpha],25[(OH).sub.2][D.sub.3] and its analogs as preventive and therapeutic anticancer agents, and a number of clinical trials [...]

Published
2009

26. The SCABRA3 nuclear gene encodes the plastid RpoTp RNA polymerase, which is required for chloroplast biogenesis and mesophyll cell proliferation in Arabidopsis (1[w])

Author

Hricoba, Andrea, Quesada, Victor, and Micol, Jose Luis

Subjects
Arabidopsis thaliana -- Genetic aspects, Arabidopsis thaliana -- Physiological aspects, Plant mutation -- Research, Cell proliferation -- Research, RNA polymerases -- Research, Growth (Plants) -- Research, Biological sciences, Science and technology
Published
2006

32. International network of cancer genome projects

Author

Hudson, Thomas J., Anderson, Warwick, Aretz, Axel, Bell, Cindy, Bernabé, Rosa R., Bhan, M. K., Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S., Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M., Jennings, Jennifer L., Kerr, David, Klatt, Peter, Kolar, Patrik, Lane, David P., Laplace, Frank, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, T. S., Remacle, Jacques, Schafer, Alan J., Shibata, Tatsuhiro, Stratton, Michael R., Watanabe, Koichi, Yuen, Matthew M. F., Cambon-Thomsen, Anne, Dressler, Lynn G., Joly, Yann, Kennedy, Karen L., Parker, Michael J., Romeo-Casabona, Carlos M., Wallace, Susan, Wiesner, Georgia L., Zeps, Nikolajs, Biankin, Andrew V., Chabannon, Christian, de Alava, Enrique, Ferguson, Martin L., Geary, Peter, Hayes, Neil D., Johns, Amber L., Kasprzyk, Arek, Nakagawa, Hidewaki, Piris, Miguel A., van de Vijver, Marc, Aburatani, Hiroyuki, Bayés, Mónica, Bowtell, David D.L., Campbell, Peter J., Hirst, Martin, López-Otín, Carlos, Marra, Marco, Ning, Zemin, Puente, Xose S., Ruan, Yijun, Stunnenberg, Hendrik G., Swerdlow, Harold, Velculescu, Victor E., Xue, Hong H., Yang, Liu, Spellman, Paul T., Bader, Gary D., Boutros, Paul C., Flicek, Paul, Getz, Gad, Guigó, Roderic, Guo, Guangwu, Haussler, David, Hubbard, Tim J., Jiang, Tao, Jones, Steven M., Li, Qibin, López-Bigas, Nuria, Luo, Ruibang, Muthuswamy, Lakshmi, Ouellette, Francis B. F., Pearson, John V., Quesada, Victor, Raphael, Benjamin J., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Teague, Jon W., Totoki, Yasushi, Tsunoda, Tatsuhiko, Valencia, Alfonso, Wheeler, David A., Wu, Honglong, Zhao, Shancen, Zhou, Guangyu, Lathrop, Mark, Axton, Myles, Dyke, Stephanie O. M., Gunter, Chris, McPherson, John D., Miller, Linda J., Zhang, Junjun, Haider, Syed A., Wang, Jianxin, Yung, Christina K., Cross, Anthony, Liang, Yong, Gnaneshan, Saravanamuttu, Guberman, Jonathan, Hsu, Jack, Bobrow, Martin, Chalmers, Don R. C., Hasel, Karl W., Kaan, Terry S. H., Knoppers, Bartha M., Lowrance, William W., Masui, Tohru, Nicolás, Pilar, Rial-Sebbag, Emmanuelle, Rodriguez, Laura Lyman, Vergely, Catherine, Grimmond, Sean M., Bowtell, David D. L., Cloonan, Nicole, deFazio, Anna, Eshleman, James R., Etemadmoghadam, Dariush, Gardiner, Brooke A., Kench, James G., Scarpa, Aldo, Sutherland, Robert L., Tempero, Margaret A., Waddell, Nicola J., Wilson, Peter J., Gallinger, Steve, Tsao, Ming-Sound, Shaw, Patricia A., Petersen, Gloria M., Mukhopadhyay, Debabrata, Chin, Lynda, DePinho, Ronald A., Thayer, Sarah, Shazand, Kamran, Beck, Timothy, Sam, Michelle, Timms, Lee, Ballin, Vanessa, Ji, Jiafu, Zhang, Xiuqing, Chen, Feng, Hu, Xueda, Yang, Qi, Tian, Geng, Zhang, Lianhai, Xing, Xiaofang, Li, Xianghong, Zhu, Zhenggang, Yu, Yingyan, Yu, Jun, Yang, Huanming, Tost, Jörg, Brennan, Paul, Holcatova, Ivana, Zaridze, David, Brazma, Alvis, Egevad, Lars, Prokhortchouk, Egor, Banks, Rosamonde Elizabeth, Uhlén, Mathias, Viksna, Juris, Ponten, Fredrik, Skryabin, Konstantin, Futreal, Andrew P., Birney, Ewan, Caldas, Carlos, Reis-Filho, Jorge S., Richardson, Andrea L., Sotiriou, Christos, Birnbaum, Daniel, Blanche, Hélène, Boucher, Pascal, Boyault, Sandrine, Masson-Jacquemier, Jocelyne D., Pauporté, Iris, Pivot, Xavier, Vincent-Salomon, Anne, Tabone, Eric, Theillet, Charles, Treilleux, Isabelle, Bioulac-Sage, Paulette, Clément, Bruno, Decaens, Thomas, Degos, Françoise, Franco, Dominique, Gut, Ivo, Gut, Marta, Heath, Simon, Samuel, Didier, Thomas, Gilles, Zucman-Rossi, Jessica, Eils, Roland, Brors, Benedikt, Korbel, Jan O., Korshunov, Andrey, Landgraf, Pablo, Lehrach, Hans, Pfister, Stefan, Radlwimmer, Bernhard, Reifenberger, Guido, Taylor, Michael D., von Kalle, Christof, Majumder, Partha P., Sarin, Rajiv, Pederzoli, Paolo, Lawlor, Rita T., Delledonne, Massimo, Bardelli, Alberto, Gress, Thomas, Klimstra, David, Zamboni, Giuseppe, Nakamura, Yusuke, Kusuda, Jun, Miyano, Satoru, Kato, Kazuto, Fujimoto, Akihiro, Yoshida, Teruhiko, Campo, Elias, Estivill, Xavier, de Sanjosé, Silvia, Montserrat, Emili, González-Díaz, Marcos, Jares, Pedro, Himmelbaue, Heinz, Bea, Silvia, Aparicio, Samuel, Borg, Ake, Børresen-Dale, Anne-Lise, Foekens, John A., vanʼt Veer, Laura, Easton, Douglas F., Martin, Sancha, Compton, Carolyn C., Lander, Eric S., Penny, Robert, Shaw, Kenna M., Speed, Terence P., Vockley, Joseph G., Lichter, Peter, Barker, Anna D., Burke, Wylie, Collins, Francis S., Green, Anthony R., Hamilton, Stanley R., Kallioniemi, Olli P., Ley, Timothy J., Liu, Edison T., Lu, Youyong, Majumder, Partha, Wainwright, Brandon J., and Wilson, Richard K.

Published
2010
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33. The genome of a songbird

Author

Warren, Wesley C., Clayton, David F., Ellegren, Hans, Arnold, Arthur P., Hillier, LaDeana W., Künstner, Axel, Searle, Steve, White, Simon, Vilella, Albert J., Fairley, Susan, Heger, Andreas, Kong, Lesheng, Ponting, Chris P., Jarvis, Erich D., Mello, Claudio V., Minx, Pat, Lovell, Peter, Velho, Tarciso A. F., Ferris, Margaret, Balakrishnan, Christopher N., Sinha, Saurabh, Blatti, Charles, London, Sarah E., Li, Yun, Lin, Ya-Chi, George, Julia, Sweedler, Jonathan, Southey, Bruce, Gunaratne, Preethi, Watson, Michael, Nam, Kiwoong, Backström, Niclas, Smeds, Linnea, Nabholz, Benoit, Itoh, Yuichiro, Whitney, Osceola, Pfenning, Andreas R., Howard, Jason, Völker, Martin, Skinner, Bejamin M., Griffin, Darren K., Ye, Liang, McLaren, William M., Flicek, Paul, Quesada, Victor, Velasco, Gloria, Lopez-Otin, Carlos, Puente, Xose S., Olender, Tsviya, Lancet, Doron, Smit, Arian F. A., Hubley, Robert, Konkel, Miriam K., Walker, Jerilyn A., Batzer, Mark A., Gu, Wanjun, Pollock, David D., Chen, Lin, Cheng, Ze, Eichler, Evan E., Stapley, Jessica, Slate, Jon, Ekblom, Robert, Birkhead, Tim, Burke, Terry, Burt, David, Scharff, Constance, Adam, Iris, Richard, Hugues, Sultan, Marc, Soldatov, Alexey, Lehrach, Hans, Edwards, Scott V., Yang, Shiaw-Pyng, Li, XiaoChing, Graves, Tina, Fulton, Lucinda, Nelson, Joanne, Chinwalla, Asif, Hou, Shunfeng, Mardis, Elaine R., and Wilson, Richard K.

Published
2010
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35. Presentación

Author

Michelle Quesada Victor

Abstract

Presentamos el volumen 9 no.2 de la Revista REDpensar “Ambiente, Territorio y Educación: investigaciones desde políticas, normas y prácticas socio culturales y ambientales”. Esta Revista es el resultado de un proceso investigativo que se promueve desde la Universidad De La Salle, a partir de una cultura de investigación crítica, comprometida de forma permanente con la transformación de las personas y la sociedad. La edición de este nuevo número de la Revista REDpensar, es un ejemplo de la diversidad de temas de investigación, las cuales proponen desde distintas miradas los esfuerzos de la humanidad por sobrellevar las crisis sociales, ambientales y pandémicas; así como la propuesta de replantear la educación en la sociedad actual que vivimos, desde una pedagogía lasallista.

Published
2020
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37. CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Author

Cortazar, Ana R., primary, Torrano, Veronica, additional, Martín-Martín, Natalia, additional, Caro-Maldonado, Alfredo, additional, Camacho, Laura, additional, Hermanova, Ivana, additional, Guruceaga, Elizabeth, additional, Lorenzo-Martín, Luis F., additional, Caloto, Ruben, additional, Gomis, Roger R., additional, Apaolaza, Iñigo, additional, Quesada, Victor, additional, Trka, Jan, additional, Gomez-Muñoz, Antonio, additional, Vincent, Silvestre, additional, Bustelo, Xose R., additional, Planes, Francisco J., additional, Aransay, Ana M., additional, and Carracedo, Arkaitz, additional

Published
2018
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39. FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition

Author

Simpson, Gordon G., Dijkwel, Paul P., Quesada, Victor, Henderson, Ian, and Dean, Caroline

Subjects
Cellular control mechanisms -- Genetic aspects, Cellular control mechanisms -- Physiological aspects, Plants, Flowering of -- Genetic aspects, Plants, Flowering of -- Physiological aspects, Developmental biology -- Research, Arabidopsis -- Genetic aspects, Arabidopsis -- Physiological aspects, Biological sciences
Abstract

Research indicates that FY protein regulates RNA 3' end processing in Arabidopsis and regulates the nuclear RNA binding protein, FCA. Results reveal that FY is involved in the negative autoregulation of FCA expression and that the FCA/FA interaction function in coordination to regulate RNA 3' end formation and control of floral transition.

Published
2003

40. Genetic Analysis of Salt-Tolerant Mutants in Arabidopsis thaliana

Author

Quesada, Victor, Ponce, Maria Rosa, and Micol, Jose Luis

Subjects
Genetic research -- Analysis, Growth (Plants) -- Genetic aspects, Plant breeding -- Research, Soils, Salts in -- Research, Agriculture -- Genetic aspects, Biological sciences
Abstract

Stress caused by the increased salinity of irrigated fields impairs plant growth and is one of the major constraints that limits crop productivity in many important agricultural areas. As a contribution to solving such agronomic problems, we have carried out a large-scale screening for Arabidopsis thaliana mutants induced on different genetic backgrounds by EMS treatment, fast neutron bombardment, or T-DNA insertions. From the 675,500 seeds we screened, 17 mutant lines were isolated, all but one of which yielded 25-70% germination levels on 250 mM NaCl medium, a condition in which their ancestor ecotypes are unable to germinate. Monogenic recessive inheritance of NaCl-tolerant germination was displayed with incomplete penetrance by all the selected mutants, which fell into five complementation groups. These were named SALOBRENO (SAN) and mapped relative to polymorphic microsatellites, the map positions of three of them suggesting that they are novel genes. Strains carrying mutations in the SAN1-SAN4 genes display similar responses to both ionic effects and osmotic pressure, their germination being NaCl and mannitol tolerant but KCl and [Na.sub.2] [SO.sub.4] sensitive. In addition, NaCl-, KCl-, and mannitol-tolerant as well as abscisic-acid-insensitive germination was displayed by san5, whose genetic and molecular characterization indicates that it carries an extremely hypomorphic or null allele of the ABI4 gene, its deduced protein product lacking the APETALA2 DNA binding domain.

Published
2000

41. Sequence variation atKLKandWFDCclusters and its association to semen hyperviscosity and other male infertility phenotypes

Author

Marques, Patrícia Isabel, primary, Fonseca, Filipa, additional, Carvalho, Ana Sofia, additional, Puente, Diana A., additional, Damião, Isabel, additional, Almeida, Vasco, additional, Barros, Nuno, additional, Barros, Alberto, additional, Carvalho, Filipa, additional, Azkargorta, Mikel, additional, Elortza, Felix, additional, Osório, Hugo, additional, Matthiesen, Rune, additional, Quesada, Victor, additional, and Seixas, Susana, additional

Published
2016
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42. Insights into the Evolution of Longevity from the Bowhead Whale Genome

Author

Keane, Michael, Semeiks, Jeremy, Webb, Andrew E., Li, Yang I., Quesada, Victor, Craig, Thomas, Madsen, Lone Bruhn, van Dam, Sipko, Brawand, David, Marques, Patricia I., Michalak, Pawel, Kang, Lin, Bhak, Jong, Yim, Hyung-Soon, Grishin, Nick V., Nielsen, Nynne Hjort, Heide-Jorgensen, Mads Peter, Oziolor, Elias M., Matson, Cole W., Church, George M., Stuart, Gary W., Patton, John C., George, J. Craig, Suydam, Robert, Larsen, Knud, Lopez-Otin, Carlos, O'Connell, Mary J., Bickham, John W., Thomsen, Bo, de Magalhaes, Joao Pedro, Keane, Michael, Semeiks, Jeremy, Webb, Andrew E., Li, Yang I., Quesada, Victor, Craig, Thomas, Madsen, Lone Bruhn, van Dam, Sipko, Brawand, David, Marques, Patricia I., Michalak, Pawel, Kang, Lin, Bhak, Jong, Yim, Hyung-Soon, Grishin, Nick V., Nielsen, Nynne Hjort, Heide-Jorgensen, Mads Peter, Oziolor, Elias M., Matson, Cole W., Church, George M., Stuart, Gary W., Patton, John C., George, J. Craig, Suydam, Robert, Larsen, Knud, Lopez-Otin, Carlos, O'Connell, Mary J., Bickham, John W., Thomsen, Bo, and de Magalhaes, Joao Pedro

Abstract

The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bow-head-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.

Published
2015
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44. Mutations in the Toll-like receptor/MYD88 pathway in young (≤50 years) CLL patients

Author

Martínez-Trillos, Alejandra, primary, Pinyol, Magda, additional, Navarro, Alba, additional, Aymerich, Marta, additional, Jares, Pedro, additional, Juan, Manel, additional, Rozman, María, additional, Colomer, Dolors, additional, Delgado, Julio, additional, Gine, Eva, additional, González-Díaz, Marcos, additional, Hernández-Rivas, Jesús M., additional, Colado, Enrique, additional, Rayón, Consolación, additional, Payer, Angel R., additional, Terol, Maria José, additional, Navarro, Blanca, additional, Quesada, Victor, additional, Puente, Xosé S., additional, Rozman, Ciril, additional, López-Otín, Carlos, additional, Campo, Elías, additional, López-Guillermo, Armando, additional, and Villamor, Neus, additional

Published
2015
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45. Abstract 20: POT1 mutations predispose to familial melanoma

Author

Robles-Espinoza, Carla Daniela, primary, Harland, Mark, additional, Ramsay, Andrew J., additional, Aoude, Lauren G., additional, Quesada, Victor, additional, Ding, Zhihao, additional, Pooley, Karen A., additional, Pritchard, Antonia L., additional, Tiffen, Jessamy C., additional, Petljak, Mia, additional, Palmer, Jane M., additional, Symmons, Judith, additional, Johansson, Peter, additional, Stark, Mitchell S., additional, Gartside, Michael G., additional, Snowden, Helen, additional, Montgomery, Grant W., additional, Martin, Nicholas G., additional, Liu, Jimmy Z., additional, Choi, Jiyeon, additional, Makowski, Matthew, additional, Brown, Kevin M., additional, Dunning, Alison M., additional, Keane, Thomas M., additional, Lopez-Otin, Carlos, additional, Gruis, Nelleke A., additional, Hayward, Nicholas K., additional, Bishop, D. Timothy, additional, Newton-Bishop, Julia A., additional, and Adams, David J., additional

Published
2014
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46. Sequence variation at KLK and WFDC clusters and its association to semen hyperviscosity and other male infertility phenotypes.

Author

Marques, Patrícia Isabel, Fonseca, Filipa, Carvalho, Ana Sofia, Puente, Diana A., Damião, Isabel, Almeida, Vasco, Barros, Nuno, Barros, Alberto, Carvalho, Filipa, Azkargorta, Mikel, Elortza, Felix, Osório, Hugo, Matthiesen, Rune, Quesada, Victor, and Seixas, Susana

Subjects
KALLIKREIN, WHEY proteins, SEMEN analysis, MALE infertility, SPERMATOZOA, BLOOD coagulation factors, HUMAN reproduction, INFERTILITY, PROTEINS, SEMEN, SPERM motility, VISCOSITY, PHENOTYPES, GENOTYPES
Abstract

Study Question: Are kallikreins (KLKs), the whey-acidic-protein four-disulfide core domain (WFDCs) and their neighbors, semenogelins (SEMGs), known to play a role in the cascade of semen coagulation and liquefaction, associated with male infertility?Summary Answer: Several KLK and SEMG variants are overrepresented among hyperviscosity, asthenozoospermia and oligozoospermia, supporting an effect of abnormal semen liquefaction on the loss of semen quality and in lowering male reproductive fitness.What Is Known Already: In the cascade of semen coagulation and liquefaction the spermatozoa coated by EPPIN (a protease inhibitor of the WFDC family) are entrapped in a cross-linked matrix established by SEMGs. After ejaculation, the SEMG matrix is hydrolyzed by KLK3/2 in a fine-tuned process regulated by other KLKs that allows the spermatozoa to increase motility.Study Design Size, Duration: This study includes a cohort of 238 infertility-related cases and 91 controls with normal spermiogram analysis. The remaining 126 controls are healthy males with unknown semen parameters. Sample collection was carried out from June 2011 to January 2015 and variant screening from May 2013 to August 2015.Participants/materials, Setting, Methods: We performed a screening by massive parallel sequencing in a pooled sample (N = 222) covering approximately 93 kb of KLK (19q13.3-13.4) and WFDC (20q13) clusters, followed by the genotyping of most promising variants in the full cohort.Main Results and the Role Of Chance: Overall, 160 common and 296 low-frequency variants passed the quality control filtering. Statistical tests disclosed an association with hyperviscosity of a KLK7 regulatory variant (P = 0.0035), and unveiled a higher burden of deleterious mutations in KLKs than expected by chance (P = 0.0106). KLK variants found to be overrepresented in cases included two substitutions likely affecting the substrate binding pocket, two nonsynonymous variants overlapping in the three-dimensional structure and two mutations mapping in consecutive N-terminal residues. Other variants identified in SEMGs possibly contributing to hyperviscosity and asthenozoospermia consisted of three replacements predicted to modify targets of proteolysis (P = 0.0442 for SEMG1 p.Gly400Asp) and a copy number variation associated with a reduced risk of oligozoospermia (P = 0.0293).Large Scale Data: Not applicable.Limitations Reasons For Caution: The sampling of a few hundred individuals has limited power to detected associations with low-frequency variants and only a small set of variants was prioritized for genotyping. Other susceptibility variants for male infertility may remain unidentified.Wider Implications Of the Findings: We provide important evidence for an effect of KLKs and SEMGs variability on semen quality and for modifications in the process of semen liquefaction as a possible cause for male infertility.Study Funding/competing Interests: This work was funded through the Portuguese Foundation for Science and Technology (FCT) and FEDER through COMPETE and QREN. The authors have no conflict of interest to declare. [ABSTRACT FROM AUTHOR]

Published
2016
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47. Mutations in TLR/MYD88 pathway identify a subset of young chronic lymphocytic leukemia patients with favorable outcome

Author

Martínez-Trillos, Alejandra, primary, Pinyol, Magda, additional, Navarro, Alba, additional, Aymerich, Marta, additional, Jares, Pedro, additional, Juan, Manel, additional, Rozman, María, additional, Colomer, Dolors, additional, Delgado, Julio, additional, Giné, Eva, additional, González-Díaz, Marcos, additional, Hernández-Rivas, Jesús M., additional, Colado, Enrique, additional, Rayón, Consolación, additional, Payer, Angel R., additional, Terol, Maria José, additional, Navarro, Blanca, additional, Quesada, Victor, additional, Puente, Xosé S., additional, Rozman, Ciril, additional, López-Otín, Carlos, additional, Campo, Elías, additional, López-Guillermo, Armando, additional, and Villamor, Neus, additional

Published
2014
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48. The genome of a songbird

Author

Warren, Wesley C, Clayton, David F, Ellegren, Hans, Arnold, Arthur P, Hillier, Ladeana W, Künstner, Axel, Searle, Steve, White, Simon, Vilella, Albert J, Fairley, Susan, Heger, Andreas, Kong, Lesheng, Ponting, Chris P, Jarvis, Erich D, Mello, Claudio V, Minx, Pat, Lovell, Peter, Velho, Tarciso A F, Ferris, Margaret, Balakrishnan, Christopher N, Sinha, Saurabh, Blatti, Charles, London, Sarah E, Li, Yun, Lin, Ya-Chi, George, Julia, Sweedler, Jonathan, Southey, Bruce, Gunaratne, Preethi, Watson, Michael, Nam, Kiwoong, Backström, Niclas, Smeds, Linnea, Nabholz, Benoit, Itoh, Yuichiro, Whitney, Osceola, Pfenning, Andreas R, Howard, Jason, Völker, Martin, Skinner, Bejamin M, Griffin, Darren K, Ye, Liang, McLaren, William M, Flicek, Paul, Quesada, Victor, Velasco, Gloria, Lopez-Otin, Carlos, Puente, Xose S, Olender, Tsviya, Lancet, Doron, Smit, Arian F A, Hubley, Robert, Konkel, Miriam K, Walker, Jerilyn A, Batzer, Mark A, Gu, Wanjun, Pollock, David D, Chen, Lin, Cheng, Ze, Eichler, Evan E, Stapley, Jessica, Slate, Jon, Ekblom, Robert, Birkhead, Tim, Burke, Terry, Burt, David, Scharff, Constance, Adam, Iris, Richard, Hugues, Sultan, Marc, Soldatov, Alexey, Lehrach, Hans, Edwards, Scott V, Yang, Shiaw-Pyng, Li, Xiaoching, Graves, Tina, Fulton, Lucinda, Nelson, Joanne, Chinwalla, Asif, Hou, Shunfeng, Mardis, Elaine R, Wilson, Richard K, Warren, Wesley C, Clayton, David F, Ellegren, Hans, Arnold, Arthur P, Hillier, Ladeana W, Künstner, Axel, Searle, Steve, White, Simon, Vilella, Albert J, Fairley, Susan, Heger, Andreas, Kong, Lesheng, Ponting, Chris P, Jarvis, Erich D, Mello, Claudio V, Minx, Pat, Lovell, Peter, Velho, Tarciso A F, Ferris, Margaret, Balakrishnan, Christopher N, Sinha, Saurabh, Blatti, Charles, London, Sarah E, Li, Yun, Lin, Ya-Chi, George, Julia, Sweedler, Jonathan, Southey, Bruce, Gunaratne, Preethi, Watson, Michael, Nam, Kiwoong, Backström, Niclas, Smeds, Linnea, Nabholz, Benoit, Itoh, Yuichiro, Whitney, Osceola, Pfenning, Andreas R, Howard, Jason, Völker, Martin, Skinner, Bejamin M, Griffin, Darren K, Ye, Liang, McLaren, William M, Flicek, Paul, Quesada, Victor, Velasco, Gloria, Lopez-Otin, Carlos, Puente, Xose S, Olender, Tsviya, Lancet, Doron, Smit, Arian F A, Hubley, Robert, Konkel, Miriam K, Walker, Jerilyn A, Batzer, Mark A, Gu, Wanjun, Pollock, David D, Chen, Lin, Cheng, Ze, Eichler, Evan E, Stapley, Jessica, Slate, Jon, Ekblom, Robert, Birkhead, Tim, Burke, Terry, Burt, David, Scharff, Constance, Adam, Iris, Richard, Hugues, Sultan, Marc, Soldatov, Alexey, Lehrach, Hans, Edwards, Scott V, Yang, Shiaw-Pyng, Li, Xiaoching, Graves, Tina, Fulton, Lucinda, Nelson, Joanne, Chinwalla, Asif, Hou, Shunfeng, Mardis, Elaine R, and Wilson, Richard K

Abstract

The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.

Published
2010
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49. Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Author

Ferreira, Pedro G., primary, Jares, Pedro, additional, Rico, Daniel, additional, Gómez-López, Gonzalo, additional, Martínez-Trillos, Alejandra, additional, Villamor, Neus, additional, Ecker, Simone, additional, González-Pérez, Abel, additional, Knowles, David G., additional, Monlong, Jean, additional, Johnson, Rory, additional, Quesada, Victor, additional, Djebali, Sarah, additional, Papasaikas, Panagiotis, additional, López-Guerra, Mónica, additional, Colomer, Dolors, additional, Royo, Cristina, additional, Cazorla, Maite, additional, Pinyol, Magda, additional, Clot, Guillem, additional, Aymerich, Marta, additional, Rozman, Maria, additional, Kulis, Marta, additional, Tamborero, David, additional, Gouin, Anaïs, additional, Blanc, Julie, additional, Gut, Marta, additional, Gut, Ivo, additional, Puente, Xose S., additional, Pisano, David G., additional, Martin-Subero, José Ignacio, additional, López-Bigas, Nuria, additional, López-Guillermo, Armando, additional, Valencia, Alfonso, additional, López-Otín, Carlos, additional, Campo, Elías, additional, and Guigó, Roderic, additional

Published
2013
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50. Exome Sequencing and Functional Analysis Identifies BANF1 Mutation as the Cause of a Hereditary Progeroid Syndrome

Author

Puente, Xose S., primary, Quesada, Victor, additional, Osorio, Fernando G., additional, Cabanillas, Rubén, additional, Cadiñanos, Juan, additional, Fraile, Julia M., additional, Ordóñez, Gonzalo R., additional, Puente, Diana A., additional, Gutiérrez-Fernández, Ana, additional, Fanjul-Fernández, Miriam, additional, Lévy, Nicolas, additional, Freije, José M.P., additional, and López-Otín, Carlos, additional

Published
2011
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