Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Cell Specific Gene Expression

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...

Cell Specific Gene Expression

Cell Specific Gene Expression

C4 Pathway and CAM

C4 Pathway and CAM

Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...

Overview of Advanced Functional Groups

Overview of Advanced Functional Groups

Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.

Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

Computed Tomography

Computed Tomography

Tomography refers to imaging by sections. Computed tomography (CT) is a non-invasive imaging technique that uses computers to analyze several cross-sectional X-rays to reveal minute details about structures in the body.
The technique was invented in the 1970s and is based on the principle that as X-rays pass through the body, they are absorbed or reflected at different levels. In the technique, a patient lies on a motorized platform while a computerized axial tomography (CAT) scanner rotates...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

An AI-Powered Trisomy 21 Research Assistant.

bioRxiv : the preprint server for biology·2026

Same author

Metab8D: a metabolic regulome network from multiomics and machine learning.

Communications biology·2026

Same author

Glucagon-Like Peptide 1 Receptor Agonists are Associated With Reduced Risk of Hepatic Encephalopathy in Cirrhosis.

Journal of clinical gastroenterology·2026

Same author

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026

Same author

Targeting metabolism to combat anticancer and antibacterial drug resistance.

Trends in pharmacological sciences·2026

Same author

Photothermal digital holography for imaging and characterization of multilayered structures.

Optics express·2025

Search research articles

Related Experiment Video

Updated: Feb 13, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform.

Saikat Chowdhury^1,2, Noopur Sinha^1,2, Piyali Ganguli^1,2

¹CSIR- National Chemical Laboratory, Chemical Engineering and Process Development Division, Pune, Maharashtra 411008, India.

Journal of Integrative Bioinformatics

|March 17, 2018

Summary

The BIOchemical PathwaY DataBase (BIOPYDB) offers curated human cell pathway data and computational tools for biological pathway analysis. It aids researchers in understanding cellular signaling cascades and disease links.

Keywords:

Computational Platform Pathway Nomenclature and Ontology Protein-Disease Mapping Protein-Protein Interaction Data RESTful API

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance

Published on: October 21, 2021

Related Experiment Videos

Last Updated: Feb 13, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance

Published on: October 21, 2021

Area of Science:

Biochemistry
Systems Biology
Bioinformatics

Background:

Pathway databases are crucial for understanding cellular processes.
Existing resources may lack comprehensive, integrated analysis tools.
Human cell-specific pathway data requires dynamic curation.

Purpose of the Study:

To develop a manually curated, dynamic database of human cell-specific pathway information.
To integrate a computational platform for various pathway analyses.
To provide a comprehensive resource for experimental and computational biologists.

Main Methods:

Manual curation of biochemical pathway data.
Integration of computational tools for Topological, Logical, and Dynamic analyses.
Development of automated pathway image reconstruction and cross-referencing features.

Main Results:

The BIOchemical PathwaY DataBase (BIOPYDB) contains 46 pathways, 3189 molecules, and 5742 reactions.
It links 6897 diseases to pathway proteins, referencing 520 literature sources and 17 databases.
Features include automated reconstruction, cross-referencing, complex search, data sharing, and a RESTful API.

Conclusions:

BIOPYDB provides a valuable, integrated resource for understanding human cellular signaling.
The database facilitates comprehensive pathway analysis for researchers.
Novel features enhance user accessibility and data integration for the research community.