Related papers: Misassembly Detection using Paired-End Sequence Re…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
High-dimensional compositional covariates, often derived from count data, are subject to measurement error and are frequently analyzed after aggregation along a prespecified tree to improve interpretability in applications such as…
We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
In microbiome and genomic studies, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
Genomic imprinting and maternal effects are two epigenetic factors that have been increasingly explored for their roles in the etiology of complex diseases. This is part of a concerted effort to find the "missing heritability." Accordingly,…
The performance of coverage-based fault localization greatly depends on the quality of test cases being executed. These test cases execute some lines of the given program and determine whether the underlying tests are passed or failed. In…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…