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Millions of cells are present in thousands of images created in high-throughput screening (HTS). Biologists could classify each of these cells into a phenotype by visual inspection. But in the presence of mill...
Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of...
This article is part of a Supplement: Volume 15 Supplement 11
Laccases (E.C. 1.10.3.2) are multi-copper oxidases that have gained importance in many industries such as biofuels, pulp production, textile dye bleaching, bioremediation, and food production. Their usefulness...
This article is part of a Supplement: Volume 15 Supplement 11
Every year pathogenic organisms cause billions of dollars' worth damage to crops and livestock. In agriculture, study of plant-microbe interactions is demanding a special attention to develop management strate...
This article is part of a Supplement: Volume 15 Supplement 11
Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multipl...
This article is part of a Supplement: Volume 15 Supplement 11
The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, fo...
This article is part of a Supplement: Volume 15 Supplement 11
While next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an e...
This article is part of a Supplement: Volume 15 Supplement 11
Tumors are heterogeneous in composition. They are composed of cancer cells proper, along with stromal elements that collectively form a microenvironment, all of which are necessary to nurture the malignant pro...
This article is part of a Supplement: Volume 15 Supplement 11
The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organ...
This article is part of a Supplement: Volume 15 Supplement 11
As the amount of scientific data grows, peer-reviewed Scientific Data Analysis Resources (SDARs) such as published software programs, databases and web servers have had a strong impact on the productivity of s...
This article is part of a Supplement: Volume 15 Supplement 11
Due to a significant decline in the costs associated with next-generation sequencing, it has become possible to decipher the genetic architecture of a population by sequencing a large number of individuals to ...
This article is part of a Supplement: Volume 15 Supplement 11
Extracted ion chromatogram (EIC) extraction and chromatographic peak detection are two important processing procedures in liquid chromatography/mass spectrometry (LC/MS)-based metabolomics data analysis. Most ...
This article is part of a Supplement: Volume 15 Supplement 11
Endocrine disrupting chemicals (EDCs) are exogenous compounds that interfere with the endocrine system of vertebrates, often through direct or indirect interactions with nuclear receptor proteins. Estrogen rec...
This article is part of a Supplement: Volume 15 Supplement 11
Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. However, the scientific discovery offered by NGS also include...
This article is part of a Supplement: Volume 15 Supplement 11
The analysis of gene expression has played an important role in medical and bioinformatics research. Although it is known that a large number of samples is needed to determine the patterns of gene expression a...
This article is part of a Supplement: Volume 15 Supplement 11
We developed a new computational technique called S tep-L evel D ifferential R esponse (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same ...
This article is part of a Supplement: Volume 15 Supplement 11
This article is part of a Supplement: Volume 15 Supplement 11
DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation...
Exome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is int...
Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. Illustra...
Quantification of a transcriptional profile is a useful way to evaluate the activity of a cell at a given point in time. Although RNA-Seq has revolutionized transcriptional profiling, the costs of RNA-Seq are ...
Signatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithm...
The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can...
Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determi...
Respiratory epithelial cells are the primary target of influenza virus infection in human. However, the molecular mechanisms of airway epithelial cell responses to viral infection are not fully understood. Rev...
Proteins dynamically interact with each other to perform their biological functions. The dynamic operations of protein interaction networks (PPI) are also reflected in the dynamic formations of protein complex...
Neural stem cells are motile and proliferative cells that undergo mitosis, dividing to produce daughter cells and ultimately generating differentiated neurons and glia. Understanding the mechanisms controlling...
To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell li...
In past number of methods have been developed for predicting post-translational modifications in proteins. In contrast, limited attempt has been made to understand post-transcriptional modifications. Recently ...
Studies of functional modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approache...
Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the st...
Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using...
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
This article is part of a Supplement: Volume 15 Supplement 10
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