COMPUTATIONAL BIOLOGY

2018 ◽  
Vol 8 (6) ◽  
pp. 66
Author(s):  
Matthew N. O. Sadiku ◽  
Yonghui Wang ◽  
Suxia Cui ◽  
Sarhan M. Musa
Keyword(s):  
Molecular Biology ◽  
Computational Biology ◽  
Computational Tools

Computation is an integral part of a larger revolution that will affect how science is conducted.  Computational biology is an important emerging field of biology which is uniquely enabled by computation. It involves using computers to model biological problems and interpret data, especially problems in evolutionary and molecular biology. The application of computational tools to all areas of biology is producing excitements and insights into biological problems too complex for conventional approaches. This paper provides a brief introduction on computational biology.

scholarly journals 2017 Outstanding Contributions to ISCB Award: Fran Lewitter

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1000 ◽  
Author(s):  
Christiana N. Fogg ◽  
Diane E. Kovats ◽  
Bonnie Berger
Keyword(s):  
Czech Republic ◽  
Molecular Biology ◽  
Computational Biology ◽  
International Society ◽  
Intelligent Systems ◽  
Educational Work ◽  
European Conference

The Outstanding Contributions to the International Society for Computational Biology (ISCB) Award was launched in 2015 to recognize individuals who have made lasting and valuable contributions to the Society through their leadership, service, and educational work, or a combination of these areas. Fran Lewitter is the 2017 winner of the Outstanding Contributions to ISCB Award and will be recognized at the 2017 Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology, meeting in Prague, Czech Republic being held from July 21-25, 2017.

FPGA-Based Accelerators for Bioinformatics Applications

2013 ◽  
pp. 605-635
Author(s):  
Alba Cristina Magalhaes Alves de Melo ◽  
Nahri Moreano
Keyword(s):  
Molecular Biology ◽  
Research Area ◽  
Sequence Profile ◽  
Huge Amount ◽  
Computational Tools ◽  
Computing Power ◽  
Open Questions ◽  
Similarities And Differences

The recent and astonishing advances in Molecular Biology, which led to the sequencing of an unprecedented number of genomes, including the human, would not have been possible without the help of Bioinformatics. Bioinformatics can be defined as a research area where computational tools and algorithms are developed to help biologists in the task of understanding the organisms. Some Bioinformatics applications, such as pairwise and sequence-profile comparison, require a huge amount of computing power and, therefore, are excellent candidates to run in FPGA platforms. This chapter discusses in detail several recent proposals on FPGA-based accelerators for these two Bioinformatics applications, highlighting the similarities and differences among them. At the end of the chapter, research tendencies and open questions are presented.

scholarly journals 2017 ISCB Overton Prize: Christoph Bock

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 999
Author(s):  
Christiana N. Fogg ◽  
Diane E. Kovats ◽  
Bonnie Berger
Keyword(s):  
Czech Republic ◽  
Molecular Biology ◽  
Computational Biology ◽  
International Society ◽  
Intelligent Systems ◽  
Board Member ◽  
Molecular Medicine ◽  
Keynote Presentation ◽  
Academy Of Sciences ◽  
Computational Biologist

The International Society for Computational Biology (ISCB) each year recognizes the achievements of an early to mid-career scientist with the Overton Prize. This prize honors the untimely death of Dr. G. Christian Overton, an admired computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators who are in the early to middle phases of their careers and are selected because of their significant contributions to computational biology through research, teaching, and service. ISCB is pleased to recognize Dr. Christoph Bock, Principal Investigator at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, Austria, as the 2017 winner of the Overton Prize. Bock will be presenting a keynote presentation at the 2017 International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) in Prague, Czech Republic being held during July 21-25, 2017.

scholarly journals Computational biology for enzymatic removal of mycotoxins

2021 ◽  
Author(s):  
Natalie Sandlin ◽  
Darius Russell Kish ◽  
John Kim ◽  
Marco Zaccaria ◽  
Babak Momeni
Keyword(s):  
Computational Biology ◽  
Empirical Data ◽  
Computational Tools ◽  
Cellular Processes ◽  
Food And Feed ◽  
Biological Organisms

Biological organisms carry a rich potential for removing toxins from our environment, but the search to identify suitable candidates remains challenging. We survey and explore the use of computational tools to discover and optimize the detoxification of harmful compounds. In particular, we will focus on mycotoxins—fungi-produced toxins that contaminate food and feed—and biological enzymes that are capable of rendering them less harmful. We discuss the use of computational tools to complement existing empirical data in three main directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and optimizing the performance of enzymes with detoxification capability.

scholarly journals Swabs to genomes: a comprehensive workflow

2015 ◽  
Author(s):  
Madison I Dunitz ◽  
Jenna M Lang ◽  
Guillaume Jospin ◽  
Aaron E Darling ◽  
Jonathan A Eisen ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Environmental Sample ◽  
Limited Resources ◽  
Library Preparation ◽  
Computational Tools ◽  
Microbial Genomes ◽  
Dna Library ◽  
Significant Barrier ◽  
Barrier To Entry ◽  
Standard Molecular Biology

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

scholarly journals Challenges and Limitations in the Studies of Glycoproteins: A Computational Chemist’s Perspective

2021 ◽  
Author(s):  
Oyku Balli ◽  
Vladimir Uversky ◽  
Serdar Durdagi ◽  
Orkid Coskuner-Weber
Keyword(s):  
Computational Biology ◽  
Structural Properties ◽  
Structural Property ◽  
Computational Studies ◽  
Computational Tools ◽  
Future Developments ◽  
High Flexibility

Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycopro-teins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.

Current and emerging tools of computational biology to improve the detoxification of mycotoxins

2021 ◽  
Author(s):  
Natalie Sandlin ◽  
Darius Russell Kish ◽  
John Kim ◽  
Marco Zaccaria ◽  
Babak Momeni
Keyword(s):  
Computational Biology ◽  
Empirical Data ◽  
Detoxifying Enzymes ◽  
Computational Tools ◽  
Cellular Processes ◽  
Food And Feed ◽  
Biological Organisms

Biological organisms carry a rich potential for removing toxins from our environment, but identifying suitable candidates and improving them remain challenging. We explore the use of computational tools to discover strains and enzymes that detoxify harmful compounds. In particular, we will focus on mycotoxins—fungi-produced toxins that contaminate food and feed—and biological enzymes that are capable of rendering them less harmful. We discuss the use of established and novel computational tools to complement existing empirical data in three directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and improving the performance of detoxifying enzymes. We hope to create a synergistic conversation between researchers in computational biology and those in the bioremediation field. We showcase open bioremediation questions where computational researchers can contribute and highlight relevant existing and emerging computational tools that could benefit bioremediation researchers.

scholarly journals Tools and strategies for physiological genomics: the Rat Genome Database

2005 ◽  
Vol 23 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Simon N. Twigger ◽  
Dean Pasko ◽  
Jeff Nie ◽  
Mary Shimoyama ◽  
Susan Bromberg ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Computational Biology ◽  
Computational Techniques ◽  
Genome Database ◽  
Computational Tools ◽  
Functional Roles ◽  
Genomics Research ◽  
Human And Mouse ◽  
Rat Genome

The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu ) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.

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