Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.

Autor: Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi

Publikováno v: PLoS Computational Biology, Vol 11, Iss 8, p e1004403 (2015)

Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. In a typical phosphoproteomics study, phos

Externí odkaz: https://doaj.org/article/2bac6a24fed24e19b888a09e2ca28889

Intraspecific Transcriptome Variation and Sex-Biased Expression in Anopheles arabiensis

Autor: José M. Ranz, Cyrille Ndo, Kevin Cabrera, Roch K. Dabiré, Bryan D. Clifton, Diego Ayala, Hsiu-Ching Ma, Vivek Jayaswal, Marco Pombi, Karine Mouline, Abdoulaye Diabaté, Anna Couhet

Publikováno v: Genome Biology and Evolution
Genome biology and evolution, vol 13, iss 9

The magnitude and functional patterns of intraspecific transcriptional variation in the anophelines, including those of sex-biased genes underlying sex-specific traits relevant for malaria transmission, remain understudied. As a result, how changes i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0e05484012fbcb0103ba369ae0fb649
https://pubmed.ncbi.nlm.nih.gov/35182427

Identification and stratification of systemic lupus erythematosus patients into two transcriptionally distinct clusters based on IFN-I signature

Autor: Nadine Lemos, Debarati Mazumder Tagore, Vivek Jayaswal, Puneet Chopra, Avisek Deyati, Anu Mohan, Siva Subramani Thulasingam, Manjunath Ramarao, Shailesh Dudhgaonkar, Vineeta Shobha, S Margaret Sunitha, Amit Anand, Preethi Karunanithi, Ratika Srivastava, Sabariya Selvam, A V Malini, Saumya Pant, Sushma Basavanthappa

Publikováno v: Lupus. 30(5)

Objective Despite the significant advancement in the understanding of the pathophysiology of systemic lupus erythematosus (SLE) variable clinical response to newer therapies remain a major concern, especially for patients with lupus nephritis and neu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1dd2c9a7174ba64c68e8001b1302fda
https://pubmed.ncbi.nlm.nih.gov/33497307

A species‐specific multigene family mediates differential sperm displacement in Drosophila melanogaster

Autor: Jamie Jimenez, Bryan D. Clifton, Kien Nguyen, Robert D. Magie, Shu Dan Yeh, José M. Ranz, Vivek Jayaswal

Publikováno v: Evolution. 72:399-403

Sperm competition is a postcopulatory sexual selection mechanism in species in which females mate with multiple males. Despite its evolutionary relevance in shaping male traits, the genetic mechanisms underlying sperm competition are poorly understoo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::787b5080119dd0eabaf3648830484b03
https://doi.org/10.1111/evo.13417

Assessment of network module identification across complex diseases

Autor: Choobdar, Sarvenaz, Ahsen, Mehmet E., Natoli, Ted, Lysenko, Artem, Ma, Tianle, Mall, Raghvendra, Marbach, Daniel, Mattia, Tomasoni, Medvedovic, Mario, Menche, Jörg, Mercer, Johnathan, Micarelli, Elisa, Monaco, Alfonso, Narayan, Rajiv, Müller, Felix, Narykov, Oleksandr, Norman, Thea, Park, Sungjoon, Perfetto, Livia, Perrin, Dimitri, Pirrò, Stefano, Przytycka, Teresa M., DREAM Module Identification Challenge Consortium, Qian, Xiaoning, Raman, Karthik, Ramazzotti, Daniele, Ramsahai, Emilie, Ravindran, Balaraman, Rennert, Philip, Sáez Rodríguez, Julio, Schärfe, Charlotta, Sharan, Roded, Shi, Ning, Subramanian, Aravind, Shin, Wonho, Shu, Hai, Sinha, Himanshu, Slonim, Donna K., Spinelli, Lionel, Srinivasan, Suhas, Suver, Christine, Szklarczyk, Damian, Tangaro, Sabina, Zhang, Jitao D., Thiagarajan, Suresh, Tichit, Laurent, Tiede, Thorsten, Tripathi, Beethika, Tsherniak, Aviad, Tsunoda, Tatsuhiko, Türei, Dénes, Ullah, Ehsan, Vahedi, Golnaz, Valdeolivas, Alberto, Stolovitzky, Gustavo, Vivek, Jayaswal, von Mering, Christian, Waagmeester, Andra, Wang, Bo, Wang, Yijie, Weir, Barbara A., White, Shana, Winkler, Sebastian, Xu, Ke, Xu, Taosheng, Kutalik, Zoltán, Yan, Chunhua, Yang, Liuqing, Yu, Kaixian, Yu, Xiangtian, Zaffaroni, Gaia, Zaslavskiy, Mikhail, Zeng, Tao, Zhang, Lu, Zhang, Weijia, Lage, Kasper, Zhang, Lixia, Zhang, Xinyu, Zhang, Junpeng, Zhou, Xin, Zhou, Jiarui, Zhu, Hongtu, Zhu, Junjie, Zuccon, Guido, Crawford, Jake, Cowen, Lenore J., Bergmann, Sven, Aicheler, Fabian, Amoroso, Nicola, Arenas, Alex, Azhagesan, Karthik, Baker, Aaron, Banf, Michael, Batzoglou, Serafim, Tomasoni, Mattia, Baudot, Anaïs, Bellotti, Roberto, Boroevich, Keith A., Brun, Christine, Cai, Stanley, Caldera, Michael, Calderone, Alberto, Cesareni, Gianni, Chen, Weiqi, Fang, Tao, Chichester, Christine, Cowen, Lenore, Cui, Hongzhu, Dao, Phuong, De Domenico, Manlio, Dhroso, Andi, Didier, Gilles, Divine, Mathew, Lamparter, David, Del Sol, Antonio, Feng, Xuyang, Flores-Canales, Jose C., Fortunato, Santo, Gitter, Anthony, Gorska, Anna, Guan, Yuanfang, Guénoche, Alain, Gómez, Sergio, Lin, Junyuan, Hamza, Hatem, Hartmann, András, He, Shan, Heijs, Anton, Heinrich, Julian, Hescott, Benjamin, Hu, Xiaozhe, Hu, Ying, Huang, Xiaoqing, Hughitt, V. Keith, Jeon, Minji, Jeub, Lucas, Johnson, Nathan T., Joo, Keehyoung, Joung, InSuk, Jung, Sascha, Kalko, Susana G., Kamola, Piotr J., Kang, Jaewoo, Kaveelerdpotjana, Benjapun, Kim, Minjun, Kim, Yoo-Ah, Kohlbacher, Oliver, Korkin, Dmitry, Krzysztof, Kiryluk, Kunji, Khalid, Kutalik, Zoltàn, Lang-Brown, Sean, Le, Thuc Duy, Lee, Jooyoung, Lee, Sunwon, Lee, Juyong, Li, Dong, Li, Jiuyong, Liu, Lin, Loizou, Antonis, Luo, Zhenhua

Publikováno v: Nature Methods
Nature methods 16(9), 843-852 (2019). doi:10.1038/s41592-019-0509-5
Nature Methods, 2019, 16 (9), pp.843-852. ⟨10.1038/s41592-019-0509-5⟩
Nature Methods, Nature Publishing Group, 2019, 16 (9), pp.843-852. ⟨10.1038/s41592-019-0509-5⟩
Nature methods, vol. 16, no. 9, pp. 843-852

Many bioinformatics methods have been proposed for reducing the complexity of large gene or protein networks into relevant subnetworks or modules. Yet, how such methods compare to each other in terms of their ability to identify disease-relevant modu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::31ab672e0c945979c1daea08c7529bc9
https://hdl.handle.net/11573/1660164