awesome-biology

Biology reference

A curated collection of resources and references for learning biology and its applications.

Curated (meta)list of resources for Biology.

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last commit: almost 2 years ago
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awesome-listbioinformaticsbiologybooksevolutionsciencesystems-biology

Table of Contents / Awesome
Awesome Bioinformatics 3,232 over 1 year ago
Awesome Biological Image Analysis 126 about 1 year ago
Awesome Multi-Omics 741 over 1 year ago
Awesome Single-Cell 3,246 11 months ago
Awesome-Computational-Neuroscience 757 about 1 year ago
Awesome Cancer Variant Databases 297 about 2 years ago
Awesome DeepBio 1,892 almost 4 years ago
Awesome Nextflow 575 about 3 years ago
Awesome Reproducible Research 326 12 months ago
Awesome Synthetic Biology 189 almost 3 years ago

Table of Contents / Lists
Biotools by John Didion 590 about 2 years ago

Table of Contents / General Reading
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
Life on Earth and The Living Planet by David Attenborough
The Secret Life of The Brain by PBS

Table of Contents / 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

Table of Contents / Biochemistry
Biochemistry by Berg
Principles of Biochemistry by Lehninger

Table of Contents / Biophysics
Feynman Lectures On Computation by Richard Feynman
Physics in Molecular Biology by Kim Sneppen
Physics of Living Systems by Fabrizio Cleri

Table of Contents / Bioprocess Engineering
Bioprocess Engineering Principles by Pauline M. Doran

Table of Contents / 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

Table of Contents / Molecular Biology
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

Table of Contents / Neuroscience
Awesome-Computational-Neuroscience 757 about 1 year ago :
Principles of Neural Science by Kandel and Schwartz
Theoretical Neuroscience by Dayan and Abbott

Table of Contents / Physical Biology
Pedagogical/review papers on Physical Biology (60+ papers) :
Cell Biology by The Numbers ( )
Physical Biology of the Cell by Phillips et al

Table of Contents / Immunology
How the Immune System Works?
Janeway's Immunobiology
Kuby Immunology

Table of Contents / Omics
http://www.pnas.org/lookup/doi/10.1073/pnas.042692499 Waterston, R. H. (2002). . Proceedings of the National Academy of Sciences, 99(6), 3712–3716
http://www.pnas.org/cgi/doi/10.1073/pnas.092136699 Myers, E. W. (2002). Proceedings of the National Academy of Sciences, 99(7), 4145–4146
http://linkinghub.elsevier.com/retrieve/pii/S0092867412005284 Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., Jones, D., et al. (2012). Cell, 149(5), 979–993
http://www.nature.com/doifinder/10.1038/nature11232 Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., et al. (2012). . Nature, 489(7414), 75–82
http://www.nature.com/doifinder/10.1038/nrg2484 Wang, Z., Gerstein, M. & Snyder, M. . Nat. Rev. Genet. 10, 57–63 (2009)

Table of Contents / 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

Table of Contents / Deep Learning
Deep Learning in Computational Biology 185 over 9 years ago List:
Deep Learning in Neuronal Image Analysis 151 over 7 years ago List:
Deep Learning in Biology 2,026 about 1 year ago List:
Deep Learning Applications in Computational Biology 1,892 almost 4 years ago :

Table of Contents / Bioinformatics
Curated list of papers for Computational Genomics 473 almost 7 years ago :
Awesome-Bioinformatics 3,232 over 1 year ago :
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

Table of Contents / 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

Table of Contents / 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

Table of Contents / 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

Table of Contents / Laboratory Protocol Manuals
Molecular Cloning: A Laboratory Manual by Sambrook
Prescott's Microbiology
Nature Protocols
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 5 almost 10 years ago , 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
Virology, immunology, biology @ Quota by Ian York
Quorky Biology
Biophysics Research Blog
reddit/biology
reddit/bioinformatics
reddit/learnbioinformatics
Biostars Tutorials
Rosalind

Table of Contents / 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

Table of Contents / Tools
ResearchKit 5,618 12 months ago , Framework to create apps for medical research
OMICS Tools , A huge collection of tools
bioconda-recipes 1,653 11 months ago , Conda recipes to install bioinformatics software
PDBREMIX 62 over 7 years ago , 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

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

Table of Contents / 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

Table of Contents / Competitions
International Genetically Engineered Machines (iGEM)
DREAM Challenges
ISCB Wikipedia Competition
Open Science Prize
sbv IMPROVER Challenges

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

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