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Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have b...
Processing of reads from high throughput sequencing is often done in terms of edges in the de Bruijn graph representing all k-mers from the reads. The memory requirements for storing all k-mers in a lookup table ...
Testing for marginal associations between numerous genetic variants and disease may miss complex relationships among variables (e.g., gene-gene interactions). Bayesian approaches can model multiple variables t...
Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve net...
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
Cell survival and development are orchestrated by complex interlocking programs of gene activation and repression. Understanding how this gene regulatory network (GRN) functions in normal states, and is altered i...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Identification of good metaphase spreads is an important step in chromosome analysis for identifying individuals with genetic disorders. The process of finding suitable metaphase chromosomes for accurate clini...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
High-content screening (HCS) has become a powerful tool for drug discovery. However, the discovery of drugs targeting neurons is still hampered by the inability to accurately identify and quantify the phenotyp...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-su...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
The phosphorylation of virus proteins by host kinases is linked to viral replication. This leads to an inhibition of normal host-cell functions. Further elucidation of phosphorylation in virus proteins is requ...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Multiple sclerosis (MS) is a disease of central nervous system that causes the removal of fatty myelin sheath from axons of the brain and spinal cord. Autoimmunity plays an important role in this pathology out...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational me...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Since late March 2013, there has been another global health concern with a sudden wave of flu infections by a novel strain of avian influenza A (H7N9) virus in China. To-date, there have been more than 100 inf...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Multivariate quantitative traits arise naturally in recent neuroimaging genetics studies, in which both structural and functional variability of the human brain is measured non-invasively through techniques su...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
An increasing number of genetic components are available in several depositories of such components to facilitate synthetic biology research, but picking out those that will allow a designed circuit to achieve...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
High-throughput, image-based screens of cellular responses to genetic or chemical perturbations generate huge numbers of cell images. Automated analysis is required to quantify and compare the effects of these...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Recent in vivo studies showed new hopes of drug repositioning through causality inference from drugs to disease. Inspired by their success, here we present an in silico method for building a causal network (Cause...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in cellular processes. Given the high-throughput mass spectrometry-based experiments, the desire to annotate the catalytic kinases for i...
This article is part of a Supplement: Volume 14 Supplement 16
This article is part of a Supplement: Volume 14 Supplement 17
This article is part of a Supplement: Volume 14 Supplement 17
Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biolo...
Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of indi...
The combination of time-lapse imaging of live cells with high-throughput perturbation assays is a powerful tool for genetics and cell biology. The Mitocheck project employed this technique to associate thousan...
Viruses that infect bacteria, called phages, are well-known for their extreme mosaicism, in which an individual genome shares many different parts with many others. The mechanisms for creating these mosaics are l...
This article is part of a Supplement: Volume 14 Supplement 15
Using Next Generation Sequencing, SNP discovery is relatively easy on diploid species and still hampered in polyploid species by the confusion due to homeology. We develop HomeoSplitter; a fast and effective s...
This article is part of a Supplement: Volume 14 Supplement 15
Variation calling is the process of detecting differences between donor and consensus DNA via high-throughput sequencing read mapping. When evaluating the performance of different variation calling methods, a ...
This article is part of a Supplement: Volume 14 Supplement 15
Clustering sequences into families has long been an important step in characterization of genes and proteins. There are many algorithms developed for this purpose, most of which are based on either direct simi...
This article is part of a Supplement: Volume 14 Supplement 15
We study the problem of sorting genomes under an evolutionary model that includes genomic rearrangements and segmental duplications. We propose an iterative algorithm to improve any initial evolutionary trajec...
This article is part of a Supplement: Volume 14 Supplement 15
We pose the problem of dissecting an ancient polyploid genome into its constituent subgenomes despite fragmentation and noise caused by genome rearrangements and fractionation of multi-copy genes. We formulate...
This article is part of a Supplement: Volume 14 Supplement 15
We prove that for general models of random gene-order evolution of k ≥ 3 genomes, as the number of genes n goes to ∞, the median value approximates k times the divergence time if the number of rearrangements is l...
This article is part of a Supplement: Volume 14 Supplement 15
Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via ...
This article is part of a Supplement: Volume 14 Supplement 15
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