Bioinformatics

Early bioinformatics—computational alignment of experimentally determined

sequences of a class of related proteins; see § Sequence analysis for further
information.

Bioinformatics (/ˌbaɪ.oʊˌɪnfərˈmætɪks/ ( listen)) 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 subsequent process of analyzing and
interpreting data is referred to as computational biology.

Computational, statistical, and computer programming techniques

have been used for computer simulation analyses of biological
queries. They include reused specific analysis "pipelines",
particularly in the field of genomics, such as by the identification of
genes and single nucleotide polymorphisms (SNPs). These
Map of the human X chromosome
pipelines are used to better understand the genetic basis of disease, (from the National Center for
unique adaptations, desirable properties (esp. in agricultural Biotechnology Information website)
species), or differences between populations. Bioinformatics also
includes proteomics, which tries to understand the organizational
principles within nucleic acid and protein sequences.[1]

Image and signal processing allow extraction of useful results from large amounts of raw data. In the field
of genetics, it aids in sequencing and annotating genomes and their observed mutations. Bioinformatics
includes text mining of biological literature and the development of biological and gene ontologies to
organize and query biological data. It also plays a role in the analysis of gene and protein expression and
regulation. Bioinformatics tools aid in comparing, analyzing and interpreting genetic and genomic data and
more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative
level, it helps analyze and catalogue the biological pathways and networks that are an important part of
systems biology. In structural biology, it aids in the simulation and modeling of DNA,[2] RNA,[2][3]
proteins[4] as well as biomolecular interactions.[5][6][7][8]

History
The first definition of the term bioinformatics was coined by Paulien Hogeweg and Ben Hesper in 1970, to
refer to the study of information processes in biotic systems.[9][10][11][12][13] This definition placed
bioinformatics as a field parallel to biochemistry (the study of chemical processes in biological systems).[10]

Bioinformatics and computational biology involved the analysis of biological data, particularly DNA,
RNA, and protein sequences. The field of bioinformatics experienced explosive growth starting in the mid-
1990s, driven largely by the Human Genome Project and by rapid advances in DNA sequencing
technology.

Analyzing biological data to produce meaningful information involves writing and running software
programs that use algorithms from graph theory, artificial intelligence, soft computing, data mining, image
processing, and computer simulation. The algorithms in turn depend on theoretical foundations such as
discrete mathematics, control theory, system theory, information theory, and statistics.

Sequences

There has been a tremendous advance in speed and cost reduction

since the completion of the Human Genome Project, with some labs
able to sequence over 100,000 billion bases each year, and a full
genome can be sequenced for $1,000 or less.[14] Sequences of genetic material are
frequently used in bioinformatics and
Computers became essential in molecular biology when protein are easier to manage using
sequences became available after Frederick Sanger determined the computers than manually.
sequence of insulin in the early 1950s. Comparing multiple
sequences manually turned out to be impractical. Margaret Oakley
Dayhoff, a pioneer in the field,[15] compiled one of the first protein sequence databases, initially published
as books[16] as well as methods of sequence alignment and molecular evolution.[17] Another early
contributor to bioinformatics was Elvin A. Kabat, who pioneered biological sequence analysis in 1970 with
his comprehensive volumes of antibody sequences released online with Tai Te Wu between 1980 and
1991.[18]

In the 1970s, new techniques for sequencing DNA were applied to bacteriophage MS2 and øX174, and the
extended nucleotide sequences were then parsed with informational and statistical algorithms. These studies
illustrated that well known features, such as the coding segments and the triplet code, are revealed in
straightforward statistical analyses and were the proof of the concept that bioinformatics would be
insightful.[19][20]

Goals
In order to study how normal cellular
activities are altered in different disease
states, raw biological data must be
combined to form a comprehensive picture
of these activities. Therefore, the field of These are sequences being compared in a MUSCLE multiple
bioinformatics has evolved such that the sequence alignment (MSA). Each sequence name (leftmost
most pressing task now involves the column) is from various louse species, while the sequences
analysis and interpretation of various types themselves are in the second column.
of data. This also includes nucleotide and
amino acid sequences, protein domains, and
protein structures.[21]
Important sub-disciplines within bioinformatics and computational biology include:

Development and implementation of computer programs to efficiently access, manage, and

use various types of information.
Development of new mathematical algorithms and statistical measures to assess
relationships among members of large data sets. For example, there are methods to locate a
gene within a sequence, to predict protein structure and/or function, and to cluster protein
sequences into families of related sequences.

The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it
apart from other approaches is its focus on developing and applying computationally intensive techniques
to achieve this goal. Examples include: pattern recognition, data mining, machine learning algorithms, and
visualization. Major research efforts in the field include sequence alignment, gene finding, genome
assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction
of gene expression and protein–protein interactions, genome-wide association studies, the modeling of
evolution and cell division/mitosis.

Bioinformatics entails the creation and advancement of databases, algorithms, computational and statistical
techniques, and theory to solve formal and practical problems arising from the management and analysis of
biological data.

Over the past few decades, rapid developments in genomic and other molecular research technologies and
developments in information technologies have combined to produce a tremendous amount of information
related to molecular biology. Bioinformatics is the name given to these mathematical and computing
approaches used to glean understanding of biological processes.

Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning
DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures.

Sequence analysis
Since the bacteriophage Phage Φ-X174 was sequenced in 1977,[22] the DNA sequences of thousands of
organisms have been decoded and stored in databases. This sequence information is analyzed to determine
genes that encode proteins, RNA genes, regulatory sequences, structural motifs, and repetitive sequences. A
comparison of genes within a species or between different species can show similarities between protein
functions, or relations between species (the use of molecular systematics to construct phylogenetic trees).
With the growing amount of data, it long ago became impractical to analyze DNA sequences manually.
Computer programs such as BLAST are used routinely to search sequences—as of 2008, from more than
260,000 organisms, containing over 190 billion nucleotides.[23]
DNA sequencing

Before sequences can be analyzed, they are obtained from a data storage bank, such as Genbank. DNA
sequencing is still a non-trivial problem as the raw data may be noisy or affected by weak signals.
Algorithms have been developed for base calling for the various experimental approaches to DNA
sequencing.

Sequence assembly

Most DNA sequencing techniques produce short fragments of sequence that need to be assembled to obtain
complete gene or genome sequences. The shotgun sequencing technique (used by The Institute for
Genomic Research (TIGR) to sequence the first bacterial genome, Haemophilus influenzae)[24] generates
the sequences of many thousands of small DNA fragments (ranging from 35 to 900 nucleotides long,
depending on the sequencing technology). The ends of these fragments overlap and, when aligned properly
by a genome assembly program, can be used to reconstruct the complete genome. Shotgun sequencing
yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger
genomes. For a genome as large as the human genome, it may take many days of CPU time on large-
memory, multiprocessor computers to assemble the fragments, and the resulting assembly usually contains
numerous gaps that must be filled in later. Shotgun sequencing is the method of choice for virtually all
genomes sequenced (rather than chain-termination or chemical degradation methods), and genome
assembly algorithms are a critical area of bioinformatics research.

Genome annotation

In genomics, annotation refers to the process of marking the stop and start regions of genes and other
biological features in a sequenced DNA sequence. Many genomes are too large to be annotated by hand.
As the rate of sequencing exceeds the rate of genome annotation, genome annotation has become the new
bottleneck in bioinformatics.

Genome annotation can be classified into three levels: the nucleotide, protein, and process levels.

Gene finding is a chief aspect of nucleotide-level annotation. For complex genomes, a combination of ab
initio gene prediction and sequence comparison with expressed sequence databases and other organisms
can be successful. Nucleotide-level annotation also allows the integration of genome sequence with other
genetic and physical maps of the genome.
The principal aim of protein-level annotation is to assign function to the protein products of the genome.
Databases of protein sequences and functional domains and motifs are used for this type of annotation.
About half of the predicted proteins in a new genome sequence tend to have no obvious function.

Understanding the function of genes and their products in the context of cellular and organismal physiology
is the goal of process-level annotation. An obstacle of process-level annotation has been the inconsistency
of terms used by different model systems. The Gene Ontology Consortium is helping to solve this
problem.[25]

The first description of a comprehensive annotation system was published in 1995[24] by the The Institute
for Genomic Research, which performed the first complete sequencing and analysis of the genome of a
free-living organism, the bacterium Haemophilus influenzae.[24] The system identifies the genes encoding
all proteins, transfer RNAs, ribosomal RNAs, in order to make initial functional assignments. The
GeneMark program trained to find protein-coding genes in Haemophilus influenzae is constantly changing
and improving.

Following the goals that the Human Genome Project left to achieve after its closure in 2003, the ENCODE
project was developed by the National Human Genome Research Institute. This project is a collaborative
data collection of the functional elements of the human genome that uses next-generation DNA-sequencing
technologies and genomic tiling arrays, technologies able to automatically generate large amounts of data at
a dramatically reduced per-base cost but with the same accuracy (base call error) and fidelity (assembly
error).

Gene function prediction

While genome annotation is primarily based on sequence similarity (and thus homology), other properties
of sequences can be used to predict the function of genes. In fact, most gene function prediction methods
focus on protein sequences as they are more informative and more feature-rich. For instance, the
distribution of hydrophobic amino acids predicts transmembrane segments in proteins. However, protein
function prediction can also use external information such as gene (or protein) expression data, protein
structure, or protein-protein interactions.[26]

Computational evolutionary biology

Evolutionary biology is the study of the origin and descent of species, as well as their change over time.
Informatics has assisted evolutionary biologists by enabling researchers to:

trace the evolution of a large number of organisms by measuring changes in their DNA,
rather than through physical taxonomy or physiological observations alone,
compare entire genomes, which permits the study of more complex evolutionary events,
such as gene duplication, horizontal gene transfer, and the prediction of factors important in
bacterial speciation,
build complex computational population genetics models to predict the outcome of the
system over time[27]
track and share information on an increasingly large number of species and organisms

Future work endeavours to reconstruct the now more complex tree of life.

Comparative genomics
The core of comparative genome analysis is the establishment of the correspondence between genes
(orthology analysis) or other genomic features in different organisms. Intergenomic maps are made to trace
the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary
events acting at various organizational levels shape genome evolution. At the lowest level, point mutations
affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral
transfer, inversion, transposition, deletion and insertion.[28] Entire genomes are involved in processes of
hybridization, polyploidization and endosymbiosis that lead to rapid speciation. The complexity of genome
evolution poses many exciting challenges to developers of mathematical models and algorithms, who have
recourse to a spectrum of algorithmic, statistical and mathematical techniques, ranging from exact,
heuristics, fixed parameter and approximation algorithms for problems based on parsimony models to
Markov chain Monte Carlo algorithms for Bayesian analysis of problems based on probabilistic models.

Many of these studies are based on the detection of sequence homology to assign sequences to protein
families.[29]

Pan genomics

Pan genomics is a concept introduced in 2005 by Tettelin and Medini. Pan genome is the complete gene
repertoire of a particular monophyletic taxonomic group. Although initially applied to closely related strains
of a species, it can be applied to a larger context like genus, phylum, etc. It is divided in two parts: the Core
genome, a set of genes common to all the genomes under study (often housekeeping genes vital for
survival), and the Dispensable/Flexible genome: a set of genes not present in all but one or some genomes
under study. A bioinformatics tool BPGA can be used to characterize the Pan Genome of bacterial
species.[30]

Genetics of disease

As of 2013, the existence of efficient high-throughput next-generation sequencing technology allows for
the identification of cause many different human disorders. Simple Mendelian inheritance has been
observed for over 3,000 disorders that have been identified at the Online Mendelian Inheritance in Man
database, but complex diseases are more difficult. Association studies have found many individual genetic
regions that individually are weakly associated with complex diseases (such as infertility,[31] breast
cancer[32] and Alzheimer's disease[33]), rather than a single cause.[34][35] There are currently many
challenges to using genes for diagnosis and treatment, such as how we don't know which genes are
important, or how stable the choices an algorithm provides. [36]

Genome-wide association studies have successfully identified thousands of common genetic variants for
complex diseases and traits; however, these common variants only explain a small fraction of
heritability.[37] Rare variants may account for some of the missing heritability.[38] Large-scale whole
genome sequencing studies have rapidly sequenced millions of whole genomes, and such studies have
identified hundreds of millions of rare variants.[39] Functional annotations predict the effect or function of a
genetic variant and help to prioritize rare functional variants, and incorporating these annotations can
effectively boost the power of genetic association of rare variants analysis of whole genome sequencing
studies.[40] Some tools have been developed to provide all-in-one rare variant association analysis for
whole-genome sequencing data, including integration of genotype data and their functional annotations,
association analysis, result summary and visualization.[41][42] Meta-analysis of whole genome sequencing
studies provides an attractive solution to the problem of collecting large sample sizes for discovering rare
variants associated with complex phenotypes.[43]

Analysis of mutations in cancer

In cancer, the genomes of affected cells are rearranged in complex or unpredictable ways. In addition to
single-nucleotide polymorphism arrays identifying point mutations that cause cancer, oligonucleotide
microarrays can be used to identify chromosomal gains and losses (called comparative genomic
hybridization). These detection methods generate terabytes of data per experiment. The data is often found
to contain considerable variability, or noise, and thus Hidden Markov model and change-point analysis
methods are being developed to infer real copy number changes.

Two important principles can be used to identify cancer by mutations in the exome. First, cancer is a
disease of accumulated somatic mutations in genes. Second, cancer contains driver mutations which need to
be distinguished from passengers.[44]

Further improvements in bioinformatics could allow for classifying types of cancer by analysis of cancer
driven mutations in the genome. Furthermore, tracking of patients while the disease progresses may be
possible in the future with the sequence of cancer samples. Another type of data that requires novel
informatics development is the analysis of lesions found to be recurrent among many tumors.[45]

Gene and protein expression

Analysis of gene expression

The expression of many genes can be determined by measuring mRNA levels with multiple techniques
including microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression
(SAGE) tag sequencing, massively parallel signature sequencing (MPSS), RNA-Seq, also known as
"Whole Transcriptome Shotgun Sequencing" (WTSS), or various applications of multiplexed in-situ
hybridization. All of these techniques are extremely noise-prone and/or subject to bias in the biological
measurement, and a major research area in computational biology involves developing statistical tools to
separate signal from noise in high-throughput gene expression studies.[46] Such studies are often used to
determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial
cells to data from non-cancerous cells to determine the transcripts that are up-regulated and down-regulated
in a particular population of cancer cells.
 MIcroarray vs RNA-Seq

Analysis of protein expression

Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the
proteins present in a biological sample. The former approach faces similar problems as with microarrays
targeted at mRNA, the latter involves the problem of matching large amounts of mass data against predicted
masses from protein sequence databases, and the complicated statistical analysis of samples when multiple
incomplete peptides from each protein are detected. Cellular protein localization in a tissue context can be
achieved through affinity proteomics displayed as spatial data based on immunohistochemistry and tissue
microarrays.[47]

Analysis of regulation

Gene regulation is a complex process where a signal, such as an extracellular signal such as a hormone,
eventually leads to an increase or decrease in the activity of one or more proteins. Bioinformatics
techniques have been applied to explore various steps in this process.

For example, gene expression can be regulated by nearby elements in the genome. Promoter analysis
involves the identification and study of sequence motifs in the DNA surrounding the protein-coding region
of a gene. These motifs influence the extent to which that region is transcribed into mRNA. Enhancer
elements far away from the promoter can also regulate gene expression, through three-dimensional looping
interactions. These interactions can be determined by bioinformatic analysis of chromosome conformation
capture experiments.

Expression data can be used to infer gene regulation: one might compare microarray data from a wide
variety of states of an organism to form hypotheses about the genes involved in each state. In a single-cell
organism, one might compare stages of the cell cycle, along with various stress conditions (heat shock,
starvation, etc.). Clustering algorithms can be then applied to expression data to determine which genes are
co-expressed. For example, the upstream regions (promoters) of co-expressed genes can be searched for
over-represented regulatory elements. Examples of clustering algorithms applied in gene clustering are k-
means clustering, self-organizing maps (SOMs), hierarchical clustering, and consensus clustering methods.

Analysis of cellular organization

Several approaches have been developed to analyze the location of organelles, genes, proteins, and other
components within cells. A gene ontology category, cellular component, has been devised to capture
subcellular localization in many biological databases.

Microscopy and image analysis

Microscopic pictures allow for the location of organelles as well as molecules, which may be the source of
abnormalities in diseases.

Protein localization

Finding the location of proteins allows us to predict what they do. This is called protein function prediction.
For instance, if a protein is found in the nucleus it may be involved in gene regulation or splicing. By
contrast, if a protein is found in mitochondria, it may be involved in respiration or other metabolic
processes. There are well developed protein subcellular localization prediction resources available,
including protein subcellular location databases, and prediction tools.[48][49]

Nuclear organization of chromatin

Data from high-throughput chromosome conformation capture experiments, such as Hi-C (experiment) and
ChIA-PET, can provide information on the three-dimensional structure and nuclear organization of
chromatin. Bioinformatic challenges in this field include partitioning the genome into domains, such as
Topologically Associating Domains (TADs), that are organised together in three-dimensional space.[50]

Structural bioinformatics
Finding the structure of proteins important application of bioinformatics. The Critical Assessment of Protein
Structure Prediction (CASP) is an open competition where worldwide research groups submit protein
models for evaluating unknown protein models.[51][52]

Amino acid sequence

The linear amino acid sequence of a protein is called the primary structure, can be easily determined from
the sequence of codons on the DNA gene that codes for it. In most proteins, the primary structure uniquely
determines the 3-dimensional structure of a protein in its native environment. An exception is the misfolded
protein involved in bovine spongiform encephalopathy. This structure is linked to the function of the
 protein. Additional structural information includes the secondary,
tertiary and quaternary structure. A viable general solution to the
prediction of the function of a protein remains an open problem.
Most efforts have so far been directed towards heuristics that work
most of the time.

Homology

In the genomic branch of bioinformatics, homology is used to

predict the function of a gene: if the sequence of gene A, whose
function is known, is homologous to the sequence of gene B,
whose function is unknown, one could infer that B may share A's
function. In structural bioinformatics, homology is used to
determine which parts of a protein are important in structure
3-dimensional protein structures
formation and interaction with other proteins. Homology modeling
such as this one are common
is used to predict the structure of an unknown protein from existing
subjects in bioinformatic analyses.
homologous proteins.

One example of this is hemoglobin in humans and the hemoglobin

in legumes (leghemoglobin), which are distant relatives from the same protein superfamily. Both serve the
same purpose of transporting oxygen in the organism. Although both of these proteins have completely
different amino acid sequences, their protein structures are virtually identical, which reflects their near
identical purposes and shared ancestor.[53]

Other techniques for predicting protein structure include protein threading and de novo (from scratch)
physics-based modeling.

Another aspect of structural bioinformatics include the use of protein structures for Virtual Screening
models such as Quantitative Structure-Activity Relationship models and proteochemometric models
(PCM). Furthermore, a protein's crystal structure can be used in simulation of for example ligand-binding
studies and in silico mutagenesis studies.

A 2021 deep-learning algorithms-based software called AlphaFold, developed by Google's DeepMind,

greatly outperforms all other prediction software methods[54], and has released predicted structures for
hundreds of millions of proteins in the AlphaFold protein structure database.[55]

Network and systems biology

Network analysis seeks to understand the relationships within biological networks such as metabolic or
protein–protein interaction networks. Although biological networks can be constructed from a single type
of molecule or entity (such as genes), network biology often attempts to integrate many different data types,
such as proteins, small molecules, gene expression data, and others, which are all connected physically,
functionally, or both.
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of
metabolites and enzymes that comprise metabolism, signal transduction pathways and gene regulatory
networks) to both analyze and visualize the complex connections of these cellular processes. Artificial life
or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple
(artificial) life forms.

Molecular interaction networks

Tens of thousands of three-dimensional protein structures have been

determined by X-ray crystallography and protein nuclear magnetic
resonance spectroscopy (protein NMR) and a central question in
structural bioinformatics is whether it is practical to predict possible
protein–protein interactions only based on these 3D shapes, without
performing protein–protein interaction experiments. A variety of
methods have been developed to tackle the protein–protein docking
problem, though it seems that there is still much work to be done in this
field.

Other interactions encountered in the field include Protein–ligand Interactions between proteins are
(including drug) and protein–peptide. Molecular dynamic simulation of frequently visualized and
movement of atoms about rotatable bonds is the fundamental principle analyzed using networks. This
behind computational algorithms, termed docking algorithms, for network is made up of protein–
protein interactions from
studying molecular interactions.
Treponema pallidum, the
causative agent of syphilis and
Others other diseases.[56]

Literature analysis

The enormous number of published literature makes it virtually impossible for individuals to read every
paper, resulting in disjointed sub-fields of research. Literature analysis aims to employ computational and
statistical linguistics to mine this growing library of text resources. For example:

Abbreviation recognition – identify the long-form and abbreviation of biological terms

Named-entity recognition – recognizing biological terms such as gene names
Protein–protein interaction – identify which proteins interact with which proteins from text

The area of research draws from statistics and computational linguistics.

High-throughput image analysis

Computational technologies are used to automate the processing, quantification and analysis of large
amounts of high-information-content biomedical imagery. Modern image analysis systems can improve an
observer's accuracy, objectivity, or speed. Image analysis is important for both diagnostics and research.
Some examples are:

high-throughput and high-fidelity quantification and sub-cellular localization (high-content

screening, cytohistopathology, Bioimage informatics)
morphometrics
 clinical image analysis and visualization
determining the real-time air-flow patterns in breathing lungs of living animals
quantifying occlusion size in real-time imagery from the development of and recovery during
arterial injury
making behavioral observations from extended video recordings of laboratory animals
infrared measurements for metabolic activity determination
inferring clone overlaps in DNA mapping, e.g. the Sulston score

High-throughput single cell data analysis

Computational techniques are used to analyse high-throughput, low-measurement single cell data, such as
that obtained from flow cytometry. These methods typically involve finding populations of cells that are
relevant to a particular disease state or experimental condition.

Biodiversity informatics

Biodiversity informatics deals with the collection and analysis of biodiversity data, such as taxonomic
databases, or microbiome data. Examples of such analyses include phylogenetics, niche modelling, species
richness mapping, DNA barcoding, or species identification tools.

Ontologies and data integration

Biological ontologies are directed acyclic graphs of controlled vocabularies. They create categories for
biological concepts and descriptions so they can be easily analyzed with computers. When categorised in
this way, it is possible to gain added value from holistic and integrated analysis.

The OBO Foundry was an effort to standardise certain ontologies. One of the most widespread is the Gene
ontology which describes gene function. There are also ontologies which describe phenotypes.

Databases
Databases are essential for bioinformatics research and applications. Databases exist for many different
information types, including DNA and protein sequences, molecular structures, phenotypes and
biodiversity. Databases can contain both empirical data (obtained directly from experiments) and predicted
data (obtained from analysis of existing data). They may be specific to a particular organism, pathway or
molecule of interest. Alternatively, they can incorporate data compiled from multiple other databases.
Databases can have different formats, access mechanisms, and be public or private.

Some of the most commonly used databases are listed below:

Used in biological sequence analysis: Genbank, UniProt

Used in structure analysis: Protein Data Bank (PDB)
Used in finding Protein Families and Motif Finding: InterPro, Pfam
Used for Next Generation Sequencing: Sequence Read Archive
Used in Network Analysis: Metabolic Pathway Databases (KEGG, BioCyc), Interaction
Analysis Databases, Functional Networks
 Used in design of synthetic genetic circuits: GenoCAD

Software and tools

Software tools for bioinformatics include simple command-line tools, more complex graphical programs,
and standalone web-services. They are made by bioinformatics companies or by public institutions.

Open-source bioinformatics software

Many free and open-source software tools have existed and continued to grow since the 1980s.[57] The
combination of a continued need for new algorithms for the analysis of emerging types of biological
readouts, the potential for innovative in silico experiments, and freely available open code bases have
created opportunities for research groups to contribute to both bioinformatics regardless of funding. The
open source tools often act as incubators of ideas, or community-supported plug-ins in commercial
applications. They may also provide de facto standards and shared object models for assisting with the
challenge of bioinformation integration.

Open-source bioinformatics software includes Bioconductor, BioPerl, Biopython, BioJava, BioJS,

BioRuby, Bioclipse, EMBOSS, .NET Bio, Orange with its bioinformatics add-on, Apache Taverna,
UGENE and GenoCAD.

The non-profit Open Bioinformatics Foundation[57] and the annual Bioinformatics Open Source
Conference promote open-source bioinformatics software.[58]

Web services in bioinformatics

SOAP- and REST-based interfaces have been developed to allow client computers to use algorithms, data
and computing resources from servers in other parts of the world. The main advantage are that end users do
not have to deal with software and database maintenance overheads.

Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search
Services), MSA (Multiple Sequence Alignment), and BSA (Biological Sequence Analysis).[59] The
availability of these service-oriented bioinformatics resources demonstrate the applicability of web-based
bioinformatics solutions, and range from a collection of standalone tools with a common data format under
a single web-based interface, to integrative, distributed and extensible bioinformatics workflow
management systems.

Bioinformatics workflow management systems

A bioinformatics workflow management system is a specialized form of a workflow management system

designed specifically to compose and execute a series of computational or data manipulation steps, or a
workflow, in a Bioinformatics application. Such systems are designed to

provide an easy-to-use environment for individual application scientists themselves to create

their own workflows,
provide interactive tools for the scientists enabling them to execute their workflows and view
their results in real-time,
simplify the process of sharing and reusing workflows between the scientists, and
 enable scientists to track the provenance of the workflow execution results and the workflow
creation steps.

Some of the platforms giving this service: Galaxy, Kepler, Taverna, UGENE, Anduril, HIVE.

BioCompute and BioCompute Objects

In 2014, the US Food and Drug Administration sponsored a conference held at the National Institutes of
Health Bethesda Campus to discuss reproducibility in bioinformatics.[60] Over the next three years, a
consortium of stakeholders met regularly to discuss what would become BioCompute paradigm.[61] These
stakeholders included representatives from government, industry, and academic entities. Session leaders
represented numerous branches of the FDA and NIH Institutes and Centers, non-profit entities including
the Human Variome Project and the European Federation for Medical Informatics, and research institutions
including Stanford, the New York Genome Center, and the George Washington University.

It was decided that the BioCompute paradigm would be in the form of digital 'lab notebooks' which allow
for the reproducibility, replication, review, and reuse, of bioinformatics protocols. This was proposed to
enable greater continuity within a research group over the course of normal personnel flux while furthering
the exchange of ideas between groups. The US FDA funded this work so that information on pipelines
would be more transparent and accessible to their regulatory staff.[62]

In 2016, the group reconvened at the NIH in Bethesda and discussed the potential for a BioCompute
Object, an instance of the BioCompute paradigm. This work was copied as both a "standard trial use"
document and a preprint paper uploaded to bioRxiv. The BioCompute object allows for the JSON-ized
record to be shared among employees, collaborators, and regulators.[63][64]

Education platforms
Bioinformatics is not only taught as in-person masters degree at many universities. The computational
nature of bioinformatics lends it to computer-aided and online learning.[65][66] Software platforms designed
to teach bioinformatics concepts and methods include Rosalind and online courses offered through the
Swiss Institute of Bioinformatics Training Portal. The Canadian Bioinformatics Workshops provides videos
and slides from training workshops on their website under a Creative Commons license. The 4273π project
or 4273pi project[67] also offers open source educational materials for free. The course runs on low cost
Raspberry Pi computers and has been used to teach adults and school pupils.[68][69] 4283 is actively
developed by a consortium of academics and research staff who have run research level bioinformatics
using Raspberry Pi computers and the 4283π operating system.[70][71]

MOOC platforms also provide online certifications in bioinformatics and related disciplines, including
Coursera's Bioinformatics Specialization (UC San Diego) and Genomic Data Science Specialization (Johns
Hopkins) as well as EdX's Data Analysis for Life Sciences XSeries (Harvard).

Conferences
There are several large conferences that are concerned with bioinformatics. Some of the most notable
examples are Intelligent Systems for Molecular Biology (ISMB), European Conference on Computational
Biology (ECCB), and Research in Computational Molecular Biology (RECOMB).

See also
 Biodiversity informatics
Bioinformatics companies
Computational biology
Computational biomodeling
Computational genomics
Cyberbiosecurity
Functional genomics
Health informatics
International Society for Computational Biology
Jumping library
List of bioinformatics institutions
List of open-source bioinformatics software
List of bioinformatics journals
Metabolomics
Nucleic acid sequence
Phylogenetics
Proteomics
Gene Disease Database

References
1. Lesk AM (26 July 2013). "Bioinformatics" (https://www.britannica.com/science/bioinformatic
s). Encyclopaedia Britannica. Archived (https://web.archive.org/web/20210414103621/http
s://www.britannica.com/science/bioinformatics) from the original on 14 April 2021. Retrieved
17 April 2017.
2. Sim AY, Minary P, Levitt M (June 2012). "Modeling nucleic acids" (https://www.ncbi.nlm.nih.g
ov/pmc/articles/PMC4028509). Current Opinion in Structural Biology. 22 (3): 273–8.
doi:10.1016/j.sbi.2012.03.012 (https://doi.org/10.1016%2Fj.sbi.2012.03.012). PMC 4028509
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028509). PMID 22538125 (https://pubmed.
ncbi.nlm.nih.gov/22538125).
3. Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM (July 2016). "Coarse-grained
modeling of RNA 3D structure" (https://doi.org/10.1016%2Fj.ymeth.2016.04.026). Methods.
103: 138–56. doi:10.1016/j.ymeth.2016.04.026 (https://doi.org/10.1016%2Fj.ymeth.2016.04.
026). PMID 27125734 (https://pubmed.ncbi.nlm.nih.gov/27125734).
4. Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (July 2016). "Coarse-
Grained Protein Models and Their Applications" (https://doi.org/10.1021%2Facs.chemrev.6b
00163). Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163 (https://
doi.org/10.1021%2Facs.chemrev.6b00163). PMID 27333362 (https://pubmed.ncbi.nlm.nih.g
ov/27333362).
5. Wong KC (2016). Computational Biology and Bioinformatics: Gene Regulation. CRC
Press/Taylor & Francis Group. ISBN 9781498724975.
6. Joyce AP, Zhang C, Bradley P, Havranek JJ (January 2015). "Structure-based modeling of
protein: DNA specificity" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366589). Briefings
in Functional Genomics. 14 (1): 39–49. doi:10.1093/bfgp/elu044 (https://doi.org/10.1093%2F
bfgp%2Felu044). PMC 4366589 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366589).
PMID 25414269 (https://pubmed.ncbi.nlm.nih.gov/25414269).
 7. Spiga E, Degiacomi MT, Dal Peraro M (2014). "New Strategies for Integrative Dynamic
Modeling of Macromolecular Assembly". In Karabencheva-Christova T (ed.). Biomolecular
Modelling and Simulations. Advances in Protein Chemistry and Structural Biology. Vol. 96.
Academic Press. pp. 77–111. doi:10.1016/bs.apcsb.2014.06.008 (https://doi.org/10.1016%2
Fbs.apcsb.2014.06.008). ISBN 9780128000137. PMID 25443955 (https://pubmed.ncbi.nlm.
nih.gov/25443955).
8. Ciemny M, Kurcinski M, Kamel K, Kolinski A, Alam N, Schueler-Furman O, Kmiecik S
(August 2018). "Protein-peptide docking: opportunities and challenges" (https://doi.org/10.10
16%2Fj.drudis.2018.05.006). Drug Discovery Today. 23 (8): 1530–1537.
doi:10.1016/j.drudis.2018.05.006 (https://doi.org/10.1016%2Fj.drudis.2018.05.006).
PMID 29733895 (https://pubmed.ncbi.nlm.nih.gov/29733895).
9. Ouzounis, C. A.; Valencia, A. (2003). "Early bioinformatics: the birth of a discipline—a
personal view" (https://doi.org/10.1093%2Fbioinformatics%2Fbtg309). Bioinformatics. 19
(17): 2176–2190. doi:10.1093/bioinformatics/btg309 (https://doi.org/10.1093%2Fbioinformati
cs%2Fbtg309). PMID 14630646 (https://pubmed.ncbi.nlm.nih.gov/14630646).
10. Hogeweg P (March 2011). Searls DB (ed.). "The roots of bioinformatics in theoretical
biology" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068925). PLOS Computational
Biology. 7 (3): e1002021. Bibcode:2011PLSCB...7E2021H (https://ui.adsabs.harvard.edu/ab
s/2011PLSCB...7E2021H). doi:10.1371/journal.pcbi.1002021 (https://doi.org/10.1371%2Fjo
urnal.pcbi.1002021). PMC 3068925 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC306892
5). PMID 21483479 (https://pubmed.ncbi.nlm.nih.gov/21483479).
11. Hesper B, Hogeweg P (1970). "Bio-informatica: een werkconcept". Kameleon. 1 (6): 28–29.
12. Hesper B, Hogeweg P (2021). "Bio-informatics: a working concept. A translation of "Bio-
informatica: een werkconcept" by B. Hesper and P. Hogeweg". arXiv:2111.11832v1 (https://a
rxiv.org/abs/2111.11832v1) [q-bio.OT (https://arxiv.org/archive/q-bio.OT)].
13. Hogeweg P (1978). "Simulating the growth of cellular forms". Simulation. 31 (3): 90–96.
doi:10.1177/003754977803100305 (https://doi.org/10.1177%2F003754977803100305).
S2CID 61206099 (https://api.semanticscholar.org/CorpusID:61206099).
14. Colby B (2022). "Whole Genome Sequencing Cost" (https://sequencing.com/education-cent
er/whole-genome-sequencing/whole-genome-sequencing-cost). Sequencing.com. Archived
(https://web.archive.org/web/20220315025036/https://sequencing.com/education-center/wh
ole-genome-sequencing/whole-genome-sequencing-cost) from the original on 15 March
2022. Retrieved 8 April 2022.
15. Moody G (2004). Digital Code of Life: How Bioinformatics is Revolutionizing Science,
Medicine, and Business (https://archive.org/details/digitalcodeoflif0000mood). ISBN 978-0-
471-32788-2.
16. Dayhoff, M.O. (1966) Atlas of protein sequence and structure. National Biomedical Research
Foundation, 215 pp.
17. Eck RV, Dayhoff MO (April 1966). "Evolution of the structure of ferredoxin based on living
relics of primitive amino Acid sequences". Science. 152 (3720): 363–6.
Bibcode:1966Sci...152..363E (https://ui.adsabs.harvard.edu/abs/1966Sci...152..363E).
doi:10.1126/science.152.3720.363 (https://doi.org/10.1126%2Fscience.152.3720.363).
PMID 17775169 (https://pubmed.ncbi.nlm.nih.gov/17775169). S2CID 23208558 (https://api.s
emanticscholar.org/CorpusID:23208558).
18. Johnson G, Wu TT (January 2000). "Kabat database and its applications: 30 years after the
first variability plot" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102431). Nucleic Acids
Research. 28 (1): 214–8. doi:10.1093/nar/28.1.214 (https://doi.org/10.1093%2Fnar%2F28.1.
214). PMC 102431 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102431).
PMID 10592229 (https://pubmed.ncbi.nlm.nih.gov/10592229).
19. Erickson JW, Altman GG (1979). "A Search for Patterns in the Nucleotide Sequence of the
MS2 Genome". Journal of Mathematical Biology. 7 (3): 219–230. doi:10.1007/BF00275725
(https://doi.org/10.1007%2FBF00275725). S2CID 85199492 (https://api.semanticscholar.or
g/CorpusID:85199492).
20. Shulman MJ, Steinberg CM, Westmoreland N (February 1981). "The coding function of
nucleotide sequences can be discerned by statistical analysis". Journal of Theoretical
Biology. 88 (3): 409–20. Bibcode:1981JThBi..88..409S (https://ui.adsabs.harvard.edu/abs/19
81JThBi..88..409S). doi:10.1016/0022-5193(81)90274-5 (https://doi.org/10.1016%2F0022-5
193%2881%2990274-5). PMID 6456380 (https://pubmed.ncbi.nlm.nih.gov/6456380).
21. Xiong J (2006). Essential Bioinformatics (https://archive.org/details/essentialbioinfo00xion).
Cambridge, United Kingdom: Cambridge University Press. pp. 4 (https://archive.org/details/e
ssentialbioinfo00xion/page/n13). ISBN 978-0-511-16815-4 – via Internet Archive.
22. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, et al. (February 1977).
"Nucleotide sequence of bacteriophage phi X174 DNA". Nature. 265 (5596): 687–95.
Bibcode:1977Natur.265..687S (https://ui.adsabs.harvard.edu/abs/1977Natur.265..687S).
doi:10.1038/265687a0 (https://doi.org/10.1038%2F265687a0). PMID 870828 (https://pubme
d.ncbi.nlm.nih.gov/870828). S2CID 4206886 (https://api.semanticscholar.org/CorpusID:4206
886).
23. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (January 2008). "GenBank"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238942). Nucleic Acids Research. 36
(Database issue): D25-30. doi:10.1093/nar/gkm929 (https://doi.org/10.1093%2Fnar%2Fgkm
929). PMC 2238942 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238942).
PMID 18073190 (https://pubmed.ncbi.nlm.nih.gov/18073190).
24. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July
1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd".
Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F (https://ui.adsabs.harvard.edu/
abs/1995Sci...269..496F). doi:10.1126/science.7542800 (https://doi.org/10.1126%2Fscienc
e.7542800). PMID 7542800 (https://pubmed.ncbi.nlm.nih.gov/7542800).
25. Stein, Lincoln (2001). "Genome annotation: from sequence to biology". Nature. 2 (7): 493–
503. doi:10.1038/35080529 (https://doi.org/10.1038%2F35080529). PMID 11433356 (https://
pubmed.ncbi.nlm.nih.gov/11433356). S2CID 12044602 (https://api.semanticscholar.org/Cor
pusID:12044602).
26. Erdin S, Lisewski AM, Lichtarge O (April 2011). "Protein function prediction: towards
integration of similarity metrics" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120633).
Current Opinion in Structural Biology. 21 (2): 180–8. doi:10.1016/j.sbi.2011.02.001 (https://d
oi.org/10.1016%2Fj.sbi.2011.02.001). PMC 3120633 (https://www.ncbi.nlm.nih.gov/pmc/artic
les/PMC3120633). PMID 21353529 (https://pubmed.ncbi.nlm.nih.gov/21353529).
27. Carvajal-Rodríguez A (March 2010). "Simulation of genes and genomes forward in time" (htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851118). Current Genomics. 11 (1): 58–61.
doi:10.2174/138920210790218007 (https://doi.org/10.2174%2F138920210790218007).
PMC 2851118 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851118). PMID 20808525
(https://pubmed.ncbi.nlm.nih.gov/20808525).
28. Brown TA (2002). "Mutation, Repair and Recombination". Genomes (2nd ed.). Manchester
(UK): Oxford.
29. Carter NP, Fiegler H, Piper J (October 2002). "Comparative analysis of comparative
genomic hybridization microarray technologies: report of a workshop sponsored by the
Wellcome Trust". Cytometry. 49 (2): 43–8. doi:10.1002/cyto.10153 (https://doi.org/10.1002%
2Fcyto.10153). PMID 12357458 (https://pubmed.ncbi.nlm.nih.gov/12357458).
30. Chaudhari NM, Gupta VK, Dutta C (April 2016). "BPGA- an ultra-fast pan-genome analysis
pipeline" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829868). Scientific Reports. 6:
24373. Bibcode:2016NatSR...624373C (https://ui.adsabs.harvard.edu/abs/2016NatSR...624
373C). doi:10.1038/srep24373 (https://doi.org/10.1038%2Fsrep24373). PMC 4829868 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829868). PMID 27071527 (https://pubmed.ncbi.
nlm.nih.gov/27071527).
31. Aston KI (May 2014). "Genetic susceptibility to male infertility: news from genome-wide
association studies" (https://doi.org/10.1111%2Fj.2047-2927.2014.00188.x). Andrology. 2
(3): 315–21. doi:10.1111/j.2047-2927.2014.00188.x (https://doi.org/10.1111%2Fj.2047-2927.
2014.00188.x). PMID 24574159 (https://pubmed.ncbi.nlm.nih.gov/24574159).
S2CID 206007180 (https://api.semanticscholar.org/CorpusID:206007180).
32. Véron A, Blein S, Cox DG (2014). "Genome-wide association studies and the clinic: a focus
on breast cancer". Biomarkers in Medicine. 8 (2): 287–96. doi:10.2217/bmm.13.121 (https://d
oi.org/10.2217%2Fbmm.13.121). PMID 24521025 (https://pubmed.ncbi.nlm.nih.gov/245210
25).
33. Tosto G, Reitz C (October 2013). "Genome-wide association studies in Alzheimer's disease:
a review" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809844). Current Neurology and
Neuroscience Reports. 13 (10): 381. doi:10.1007/s11910-013-0381-0 (https://doi.org/10.100
7%2Fs11910-013-0381-0). PMC 3809844 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3
809844). PMID 23954969 (https://pubmed.ncbi.nlm.nih.gov/23954969).
34. Londin E, Yadav P, Surrey S, Kricka LJ, Fortina P (2013). "Use of linkage analysis, genome-
wide association studies, and next-generation sequencing in the identification of disease-
causing mutations". Pharmacogenomics. Methods in Molecular Biology. Vol. 1015. pp. 127–
46. doi:10.1007/978-1-62703-435-7_8 (https://doi.org/10.1007%2F978-1-62703-435-7_8).
ISBN 978-1-62703-434-0. PMID 23824853 (https://pubmed.ncbi.nlm.nih.gov/23824853).
35. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA (June
2009). "Potential etiologic and functional implications of genome-wide association loci for
human diseases and traits" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687147).
Proceedings of the National Academy of Sciences of the United States of America. 106 (23):
9362–7. Bibcode:2009PNAS..106.9362H (https://ui.adsabs.harvard.edu/abs/2009PNAS..10
6.9362H). doi:10.1073/pnas.0903103106 (https://doi.org/10.1073%2Fpnas.0903103106).
PMC 2687147 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687147). PMID 19474294
(https://pubmed.ncbi.nlm.nih.gov/19474294).
36. Hall LO (2010). "Finding the right genes for disease and prognosis prediction". 2010
International Conference on System Science and Engineering. System Science and
Engineering (ICSSE),2010 International Conference. pp. 1–2.
doi:10.1109/ICSSE.2010.5551766 (https://doi.org/10.1109%2FICSSE.2010.5551766).
ISBN 978-1-4244-6472-2. S2CID 21622726 (https://api.semanticscholar.org/CorpusID:2162
2726).
37. Manolio, Teri A.; Collins, Francis S.; Cox, Nancy J.; et al. (October 2009). "Finding the
missing heritability of complex diseases" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC28
31613). Nature. 461 (7265): 747–753. Bibcode:2009Natur.461..747M (https://ui.adsabs.harv
ard.edu/abs/2009Natur.461..747M). doi:10.1038/nature08494 (https://doi.org/10.1038%2Fna
ture08494). PMC 2831613 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831613).
PMID 19812666 (https://pubmed.ncbi.nlm.nih.gov/19812666).
38. Wainschtein, Pierrick; Jain, Deepti; Zheng, Zhili; et al. (March 2022). "Assessing the
contribution of rare variants to complex trait heritability from whole-genome sequence data"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9119698). Nature Genetics. 54 (3): 263–273.
doi:10.1038/s41588-021-00997-7 (https://doi.org/10.1038%2Fs41588-021-00997-7).
PMC 9119698 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9119698). PMID 35256806
(https://pubmed.ncbi.nlm.nih.gov/35256806).
39. Taliun, Daniel; Harris, Daniel N.; Kessler, Michael D.; et al. (February 2021). "Sequencing of
53,831 diverse genomes from the NHLBI TOPMed Program" (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC7875770). Nature. 590 (7845): 290–299. Bibcode:2021Natur.590..290T (htt
ps://ui.adsabs.harvard.edu/abs/2021Natur.590..290T). doi:10.1038/s41586-021-03205-y (htt
ps://doi.org/10.1038%2Fs41586-021-03205-y). PMC 7875770 (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC7875770). PMID 33568819 (https://pubmed.ncbi.nlm.nih.gov/33568819).
40. Li, Xihao; Li, Zilin; Zhou, Hufeng; et al. (September 2020). "Dynamic incorporation of
multiple in silico functional annotations empowers rare variant association analysis of large
whole-genome sequencing studies at scale" (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C7483769). Nature Genetics. 52 (9): 969–983. doi:10.1038/s41588-020-0676-4 (https://doi.o
rg/10.1038%2Fs41588-020-0676-4). PMC 7483769 (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC7483769). PMID 32839606 (https://pubmed.ncbi.nlm.nih.gov/32839606).
41. Li, Zilin; Li, Xihao; Zhou, Hufeng; et al. (December 2022). "A framework for detecting
noncoding rare-variant associations of large-scale whole-genome sequencing studies" (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008172). Nature Methods. 19 (12): 1599–
1611. doi:10.1038/s41592-022-01640-x (https://doi.org/10.1038%2Fs41592-022-01640-x).
PMC 10008172 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008172).
PMID 36303018 (https://pubmed.ncbi.nlm.nih.gov/36303018). S2CID 243873361 (https://ap
i.semanticscholar.org/CorpusID:243873361).
42. "STAARpipeline: an all-in-one rare-variant tool for biobank-scale whole-genome
sequencing data". Nature Methods. 19 (12): 1532–1533. December 2022.
doi:10.1038/s41592-022-01641-w (https://doi.org/10.1038%2Fs41592-022-01641-w).
PMID 36316564 (https://pubmed.ncbi.nlm.nih.gov/36316564). S2CID 253246835 (https://ap
i.semanticscholar.org/CorpusID:253246835).
43. Li, Xihao; Quick, Corbin; Zhou, Hufeng; Gaynor, Sheila M.; Liu, Yaowu; Chen, Han; Selvaraj,
Margaret Sunitha; Sun, Ryan; Dey, Rounak; Arnett, Donna K.; Bielak, Lawrence F.; Bis,
Joshua C.; Blangero, John; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer A.; Cade,
Brian E.; Correa, Adolfo; Cupples, L. Adrienne; Curran, Joanne E.; de Vries, Paul S.;
Duggirala, Ravindranath; Freedman, Barry I.; Göring, Harald H. H.; Guo, Xiuqing; Haessler,
Jeffrey; Kalyani, Rita R.; Kooperberg, Charles; Kral, Brian G.; Lange, Leslie A.; Manichaikul,
Ani; Martin, Lisa W.; McGarvey, Stephen T.; Mitchell, Braxton D.; Montasser, May E.;
Morrison, Alanna C.; Naseri, Take; O’Connell, Jeffrey R.; Palmer, Nicholette D.; Peyser,
Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Redline, Susan; Reiner, Alexander P.;
Reupena, Muagututi’a Sefuiva; Rice, Kenneth M.; Rich, Stephen S.; Sitlani, Colleen M.;
Smith, Jennifer A.; Taylor, Kent D.; Vasan, Ramachandran S.; Willer, Cristen J.; Wilson,
James G.; Yanek, Lisa R.; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed)
Consortium; TOPMed Lipids Working Group; Rotter, Jerome I.; Natarajan, Pradeep; Peloso,
Gina M.; Li, Zilin; Lin, Xihong (January 2023). "Powerful, scalable and resource-efficient
meta-analysis of rare variant associations in large whole genome sequencing studies" (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC10084891). Nature Genetics. 55 (1): 154–164.
doi:10.1038/s41588-022-01225-6 (https://doi.org/10.1038%2Fs41588-022-01225-6).
PMC 10084891 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10084891).
PMID 36564505 (https://pubmed.ncbi.nlm.nih.gov/36564505). S2CID 255084231 (https://ap
i.semanticscholar.org/CorpusID:255084231).
44. Vazquez M, de la Torre V, Valencia A (27 December 2012). "Chapter 14: Cancer genome
analysis" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531315). PLOS Computational
Biology. 8 (12): e1002824. Bibcode:2012PLSCB...8E2824V (https://ui.adsabs.harvard.edu/a
bs/2012PLSCB...8E2824V). doi:10.1371/journal.pcbi.1002824 (https://doi.org/10.1371%2Fj
ournal.pcbi.1002824). PMC 3531315 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35313
15). PMID 23300415 (https://pubmed.ncbi.nlm.nih.gov/23300415).
45. Hye-Jung EC, Jaswinder K, Martin K, Samuel AA, Marco AM (2014). "Second-Generation
Sequencing for Cancer Genome Analysis". In Dellaire G, Berman JN, Arceci RJ (eds.).
Cancer Genomics. Boston (US): Academic Press. pp. 13–30. doi:10.1016/B978-0-12-
396967-5.00002-5 (https://doi.org/10.1016%2FB978-0-12-396967-5.00002-5).
ISBN 9780123969675.
46. Grau J, Ben-Gal I, Posch S, Grosse I (July 2006). "VOMBAT: prediction of transcription factor
binding sites using variable order Bayesian trees" (https://www.ncbi.nlm.nih.gov/pmc/article
s/PMC1538886). Nucleic Acids Research. 34 (Web Server issue): W529-33.
doi:10.1093/nar/gkl212 (https://doi.org/10.1093%2Fnar%2Fgkl212). PMC 1538886 (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC1538886). PMID 16845064 (https://pubmed.ncbi.nlm.
nih.gov/16845064).
47. "The Human Protein Atlas" (https://www.proteinatlas.org/). www.proteinatlas.org. Archived (h
ttps://web.archive.org/web/20200304041657/http://www.proteinatlas.org/) from the original
on 4 March 2020. Retrieved 2 October 2017.
48. "The human cell" (https://www.proteinatlas.org/humancell). www.proteinatlas.org. Archived
(https://web.archive.org/web/20171002215345/https://www.proteinatlas.org/humancell) from
the original on 2 October 2017. Retrieved 2 October 2017.
49. Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, et al. (May 2017). "A
subcellular map of the human proteome". Science. 356 (6340): eaal3321.
doi:10.1126/science.aal3321 (https://doi.org/10.1126%2Fscience.aal3321). PMID 28495876
(https://pubmed.ncbi.nlm.nih.gov/28495876). S2CID 10744558 (https://api.semanticscholar.o
rg/CorpusID:10744558).
50. Ay F, Noble WS (September 2015). "Analysis methods for studying the 3D architecture of the
genome" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556012). Genome Biology. 16 (1):
183. doi:10.1186/s13059-015-0745-7 (https://doi.org/10.1186%2Fs13059-015-0745-7).
PMC 4556012 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556012). PMID 26328929
(https://pubmed.ncbi.nlm.nih.gov/26328929).
51. Kryshtafovych, A.; Schwede, T.; Topf, M.; Fidelis, K.; Moult, J. (2019). "Critical Assessment of
Methods of Protein Structure Prediction (CASP) – Round XIII" (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC6927249). Proteins. 87 (12): 1011–1020. doi:10.1002/prot.25823 (https://d
oi.org/10.1002%2Fprot.25823). PMC 6927249 (https://www.ncbi.nlm.nih.gov/pmc/articles/P
MC6927249). PMID 31589781 (https://pubmed.ncbi.nlm.nih.gov/31589781).
52. "Home - CASP14" (https://predictioncenter.org/casp14/). predictioncenter.org. Archived (http
s://web.archive.org/web/20230130200222/https://predictioncenter.org/casp14/) from the
original on 30 January 2023. Retrieved 12 June 2023.
53. Hoy JA, Robinson H, Trent JT, Kakar S, Smagghe BJ, Hargrove MS (August 2007). "Plant
hemoglobins: a molecular fossil record for the evolution of oxygen transport". Journal of
Molecular Biology. 371 (1): 168–79. doi:10.1016/j.jmb.2007.05.029 (https://doi.org/10.1016%
2Fj.jmb.2007.05.029). PMID 17560601 (https://pubmed.ncbi.nlm.nih.gov/17560601).
54. Jumper, John; Evans, Richard; Pritzel, Alexander; Green, Tim; Figurnov, Michael;
Ronneberger, Olaf; Tunyasuvunakool, Kathryn; Bates, Russ; Žídek, Augustin; Potapenko,
Anna; Bridgland, Alex; Meyer, Clemens; Kohl, Simon A. A.; Ballard, Andrew J.; Cowie,
Andrew (August 2021). "Highly accurate protein structure prediction with AlphaFold" (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC8371605). Nature. 596 (7873): 583–589.
Bibcode:2021Natur.596..583J (https://ui.adsabs.harvard.edu/abs/2021Natur.596..583J).
doi:10.1038/s41586-021-03819-2 (https://doi.org/10.1038%2Fs41586-021-03819-2).
ISSN 1476-4687 (https://www.worldcat.org/issn/1476-4687). PMC 8371605 (https://www.ncb
i.nlm.nih.gov/pmc/articles/PMC8371605). PMID 34265844 (https://pubmed.ncbi.nlm.nih.gov/
34265844).
55. "AlphaFold Protein Structure Database" (https://alphafold.ebi.ac.uk/). alphafold.ebi.ac.uk.
Archived (https://web.archive.org/web/20210724013505/https://alphafold.ebi.ac.uk/) from the
original on 24 July 2021. Retrieved 10 October 2022.
56. Titz B, Rajagopala SV, Goll J, Häuser R, McKevitt MT, Palzkill T, Uetz P (May 2008). Hall N
(ed.). "The binary protein interactome of Treponema pallidum--the syphilis spirochete" (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386257). PLOS ONE. 3 (5): e2292.
Bibcode:2008PLoSO...3.2292T (https://ui.adsabs.harvard.edu/abs/2008PLoSO...3.2292T).
doi:10.1371/journal.pone.0002292 (https://doi.org/10.1371%2Fjournal.pone.0002292).
PMC 2386257 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386257). PMID 18509523
(https://pubmed.ncbi.nlm.nih.gov/18509523).
57. "Open Bioinformatics Foundation: About us" (http://www.open-bio.org/wiki/Main_Page).
Official website. Open Bioinformatics Foundation. Archived (https://web.archive.org/web/201
10512022059/http://open-bio.org/wiki/Main_Page) from the original on 12 May 2011.
Retrieved 10 May 2011.
58. "Open Bioinformatics Foundation: BOSC" (http://www.open-bio.org/wiki/BOSC). Official
website. Open Bioinformatics Foundation. Archived (https://web.archive.org/web/201107181
75922/http://www.open-bio.org/wiki/BOSC) from the original on 18 July 2011. Retrieved
10 May 2011.
59. Nisbet R, Elder IV J, Miner G (2009). "Bioinformatics" (https://books.google.com/books?id=U
5np34a5fmQC&q=bioinformatics%20service%20categories%20EBI&pg=PA328).
Handbook of Statistical Analysis and Data Mining Applications. Academic Press. p. 328.
ISBN 978-0080912035.
60. Office of the Commissioner. "Advancing Regulatory Science – Sept. 24–25, 2014 Public
Workshop: Next Generation Sequencing Standards" (https://www.fda.gov/ScienceResearch/
SpecialTopics/RegulatoryScience/ucm389561.htm). www.fda.gov. Archived (https://web.arc
hive.org/web/20171114200347/https://www.fda.gov/ScienceResearch/SpecialTopics/Regul
atoryScience/ucm389561.htm) from the original on 14 November 2017. Retrieved
30 November 2017.
61. Simonyan V, Goecks J, Mazumder R (2017). "Biocompute Objects-A Step towards
Evaluation and Validation of Biomedical Scientific Computations" (https://www.ncbi.nlm.nih.
gov/pmc/articles/PMC5510742). PDA Journal of Pharmaceutical Science and Technology.
71 (2): 136–146. doi:10.5731/pdajpst.2016.006734 (https://doi.org/10.5731%2Fpdajpst.201
6.006734). PMC 5510742 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510742).
PMID 27974626 (https://pubmed.ncbi.nlm.nih.gov/27974626).
62. Office of the Commissioner. "Advancing Regulatory Science – Community-based
development of HTS standards for validating data and computation and encouraging
interoperability" (https://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/u
cm491893.htm). www.fda.gov. Archived (https://web.archive.org/web/20180126133504/http
s://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm491893.htm) from
the original on 26 January 2018. Retrieved 30 November 2017.
63. Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, et al. (December
2018). "Enabling precision medicine via standard communication of HTS provenance,
analysis, and results" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338479). PLOS
Biology. 16 (12): e3000099. doi:10.1371/journal.pbio.3000099 (https://doi.org/10.1371%2Fjo
urnal.pbio.3000099). PMC 6338479 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC633847
9). PMID 30596645 (https://pubmed.ncbi.nlm.nih.gov/30596645).
64. BioCompute Object (BCO) project is a collaborative and community-driven framework to
standardize HTS computational data. 1. BCO Specification Document: user manual for
understanding and creating B. (https://github.com/biocompute-objects/HTS-CSRS),
biocompute-objects, 3 September 2017, archived (https://web.archive.org/web/2018062708
1221/https://github.com/biocompute-objects/HTS-CSRS) from the original on 27 June 2018,
retrieved 30 November 2017
65. Campbell, A. Malcolm (1 June 2003). "Public Access for Teaching Genomics, Proteomics,
and Bioinformatics" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC162192). Cell Biology
Education. 2 (2): 98–111. doi:10.1187/cbe.03-02-0007 (https://doi.org/10.1187%2Fcbe.03-0
2-0007). PMC 162192 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC162192).
PMID 12888845 (https://pubmed.ncbi.nlm.nih.gov/12888845).
66. Arenas, Miguel (September 2021). "General considerations for online teaching practices in
bioinformatics in the time of COVID ‐19" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC842
6940). Biochemistry and Molecular Biology Education. 49 (5): 683–684.
doi:10.1002/bmb.21558 (https://doi.org/10.1002%2Fbmb.21558). ISSN 1470-8175 (https://w
ww.worldcat.org/issn/1470-8175). PMC 8426940 (https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC8426940). PMID 34231941 (https://pubmed.ncbi.nlm.nih.gov/34231941).
67. Barker D, Ferrier DE, Holland PW, Mitchell JB, Plaisier H, Ritchie MG, Smart SD (August
2013). "4273π: bioinformatics education on low cost ARM hardware" (https://www.ncbi.nlm.n
ih.gov/pmc/articles/PMC3751261). BMC Bioinformatics. 13: 522. doi:10.1186/1471-2105-14-
243 (https://doi.org/10.1186%2F1471-2105-14-243). PMC 3751261 (https://www.ncbi.nlm.ni
h.gov/pmc/articles/PMC3751261). PMID 23937194 (https://pubmed.ncbi.nlm.nih.gov/239371
94).
68. Barker D, Alderson RG, McDonagh JL, Plaisier H, Comrie MM, Duncan L, et al. (2015).
"University-level practical activities in bioinformatics benefit voluntary groups of pupils in the
last 2 years of school". International Journal of STEM Education. 2 (17).
doi:10.1186/s40594-015-0030-z (https://doi.org/10.1186%2Fs40594-015-0030-z).
S2CID 256396656 (https://api.semanticscholar.org/CorpusID:256396656).
69. McDonagh JL, Barker D, Alderson RG (2016). "Bringing computational science to the
public" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775721). SpringerPlus. 5 (259):
259. doi:10.1186/s40064-016-1856-7 (https://doi.org/10.1186%2Fs40064-016-1856-7).
PMC 4775721 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775721). PMID 27006868
(https://pubmed.ncbi.nlm.nih.gov/27006868).
70. Robson JF, Barker D (October 2015). "Comparison of the protein-coding gene content of
Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604092). BMC Research Notes. 8 (561):
561. doi:10.1186/s13104-015-1476-2 (https://doi.org/10.1186%2Fs13104-015-1476-2).
PMC 4604092 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604092). PMID 26462790
(https://pubmed.ncbi.nlm.nih.gov/26462790).
71. Wreggelsworth KM, Barker D (October 2015). "A comparison of the protein-coding genomes
of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon
phaeoclathratiforme BU-1" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4606965). BMC
Research Notes. 8 (565): 565. doi:10.1186/s13104-015-1535-8 (https://doi.org/10.1186%2Fs
13104-015-1535-8). PMC 4606965 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC460696
5). PMID 26467441 (https://pubmed.ncbi.nlm.nih.gov/26467441).

Further reading
Sehgal et al. : Structural, phylogenetic and docking studies of D-amino acid oxidase
activator(DAOA ), a candidate schizophrenia gene. Theoretical Biology and Medical
Modelling 2013 10 :3.
Achuthsankar S Nair Computational Biology & Bioinformatics – A gentle Overview (http://pri
nt.achuth.googlepages.com/BINFTutorialV5.0CSI07.pdf) Archived (https://web.archive.org/w
eb/20081216212125/http://print.achuth.googlepages.com/BINFTutorialV5.0CSI07.pdf) 16
December 2008 at the Wayback Machine, Communications of Computer Society of India,
January 2007
Aluru, Srinivas, ed. Handbook of Computational Molecular Biology. Chapman & Hall/Crc,
2006. ISBN 1-58488-406-1 (Chapman & Hall/Crc Computer and Information Science
Series)
Baldi, P and Brunak, S, Bioinformatics: The Machine Learning Approach, 2nd edition. MIT
Press, 2001. ISBN 0-262-02506-X
Barnes, M.R. and Gray, I.C., eds., Bioinformatics for Geneticists, first edition. Wiley, 2003.
ISBN 0-470-84394-2
Baxevanis, A.D. and Ouellette, B.F.F., eds., Bioinformatics: A Practical Guide to the Analysis
of Genes and Proteins, third edition. Wiley, 2005. ISBN 0-471-47878-4
Baxevanis, A.D., Petsko, G.A., Stein, L.D., and Stormo, G.D., eds., Current Protocols in
Bioinformatics. Wiley, 2007. ISBN 0-471-25093-7
Cristianini, N. and Hahn, M. Introduction to Computational Genomics (http://www.computatio
nal-genomics.net/) Archived (https://web.archive.org/web/20090104042023/http://www.comp
utational-genomics.net/) 4 January 2009 at the Wayback Machine, Cambridge University
Press, 2006. (ISBN 9780521671910 |ISBN 0-521-67191-4)
Durbin, R., S. Eddy, A. Krogh and G. Mitchison, Biological sequence analysis. Cambridge
University Press, 1998. ISBN 0-521-62971-3
Gilbert D (September 2004). "Bioinformatics software resources" (https://doi.org/10.1093%2
Fbib%2F5.3.300). Briefings in Bioinformatics. 5 (3): 300–4. doi:10.1093/bib/5.3.300 (https://d
oi.org/10.1093%2Fbib%2F5.3.300). PMID 15383216 (https://pubmed.ncbi.nlm.nih.gov/1538
3216).
Keedwell, E., Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques
to Bioinformatics Problems. Wiley, 2005. ISBN 0-470-02175-6
Kohane, et al. Microarrays for an Integrative Genomics. The MIT Press, 2002. ISBN 0-262-
11271-X
Lund, O. et al. Immunological Bioinformatics. The MIT Press, 2005. ISBN 0-262-12280-4
Pachter, Lior and Sturmfels, Bernd. "Algebraic Statistics for Computational Biology"
Cambridge University Press, 2005. ISBN 0-521-85700-7
Pevzner, Pavel A. Computational Molecular Biology: An Algorithmic Approach The MIT
Press, 2000. ISBN 0-262-16197-4
Soinov, L. Bioinformatics and Pattern Recognition Come Together (http://jprr.org/index.php/jp
rr/article/view/8/5) Archived (https://web.archive.org/web/20130510213503/http://jprr.org/inde
x.php/jprr/article/view/8/5) 10 May 2013 at the Wayback Machine Journal of Pattern
Recognition Research (JPRR (http://www.jprr.org) Archived (https://web.archive.org/web/200
80908110041/http://www.jprr.org/) 8 September 2008 at the Wayback Machine), Vol 1 (1)
2006 p. 37–41
Stevens, Hallam, Life Out of Sequence: A Data-Driven History of Bioinformatics, Chicago:
The University of Chicago Press, 2013, ISBN 9780226080208
Tisdall, James. "Beginning Perl for Bioinformatics" O'Reilly, 2001. ISBN 0-596-00080-4
Catalyzing Inquiry at the Interface of Computing and Biology (2005) CSTB report (http://ww
w.nap.edu/catalog/11480.html) Archived (https://web.archive.org/web/20070128222920/htt
p://www.nap.edu/catalog/11480.html) 28 January 2007 at the Wayback Machine
 Calculating the Secrets of Life: Contributions of the Mathematical Sciences and computing
to Molecular Biology (1995) (http://www.nap.edu/catalog/2121.html) Archived (https://web.arc
hive.org/web/20080706035211/http://www.nap.edu/catalog/2121.html) 6 July 2008 at the
Wayback Machine
Foundations of Computational and Systems Biology MIT Course (https://web.archive.org/we
b/20071222091912/http://ocw.mit.edu/OcwWeb/Biology/7-91JSpring2004/LectureNotes/ind
ex.htm)
Computational Biology: Genomes, Networks, Evolution Free MIT Course (http://compbio.mit.
edu/6.047/) Archived (https://web.archive.org/web/20130408034631/http://compbio.mit.edu/
6.047/) 8 April 2013 at the Wayback Machine

External links
The dictionary definition of bioinformatics at Wiktionary
Learning materials related to Bioinformatics at Wikiversity
Media related to Bioinformatics at Wikimedia Commons
Bioinformatics Resource Portal (SIB) (http://expasy.org)

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