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419 results on '"Novikov, Ilya A."'

10. Calculation of sample size guaranteeing the required width of the empirical confidence interval with predefined probability

Author

Novikov, Ilya

Subjects
Statistics - Methodology
Abstract

The goal of any estimation study is an interval estimation of a the parameter(s) of interest. These estimations are mostly expressed using empirical confidence intervals that are based on sample point estimates of the corresponding parameter(s). In contrast, calculations of the necessary sample size usually use expected confidence intervals that are based on the expected value of the parameter(s). The approach that guarantees the required probability of the required width of empirical confidence interval is known at least since 1989. However, till now, this approach is not implemented for most software and is not even described in many modern papers and textbooks. Here we present the concise description of the approach to sample size calculation for obtaining empirical confidence interval of the required width with the predefined probability and give a framework of its general implementation. We illustrate the approach in Normal, Poisson, and Binomial distributions. The numeric results showed that the sample size necessary to obtain the required width of empirical confidence interval with the standard probability of $0.8$ or $0.9$ may be more than 20\% larger than the sample size calculated for the expected values of the parameters.

Published
2018

11. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, and Lavezzo, Enrico

Subjects
Human Genome, Networking and Information Technology R&D (NITRD), Genetics, Generic health relevance, Animals, Biofilms, Candida albicans, Drosophila melanogaster, Genome, Bacterial, Genome, Fungal, Humans, Locomotion, Memory, Long-Term, Molecular Sequence Annotation, Pseudomonas aeruginosa, Protein function prediction, Long-term memory, Biofilm, Critical assessment, Community challenge, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

Published
2019

31. Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2

Author

Choi, Byung-Kwon, Dayaram, Tajhal, Parikh, Neha, Wilkins, Angela D., Nagarajan, Meena, Novikov, Ilya B., Bachman, Benjamin J., Jung, Sung Yun, Haas, Peter J., Labrie, Jacques L., Pickering, Curtis R., Adikesavan, Anbu K., Regenbogen, Sam, Kato, Linda, Lelescu, Ana, Buchovecky, Christie M., Zhang, Houyin, Bao, Sheng Hua, Boyer, Stephen, Weber, Griff, Scott, Kenneth L., Chen, Ying, Spangler, Scott, Donehower, Lawrence A., and Lichtarge, Olivier

Published
2018

45. Four Most Pathogenic Superfamilies of Insect Pests of Suborder Sternorrhyncha: Invisible Superplunderers of Plant Vitality

Author

Oberemok, Volodymyr V., primary, Gal’chinsky, Nikita V., additional, Useinov, Refat Z., additional, Novikov, Ilya A., additional, Puzanova, Yelizaveta V., additional, Filatov, Roman I., additional, Kouakou, Nanan J., additional, Kouame, Kra F., additional, Kra, Kouadio D., additional, and Laikova, Kateryna V., additional

Published
2023
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49. DNA insecticide developed from the Lymantria dispar 5.8S ribosomal RNA gene provides a novel biotechnology for plant protection

Author

Oberemok, Volodymyr V., Laikova, Kateryna V., Gal’chinsky, Nikita V., Useinov, Refat Z., Novikov, Ilya A., Temirova, Zenure Z., Shumskykh, Maksym N., Krasnodubets, Alisa M., Repetskaya, Anna I., Dyadichev, Valeriy V., Fomochkina, Iryna I., Bessalova, Evgenia Y., Makalish, Tatiana P., Gninenko, Yuri I., and Kubyshkin, Anatoly V.

Published
2019
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