Literature DB >> 31964852

Clarifying the effect of library batch on extracellular RNA sequencing.

Christopher Hartl1, Yuan Gao2,3.   

Abstract

Mesh：

Substances：

Year:  2020        PMID： 31964852      PMCID： PMC6994997          DOI： 10.1073/pnas.1916312117

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


× No keyword cloud information.
  10 in total

1.  qSVA framework for RNA quality correction in differential expression analysis.

Authors:  Andrew E Jaffe; Ran Tao; Alexis L Norris; Marc Kealhofer; Abhinav Nellore; Joo Heon Shin; Dewey Kim; Yankai Jia; Thomas M Hyde; Joel E Kleinman; Richard E Straub; Jeffrey T Leek; Daniel R Weinberger
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-20       Impact factor: 11.205

Review 2.  Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.

Authors:  Francesca Finotello; Barbara Di Camillo
Journal:  Brief Funct Genomics       Date:  2014-09-18       Impact factor: 4.241

Review 3.  Tackling the widespread and critical impact of batch effects in high-throughput data.

Authors:  Jeffrey T Leek; Robert B Scharpf; Héctor Corrada Bravo; David Simcha; Benjamin Langmead; W Evan Johnson; Donald Geman; Keith Baggerly; Rafael A Irizarry
Journal:  Nat Rev Genet       Date:  2010-09-14       Impact factor: 53.242

4.  Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates.

Authors:  Yet Nguyen; Dan Nettleton; Haibo Liu; Christopher K Tuggle
Journal:  J Agric Biol Environ Stat       Date:  2015-10-01       Impact factor: 1.524

5.  Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets.

Authors:  Yalchin Oytam; Fariborz Sobhanmanesh; Konsta Duesing; Joshua C Bowden; Megan Osmond-McLeod; Jason Ross
Journal:  BMC Bioinformatics       Date:  2016-09-01       Impact factor: 3.169

6.  variancePartition: interpreting drivers of variation in complex gene expression studies.

Authors:  Gabriel E Hoffman; Eric E Schadt
Journal:  BMC Bioinformatics       Date:  2016-11-25       Impact factor: 3.169

7.  Extracellular RNA in a single droplet of human serum reflects physiologic and disease states.

Authors:  Zixu Zhou; Qiuyang Wu; Zhangming Yan; Haizi Zheng; Chien-Ju Chen; Yuan Liu; Zhijie Qi; Riccardo Calandrelli; Zhen Chen; Shu Chien; H Irene Su; Sheng Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-03       Impact factor: 11.205

8.  A Digital RNA Signature of Circulating Tumor Cells Predicting Early Therapeutic Response in Localized and Metastatic Breast Cancer.

Authors:  Tanya T Kwan; Aditya Bardia; Laura M Spring; Anita Giobbie-Hurder; Mark Kalinich; Taronish Dubash; Tilak Sundaresan; Xin Hong; Joseph A LiCausi; Uyen Ho; Erin J Silva; Ben S Wittner; Lecia V Sequist; Ravi Kapur; David T Miyamoto; Mehmet Toner; Daniel A Haber; Shyamala Maheswaran
Journal:  Cancer Discov       Date:  2018-08-13       Impact factor: 39.397

9.  Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge.

Authors:  Sara Mostafavi; Alexis Battle; Xiaowei Zhu; Alexander E Urban; Douglas Levinson; Stephen B Montgomery; Daphne Koller
Journal:  PLoS One       Date:  2013-07-18       Impact factor: 3.240

10.  BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm.

Authors:  Anna Papiez; Michal Marczyk; Joanna Polanska; Andrzej Polanski
Journal:  Bioinformatics       Date:  2019-06-01       Impact factor: 6.937
  10 in total
  1 in total

1.  Reply to Hartl and Gao: Lack of between-batch difference in the distributions of measured extracellular RNA levels.

Authors:  Zixu Zhou; Qiuyang Wu; Zhangming Yan; Haizi Zheng; Chien-Ju Chen; Yuan Liu; Zhijie Qi; Riccardo Calandrelli; Zhen Chen; Shu Chien; H Irene Su; Sheng Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-21       Impact factor: 11.205
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.