Significance evaluation in factor graphs

Autor: Tobias Madsen, Asger Hobolth, Jens Ledet Jensen, Jakob Skou Pedersen

Publikováno v: BMC Bioinformatics, Vol 18, Iss 1, Pp 1-12 (2017)

Abstract Background Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of both genomics data as well as data from other scientific fields

Externí odkaz: https://doaj.org/article/83dc351f360e4472a0815e87d14da2d3

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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Husen, M Umer, Timothy, J Underwood, Lara, Urban, Tomoko, Urushidate, Tetsuo, Ushiku, Liis, Uusküla-Reimand, Alfonso, Valencia, David, J Van Den Berg, Steven Van Laere, Peter Van Loo, Erwin, G Van Meir, Gert, G Van den Eynden, Theodorus Van der Kwast, Naveen, Vasudev, Miguel, Vazquez, Ravikiran, Vedururu, Umadevi, Veluvolu, Shankar, Vembu, Lieven P, C Verbeke, Peter, Vermeulen, Clare, Verrill, Alain, Viari, David, Vicente, Caterina, Vicentini, K Vijay Raghavan, Juris, Viksna, Ricardo, E Vilain, Izar, Villasante, Anne, Vincent-Salomon, Tapio, Visakorpi, Douglas, Voet, Paresh, Vyas, Ignacio, Vázquez-García, Nick, M Waddell, Nicola, Waddell, Claes, Wadelius, Lina, Wadi, Rabea, Wagener, Jian, Wang, Linghua, Wang, Wang, Qi, Yumeng, Wang, Zhining, Wang, Paul, M Waring, Hans-Jörg, Warnatz, Jonathan, Warrell, Anne, Y Warren, David, C Wedge, Dieter, Weichenhan, Paul, Weinberger, Daniel, J Weisenberger, Ian, Welch, Justin, P Whalley, Hayley, C Whitaker, Dennis, Wigle, Matthew, D Wilkerson, Ashley, Williams, James, S Wilmott, Gavin, W Wilson, Julie, M Wilson, Richard, K Wilson, Boris, Winterhoff, Jeffrey, A Wintersinger, Maciej, Wiznerowicz, Stephan, Wolf, Bernice, H Wong, Tina, Wong, Winghing, Wong, Youngchoon, Woo, Scott, Wood, Bradly, G Wouters, Adam, J Wright, Derek, W Wright, Mark, H Wright, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Tian, Xia, Qian, Xiang, Xiao, Xiao, Rui, Xing, Heng, Xiong, Qinying, Xu, Yanxun, Xu, Shinichi, Yachida, Rui, Yamaguchi, Masakazu, Yamamoto, Shogo, Yamamoto, Hiroki, Yamaue, Fan, Yang, Huanming, Yang, Jean, Y Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yang, Xiaotong, Yao, Marie-Laure, Yaspo, Lucy, Yates, Christina, Yau, Chen, Ye, Christopher, J Yoon, Sung-Soo, Yoon, Fouad, Yousif, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yu, Yuan, Ke, Yuan, Yuan, Denis, Yuen, Olga, Zaikova, Jorge, Zamora, Marc, Zapatka, Jean, C Zenklusen, Thorsten, Zenz, Nikolajs, Zeps, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhang, Zhongming, Zhao, Liangtao, Zheng, Xiuqing, Zheng, Wanding, Zhou, Yong, Zhou, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zhu, Lihua, Zou, Xueqing, Zou, Anna, Defazio, Nicholas van As, Carolien H, M van Deurzen, Marc, J van de Vijver, L Van't Veer, Christian von Mering

Publikováno v: Nature Communications, 11(1):4748. Nature Publishing Group
Nature communications, 11(1):4748. Nature Publishing Group
Nature communications, 11 (1
NATURE COMMUNICATIONS
Nature Communications, 11 (1)
Nature Communications, Vol 11, Iss 1, Pp 1-27 (2020)
Bailey, M H, Meyerson, W U, Dursi, L J, Wang, L B, Dong, G, Liang, W W, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, M H, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, Weischenfeldt, J, Brunak, S, Ding, L, Favero, F, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ', Nature Communications, vol. 11, no. 1, 4748 . https://doi.org/10.1038/s41467-020-18151-y
Bailey, Matthew H; Meyerson, William U; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan; Liang, Wen-Wei; Weerasinghe, Amila; Li, Shantao; Kelso, Sean; Saksena, Gordon; Ellrott, Kyle; Wendl, Michael C; Wheeler, David A; Getz, Gad; Simpson, Jared T; Gerstein, Mark B; Ding, Li (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1), p. 4748. Springer Nature 10.1038/s41467-020-18151-y
Nature communications, vol 11, iss 1
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
RUO. Repositorio Institucional de la Universidad de Oviedo
instname
Nature Communications
Dipòsit Digital de la UB
Universidad de Barcelona
Nature Communications, 11, 1
Recercat. Dipósit de la Recerca de Catalunya
Digital.CSIC. Repositorio Institucional del CSIC
Nature Communications, 11
RUO: Repositorio Institucional de la Universidad de Oviedo
Universidad de Oviedo (UNIOVI)
Bailey, M H, Meyerson, W U, Dursi, L J, Wang, L B, Dong, G, Liang, W W, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, M H, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ', Nature Communications, vol. 11, no. 1, 4748 . https://doi.org/10.1038/s41467-020-18151-y
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)

MC3 Working Group: Rehan Akbani21, Pavana Anur22, Matthew H. Bailey1,2,3, Alex Buchanan9, Kami Chiotti9, Kyle Covington12,23, Allison Creason9, Li Ding1,2,3,20, Kyle Ellrott9, Yu Fan21, Steven Foltz1,2, Gad Getz8,14,15,16, Walker Hale12, David Haussl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79caf69aa08507159a37977adcb4937b
https://www.bib.irb.hr/1104730

EBADIMEX: An empirical Bayes approach to detect joint differential expression and methylation and to classify samples

Autor: Malene Juul, Tobias Madsen, Michał P. Świtnicki, Jakob Skou Pedersen

Publikováno v: Madsen, T, Świtnicki, M, Juul, M & Pedersen, J S 2019, ' EBADIMEX : an empirical Bayes approach to detect joint differential expression and methylation and to classify samples ', Statistical Applications in Genetics and Molecular Biology, vol. 18, no. 6, 20180050 . https://doi.org/10.1515/sagmb-2018-0050

1AbstractDNA methylation and gene expression are interdependent and both implicated in cancer development and progression, with many individual biomarkers discovered. A joint analysis of the two data types can potentially lead to biological insights

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8677ec1d3c0e670c970ad43a18b9d6ac

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Autor: Pcawg Drivers, Chris Sander, Todd A. Johnson, Jüri Reimand, Lina Wadi, Dimple Chakravarty, Claes Wadelius, Rory Johnson, Abel Gonzalez-Perez, Jing Zhang, Nicholas A Sinnott-Armstrong, Icgc, Abdullah Kahraman, Nicholas J. Haradhvala, Husen M. Umer, Priyanka Dhingra, Michael S. Lawrence, Inigo Martincorena, Ben Raphael, André Kahles, Chen Hong, Esther Rheinbay, Joana Carlevaro-Fita, Loris Mularoni, Tatsuhiko Tsunoda, Qianyun Guo, Andrés Arturo Lanzós Camaioni, Yosef E. Maruvka, Josh Stuart, Dong-Hoon Lee, Jakob Skou Pedersen, Jaegil Kim, Klev Diamanti, Nuno A. Fonseca, Julian M. Hess, Federico Abascal, Samir B. Amin, Kjong-Van Lehmann, Carl Herrmann, Ekta Khurana, Mark Gerstein, Mark A. Rubin, Mark P. Hamilton, Lars Feuerbach, Oriol Pich, Lincoln Stein, Keunchil Park, Keith A. Boroevich, Liis Uusküla-Reimand, Ciyue Shen, Lucas Lochovsky, David Tamborero, Gad Getz, Shimin Shuai, Randi Istrup Istrup Pedersen, Johanna Bertl, Lina Sieverling, Young-Wook Kim, Morten Muhlig Nielsen, Keren Isaev, Calvin Wing Yiu Chan, Asger Hobolth, Malene Juul, Eric Minwei Liu, Henrik Hornshøj, Jan Komorowski, Sushant Kumar, Nuria Lopez-Bigas, David A. Wheeler, Manolis Kellis, Peter J. Campbell, Radhakrishnan Sabarinathan, Grace Tiao, Gordon Saksena, Henrik Tobias Madsen

Publikováno v: bioRxiv
pre

Discovery of cancer drivers has traditionally focused on the identification of protein-coding genes. Here we present a comprehensive analysis of putative cancer driver mutations in both protein-coding and non-coding genomic regions across >2,500 whol

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eaec91ebd7eaa8c5486f9e530572e585
https://doi.org/10.1101/237313

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

Autor: Michał P. Świtnicki, Tobias Madsen, Johanna Bertl, Qianyun Guo, Morten Muhlig Nielsen, Jakob Skou Pedersen, Henrik Hornshøj, Malene Juul, Asger Hobolth

Publikováno v: eLife, Vol 6 (2017)
eLife
Rasmussen, M J, Bertl, J, Guo, Q, Nielsen, M M, Świtnicki, M, Hornshøj, H, Madsen, T, Hobolth, A & Pedersen, J S 2017, ' Non-coding cancer driver candidates identified with a sample-and position-specific model of the somatic mutation rate ', eLife, vol. 6 . https://doi.org/10.7554/eLife.21778

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1fe8856c30e06cdb52f134a3d9cc861c
https://elifesciences.org/articles/21778