CORRECTING FOR AMPLIFICATION BIAS IN NEXT-GENERATION SEQUENCING DATA

[1]  S. Bennett Solexa Ltd. , 2004, Pharmacogenomics.

[2]  Naiwen Ye,et al.  Robustness of Canberra Metric in Computer Intrusion Detection W , 2001 .

[3]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[4]  W. Huber,et al.  Differential expression analysis for sequence count data , 2010 .

[5]  G. N. Lance,et al.  Computer Programs for Hierarchical Polythetic Classification ("Similarity Analyses") , 1966, Comput. J..

[6]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[7]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[8]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[9]  Susan M. Bridges,et al.  Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data , 2009, BMC Bioinformatics.

[10]  G. N. Lance,et al.  Mixed-Data Classificatory Programs I - Agglomerative Systems , 1967, Aust. Comput. J..

[11]  M. Friedman A Comparison of Alternative Tests of Significance for the Problem of $m$ Rankings , 1940 .

[12]  Piotr J. Balwierz,et al.  Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data , 2009, Genome Biology.

[13]  T. Jenuwein,et al.  In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases , 2012, PLoS genetics.

[14]  R. Doerge,et al.  Statistical Applications in Genetics and Molecular Biology A Two-Stage Poisson Model for Testing RNA-Seq Data , 2011 .

[15]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[16]  Zhou Du,et al.  agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..

[17]  K. Robertson DNA methylation and human disease , 2005, Nature Reviews Genetics.

[18]  Daniel Rios,et al.  Ensembl 2011 , 2010, Nucleic Acids Res..

[19]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[20]  M. Friedman The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance , 1937 .

[21]  E. Mardis Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[22]  K. Zhao,et al.  Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq , 2009, Nucleic acids research.