Bioinformatics Data Management and Data Mining

2008 ◽  
pp. 1714-1721
Author(s):  
Boris Galitsky
Keyword(s):  
Data Mining ◽  
Human Genetics ◽  
Genome Mapping ◽  
Biological Information ◽  
Model Organisms ◽  
Functional Study ◽  
Biological Research ◽  
Biochemical Processes ◽  
E Coli ◽  
Mapping Techniques

Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting, and utilizing information from biological sequences and molecules.  The focus of bioinformatics is the application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics. It has been mainly stimulated by advances in DNA sequencing and genome mapping techniques (Adams, Fields & Venter, 1994). Genomics is the discipline that studies genes and their functions, including the functional study of genes, their resulting proteins, and the role played by the proteins in the biochemical processes, as well as the study of human genetics by comparisons with model organisms such as mice, fruit flies, and the bacterium E. coli

Bioinformatics Data Management and Data Mining

2005 ◽  
pp. 29-34 ◽  
Author(s):  
Boris Galitsky
Keyword(s):  
Data Mining ◽  
Human Genetics ◽  
Genome Mapping ◽  
Biological Information ◽  
Model Organisms ◽  
Functional Study ◽  
Biological Research ◽  
Biochemical Processes ◽  
E Coli ◽  
Mapping Techniques

Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting, and utilizing information from biological sequences and molecules.  The focus of bioinformatics is the application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics. It has been mainly stimulated by advances in DNA sequencing and genome mapping techniques (Adams, Fields & Venter, 1994). Genomics is the discipline that studies genes and their functions, including the functional study of genes, their resulting proteins, and the role played by the proteins in the biochemical processes, as well as the study of human genetics by comparisons with model organisms such as mice, fruit flies, and the bacterium E. coli

scholarly journals Targeting protein function: the expanding toolkit for conditional disruption

2016 ◽  
Vol 473 (17) ◽  
pp. 2573-2589 ◽  
Author(s):  
Amy E. Campbell ◽  
Daimark Bennett
Keyword(s):  
Protein Function ◽  
Fundamental Problem ◽  
Model Organisms ◽  
Biological Research ◽  
Protein Cleavage ◽  
Biochemical Processes ◽  
Division Cell ◽  
Time Frames ◽  
Fast Acting ◽  
Gene Perturbation

A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.

The Human Genome Project and public policy

1999 ◽  
Vol 8 (3) ◽  
pp. 161-168 ◽  
Author(s):  
Glen A. Evans
Keyword(s):  
Human Genome ◽  
Human Genome Project ◽  
Social Issues ◽  
Genome Project ◽  
Biological Information ◽  
Biological Research ◽  
Genetic Privacy ◽  
Emerging Issues ◽  
The Many ◽  
The Human Genome Project

The Human Genome Project is a massive government and privately funded undertaking to sequence the entire human genome and discover all 80,000 human genes in less than 15 years. As the project nears completion in the first decade of the 21st century, the ramifications of public availability of this vast amount of biological information are likely to pervade society. The legal, ethical and social issues raised by the genome project and associated biological research are expected to have a profound and long lasting impact on daily life. How society deals with the many emerging issues involving genetic privacy, designer babies, and the transformation of medical care among others will be a major focus of public and governmental discussion in the next decade.

scholarly journals Dysregulation of the PDGFRA gene causes inflow tract anomalies including TAPVR: integrating evidence from human genetics and model organisms

2010 ◽  
Vol 19 (7) ◽  
pp. 1286-1301 ◽  
Author(s):  
Steven B. Bleyl ◽  
Yukio Saijoh ◽  
Noortje A.M. Bax ◽  
Adriana C. Gittenberger-de Groot ◽  
Lambertus J. Wisse ◽  
...  
Keyword(s):  
Human Genetics ◽  
Model Organisms ◽  
Pdgfra Gene

scholarly journals Escherichia coli as a genetic tool

1985 ◽  
Vol 95 (3) ◽  
pp. 611-618
Author(s):  
Naomi Datta
Keyword(s):  
Escherichia Coli ◽  
Academic Research ◽  
Genetically Engineered ◽  
Cloning And Expression ◽  
Biological Research ◽  
New Techniques ◽  
E Coli ◽  
Genetic Tool ◽  
The Past ◽  
Made In

SUMMARYThe study of Escherichia coli and its plasmids and bacteriophages has provided a vast body of genetical information, much of it relevant to the whole of biology. This was true even before the development of the new techniques, for cloning and analysing DNA, that have revolutionized biological research during the past decade. Thousands of millions of dollars are now invested in industrial uses of these techniques, which all depend on discoveries made in the course of academic research on E. coli. Much of the background of knowledge necessary for the cloning and expression of genetically engineered information, as well as the techniques themselves, came from work with this organism.

scholarly journals Responses to Developmental Temperature Fluctuation in Life History Traits of Five Drosophila Species (Diptera: Drosophilidae) from Different Thermal Niches

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 925
Author(s):  
Tommaso Manenti ◽  
Anders Kjærsgaard ◽  
Toke Munk Schou ◽  
Cino Pertoldi ◽  
Neda N. Moghadam ◽  
...  
Keyword(s):  
Thermal Resistance ◽  
Temperature Fluctuation ◽  
Developmental Time ◽  
Drosophila Species ◽  
Model Organisms ◽  
Wing Size ◽  
Multiple Traits ◽  
Biochemical Processes ◽  
Developmental Temperature ◽  
The Impact

Temperature has profound effects on biochemical processes as suggested by the extensive variation in performance of organisms across temperatures. Nonetheless, the use of fluctuating temperature (FT) regimes in laboratory experiments compared to constant temperature (CT) regimes is still mainly applied in studies of model organisms. We investigated how two amplitudes of developmental temperature fluctuation (22.5/27.5 °C and 20/30 °C, 12/12 h) affected several fitness-related traits in five Drosophila species with markedly different thermal resistance. Egg-to-adult viability did not change much with temperature except in the cold-adapted D. immigrans. Developmental time increased with FT among all species compared to the same mean CT. The impact of FT on wing size was quite diverse among species. Whereas wing size decreased quasi-linearly with CT in all species, there were large qualitative differences with FT. Changes in wing aspect ratio due to FT were large compared to the other traits and presumably a consequence of thermal stress. These results demonstrate that species of the same genus but with different thermal resistance can show substantial differences in responses to fluctuating developmental temperatures not predictable by constant developmental temperatures. Testing multiple traits facilitated the interpretation of responses to FT in a broader context.

An Overview of Biological Data Mining

Biotechnology ◽  
2019 ◽  
pp. 120-139
Author(s):  
Seetharaman Balaji
Keyword(s):  
Data Mining ◽  
Information Retrieval ◽  
Biological Networks ◽  
Web Mining ◽  
Biological Data ◽  
Biological Research ◽  
Digital Repository ◽  
Domain Specific ◽  
Novice Learner ◽  
Integration Data

The largest digital repository of information, the World Wide Web keeps growing exponentially and calls for data mining services to provide tailored web experiences. This chapter discusses the overview of information retrieval, knowledge discovery and data mining. It reviews the different stages of data mining and introduces the wide spread biological databanks, their explosion, integration, data warehousing, information retrieval, text mining, text repositories for biological research publications, domain specific search engines, web mining, biological networks and visualization, ontology and systems biology. This chapter also illustrates some technical jargon with picture analogy for a novice learner to understand the concepts clearly.

Data Mining in Gene Expression Analysis

2008 ◽  
pp. 1643-1673
Author(s):  
Jilin Han ◽  
Le Gruenwald ◽  
Tyrrell Conway
Keyword(s):  
Gene Expression ◽  
Data Mining ◽  
Biological Information ◽  
Future Research ◽  
Gene Expression Data Analysis ◽  
Experimental Conditions ◽  
Single Experiment ◽  
Important Approach ◽  
Future Research Directions ◽  
Gene Expression Levels

The study of gene expression levels under defined experimental conditions is an important approach to understand how a living cell works. High-throughput microarray technology is a very powerful tool for simultaneously studying thousands of genes in a single experiment. This revolutionary technology results in an extensive amount of data, which raises an important question: how to extract meaningful biological information from these data? In this chapter, we survey data mining techniques that have been used for clustering, classification and association rules for gene expression data analysis. In addition, we provide a comprehensive list of currently available commercial and academic data mining software together with their features. Lastly, we suggest future research directions.

Human Genetics

2005 ◽  
Author(s):  
Antonio Regalado
Keyword(s):  
Heart Attack ◽  
Fluorescent Protein ◽  
Human Genetics ◽  
New Technology ◽  
Genetic Research ◽  
Biological Research ◽  
Scientific Journals ◽  
Big Picture ◽  
New Gene ◽  
Green Fluorescent

Genetic research is moving faster than a nematode poked by a platinum needle. Every week, the scientific journals report a score of new gene discoveries made in mice, worms, and men. How can a science journalist cover it all? It's hopeless, of course. So one thing I always keep in mind is it's often the methods or scientific tools behind these molecular discoveries, not the discoveries themselves, that present the best story possibilities. Examples of topics for such “tool stories” include DNA chips, proteomics, and new imaging technologies like the green-fluorescent protein used to make zebrafish and other laboratory critters glow. In writing about the technologies that drive biological research, I've found a formula that has worked well for me, time and again. Of course, not every story fits the same mold, and the best ones break it. But it's important to be familiar with how a tool story typically comes to be, and how to write one. I like to think about biology as a big onion that's rapidly being peeled. There are tens of thousands of biologists peeling away every day, figuring out all of life's working parts. But I never saw much sense in inspecting every peel for its news potential. (And some editors I know refer dismissively to the latest uncovering of a gene for heart attack or schizophrenia as “gene-of-the-week” stories.) It's better, sometimes, to focus on the new techniques and ideas for peeling the onion. Tool stories are big-picture stories that can be newsy, but the trends tend to have a long shelf life. They endure through numerous news cycles, and ultimately nearly every outlet in the journalistic food chain will cover the big ones. Your decision is when to catch the wave. Some reporters put a big emphasis on being first, but others will be content to watch the story unfold and cover their piece of it when it's right for whatever market they happen to be writing for. Either way, a tale of how a new technology is changing biological research is a great way to teach your readers—and yourself—about how science really works.

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