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Computational biology and protein modeling of cyanobacteria using bioinformatics tools and techniques
Padhi S.B.,Behera S.,Swain P.,Behura S.
International Journal of Bioinformatics Research , 2010,
Abstract: Computational biology is a term coined from analogy to the role of physical sciences, is nowcoming into its own as a major element of contemporary biological and biomedical research. In the sharp inthis pattern, over past few years, experiments in life sciences in the academic institutions have begun torecognize the value of bioinformatics and computational biology in the field of algology. Cyanobacteria (alsoknown as blue–green algae) are a group of extraordinarily diverse Gram-negative prokaryotes thatoriginated 3.5 billion years ago. After the advent of bioinformatics in the field of algology, complete genomesequences of Cyanobacteria have been reported in more than 30 species and strains including unicellular.The filamentous cyanobacterium Anabaena sp. PCC 7120 (further referred to as Anabaena sp.) is a modelsystem to study nitrogen fixation, cell differentiation, cell pattern formation and evolution of plastids. It is amulticellular photosynthetic microorganism consisting of two cell types, vegetative cells and nitrogen fixingheterocysts. The nucleotide sequence of the entire genome of a filamentous Cyanobacterium, Anabaena sp.Strain PCC 7120, was determined. This study focuses on the function and dynamics of the proteome of theGram-negative outer membrane in Anabaena sp.
Bioinformatics meets systems biology
Carlos Salazar, Jana Schütze, Oliver Ebenh?h
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-1-303
Abstract: The efficient integration of bioinformatics and systems biology requires worldwide cooperation not only in the research of senior scientists but also in the research training of young scientists. To this end, a student-focused workshop on bioinformatics and systems biology http://www.biologie.hu-berlin.de/gk/ibsb2005 webcite was held last August at Humboldt University in Berlin, Germany. This was the fifth annual workshop held as part of a research collaboration between the Bioinformatics Program of Boston University in the USA, the Bioinformatics Center of Kyoto University in Japan, and the Berlin-located graduate program 'Dynamics and Evolution of Cellular and Macromolecular Processes'. This time the meeting had two main themes - the integration of genomic and chemical information in the analysis of the dynamics and topology of cellular regulatory networks, and the development of more accurate computational tools for the analysis of gene expression and the prediction of transcription-factor binding sites. Full papers accepted for the fifth workshop have been published in the Genome Informatics Series of the Japanese Society of Bioinformatics, edited by Satoru Miyano (University of Tokyo, Japan) http://www.jsbi.org/journal/GI16_1.html webcite.Trends in genome biology and bioinformatics were highlighted in the opening talk by Minoru Kanehisa (Kyoto University Bioinformatics Center, Japan), whose group is responsible for the Kyoto Encyclopedia of Genes and Genomes (KEGG) database http://www.genome.ad.jp/kegg webcite. This stores molecular interaction networks and graphics, including metabolic pathways, regulatory pathways and molecular complexes. Kanehisa emphasized the importance of an integrated analysis of genomic and chemical information to predict the complete functional behaviors of cells, organisms and ecosystems. While traditional genomics and other 'omics' have contributed to our knowledge of the genes and proteins that make up a biological system, new chemi
Computational Biology and Bioinformatics in Nigeria  [PDF]
Segun A. Fatumo ,Moses P. Adoga,Opeolu O. Ojo,Olugbenga Oluwagbemi,Tolulope Adeoye,Itunuoluwa Ewejobi,Marion Adebiyi,Ezekiel Adebiyi ?,Clement Bewaji ?,Oyekanmi Nashiru ?
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003516
Abstract: Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.
Bioinformatics Resources and Tools for Phage Display  [PDF]
Jian Huang,Beibei Ru,Ping Dai
Molecules , 2011, DOI: 10.3390/molecules16010694
Abstract: Databases and computational tools for mimotopes have been an important part of phage display study. Five special databases and eighteen algorithms, programs and web servers and their applications are reviewed in this paper. Although these bioinformatics resources have been widely used to exclude target-unrelated peptides, characterize small molecules-protein interactions and map protein-protein interactions, a lot of problems are still waiting to be solved. With the improvement of these tools, they are expected to serve the phage display community better.
Teaching Botany Using Bioinformatics Tools  [PDF]
Xiaorong Zhang
Creative Education (CE) , 2019, DOI: 10.4236/ce.2019.1010155
Abstract: Two laboratory activities are designed to reinforce several important concepts in General Botany course, which is a required course for biology majors at Savannah State University (SSU). The first activity requires students to study the relationship between protein structure and function through observing the 3D structure of Rubisco (ribulose-1,5-biphosphate carboxylase and oxygenase)—the enzyme that catalyzes the first step of the Calvin cycle for photosynthesis. This activity also helps students understand the mechanism of enzymatic action through examining the interaction of Rubisco with its cofactor, substrate, competitive inhibitor, and product. The second activity is designed to help students grasp the concept of plant evolution and phylogeny through analyzing the genetic sequences of Rubisco collected from representative species and determining the evolutionary relationships of these species using bioinformatics tools. Through these two laboratory activities, several important topics are linked together, with Rubisco as a common theme, so that students would develop a holistic and coherent view of plant sciences. Furthermore, students would also gain several important bioinformatics skills that they could use and apply in their future studies and careers.
Glycosylation and Bioinformatics: current status for glycosylation prediction tools
Mazola,Yuliet; Chinea,Glay; Musacchio,Alexis;
Biotecnolog?-a Aplicada , 2011,
Abstract: glycosylation is an important co-and post-translational modification involved in a variety of critical biological processes. the development of computational algorithms for protein glycosylation prediction has been propelled in the latest years. the localization of potential glycosylated sites facilitates the rational alteration of glycosylationrelated functions in cells. this manuscript gives an overview of current available bioinformatics resources and databases for glycobiology, focusing on glycosylation predictors. as a complement, general features about the different glycosylation types are also exposed.
The aryl hydrocarbon receptor meets immunology: friend or foe? A little of both  [PDF]
Joshua D. Mezrich
Frontiers in Immunology , 2014, DOI: 10.3389/fimmu.2014.00458
Abstract: The aryl hydrocarbon receptor (AHR) has long been studied by toxicologists as a ligand-activated transcription factor that is activated by dioxin and other environmental pollutants such as polycyclic aromatic hydrocarbons. The hallmark of AHR activation is the upregulation of the cytochrome P450 enzymes that metabolize many of these toxic compounds. However, recent findings demonstrate that both exogenous and endogenous AHR ligands can alter innate and adaptive immune responses including effects on T-cell differentiation. Kynurenine, a tryptophan breakdown product, is one such endogenous ligand of the AHR. Expression of indoleamine 2,3-dioxygenase by dendritic cells causes accumulation of kynurenine and results in subsequent tolerogenic effects including increased regulatory T cell activity. At the same time, polycyclic aromatic hydrocarbons found in pollution enhance Th17 differentiation in the lungs of exposed mice via the AHR. In this perspective, we will discuss the importance of the AHR in the immune system and the role this might play in normal physiology and response to disease.
Bioconductor: open software development for computational biology and bioinformatics
Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang
Genome Biology , 2004, DOI: 10.1186/gb-2004-5-10-r80
Abstract: The Bioconductor project [1] is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics (CBB). Biology, molecular biology in particular, is undergoing two related transformations. First, there is a growing awareness of the computational nature of many biological processes and that computational and statistical models can be used to great benefit. Second, developments in high-throughput data acquisition produce requirements for computational and statistical sophistication at each stage of the biological research pipeline. The main goal of the Bioconductor project is creation of a durable and flexible software development and deployment environment that meets these new conceptual, computational and inferential challenges. We strive to reduce barriers to entry to research in CBB. A key aim is simplification of the processes by which statistical researchers can explore and interact fruitfully with data resources and algorithms of CBB, and by which working biologists obtain access to and use of state-of-the-art statistical methods for accurate inference in CBB.Among the many challenges that arise for both statisticians and biologists are tasks of data acquisition, data management, data transformation, data modeling, combining different data sources, making use of evolving machine learning methods, and developing new modeling strategies suitable to CBB. We have emphasized transparency, reproducibility, and efficiency of development in our response to these challenges. Fundamental to all these tasks is the need for software; ideas alone cannot solve the substantial problems that arise.The primary motivations for an open-source computing environment for statistical genomics are transparency, pursuit of reproducibility and efficiency of development.High-throughput methodologies in CBB are extremely complex, and many steps are involved in the conversion of information from low-level information structures (for example,
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools
Daisuke Kihara,Yifeng David Yang,Troy Hawkins
Cancer Informatics , 2006,
Abstract: The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases), pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that may be unfamiliar to most cancer researchers wanting to incorporate bioinformatics tools and analyses into their work, and also to bioinformaticians looking for real data to develop and test algorithms. This review reveals the interdependence of cancer research and bioinformatics, and highlight the most appropriate and useful resources available to cancer researchers. These include not only public databases, but general and specific bioinformatics tools which can be useful to the cancer researcher. The primary foci are function and structure prediction tools of protein genes. The result is a useful reference to cancer researchers and bioinformaticians studying cancer alike.
Bioinformatics Meets User-Centred Design: A Perspective  [PDF]
Katrina Pavelin,Jennifer A. Cham ,Paula de Matos,Cath Brooksbank,Graham Cameron,Christoph Steinbeck
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002554
Abstract: Designers have a saying that “the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years.” It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.
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