A curated collection of resources for Biotechnology, Bioinformatics, Synthetic Biology, CRISPR, and AI in Drug Discovery.
- Overview
- Bioinformatics & Computational Biology
- CRISPR & Gene Editing
- Synthetic Biology
- AI in Drug Discovery
- GitHub Repositories
- Datasets & Databases
- Educational Resources
- Timeline & Milestones
Biotechnology merges biology with technology to improve healthcare, agriculture, and industrial processes. This repository focuses on the computational and high-tech aspects, including genetic engineering, AI-driven drug design, and genomic data analysis.
- Biopython: Foundational Python library for biological computation.
- Bioconductor: R packages for analysis of high-throughput genomic data.
- GROMACS: High-performance molecular dynamics simulator.
- RDKit: Cheminformatics and machine learning for chemistry.
- Galaxy: Web-based platform for accessible, reproducible biomedical research.
- GATK (Genome Analysis Toolkit): Standard for variant discovery.
- Nextflow: Workflow system for scalable and reproducible pipelines.
- DeepVariant: Google's deep learning-based variant caller.
- CRISPR-Cas9: The revolutionary gene-editing tool derived from bacterial immune systems.
- Prime Editing: "Search-and-replace" genome editing without double-strand breaks.
- Base Editing: Precise conversion of one DNA letter to another.
- Innovative Genomics Institute (IGI): Founded by Jennifer Doudna, offers extensive educational guides.
- Synthego CRISPR 101: Comprehensive eBook and guides for beginners and experts.
- Addgene CRISPR Guide: Repository for plasmids and practical lab protocols.
- CRISPR Therapeutics: Developing gene-based medicines (e.g., for Sickle Cell Disease).
- Intellia Therapeutics: In vivo genome editing.
- Editas Medicine: Genome editing for ocular and blood diseases.
- Design-Build-Test-Learn (DBTL): The engineering cycle for biological systems.
- BioBricks: Standardized DNA sequences for assembling biological circuits.
- TinkerCell: CAD for synthetic biology.
- Benchling: Cloud-based platform for life science R&D (electronic lab notebook + molecular biology suite).
- Ginkgo Bioworks: "The Organism Company" - platform for cell programming.
- Twist Bioscience: High-throughput DNA synthesis on silicon.
- Zymergen (Acquired by Ginkgo): Biofacturing and materials.
- AlphaFold (DeepMind): Solved the protein folding problem; predicts 3D structure from amino acid sequence.
- RoseTTAFold: Protein structure prediction tool from the Baker Lab.
- DeepChem: Open-source library for deep learning in drug discovery, materials science, and quantum chemistry.
- Recursion Pharmaceuticals: AI-driven decoding of biology to discover new medicines.
- Insilico Medicine: End-to-end AI for target discovery and generative chemistry.
- Isomorphic Labs: Alphabet company re-imagining drug discovery with AI (built on AlphaFold).
- Exscientia: First AI-designed drug to enter clinical trials.
- Relay Therapeutics: Combining computation with experimentation for protein motion.
| Project | Description | Language |
|---|---|---|
| alphafold | Protein structure prediction system | Python |
| biopython | Tools for biological computation | Python |
| deepchem | Democratizing deep learning for science | Python |
| rdkit | Cheminformatics and machine learning | C++/Python |
| awesome-bioinformatics | Curated list of bioinformatics software | Markdown |
| nf-core | Community effort for Nextflow pipelines | Nextflow |
- GenBank (NCBI): The NIH genetic sequence database.
- UniProt: Comprehensive resource for protein sequence and functional information.
- PDB (Protein Data Bank): Archive of 3D structural data of biological macromolecules.
- Human Cell Atlas: Mapping every cell type in the human body.
- ChEMBL: Database of bioactive drug-like small molecules.
- MIT OpenCourseWare: "Computational Biology: Genomes, Networks, Evolution."
- Coursera: "Genomic Data Science Specialization" (Johns Hopkins).
- Rosalind: Platform for learning bioinformatics through problem-solving.
- StatQuest with Josh Starmer: Brilliant explanations of statistics and ML in biology.
- iBiology: Talks by the world's leading biologists.
- OmicsLogic: Bioinformatics and data science training.
- Evolutionary and Structural Constraints Define a Mutation-Resistant Catalytic Core in E. coli Serine Hydroxy methyltransferase (SHMT) (2026-01-02)
Serine hydroxymethyltransferase is an essential enzyme in the Escherichia coli folate pathway, yet it has not been adopted as an antibacterial target, unlike DHFR, DHPS, or thymidylate synthase. To in...
- Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited (2026-01-02)
We have previously shown that Good-Turing statistics can be applied to molecular dynamics trajectories to estimate the probability of observing completely new (thus far unobserved) biomolecular struct...
- The thermodynamics of pressure activated assembly of supramolecules in isochoric and isobaric systems (2026-01-02)
The efficacy of cryopreservation is constrained by the difficulty of achieving sufficiently high intracellular concentrations of cryoprotective solutes without inducing osmotic injury or chemical toxi...
- The Physics of Causation (2026-01-02)
Assembly theory (AT) introduces a concept of causation as a material property, constitutive of a metrology of evolution and selection. The physical scale for causation is quantified with the assembly ...
- MethConvTransformer: A Deep Learning Framework for Cross-Tissue Alzheimer's Disease Detection (2026-01-01)
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by progressive cognitive decline and widespread epigenetic dysregulation in the brain. DNA methylation, as a stabl...
gantt
title Biotechnology & Genomics Timeline
dateFormat YYYY
section Genomics
Human Genome Project Completed :done, 2003, 2003
Next-Gen Sequencing (NGS) :done, 2005, 2010
Human Pangenome Draft :done, 2023, 2023
section CRISPR
CRISPR-Cas9 as Tool (Doudna/Charpentier) :done, 2012, 2012
First CRISPR Clinical Trials :done, 2018, 2020
FDA Approves Casgevy (Sickle Cell) :done, 2023, 2024
section AI in Bio
AlphaFold 2 Release :done, 2020, 2021
AlphaFold 3 Release :done, 2024, 2025
First AI-designed Drug in Trials :done, 2021, 2022
This repository is equipped with an automated research feed that fetches the latest Quantitative Biology papers from arXiv.
To run manually:
python3 scripts/update_feed.pyLast Updated: January 2026 Maintained by: @nbajpai-code