bioinformatics.md

title	Bioinformatics

Bioinformatics

Personally quite excited about developments of Foregen & am donating to the cause. Regenerating tissue/organs fully is incredibly exciting.

Links

• Rosalind - Platform for learning bioinformatics and programming through problem solving.
• Awesome Bioinformatics
• STUDY WITH ME | Computational Biology (2019)
• Primer on statistical mechanics for biochemists
• 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)