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BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data

Jinghua Gu, Xiao Wang, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
2014 BMC Bioinformatics  
A novel Bayesian framework is developed for joint estimate of gene level mRNA abundance and differential state, which models the intrinsic variability in RNA-Seq to improve the estimation.  ...  However, precise quantification of mRNA abundance and identification of differentially expressed genes are complicated due to biological and technical variations in RNA-Seq data.  ...  We propose a computational method, namely Bayesian Analysis of Dispersed Gene Expression ('BADGE'), to model variability in RNA-Seq data.  ... 
doi:10.1186/1471-2105-15-s9-s6 pmid:25252852 pmcid:PMC4168709 fatcat:smmaak7zoze6pnkwc7jp4a346q

RNA-seq data science: From raw data to effective interpretation [article]

Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin (+4 others)
2021 arXiv   pre-print
RNA-seq analysis enables the probing of genes and corresponding transcripts which is essential for answering important biological questions, such as detecting novel exons, transcripts, gene expressions  ...  RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms.  ...  Patro for his valuable comments and suggestions on the manuscript. Competing Interests The authors declare no competing interests. References  ... 
arXiv:2010.02391v3 fatcat:krgm7uzmibdlfh2ylgqxmnh2qu

a need to know

William A. Spencer, Larry R. Gettman, H. H. Bridge, Allan J. Ryan
1983 Physician and sportsmedicine  
Testing for Differentially Expressed Pathways from Within-Subject Matched Pairs of RNA-Seq Data Sets-FGrant Schissler, Statistics GIDP; Walter W. Piegorsch, University of Arizona; Yves A.  ...  Power Analysis for RNA-Seq Differential Expression Studies-FLianbo Yu, The Ohio State University; Soledad Fernandez, The Ohio State University; Guy N.  ...  Professional Development This year marks the centennial of Statistics of Income (SOI), a principal Federal statistical agency responsible for the statistical policies and programs of the U.S.  ... 
doi:10.1080/00913847.1983.11708423 pmid:27409254 fatcat:7rlbreoerngb3epmighz7l5vr4

HGM 2010 Programme / Abstract

2010 The HUGO Journal  
The identification of an EYS mutation in a dog affected with retinal progressive atrophy would provide a useful model for establishing future therapies for retinitis pigmentosa.  ...  We are currently RT-PCR-amplifying RNA from the lymphocytes of patients to identify aberrant transcripts.  ...  Therefore, we propose a new pipeline to analyze SAGE, DGE and RNA-Seq data.  ... 
doi:10.1007/s11568-010-9143-0 fatcat:oykxd6u7snfi5o7m6tst7wi6yq

第57回年会予稿集

2019 Seibutsu Butsuri  
for brain disorders. 2SCP-4 顕微鏡ライブイメージングと 1 細胞 RNA-seq を組み合わせた自動化システムの開発とシンギュラ リティ生物学への応用 An automated system for combining single-cell RNA-seq with live cell imaging and its applications for Singularity  ...  In this presentation, I will introduce our efforts to develop novel sequencing methods to read the epigenome, including PBAT-seq for DNA methylation, DMS-seq for protein-DNA interactions, and others.  ...  -S425 -Poster, Day 3 3Pos187 Three-dimensional analysis for formation process of amyloid β 42 aggregation using quantum dots nanoprobe Masahiro Kuragano, Kiyotaka Tokuraku (Div. of Sust. and Env.  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

第56回年会予稿集

2018 Seibutsu Butsuri  
Biophysical Society of Japan (BSJ) grants "Early Career Award in Biophysics" and "Early Career Presentation Award" to young BSJ members for their excellent presentations that show great potential to contribute  ...  Up to five awardees of the Early Career Award in Biophysics will be selected and announced at the banquet 3SEA-5 光遺伝子操作による単一の糸球体の活性により誘因される恐怖行動の探索 Immobility responses are induced by photoactivation of  ...  In this study, we propose a theoretical framework in which we present a fairly general model of a gene regulatory system, derive a novel solution, and provide a Bayesian approach for estimating the model  ... 
doi:10.2142/biophys.58.s1 fatcat:6slkwnu64fen7cjixehxrcmdzm

From condition-specific interactions towards the differential complexome of proteins [article]

Thorsten Will, Universität Des Saarlandes
2020
This improvement facilitates an application of the method for a large number of samples and the resulting sample-specific complexes can ultimately be assessed quantitatively with our novel differential  ...  presence of causative protein domain interactions of an underlying model.  ...  Thus, RNA-seq is also able to report novel splice variants and mutations in the sequence [67] . Figure 2 .3 sketches the basic approach of RNA-seq.  ... 
doi:10.22028/d291-32493 fatcat:f2kkrll3sfepnh2x445ixsox3a

Human endogenous retroviruses aid embryonic development [article]

Manvendra Singh, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2018
HERV-H provides binding sites for pluripotency transcription factors and serves as a major source for ncRNAs and chimeric transcripts in hPSCs.  ...  Following up, we show that diverse modes of HERV-H activity have played a pivotal role in the evolution and development of human- specific embryogenesis including pluripotency.  ...  RNA-seq data used for this analysis was published [184] C.  ... 
doi:10.17169/refubium-1312 fatcat:lwvuvlafava3vdgj6u5nxkxtw4

A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes

Charalampos Kyriakopoulos, Karl Nordström, Paula Linh Kramer, Judith Y. Gottfreund, Abdulrahman Salhab, Julia Arand, Fabian Müller, Ferdinand von Meyenn, Gabriella Ficz, Wolf Reik, Verena Wolf, Jörn Walter (+1 others)
2022
A precise understanding of DNA methylation dynamics is of great importance for a variety of biological processes including cellular reprogramming and differentiation.  ...  For this purpose we developed a pipeline for quantitative and precise estimation of Dnmt and Tet activity.  ...  sequencing data.  ... 
doi:10.3929/ethz-b-000540672 fatcat:uvjahdrgtfdefk3yb54qmpm3ai

Epigenetic effects of temperature on sex change in barramundi, Lates calcarifer

Alyssa Budd
2020
Because prebuilt indexes are not available for non-model organisms such as barramundi, a custom index was built to aid the mapping of RNA-Seq reads.  ...  control individuals for which WGBS and RNA-Seq data were obtained were additionally assessed in greater detail (Figure 4.15) .  ...  Results are derived from linear hypothesis testing to compare regression coefficients for each region specified in the comparison column based on the beta regression model specified in text and p values  ... 
doi:10.25903/95mj-pk34 fatcat:ifvxy7xegvdfhpjx35pbvk65su

THE IMPACT OF MODERN BREEDING ON KEY TRAITS ARCHITECTURE EVOLUTION THROUGH DOMESTICATION AND ITS IMPLICATION FOR THE CASSAVA BREEDING APPROACH

Alex Chukwuka Ogbonna
2021
of detected DEGs into 18 gene modules. (9) Differential expression and pathway analysis targeting cassava mosaic disease identified 27 genes observed in plant-pathogen interaction pathways, and two peroxidase  ...  Lastly, I developed a population-based transcriptomics resource for studying developmental and physiological characteristics of cassava and also providing additional insight on disease resistance.  ...  Bredeson from University of California, Berkeley, for providing helpful discussion and feedback. We thank the three anonymous reviewers and the editor for their constructive feedback.  ... 
doi:10.7298/51v5-ab56 fatcat:6jzxzmmw4zaopekpkfj6p64bmy

Yuan_columbia_0054D_16399.pdf [article]

2021
We develop a method to improve estimation of expression quantitative trait loci by joint inference over gene expression reference data and GWAS data, incorporating insights from the liability threshold  ...  rapidly increasing sample sizes and power required for GWAS.  ...  stemming from small sample sizes of current RNA-seq experiments [107] .  ... 
doi:10.7916/d8-79d1-t253 fatcat:t5yhvnpn6bbdrbq7t4osxks4bq