Top Research Papers on Bioinformatics

This journey provided an opportunity to debate on cry toxins, lipase, ibuprofen, HLA alleles, antigens, peptide vaccines, protein-protein interactions, genomes and biological knowledge discovery models.

An organized functional scheme of animal was composed and it has been used to show that the essence of the living being is the three-level informational flows for coding-decoding and control, implemented by genetic, hormonal and neural subsystems.

An introduction to major bioinformatics resources of databases and tools developed at KOBIC, classified into three main fields: genome, proteome, and literature.

This review provides an overview of the concepts of quantum biology and quantum mechanics and their intersection in quantum bioinformatics and proposes a classification of quantum bioinformatics to promote interdisciplinary collaboration and accelerate progress.

Summary Over the last decade, the areas of bioinformatics and genomics have identified, catalogued and characterised, at the molecular level, the components that make up the complex system of a cell. The next step is to describe how the many components interact to create the complex behaviour that underlies development and disease. The following article is to describe some of the research areas and challenges involved.

The results verify that the proposed Local Feature Mining in Proteins (LFM-Pro) method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.

It is shown that drug design aimed at promoting pairwise interactions between ligand and kinase target actually fosters promiscuity because of the high conservation of the partner groups on or around the ATP-binding site of the kinase.

Here, it is shown that the problem can be reformulated such that an optimal scale is straightforwardly obtained in an analytical fashion and favorably compares with others in terms of both algorithmic optimality and practical prediction accuracy.

The integration of ICA and statistical tests for detecting the differences in peak intensities between experimental groups allows to identify protein peaks that could be indicators of a diseased state.

A web application, the POODLE-S, is developed, which predicts the disordered region from amino acid sequences by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

A web server for discriminating the stability of proteins and predicting their stability changes upon single amino acid substitutions from amino acid sequence, developed using decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively.

This work uses a sampling method known as particle filtering to produce a set of all-atom protein models, and shows that this approach produces a more accurate model than three leading methods--Textal, Resolve and ARP/WARP--in terms of main chain completeness, sidechain identification and crystallographic R factor.

Having recently attended two very informative, empowering workshops on bioinformatics and translational bioinformatics with Diane C. Rein, PhD, MLS, Bioinformatics and Molecular Biology Liaison, Health Sciences Library, University of Buffalo, the top takeaways for success in handling these kinds of information requests are shared.

The development of a ltering framework designed for efficient identification of both polyclonal and independent errors within SOLiD sequence data, which utilizes the quality values reported by SOLiD’s primary analysis for the identification of the two different types of errors.

This work provides several methods to search for similar folding patterns using a concise tableau representation of proteins that encodes the relative geometry of secondary structural elements, and describes a rapid and accurate method for comparing a query structure against a database of protein domains, TableauSearch.

A new method for the identification of leucine-rich repeats by incorporating protein secondary structure prediction and application of next-generation DNA sequencing in medical discovery is proposed.

Clinicians at the point of care need to understand and integrate entities such as genotype/phenotype correlations, biomarker discovery, and pharmacogenomics; while researchers require accurate, structured, and (ideally) coded clinical data, as well as biological reference data sets.

The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study.

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Assessment of medical technology in the context of commercialization in the context of commercialization and many issues unique to biomedical products.

This chapter presents bioinformatics first from the perspective of computer science and information technology, then from the perspectives of bioscience.

The machine learning field continues to develop new applications for predicting outcomes and explaining phenomena in the domain of biology and medicine, but NNs offer limited help in explaining the features and their values for the models they produce.

Two books devoted to the state of the art in bioinformatics are covered: a one-volume work, Current Topics in Computation Molecular Biology, and a two- volume work, Bio informatics, both of which are organized collections of articles by experts in the subfields of this discipline.

Biskit simplifies the parallelization of time consuming calculations via PVM (Parallel Virtual Machine) and offers a software platform for the rapid integration of external programs and new algorithms into complex structural bioinformatics workflows.

OBJECTIVES: The NRSP-8 project was renewed as of 10/01/18, with the following objectives: 1. Advance the quality of reference genomes for all agri-animal species by providing high contiguity assemblies, deep functional annotations of these assemblies, and comparison across species to understand structure and function of animal genomes; 2. Advance genome-tophenome prediction by implementing strategies and tools to identify and validate genes and allelic variants predictive of biologically and economically important phenotypes and traits; and 3. Advance analysis, curation, storage, application, ...

A novel statistical test of whether two samples are from the same distribution, compatible with both multivariate and structured data, that is fast, easy to implement, and works well, as shown by the experiments.

ConGAS, a Bayesian probabilistic method to phase bulk DNA and single-cell RNA measurements from independent assays, is introduced and it is found that it can determine the tumour subclonal composition at the single- cell level together with clone-specific RNA phenotypes in tumour data generated from both 10x and Smart-Seq assays.

The means to facilitate automatic access to the scientific discourse of articles by automating the recognition of 11 categories at the sentence level, which are called Core Scientiﷁc Concepts (CoreSCs), can be presented.

It is argued that the so-called Hilbert curve visualization can complement genome browsers and help to get further insights into the structure of one’s data.

This work describes a kernel that is derived in a straightforward fashion from an existing structural alignment program, MAMMOTH, and finds that this kernel significantly out-performs a variety of other kernels, including several previously described kernels.

This research presents the method for identifying gateway nodes in three datasets using a high performance computing environment: quiescence in Saccharomyces cerevisiae, brain aging in Mus Musculus, and the effects of creatine on Aging in Mus musculus and finds that the parallel method improves runtime and performs equally as well as sequential approach.

How the bioinformatics services are crucial to growth and success of genomic medicine research in Taiwan is explained.

Information and resources on bioinformatics and statistics for the UCSF research community are provided.

An empirical guideline to introduce programming languages and recommend Python as first language for graduate programs in which students were from genetics and molecular biology backgrounds is reported and should be extended for other research programs.

It is argued that large-scale engineering principles can be successfully adapted from disciplines such as software engineering and data management, and that having an in-the-large perspective will be a key advantage in the next phase of bioinformatics development.

This chapter discusses the role of bioinformatics in genetics research in the post-genome era, and a stepwise approach to locus refinement and candidate gene identification.

This work focuses on the analysis of scale-free topologies, network modules and the relation of domain–domain to protein–protein interaction networks in large-scale protein interaction networks.

The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering, as robustness is increased and an optimal strategy for parameter selection emerges more naturally.

This paper compiles a list of numerous bioinformatic terms for the Applications of Bioinformatics in Cancer Detection conference to be helpful as a lexicon for the volume as a whole.

1= National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, NS, Canada, B3H 3Z1 2= National Research Council of Canada, Biotechnology Research Institute, 6100 Royalmount Avenue, Montreal, Quebec, Canada, H4P 2R2 3= National Research Council of Canada, Canada Institute for Scientific and Technical Information, M-55 Montreal Road, Ottawa, Ontario, Canada, K1A 0S2 4= National Research Council of Canada, Plant Biotechnology Institute, 110 Gymnasium Road, Saskatoon, Saskatchewan, Canada, S7N 0W9 5= Present address: Roger Foxall & Associates, 13880 18A Aven...

A new clustering algorithm is described, in which gene selection is used to derive biologically meaningful clusterings of samples by combining expression profiles and functional annotation data, and it is conjecture that this method has the potential to reveal so far unknown, clinically relevant classes of patients in an unsupervised manner.

An OpenLab learning course was used to reflect the students` and undergrads` impression of bioinformatics and found the increase of knowledge is significantly higher when doing additional data analysis and computer work than working only in the wet lab.

Although a thoughtful discussion of the relevant literature and techniques is found in each chapter, the book is not overly technical and does not present advanced mathematical, statistical, or genetic concepts in great depth.

ACGT is a genomic DNA sequence comparison viewer and analyzer that can read a pair of DNA sequences in GenBank, Embl or Fasta formats, with or without a comparison file, and provide users with many options to view and analyze the similarities between the input sequences.

This work presents a novel method for including interface information into protein docking simulations within the LightDock framework, and demonstrates the applicability of this approach on the new 55 cases of the Protein–Protein Docking Benchmark 5.

In being the Founding Dean of a new School of Data Science, what the authors do suddenly looks different, and a computational biologist with 40 years of research experience says bioinformatics is dead.

This chapter intends to provide an overview of the basic methods and bioinformatics resources available for the analysis of nucleic acids and protein sequences, and is primarily addressed to occasional users.

During 2012, next generation sequencing (NGS) has attracted great attention in the biomedical research community, especially for personalized medicine, and third generation sequencing has become available.

The rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability are described.

The results suggest that oxidative stress plays an important role in epithelial cells with BRCA1 mutations that may contribute to the later development of breast cancer.