Modeling bias and variation in the stochastic processes of small RNA sequencing

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

(2016) Sara A. Byron et al.   NATURE REVIEWS GENETICS

Empirical insights into the stochasticity of small RNA sequencing

(2016) Li-Xuan Qin et al.   Scientific Reports

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

(2015) Ruijie Liu et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

(2015) Katharine Best et al.   Scientific Reports

Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure

(2015) Ryan T. Fuchs et al.   PLoS One

Elimination of Ligation Dependent Artifacts in T4 RNA Ligase to Achieve High Efficiency and Low Bias MicroRNA Capture

(2014) Yunke Song et al.   PLoS One

Hypoxia-mediated downregulation of miRNA biogenesis promotes tumour progression

(2014) Rajesha Rupaimoole et al.   Nature Communications

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data

(2013) Yingtao Bi et al.   BMC BIOINFORMATICS

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction

(2012) Gary Cobbs   BMC BIOINFORMATICS

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Expression Is Down-Regulated and Reorganized in Prefrontal Cortex of Depressed Suicide Subjects

(2012) Neil R. Smalheiser et al.   PLoS One

Cigarette Smoking Decreases Global MicroRNA Expression in Human Alveolar Macrophages

(2012) Joel W. Graff et al.   PLoS One

A powerful and flexible approach to the analysis of RNA sequence count data

(2011) Yi-Hui Zhou et al.   BIOINFORMATICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Genomewide microRNA down-regulation as a negative feedback mechanism in the early phases of liver regeneration

(2011) Jingmin Shu et al.   HEPATOLOGY

Inference for Quantitation Parameters in Polymerase Chain Reactions via Branching Processes With Random Effects

(2011) Bret Hanlon et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Circulating microRNA expression is reduced in chronic kidney disease

(2011) Calida S. Neal et al.   NEPHROLOGY DIALYSIS TRANSPLANTATION

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

microRNA Signature and Expression of Dicer and Drosha Can Predict Prognosis and Delineate Risk Groups in Neuroblastoma

(2010) R.-J. Lin et al.   CANCER RESEARCH

Background adjustment of cDNA microarray images by Maximum Entropy distributions

(2010) Christos Argyropoulos et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models

(2010) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

(2010) Sudeep Srivastava et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Absolute quantification of microRNAs by using a universal reference

(2009) U. Bissels et al.   RNA

A quantitative approach for polymerase chain reactions based on a hidden Markov model

(2008) Nadia Lalam   JOURNAL OF MATHEMATICAL BIOLOGY

Podocyte-Specific Deletion of Dicer Alters Cytoskeletal Dynamics and Causes Glomerular Disease

(2008) S. J. Harvey et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Podocyte-Selective Deletion of Dicer Induces Proteinuria and Glomerulosclerosis

(2008) S. Shi et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY