Bioinformatics

Rosalind - Platform for learning bioinformatics and programming through problem solving.

Kindred - Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).

fastq-rs - Can process fastq files at about the speed of the coreutils.

nglview - Jupyter widget to interactively view molecular structures and trajectories.

ngl - WebGL protein viewer.

Mark Zuckerberg Live With Joe DeRisi & Steve Quake || The Future of Technology & Society (2019)

The Biostar Handbook - Introduces readers to bioinformatics, the scientific discipline at the intersection of biology, computer science, and statistical data analytics dedicated to the digital processing of genomic information.

Michael Levin | 2017 Allen Frontiers Symposium

Lattice - Creates design-automation workflows that fundamentally change engineering biology. (GitHub)

GuacaMol - Benchmarks for generative chemistry.

Single-cell RNA-seq pseudotime estimation algorithms

Allen Institute for Brain Science Toolkit

Computer-Designed Organisms - Scalable pipeline for creating functional novel lifeforms.

BioGrakn - Provides an intuitive way to query interconnected and heterogeneous biomedical data in one single place. (Article)

AlphaFold: Using AI for scientific discovery (2020) (HN)

Rust-Bio - Provides implementations of many algorithms and data structures that are useful for bioinformatics.

Low-N protein engineering with data-efficient deep learning (2020)

Machine Boss - Bioinformatics Open Source Sequence machine.

atomium - Python molecular modeller (with .pdb/.cif/.mmtf parsing and production).

PoincareMaps - Poincare maps recover continuous hierarchies in single-cell data.

OpenMM - Toolkit for molecular simulation using high performance GPU code. (OpenMM Cookbook)

Guide to help wet lab biologists learn computational biology (2020)

BiGG Models - Search the database by model, reaction, metabolite, or gene. (Code)

Systems Biology and Biotechnology Specialization course

Path to a free self-taught education in Bioinformatics

How to Build a Biotech (HN)

Unified rational protein engineering with sequence-based deep representation learning (2019)

Deep Molecular Programming: A Natural Implementation of Binary-Weight ReLU Neural Networks (2020) (HN)

Computationally Comparing Biological Networks and Reconstructing Their Evolution (2012)

Bioinformatics Specialization courses

Scanpy - Single-Cell Analysis in Python.

elPrep - High-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines.

Announcing Sylph

Interactive bioimage analysis with Python and Jupyter (2020)

Biomedical Applications of Electrical Stimulation (2020)

a16z invested bio companies

MultiQC - Searches a given directory for analysis logs and compiles a HTML report. (Code)

Diyhplus Wiki - Wiki for open source hardware, do-it-yourself biohacking and practical transhumanism. (Code)

Tellurium - Python environment for reproducible dynamical modeling of biological networks. (Web)

Chemlambda - Graph rewriting system derived from graphic lambda calculus [1] which can be seen as a simple model of chemical or biological computing. (Code)

FPbase - Fluorescent Protein Database. (HN)

Cell Biology by the Numbers

CReM - Open-source Python framework to generate chemical structures using a fragment-based approach.

QSAR modeling software and virtual screening

Axial - Founder-driven life sciences companies (2020)

Manolis Kellis research

Pumas AI - Platform for pharmaceutical modeling and simulation. (HN)

Mitochondrial dynamics in postmitotic cells regulate neurogenesis (2020) (Tweet)

PVDH Lab - Stem cell and Developmental neurobiology.

Applying tech frameworks to biotech: key differences (HN)

Europe’s biotech renaissance (2020)

Awesome DeepBio

Coming up with ideas for biotech startups (2020)

Analyzing toehold sequences for synthetic biology (2020)

R, Data Science, & Computational Biology (2020)

Bioinformatics Algorithms book

ASAP - Automatic Selection And Prediction tools for materials and molecules.

The second decade of synthetic biology: 2010–2020 (HN)

BioDesign Research Conference

Cryo–electron microscopy breaks the atomic resolution barrier at last (2020) (HN)

Deep Learning for Graphs in Chemistry and Biology

Amorphous computing - Refers to computational systems that use very large numbers of identical, parallel processors each having limited computational ability and local interactions.

Awesome Single Cell - Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

MacLean Lab - Stem Cell Systems Biology Research.

Cahan Lab - Stem cell engineering, developmental biology, and cancer biology research.

Tufts Uni: Levin Biology Lab - Investigating information storage and processing in biological systems.

Nextflow - Bioinformatics workflow manager that enables the development of portable and reproducible workflows. (Web) (GitHub)

Quantum deep field for molecule

AlQuraishi Lab at Columbia University - Machine Learning, Molecules, Systems Biology research. (GitHub)

AlphaFold: a solution to a 50-year-old grand challenge in biology, protein folding (2020) (HN) (Explained) (Lex explains)

AlphaFold2 @ CASP14: “It feels like one’s child has left home.” (2020) (Tweet) (HN)

Alphafold2 in PyTorch

ProSPr: Protein Structure Prediction

MiniFold - Deep Learning for Protein Structure Prediction inspired by DeepMind AlphaFold algorithm.

What is protein folding? A brief explanation (2020) (HN)

HH-suite3 for sensitive sequence searching - Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

Soding Lab - Quantitative and Computational Biology Research. (GitHub)

Protein folding explained (2020)

sfaira - Data and model repository for single-cell data.

Theis Lab - Institute of Computational Biology. (GitHub)

PostEra - Medicinal Chemistry Powered by Machine Learning.

Bioregistry - Integrative meta-registry of biological databases, ontologies, and nomenclatures.

Nature Biotechnology

PyMOL - Molecular visualization system. (Code)

Bioinformatics Chat - Podcast about computational biology, bioinformatics, and next generation sequencing.

OpenCADD - Python library for structural cheminformatics.

Ask HN: Best way to learn computational biology/immunology? (2021)

Lumol - Classical molecular simulation engine that provides a solid base for developing new algorithms and methods. (Web)

Tasks Assessing Protein Embeddings (TAPE) - Set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

Center for Computational Biology

Yun S. Song Research (Song Lab) (GitHub)

MolStar - Comprehensive macromolecular library. (Web)

How to Start a Biotech Company on a Budget (2021)

BioGraPy - Biological Graphic tool in Python.

FPbase - The Fluorescent Protein Database. (Code)

Cell Ontology - Structured controlled vocabulary for cell types in animals. (Code)

Squidpy - Spatial Molecular Data Analysis in Python.

TorchProteinLibrary - PyTorch library of layers acting on protein representations.

The Wilke Lab - Computational Evolutionary Biology.

parasail - Pairwise Sequence Alignment Library.

CellChat - R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data.

BiLSTM-CNN-CRF architecture for sequence tagging

scArches - Package to integrate newly produced single-cell datasets into integrated reference atlases.

Biotech for the Biocurious (2021)

The Century of Biology Newsletter

Papers on machine learning for proteins

Finding a "killer application" for novel biotech: AveXis case study (2020) (Tweet)

BioModels - Vast repository of mathematical models of biological and biomedical systems.

noodles - Bioinformatics I/O libraries in Rust.

Datamol - Molecular Manipulation Made Easy.

Role of Bioelectricity During Cell Proliferation in Different Cell Types (2020)

tidysq - Contains tools for analysis and manipulation of biological sequences (including amino acid and nucleic acid – e.g. RNA, DNA – sequences).

SeqKit - Cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Go.

TaxonKit - Practical and Efficient NCBI Taxonomy Toolkit.

unikmer - Toolkit for nucleic acid k-mer analysis, including set operations on k-mers (sketch) optional with TaxIDs but without count information.

ProteinSolver - Graph neural network capable of generating novel amino acid sequences that fold into proteins with predetermined topologies. (Docs)

Learning from Protein Structure with Geometric Vector Perceptrons (2020) (Code)

Dabble - Membrane protein builder and parameterizer.

ffq - Fetch run information from the European Nucleotide Archive (ENA). (Tweet)

MolPAL - Molecular Pool-based Active Learning.

Delocalization-Induced Molecular Equality (2021)

Molecular Assembly Index (2021)

Depth-First Blog

ChemCore - Cheminformatics toolkit for Rust. (Article)

Biochemical Pathway Maps (HN)

Awesome Biomedical Information Extraction

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences (2020) (Code)

Highly accurate protein structure prediction with AlphaFold (2021) (Code) (Tweet) (HN)

AlphaFold 2 is here: what’s behind the structure prediction miracle (2021) (HN)

AlphaFold Protein Structure Database (HN)

The AlphaFold2 Method Paper: A Fount of Good Ideas (2021) (Tweet)

AlphaFold Colab

More Protein Folding Progress – What’s It Mean? (2021) (HN)

smof - UNIX-style FASTA tools.

AlphaFold2: Are attention and symmetries all you need? (2021)

ColabFold - Making Protein folding accessible to all via Google Colab.

BioLink API - API for linked biological knowledge.

AlpahFold, a tentative review (2021)

htsget-rs - Bioinformatic file formats accessible to the web.

Synthace - Enabling life science, the way it should be done.

scispacy - Full spaCy pipeline and models for scientific/biomedical documents. (Web)

Bioinformatics Format Specimens - Collection of bioinformatics file format specimens to test against.

Single-sequence protein structure prediction using language models from deep learning (2021) (Code)

Robust, Universal Tree Balance Indices (2021) (Tweet)

Julia for Biologists (2021)

Hierarchical Generation of Molecular Graphs using Structural Motifs (2020) (Code)

Broad Institute - Unique, collaborative community pioneering a new model of biomedical science. (Twitter) (GitHub)

INDRA (Integrated Network and Dynamical Reasoning Assembler) - Automated model assembly system, originally developed for molecular systems biology and then generalized to other domains. (Web)

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

Neural Distance Embeddings for Biological Sequences (2021) (Code)

Protein complex prediction with AlphaFold-Multimer (2021) (Tweet) (HN)

A cryptography game-changer for biomedical research at scale (2021) (HN)

MoleculeX - New and rapidly growing suite of machine learning methods and software tools for molecule exploration.

Biomappings - Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.

PheKnowLator - Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models.

Computational Reproducibility with BioNix (2021)

Self-Alignment Pretraining for Biomedical Entity Representations (2021) (Code)

Bandage - Bioinformatics Application for Navigating De novo Assembly Graphs Easily. (Code)

Viv - Multiscale visualization of high-resolution multiplexed bioimaging data on the web.

PHATE - Visualizing Transitions and Structure for Biological Data Exploration.

Artificial intelligence reveals nuclear pore complexity (2021) (Tweet)

BioNix - Functional highly reproducible bioinformatics pipelines.

Awesome Bioinformatics Formats

BioShape Lab

Bioinformatics repository with more and newer packages

The History of Microbiology – A Personal Interpretation

SeqFu - General-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files.

Bioinformatics algorithms covered in Cambridge Uni Bio Course

block aligner - SIMD-accelerated library for computing global and X-drop affine gap sequence alignments using an adaptive block-based algorithm.

OpenFold - Trainable & open-source PyTorch reproduction of AlphaFold 2.

HSM (Hierarchical Statistical Mechanical model) - Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. (Web)

Foregen and the Science of Regeneration with Tyler Drzod and Eric Cunningham (2021) (Links & Transcript)

Foregen - Regenerating Foreskins. (Reddit) (Commentarium)

DeepMind releases massive protein structure database (2021)

ATOM3D: Tasks on Molecules in Three Dimensions (Code)

3D Infomax improves GNNs for Molecular Property Prediction (2021) (Code)

Regenerated crustacean limbs are precise replicas (2021) (Tweet)

Dockerfiles and documentation on tools for public health bioinformatics

Arc Institute - New institution for curiosity-driven biomedical science and technology. (Tweet) (Twitter)

SeqLike - Unified biological sequence manipulation in Python.

Deep Learning for Molecules and Materials Book (Code)

ProtTrans - State of the art pre-trained models for proteins.

sandbox.bio - Interactive bioinformatics tutorials.

Foldseek Search Server - Suite for searching and clustering protein structures. (Code) (Tweet)

AlphaFold 2 & Equivariance (2020)

AlphaFold-Powered Drug Discovery of a Novel CDK20 Inhibitor (2022) (HN)

Graphein - Protein Graph Library.

A backbone-centred energy function of neural networks for protein design (2022)

EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction (2022) (Code)

FastFold - Optimizing Protein Structure Prediction Model Training and Inference on GPU Clusters.

Graphormer - Deep learning package that allows researchers and developers to train custom models for molecule modeling tasks.

Strobealign - Fast short-read aligner. It achieves the speedup by using a dynamic seed size obtained from syncmer-thinned strobemers.

Bioinformatics training materials

3 Key Questions to Think About When Designing Proteins Computationally (2022) (Tweet)

AIMSim - Tool for visualizing diversity in your molecular data-set using structural fingerprints.

ProteInfer - Approach for predicting the functional properties of protein sequences using deep neural networks.

Learning inverse folding from millions of predicted structures (2022) (Code) (Tweet)

What's next for AlphaFold and the AI protein-folding revolution (2022)

AlphaFill - Algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models.

tiwih - Simple bioinformatics command-line tools I wished I had.

Awesome Bioinformatics Benchmarks

GLUE (Graph-Linked Unified Embedding) - Graph-linked unified embedding for single-cell multi-omics data integration.

Learning to Extend Molecular Scaffolds with Structural Motifs (2022) (Code)

Functional regeneration and repair of tendons using biomimetic scaffolds loaded with recombinant periostin (2021)

MUSCLE - Widely-used software for making multiple alignments of biological sequences.

fastBio - Deep learning library for biological sequences. Extension of Fastai and PyTorch.

glosim - Python package to compute similarities between molecules and structures.

Bioontologies - Unified access to biomedical ontologies.

PyBioPAX - Python implementation of the BioPAX object model.

AIMNet - Atoms In Molecules Neural Network Potential.

BigBIO: Biomedical Datasets - Tools for curating biomedical training data for large-scale language modeling.

molcloud - Make a bunch of molecules.

RITA: a Study on Scaling Up Generative Protein Sequence Models (2022) (Code)

Awesome Molecular Generation

Geometric Transformers for Protein Interface Contact Prediction (2022) (Code)

DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction (2021) (Code)

Carina - Fast proteomics search engine in 1000 lines of code.

Cluster Tools - Distributed segmentation for bio-image-analysis.

BCALM - Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

pyfaidx - Efficient pythonic random access to fasta subsequences.

AlphaFold reveals the structure of the protein universe (2022) (HN)

K-mer File Format: a standardized and compact disk representation of sets of k-mers (2022) (Tweet)

A Guide to Decentralized Biotech

Saez-Rodriguez Group - Develop software tools for systems level analysis and mechanistic modeling of molecular and biomedical data. (GitHub)

Collection of fold tools

Bio Embeddings - Get protein embeddings from protein sequences.

Deep Review - Collaboratively written review paper on deep learning, genomics, and precision medicine. (Web)

Uni-Fold: an open-source platform for developing protein models beyond AlphaFold

Fasten - Perform random operations on fastq files, using unix streaming.

JVARKIT - Java utilities for Bioinformatics.

Bioconda recipes - Conda recipes for the bioconda channel.

foldingdiff - Diffusion model for protein backbone generation. (Demo)

DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking (2022) (Code)

Allbase - Database for engineering organisms. Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL.

MICAN - Non-sequential structural alignment program for protein structure.

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (2022) (Code)

List of papers about Proteins Design using Deep Learning

ManyFold - Efficient and flexible library for training and validating protein folding models.

AlphaFold’s new rival? Meta AI predicts shape of 600M proteins (2022) (HN)

biogo - Bioinformatics library for Go. (Examples)

Rust-Bio-Tools - Set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio.

fastqc-rs - Quality control tool for FASTQ files written in rust.

This is biology's century. We're not ready for it (2022)

Foresight Institute - Catalyzing Transformative Technologies. (Twitter)

Why use Rust for bioinformatics? Defining the problem space. (2022) (Reddit)

Progres - Protein Graph Embedding Search.

Mega-scale experimental analysis of protein folding stability in biology and protein design (2022) (Tweet)

Representation Learning on Biomolecular Structures using Equivariant Graph Attention (2022)

On-chip on-demand delivery of K+ for in vitro bioelectronics (2022)

Nanoscale Instruments for Visualizing Small Proteins (2022)

Latch SDK - Framework to build and deploy bioinformatics workflows.

LatchBio - End-to-end biocomputing in the browser. (GitHub) (Twitter) (Hiring)

Robust deep learning based protein sequence design using ProteinMPNN (2022) (Code)

AlphaFold 2 & Equivariance (2020)

Vascularization, Survival, and Functionality of Tissue-Engineered Constructs

OpenBioLink - Resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

Bitesize Bio - Biotech how-tos.

Fierce Biotech - Biotech industry news.

Chroma PyTorch - Generative models of protein using DDPM and GNNs, in Pytorch.

Equiformer Diffusion - Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements.

BioSpaCy - SpaCy pipeline for processing biology texts.

Molecular Property Prediction - Message Passing Neural Networks for Molecule Property Prediction.

topiary - Python framework for doing ancestral sequence reconstruction.

OngLai: An Algorithm to Classify Homologous Series

BioGPT: generative pre-trained transformer for biomedical text generation and mining (2022) (Code)

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies (2022) (Code)

Awesome Biomechanics

Spateo - Spatiotemporal modeling of spatial transcriptomics.

Awesome Cytodata

Ankh - Optimized Protein Language Model Unlocks General-Purpose Modelling.

Gotree - Set of command line tools and an API to manipulate phylogenetic trees.

biopix - 3D Protein Structure Visualizer Built with Rust.