Genomics
The advent of next-generation sequencing (NGS) technologies enables researchers to sequence complex microbial communities directly from environment. Since assembly typically produces only genome fragments, also known as contigs, instead of…
Motivation: The analysis of antibodies and T-cell receptors (TCRs) concentrations in serum is a fundamental problem in immunoinformatics. Repertoire construction is a preliminary step of analysis of clonal lineages, understanding of immune…
A new method to identify all sufficiently long repeating substrings in one or several symbol sequences is proposed. The method is based on a specific gauge applied to symbol sequences that guarantees identification of the repeating…
The pathogenesis of cancer in human is still poorly understood. With the rapid development of high-throughput sequencing technologies, huge volumes of cancer genomics data have been generated. Deciphering those data poses great…
An RNA-seq experiment with 48 biological replicates in each of 2 conditions was performed to determine the number of biological replicates ($n_r$) required, and to identify the most effective statistical analysis tools for identifying…
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect…
Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the…
Constructing gene interaction networks (GINs) from high-throughput gene expression data is an important and challenging problem in systems biology. Existing algorithms produce networks that either have undirected and unweighted edges, or…
Owing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis. We review here the…
Systematic identification of protein function is a key problem in current biology. Most traditional methods fail to identify functionally equivalent proteins if they lack similar sequences, structural data or extensive manual annotations.…
Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that…
Overtreatment of early-stage low-risk prostate cancer (PC) patients represents a significant problem in disease management and has socio-economic implications. Development of genetic and molecular markers of clinically significant disease…
Isoform quantification is an important goal of RNA-seq experiments, yet it remains prob- lematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental…
Linear mixed models (LMMs) have emerged as the method of choice for confounded genome-wide association studies. However, the performance of LMMs in non-randomly ascertained case-control studies deteriorates with increasing sample size. We…
Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain…
Variability is ubiquitous in nature and a fundamental feature of complex systems. Few studies, however, have investigated variance itself as a trait under genetic control. By focusing primarily on trait means and ignoring the effect of…