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Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can some times referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer science and engineering which uses bioengineering to build computers.
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression.
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
An RNA spike-in is an RNA transcript of known sequence and quantity used to calibrate measurements in RNA hybridization assays, such as DNA microarray experiments, RT-qPCR, and RNA-Seq.
Microarray analysis techniques are used in interpreting the data generated from experiments on DNA, RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes – in many cases, an organism's entire genome – in a single experiment. Such experiments can generate very large amounts of data, allowing researchers to assess the overall state of a cell or organism. Data in such large quantities is difficult – if not impossible – to analyze without the help of computer programs.
Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science. As of 2009, he is co-director of the Yale Computational Biology and Bioinformatics program.
ChIP-on-chip is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ("chip"). Like regular ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA in vivo. Specifically, it allows the identification of the cistrome, the sum of binding sites, for DNA-binding proteins on a genome-wide basis. Whole-genome analysis can be performed to determine the locations of binding sites for almost any protein of interest. As the name of the technique suggests, such proteins are generally those operating in the context of chromatin. The most prominent representatives of this class are transcription factors, replication-related proteins, like origin recognition complex protein (ORC), histones, their variants, and histone modifications.
Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M and A scales, then plotting these values. Though originally applied in the context of two channel DNA microarray gene expression data, MA plots are also used to visualise high-throughput sequencing analysis.
Terence Paul "Terry" Speed, FAA FRS is an Australian statistician. A senior principal research scientist at the Walter and Eliza Hall Institute of Medical Research, he is known for his contributions to the analysis of variance and bioinformatics, and in particular to the analysis of microarray data.
In statistics, a volcano plot is a type of scatter-plot that is used to quickly identify changes in large data sets composed of replicate data. It plots significance versus fold-change on the y and x axes, respectively. These plots are increasingly common in omic experiments such as genomics, proteomics, and metabolomics where one often has a list of many thousands of replicate data points between two conditions and one wishes to quickly identify the most meaningful changes. A volcano plot combines a measure of statistical significance from a statistical test with the magnitude of the change, enabling quick visual identification of those data-points that display large magnitude changes that are also statistically significant.
Robert Clifford Gentleman is a Canadian statistician and bioinformatician who is currently the founding executive director of the Center for Computational Biomedicine at Harvard Medical School. He was previously the vice president of computational biology at 23andMe. Gentleman is recognized, along with Ross Ihaka, as one of the originators of the R programming language and the Bioconductor project.
Alicia Yinema Kate Nungarai Oshlack is an Australian bioinformatician and is Co-Head of Computational Biology at the Peter MacCallum Cancer Centre in Melbourne, Victoria, Australia. She is best known for her work developing methods for the analysis of transcriptome data as a measure of gene expression. She has characterized the role of gene expression in human evolution by comparisons of humans, chimpanzees, orangutans, and rhesus macaques, and works collaboratively in data analysis to improve the use of clinical sequencing of RNA samples by RNAseq for human disease diagnosis.
Pathway is the term from molecular biology for a curated schematic representation of a well characterized segment of the molecular physiological machinery, such as a metabolic pathway describing an enzymatic process within a cell or tissue or a signaling pathway model representing a regulatory process that might, in its turn, enable a metabolic or another regulatory process downstream. A typical pathway model starts with an extracellular signaling molecule that activates a specific receptor, thus triggering a chain of molecular interactions. A pathway is most often represented as a relatively small graph with gene, protein, and/or small molecule nodes connected by edges of known functional relations. While a simpler pathway might appear as a chain, complex pathway topologies with loops and alternative routes are much more common. Computational analyses employ special formats of pathway representation. In the simplest form, however, a pathway might be represented as a list of member molecules with order and relations unspecified. Such a representation, generally called Functional Gene Set (FGS), can also refer to other functionally characterised groups such as protein families, Gene Ontology (GO) and Disease Ontology (DO) terms etc. In bioinformatics, methods of pathway analysis might be used to identify key genes/ proteins within a previously known pathway in relation to a particular experiment / pathological condition or building a pathway de novo from proteins that have been identified as key affected elements. By examining changes in e.g. gene expression in a pathway, its biological activity can be explored. However most frequently, pathway analysis refers to a method of initial characterization and interpretation of an experimental condition that was studied with omics tools or genome-wide association study. Such studies might identify long lists of altered genes. A visual inspection is then challenging and the information is hard to summarize, since the altered genes map to a broad range of pathways, processes, and molecular functions. In such situations, the most productive way of exploring the list is to identify enrichment of specific FGSs in it. The general approach of enrichment analyses is to identify FGSs, members of which were most frequently or most strongly altered in the given condition, in comparison to a gene set sampled by chance. In other words, enrichment can map canonical prior knowledge structured in the form of FGSs to the condition represented by altered genes.
TopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. TopHat aligns RNA-Seq reads to mammalian-sized genomes.
Sorin Drăghici is a Romanian-American computer scientist and a program director in the Division of Information and Intelligent Systems (IIS) of the Directorate for Computer and Information Science and Engineering (CISE) at the National Science Foundation (NSF). Previous positions include: Associate Dean for Entrepreneurship and Innovation of Wayne State University's College of Engineering, the Director of the Bioinformatics and Biostatistics Core at Karmanos Cancer Institute, and the Director of the James and Patricia Anderson Engineering Ventures Institute. Draghici was elected a Fellow of the Institute of Electrical and Electronics Engineers (IEEE) in 2022, for contributions to the analysis of high-throughput genomics and proteomics data. He has also been elected a Fellow of the Asia-Pacific Artificial Intelligence Association (AAIA).
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.
Rafael Irizarry is a professor of biostatistics at the Harvard T.H. Chan School of Public Health and professor of biostatistics and computational biology at the Dana–Farber Cancer Institute. Irizarry is known as one of the founders of the Bioconductor project.
Sandrine Dudoit is a professor of statistics and public health at the University of California, Berkeley. Her research applies statistics to microarray and genetic data; she is known as one of the founders of the open-source Bioconductor project for the development of bioinformatics software.
Sündüz Keleş is a Turkish-American statistician specializing in statistical methods in genomics. She is a professor of statistics and of biostatistics and medical informatics at the University of Wisconsin–Madison. Her research has included the development of the FreeHi-C system for generating synthetic Hi-C data.
References
- 1 2 "2015 Moran Medal for research in statistics", 2015 awardees, Australian Academy of Science, retrieved 2018-02-27
- ↑ Mathematicians solving today's problems of systems biology, Garvan Institute of Medical Research, 21 March 2012
- ↑ Professor Jean Yang, School of Mathematics and Statistics, University of Sydney, retrieved 2018-02-27
- 1 2 3 4 Curriculum vitae (PDF), 2013, archived from the original (PDF) on 2018-02-28, retrieved 2018-02-27
- ↑ Jean Yang at the Mathematics Genealogy Project
