RNA-sequencing (RNA-seq) has become the tool of choice for transcriptomics. Several recent studies demonstrate its successful adaption to single cell analysis. This allows new biological insights into cell differentiation, cell-to-cell variation and gene regulation, and how these aspects depend on each other. Here, I review the current single cell RNA-seq (scRNA-seq) efforts and discuss experim...

Classical Information Extraction (IE) systems fill slots in domain-specific frames. This paper reports on SEQ, a novel open IE system that leverages a domainindependent frame to extract ordered sequences such as presidents of the United States or the most common causes of death in the U.S. SEQ leverages regularities about sequences to extract a coherent set of sequences from Web text. SEQ nearl...

RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this re...

............................................................................................................................... i DEDICATION .......................................................................................................................... iv ACKNOWLEDGEMENTS ....................................................................................................... v TABLE O...

SUPPLEMENTAL MATERIALS & METHODS: TABLE OF CONTENTS I. PRIMARY DATA GENERATION .........................................................................................3 Cell Culture and Cell Lines Assayed .....................................................................................................................................3 Sub-cellular Fractionation and RNA Isolation (CSHL)......

Despite the fact that many RNA-Seq experiments do not use biological replicates, most of the existing differential gene expression analysis for RNA-Seq data are designed to work with replicates. We present a novel method for differential gene expression analysis based on bootstrapping. We also discuss the use of different normalization methods with Fisher’s exact test. We compare the methods we...

Due to its higher resolution mapping and stronger ChIP enrichment signals, ChIP-seq tends to replace ChIP-chip technology in studying genome-wide protein-DNA interactions, while the massive digital ChIP-seq data present new challenges to statisticians. To date, most methods proposed in the literature for ChIP-seq data analysis are model based, however, finding a single model workable for all da...

ChIP-seq has become the primary method for identifying in vivo protein-DNA interactions on a genome-wide scale, with nearly 800 publications involving the technique appearing in PubMed as of December 2012. Individually and in aggregate, these data are an important and information-rich resource. However, uncertainties about data quality confound their use by the wider research community. Recentl...