Bioinformatics

Bioinformatics is an interdisciplinary field that develops methods and software tools for better understanding biological data. 🚀


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Bioinformatics

Introduction about the Bioinformatics and Fields related to bioinformatics.

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data.
This part we will focus on below list of questions:
1. What is bioinformatics?
2. What are the origins of bioinformatics?
3. What are the most common bioinformatics programs?
4. What are the most common bioinformatics technologies?
5. How are data analyzed in bioinformatics?
6. Fields related to bioinformatics

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Programming

Brifely introduce some programming language and the IDE-like software.

R is a programming language and free software environment for statistical computing and graphics that is supported by the R Foundation for Statistical Computing. The R language is widely used among statisticians and data miners for developing statistical software and data analysis.
R is a GNU package. The source code for the R software environment is written primarily in C, Fortran, and R. R is freely available under the GNU General Public License, and pre-compiled binary versions are provided for various operating systems.

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RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

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Tutorials

Bioinformatics is a computional biology, here we provide some tutorials for the common tools of bioinformatics

Getting started with R

Installation and Getting started with the R interface

Tutorials_1

Need to dicuss about the tutorials displayed here.

Tutorials_2

Need to dicuss about the tutorials displayed here..

History of Computer

This part will briefly introduce the history of computer.

Online Courses

This section will introduce online courses about R programming, data science and machine learning.

History of Internet

The Internet is a worldwide system of interconnected computer networks that use the TCP/IP set of network protocols to reach billions of users.

Other Resources

This section will introduce other resources such as tutorials, software, and online tools in the Bioinformatics field.

ClinVar Database

ClinVar aggregates information about genomic variation and its relationship to human health.

NIH Disaster Research Response (DR2)

The NIH Disaster Research Response Program (DR2) is the national framework for research on the medical and public health aspects of disasters and public health emergencies.

UCSC Genome Browser

UCSC Genome Browser is a web-based tool that provides a fast, easy way to display a specific region of a genome assembly, along with dozens of aligned annotation tracks.

Gene Expression Omnibus

GEO is a public functional genomics data repository supporting MIAME-compliant data submissions.

Colorectal Cancer Risk Assessment Tool

The Colorectal Cancer Risk Assessment Tool was designed for use by doctors and other health providers with their patients.

Breast Cancer Risk Assessment Tool

The Breast Cancer Risk Assessment Tool is an interactive tool to estimate a woman’s risk of developing invasive breast cancer.

PICO (Patient, Intervention, Comparison, Outcome)

The PICO process is a technique used in evidence based practice to frame and answer a clinical or health care related question.

Repository for Informed Decision Making (RIDeM)

Repository for Informed Decision Making (RIDeM). The long-term goal of the Repository for Informed Decision Making is to provide access to key facts needed to support clinical decision making.

State Tobacco Activities Tracking and Evaluation (STATE) System

State Tobacco Activities Tracking and Evaluation (STATE) System is an electronic data warehouse/interactive application.

US CDC FluView Interactive

US CDC FluView Interactive. The CDC FluView report provides weekly influenza surveillance information in the United States.

Database

Bioinformatics database is the starting point and operating platform for all bioinformatics work

Genome RNAi

GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens.

Bioinformatic Harvester

The Bioinformatic Harvester (PGP)was a bioinformatic meta search engine created by the European Molecular Biology and further developed by KIT Karlsruhe Institute of Technology Laboratory.

DNA Data Bank of Japan (DDBJ)

DNA database of Japan (DDBJ) Center provides sharing and analysis services for data from life science researches and advances science.

Pathogen-Host Interaction database (PHI-base)

The Pathogen-Host Interaction database (PHI-base) contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions.

Pathway Interaction Database (PID)

The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways. The database contains information about the molecular interactions and reactions that take place in cells, with a particular focus on processes that might be relevant to cancer research and treatment.

RCSB PDB

Protein Data Bank builds upon archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

Rfam

Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute.
Rfam is designed to be similar to the Pfam database for annotating protein families.

Uniport (SWISS-PROT/TrEMBL)

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information.

European Bioinformatics Institute (EMBL)

The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 22 member states, four prospect and two associate member states.

GPCRdb

GPCRdb contains data, diagrams and web tools for G protein-coupled receptors (GPCRs).

Gene Disease Database

In Bioinformatics, a Gene Disease Database is a systematized collection of data, typically structured to model aspects of reality, in a way to comprehend the underlying mechanisms of complex diseases, by understanding multiple composite interactions between phenotype-genotype relationships and gene-disease mechanisms.

MiRBase

In bioinformatics, miRBase is a biological database that acts as an archive of microRNA sequences and annotations. As of September 2010 it contained information about 15,172 microRNAs. This number has rose to 38589 by March 2018. The miRBase registry provides a centralised system for assigning new names to microRNA genes.

PIR

Protein Information Resource, part of UniProt.

Rat Genome Database (RGD)

The Rat Genome Database (RGD) is the premiere location for rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse.

Reactome

Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome.

SCOP2

SCOP2 is a successor of Structural classification of proteins (SCOP). the main focus of SCOP2 is on proteins that are structurally characterized and deposited in the PDB.

CATH/Gene3D

The CATH database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains.(95 million protein domains classified into 6,119 superfamilies)

GenBank

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

KABAT

The Kabat database includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest.

SNPedia

The SNPedia (PGP) is a wiki-based bioinformatics web site that serves as a database of single nucleotide polymorphisms (SNPs).

SWISS-2DPAGE

SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and SDS-PAGE database.

WikiPathways

WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways.

BioCyc database collection

The BioCyc database collection is an assortment of organism specific Pathway/ Genome Databases (PGDBs). They provide reference to genome and metabolic pathway information for thousands of organisms. As of December 2016, there are 9300 databases within BioCyc.

DBD

Transcription factor prediction database (DBD) is a database of predicted transcription factors in completely sequenced genomes.

Ensembl genome database project

Ensembl genome database project is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project.

PROSITE

PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

Reference Sequence (RefSeq) database

The Reference Sequence (RefSeq) database[1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products.

CMVD

China Microbiology and Virology Database (CMVD) is a comprehensive database index.

ENZYME

ENZYME is a repository of information relative to the nomenclature of enzymes.And it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided

FLYBASE

A Database of Drosophila Genes & Genomes.

OMIM

OMIM is Online Mendelian Inheritance in Manauthored and edited at the McKusick-Nathans Institute of Genetic Medicine.

SWISS-model

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline.

Biomodels Database

BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006.

Haplotype Map (HapMap)

The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation.

Interpro

InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.

KEGG

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.

PMP

Protein model portal (PMP) gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment.

Xenbase

Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs.

23andMe

23andMe is a privately held personal genomics and biotechnology company based in Mountain View, California. The company is named for the 23 pairs of chromosomes in a normal human cell.

ExoCarta

Exosomes are 30-150 nm membrane vesicles of endocytic origin secreted by most cell types in vitro. ExoCarta, an exosome database, provides with the contents that were identified in exosomes in multiple organisms.

Saccharomyces Genome Database

The Saccharomyces Genome Database is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker’s or budding yeast.

BacDive

BacDive (the Bacterial Diversity Metadatabase) is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.

WormBase

WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about other related nematodes.

EzTaxon Database

In bioinformatics, the EzTaxon database is a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences.

Zebrafish Information Network

The Zebrafish Information Network (ZFIN) is an online biological database of information about the zebrafish (Danio rerio).

Personal Genome Project

The Personal Genome Project (PGP) is a long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personal genomics and personalized medicine.

The Cancer Imaging Archive (TCIA)

The Cancer Imaging Archive (TCIA) is an open-access database of medical images for Cancer research.

Software

Here we provide some popular tools for various kinds of fields.

Bioimaging

Including: Image preprocessing, Image processing, Microscopic Phenotype Analysis, Laser Scanning Microscopy, Conventional Fluorescence microscopy, Super-resolution Imaging, Cryo-EM.

DNA Modifications

Including: DNA modification analysis, DNA methylation array analysis, Enrichment Analysis,BS-seq analysis.

Genome Annotation

Including: Gene Ontology Annotation, GO Semantic Similarity Analysis, Promoter Predication, Annotation Workflows.

Metabolic Profiles

Including: Metabolic profiles analysis, MS-based untargeted Metabolomics, NMR-based Metabolomics, MS-based targeted metabolomics.

Protein Sequence/Expression

Including: Protein Sequence Analysis, MS-based untargeted Proteomics, MS-based Metaproteomics, Antibody Array Analysis, Proteogenomics Analysis.

RNA Transcription

Including: Transcription analysis, RNA-seq analysis, CAGE Analysis,Gene expression array analysis, Metatranscriptomic sequencing analysis.

DNA Structure

Including: DNA structure analysis, DNA structure Database, Small-angle scattering.

Lipidomics

Including: Lipidomics Databases, MS-based untargeted lipidomics, MS-based targeted lipidomics.

Low-level RNA detection

Including: Low-level RNA detection, scRNA-seq analysis, Single-cell qPCR, dPCR.

Medical Imaging

Including: Medical Imaging Analysis, Magnetic Resonance Imaging, Computerized Tomography Scan Imaging, Nuclear Medicine Imaging, Ultrasonic Imaging.

Nucleosome Positioning

Including: Nucleosome positioning, MNase-seq analysis, ATAC-seq analysis.

Prediction of Protein Structure

Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its folding and its secondary and tertiary structure from its primary structure.

Computational Neuroinformatics

Including: Realistic Neuronal Network Modelling, Compartment Neuron Modelling, Model Files Conversion, Model Files Visualization, Model Building, Database.

Drug Discovery

Including: Chemical Enrichment Analysis, Drug-drug interaction prediction, Ligand-based Virtual Screening, Drug Repositioning, Chemical Toxicity, Molecular editors.

Genome Editing

Including: Genome Edition, Genome Editing Databases, CRISPR/Cas9 Screen Analysis.

Immune System

Including: Immune System Analysis, Flow Cytometry, Mass Cytometry, Peptide Array Analysis.

RNA Modifications

Including: RNA Modifications Analysis, MeRIP-seq Analysis, Degradome-seq Analysis.

Metabolic Engineering

Including: Constraint based methods, Metabolic pathway prediction, Strain design, Thermodynamics, Network analysis, 13C-fluxomics.

Neorophysiology

Including: Neurophysiology Analysis, Clinical Eletrophysiology, Patch-clamp.

Population Genomics

Including: Population genetic analysis, GBS analysis, RAD-seq analysis.

Protein Interactions

Including: Protein Interactions Analysis, FRET.

RNA-Protein Interactions

Including: CLIP-seq Analysis, Ribo-seq Analysis.

Brain Connectomics

Including: Connectivity Analysis, Functional Magnetic Resonance Imaging, Diffusion Magnetic Resonance Imaging Analysis, Neuron Tracing.

DNA-Protein Interactions

Including: HT-SELEX Analysis, DNase-seq Analysis, ChIO-seq Analysis.

DNA-Protein Interactions

Including: HT-SELEX Analysis, DNase-seq Analysis, ChIO-seq Analysis.

Membrane Protein

Including: Membrane Protein Analysis, FRAP.

Non-Coding RNA

Including: Non-Coding RNA Analysis, sRNA-seq analysis, miRNA Array analysis.

Phylogenetic Data Analysis

Including: Phylogenetic inference, Phylogenetic Network Construction, Discrete Character Evolution, Tumor Progression, Tree Visualization.

Journals

The comprehensive list of the bioinformatics and computational biology journals and conferences (in alphabetical order).

Aerican Journal of Human Genetics (AJHG)

The American Journal of Human Genetics include the application of genetics in medicine and public policy, as well as the related areas of molecular and cell biology.

Algorithms for Molecular Biology

Algorithms for Molecular Biology publishes articles on novel algorithms for biological sequence and structure analysis, phylogeny reconstruction, and combinatorial algorithms and machine learning.

Bioinformatics

Bioinformatics is the leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers.

Cancer Cell

Cancer Cell is a peer-reviewed scientific journal published by Cell Press. It covers all aspects of cancer research at the cellular-level.

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Research in Computational Molecular Biology (RECOMB)

Research in Computational Molecular Biology (RECOMB) is an annual academic conference on the subjects of bioinformatics and computational biology.

Asia Pacific Bioinformatics Conference (APBC)

Asia Pacific Bioinformatics Conference (APBC) series is an annual international forum for exploring research, development and novel applications in the field of Bioinformatics.

BMC Bioinformatics

BMC Bioinformatics is a peer-reviewed open access scientific journal covering bioinformatics and computational biology published by BioMed Central.

Cell Research

The Cell Research (CR) publishes results of unusual significance or broad conceptual or technical advances in all areas of life sciences, as long as the study is closely related to molecular and cell biology.

Basel Computational Biology Conference (BC2)

Basel Computational Biology Conference (BC2) is a scientific meeting on the subjects of bioinformatics and computational biology.

Bioinformatics and Bioengineering (BIBE)

Bioinformatics and Bioengineering (BIBE) series was found in 2000 and BIBE is the first leading Conference of its kind in IEEE/Internationally inspiring others to follow its path.

Annual International Computing and Combinatorics Conference (COCOON)

Annual International Computing and Combinatorics Conference (COCOON) series focus on the areas of algorithms, theory of computation, computational complexity, and combinatorics related to computing.

BMC Genomics

BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics.

Cell

Cell:Areas covered include molecular biology, cell biology, systems biology, stem cells, developmental biology, genetics and genomics, proteomics, cancer research, immunology, neuroscience, structural biology, microbiology, virology, physiology, biophysics, and computational biology.

Annual Symposium on Combinatorial Pattern Matching (CPM)

Annual Symposium on Combinatorial Pattern Matching (CPM) series focus on the areas related to combinatorial pattern matching and its applications.

BMC Systems Biology

BMC Systems Biology is a part of the BMC Series of journals, it has a broad scope covering the engineering of biological systems, network modelling, quantitative analyses, integration of different levels of information and synthetic biology.

Current Biology

A primary aim of Current Biology is to foster communication across fields of biology, both by publishing important findings of general interest from diverse fields and through highly accessible editorial articles that explicitly aim to inform non-specialists.

Briefing in Bioinformatics

Briefing in Bioinformatics includs reviews of databases and analytical tools for genetics and molecular biology.

Genome Biology

Genome Biology publishes outstanding research in all areas of biology and biomedicine studied from a genomic and post-genomic perspective.

European Conference on Computational Biology (ECCB)

European Conference on Computational Biology (ECCB) is the main computational biology event in Europe and will welcome scientists working in a variety of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology.

Genome Research

Genome Research is an international, continuously published, peer-reviewed journal that publishes studies on the structure, function, biology, and evolution of genomes of all organisms.

Journal of Computational Biology

Journal of Computational Biology is the leading journal covering the analysis, management, and visualization of cellular information at the molecular level.

Journal of Mathematical Biology

Papers published in Journal of Mathematical Biology should either provide biological insight as a result of mathematical analysis or identify and open up challenging new types of mathematical problems that derive from biological knowledge.

Molecular Cell

Molecular Cell aims to publish the best research in molecular biology.

The IEEE Engineering in Medicine and Biology Society (EMBC)

the IEEE Engineering in Medicine and Biology Society (EMBC) is an IEEE group dedicated to the study of Biomedical Engineering.

International Conference on Bioinformatics (InCoB)

International Conference on Bioinformatics (InCoB) is a scientific conference on bioinformatics aimed at scientists in the Asia Pacific region.

Intelligent Systems for Molecular Biology (ISMB)

Intelligent Systems for Molecular Biology (ISMB) brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems.

Journal of Theoretical Biology

The Journal of Theoretical Biology is a biweekly peer-reviewed scientific journal covering theoretical biology, as well as mathematical and computational aspects of biology.

Molecular Systems Biology

Molecular Cell aims to publish the best research in molecular biology.

Mathematical Biosciences

Mathematical Biosciences is a monthly peer-reviewed scientific journal covering research on the use of mathematical models in the biosciences.

Nature Biotechnology

The focus of Nature Biotechnology is biotechnology including research results and the commercial business sector of this field.

Pacific Symposium on Biocomputing (PSB)

Pacific Symposium on Biocomputing (PSB) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance.

Nature Cell Biology

Nature Cell Biology publishes research of the highest quality across all areas of cell biology, encouraging studies that shed light on the mechanisms underlying fundamental cell biological processes in physiology and disease.

PLOS Computational Biology

Mathematical Biosciences is a monthly peer-reviewed scientific journal covering research on the use of mathematical models in the biosciences.

Nature Chemical Biology

Nature Chemical Biology is interested in the best research from across the field of chemical biology, with their broad scope ensuring that work published reaches the widest possible audience.

The Workshop on Algorithms in Bioinformatics (WABI)

The Workshop on Algorithms in Bioinformatics (WABI), established in 2001, is one of the major annual conferences on algorithms in bioinformatics.

Nature Genetics

Nature Genetics encompasses genetic and functional genomic studies on human traits and on other model organisms, including mouse, fly, nematode and yeast.

Nature Medicine

Nature Medicine is a monthly peer-reviewed medical journal publishing research articles, reviews, news and commentaries in the biomedical area, including both basic research and early-phase clinical research covering all aspects of medicine.

Nature Methods

Nature Methods is a forum for the publication of novel methods and significant improvements to tried-and-tested basic research techniques in the life sciences.

Nature Protocols

Nature Protocols Nature Protocols, published by the Nature Publishing Group, is an on-line scientific journal publishing methods in a recipe-style format.

Nucleic Acid Research

Nucleic Acids Research is an open-access peer-reviewed scientific journal published by Oxford University Press. It covers research on nucleic acids, such as DNA and RNA, and related work.

Plos Biology

PLOS Biology was the first journal of the Public Library of Science and now it is an Open access journal published under the Creative Commons Attribution license.

Systematic Biology

Systematic Biology covers the theory, principles, and methods of systematics as well as phylogeny, evolution, morphology, biogeography, paleontology, genetics, and the classification of all living things.

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