xahiru/awesome-biology

Curated (meta)list of resources for Biology.

Awesome Biology

Meta-collection of awesome learning resources, research papers, tools and other resources across different fields in Biology. This is inspired from several such lists in programming community.

If you want to contribute to this list (please do), send a pull request, open an issue. When sending suggestions please add a short blurb/description about resource that you have personally read/benefited from. Feel free to debate quality, headings, etc. irrespective of any particular field or subject area.

All the resources need not be freely available for download.

For Q&A type of resources that share excellent insight see here.

For a list of review research articles, see awesome-reviews.

Table of Contents

• Awesome lists
• General Reading
  • Videos
• Introductory
• Biochemistry
• Biophysics
• Bioprocess Engineering
• Evolution
• Molecular Biology
• Neuroscience
• Physical Biology
• Immunology
• Genetics
• Omics & Sequencing
• Systems Biology and Genetic Networks
• Bioinformatics
• Structural Biology | Proteins
• Statistics | Data munging
• Laboratory Manuals
• Blogs/Links
• Tools
• Journals
• MOOCs
• Competitions

Awesome

• Awesome Bioinformatics
• Awesome Multi-Omics
• Awesome Single-Cell
• Awesome-Computational-Neuroscience
• Awesome Cancer Variant Databases
• Awesome DeepBio
• Awesome Nextflow
• Awesome Reproducible Research
• Awesome Synthetic Biology

Lists

Other awesome lists without the awesome branding.

Tools

• Biotools by John Didion

General Reading

Unordered list of books written in popular science style yet sufficiently technical in appropriate cases to provide you an interesting tour of all big and small process in universe and its biology.

• The Epic History of Biology by Serafini
• The Selfish Gene by Richard Dawkins
• What is Life by Erwin Schrodinger (Public Domain)
• The Immortal Life of Henrietta Lacks by Rebecca Skloot
• The Red Queen: Sex and the Evolution of Human Nature by Matt Ridley
• The Richness of Life by Stephen Jay Gould
• Guns, Germs, and Steel: The Fates of Human Societies by Jared Diamond
• The Ascent of Man by Jacob Bronowski
• Power, Sex and Suicide: Mitochondria and the Meaning of Life by Nick Lane
• Emperor of all Maladies by Siddhartha Mukherjee
• The Gene by Siddhartha Mukherjee
• The Eighth Day of Creation by H. F. Judson
• The Human Zoo by Desmond Morris
• The Equation That Couldn't be Solved by Mario Livio
• The Golden Ratio by Mario Livio
• The Complexity Paradox by Kenneth Mossman
• The Vital Question by Nick Lane
• On Growth and Form by D'Arcy Wentworth Thomsom
• The Big Questions: Evolution by Francisco Ayala
• The Making of a Fly by Peter Lawrence
• Molecular Machines in Biology by Joachim Frank
• Cell Motility from Molecules to Organisms by Ridley and Peckham
• Random Walks in Biology by Howard Berg
• Elephants on Acids and Other Bizarre Experiments by Alex Boese
• Sapiens: A Brief History of Humankind by Yuval Noah Harari
• Evolving Ourselves: Redesigning the Future of Humanity--One Gene at a Time
• The Botany of Desire by Michael Pollan
• Silent Spring by Rachel Carlson
• Soft Matter: the stuff that dreams are made of by Roberto Piazza

Videos

• Life on Earth and The Living Planet by David Attenborough
• The Secret Life of The Brain by PBS

General Biology

• Ancestors in Our Genome by Eugene E. Harris
• A Cartoon Guide to Genetics by Gonick and Wheelis
• Campbell Biology
• Clinical Microbiology Made Ridiculously Simple
• The Biology of Cancer by Weinberg
• The Deeper Genome by John Parrington
• The Developing Genome: An Introduction to Behavioral Epigenetics by Davis S. Moore
• The Systems View of Life: A Unifying Vision
• Scitable by Nature Education
• The Many Phases of the Matter by Ganeshan Venkataraman
• The Shaping of Life by Lionel G. Harrison
• The Machinery of Life by David Goodsell

Biochemistry

• Biochemistry by Berg
• Principles of Biochemistry by Lehninger

Biophysics

• Feynman Lectures On Computation by Richard Feynman
• Physics in Molecular Biology by Kim Sneppen
• Physics of Living Systems by Fabrizio Cleri

Bioprocess Engineering

• Bioprocess Engineering Principles by Pauline M. Doran

Evolution

• Arrival of the Fittest: Solving Evolution's Greatest Puzzle by Andreas Wagner
• Computational Molecular Evolution by Ziheng Yang
• Fundamentals of Molecular Evolution by Dan Graur
• Human Evolutionary Genetics by Jobling et al
• Life Ascending: The Ten Great Inventions of Evolution by Nick Lane
• Robustness and Evolvability in Living Systems by Andreas Wagner
• Mathematical Ecology of Populations and Ecosystems by John Pastor
• Man and His Future, A Ciba Foundation Volume by Wolstenholme, G. E. W.
• The Origins of Evolutionary Innovations by Andreas Wagner
• The Growth of Biological Thought

Molecular Biology

• Quora: What are the best papers in Molecular Biology?
• Molecular Biology of the Cell by Bruce Alberts
• Molecular Biology of Gene by Watson et al
• Molecular Cell Biology by Lodish
• Gene Cloning and DNA Analysis: An Introduction by T. A. Brown
• Lewin's GENES XII by Krebs et al

Neuroscience

• LIST: Awesome-Computational-Neuroscience
• Principles of Neural Science by Kandel and Schwartz
• Theoretical Neuroscience by Dayan and Abbott

Physical Biology

• List: Pedagogical/review papers on Physical Biology (60+ papers) (course) (archive)
• Cell Biology by The Numbers (Online)
• Physical Biology of the Cell by Phillips et al

Immunology

• How the Immune System Works?
• Janeway's Immunobiology

Genetics

• Genes and Genomes: A Changing Perspective by Maxine Singer and Paul Berg

  Students will like this text. The writing is clear and straight-forward so that facts are easily assimilated and arguments/discursive points easily followed. The part on recombinant DNA is particularly good. - C A Smith (Biochemical Education, Volume 19, Issue 4)

• Concepts of Genetics by Klug

• Principles of Population Genetics by Hartl and Clark

Omics

• Waterston, R. H. (2002). On the sequencing of the human genome. Proceedings of the National Academy of Sciences, 99(6), 3712–3716. http://www.pnas.org/lookup/doi/10.1073/pnas.042692499
• Myers, E. W. (2002). On the sequencing and assembly of the human genome. Proceedings of the National Academy of Sciences, 99(7), 4145–4146. http://www.pnas.org/cgi/doi/10.1073/pnas.092136699
• Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., Jones, D., et al. (2012). Mutational Processes Molding the Genomes of 21 Breast Cancers. Cell, 149(5), 979–993. http://linkinghub.elsevier.com/retrieve/pii/S0092867412005284
• Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., et al. (2012). The accessible chromatin landscape of the human genome. Nature, 489(7414), 75–82. http://www.nature.com/doifinder/10.1038/nature11232
• Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009). http://www.nature.com/doifinder/10.1038/nrg2484

Systems Biology and Genetic Networks

• An Introduction to Systems Biology by Uri Alon
• A First Course in Systems Biology by E. Voit
• A Genetic Switch by Mark Ptashne
• Lectures from Systems Biology Course by Uri Alon
• Lectures from Systems Biology: Constraint-based Reconstruction and Analysis by B. Palsson
• Life: An Introduction to Complex Systems Biology by Kunihiko Kaneko
• Mathematical Modeling in Systems Biology by Brian Ingalls
• Systems Biology: Properties of Reconstructed Networks by B. Palsson

Deep Learning

• List: Deep Learning in Computational Biology
• List: Deep Learning in Neuronal Image Analysis
• List: Deep Learning in Biology
• List: Deep Learning Applications in Computational Biology

Bioinformatics

• List: Curated list of papers for Computational Genomics
• List: Awesome-Bioinformatics
• Practical Computing for Biologists by Steven Haddock and Casey Dunn
• An Introduction to Bioinformatics Algorithms by Pavel Pevzner
• Bioinformatics and Functional Genomics by Jonathan Pevsner
• Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau and Pavel Pevzner
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
• Bioinformatics: The Machine Learning Approach by Pierre Baldi
• Current topics in Genome Analysis 2016 by NIH-NHGRI
• Statistical Methods in Bioinformatics: An Introduction by Ewens
• Introduction to Protein-DNA Interactions by Gary Stormo
• Introduction to Genomics by Arthur M. Lesk
• Theory of Basic Alignment Search Tool (BLAST)
• Translational Bioinformatics by PLOS Collections

Statistics

• Introduction to Statistical Learning (with applications in R) by Hastie et al.
• Nature's Statistics for Biologists collection
• Statistical Done Wrong by Alex Reinhart
• Statistics Inference by George Casella

Structural Biology | Proteins

• Algorithms in Structural Molecular Biology by Bruce R. Donald
• Introduction to Protein Structure by Branden and Tooze
• Proteins: Structures and Molecular Properties by Creighton

Data Analysis | Programming

• The Cartoon Guide to Statistics by Gonick
• The Analysis of Biological Data by Whitlock and Schluter
• Practical Computing for Biologists by Haddock and Dunn
• Advanced Python for Biologists by Dr Martin O Jones

Laboratory Protocol Manuals

• Molecular Cloning: A Laboratory Manual by Sambrook
• Prescott's Microbiology
• Nature Protocols

Blogs/Links

• What are some essential websites for biologists?
• Talks at ICTS, an interesting collection of talks on statistical physics, systems biology, and much more.
• Papers-per-week, my collection of papers (with reviews!)
• Protein Love @ Quora
• Bioscience club @ Quora, discusses great biology related answers on Quora
• it is NOT junk, a blog about genomes, DNA, evolution, open science by Michael Eisen
• Virology, immunology, biology @ Quota by Ian York
• Quorky Biology
• Biophysics Research Blog
• reddit/biology
• reddit/bioinformatics
• reddit/learnbioinformatics
• Biostars Tutorials
• Rosalind

Podcasts

• This Week in Microbiology by Vincent Racaniello
• Nature Podcasts
• Evolution Talk Podcast
• The Naked Scientists' Podcasts, with four biology related podcasts, The Naked Scientists, eLife, Naked Genetics, and Naked Neuroscience

Tools

• ResearchKit, Framework to create apps for medical research
• OMICS Tools, A huge collection of tools
• bioconda-recipes, Conda recipes to install bioinformatics software
• PDBREMIX, Library to analyze protein structures and protein simulations
• scikit-bio, in development Python library for bioinformatics
• BioPython, Python libraries that implement a rich set of modules to handle wide class of biological computations
• SciFeeds, Aggregates science mentioned in articles, social media, and news media to help identify important scientific advances
• Linuxbrew, port of Homebrew, a Mac OS package manager, for Linux

Journals

• Top Publications (Life Sciences) - Google Scholar
• Annual Reviews
• Cell Press
• Current Opinion
• Nature
• Oxford Journals
• PNAS
• Science

MOOCs

• Bioinformatics: Journey to the Frontier of Computational Biology Specialization
• Complexity Explorer by Santa Fe Institute
• Epigenetic Control of Gene Expression
• Experimental Genome Science
• EMBL-EBI Online Training Courses
• Fundamentals of Biology - OCW.MIT
• HarvardX's PH525-x Data Analysis Series
• Introduction to Systems Biology
• Introduction to Biomedical Imaging
• Introduction to Human Evolution
• Network Analysis in Systems Biology
• Neuronal Dynamics: Computational Neuroscience of Single Neurons
• Principles of Synthetic Biology
• Principles of Biochemistry
• Proteins: Biology's Workforce
• videolectures.net - Biology

Competitions

• International Genetically Engineered Machines (iGEM)
• DREAM Challenges
• ISCB Wikipedia Competition
• Open Science Prize
• sbv IMPROVER Challenges

Conferences

• American Society of Human Genetics (ASHG)
• Biology of Genomes
• Gordon Research Conferences
• Intelligent Systems for Molecular Biology (ISMB)
• RECOMB