Understanding bioinformatics

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1. Dn_AbAug 2012
   Just as in programming, there are no short cuts here. http://norvig.com/21-days.html

   I too think this is something to be on the curve of. You're gonna have to at least learn the basics of [organic] chemistry, genetics, molecular genetics and cellular biology. A blackbox approach will give you a very low ceiling.

   Some books to start with:

   Genes, Proteins and Computers

   A Practical Introduction to the Simulation of Molecular Systems

   Understanding Bioinformatics

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2. ly3xqhl8g9Feb 2023
   I also focused on the work done by the Levin lab after the Sean Carroll podcast [1]. In order to familiarize myself with the subject matter in a more practical manner I started writing a wrapper and a frontend, BESO [2], BioElectric Simulation Orchestrator, for BETSE [3], the Bio Electric Tissue Simulation Engine developed by Alexis Pietak which is used by the Levin lab to simulate various tissues and their responses based on world/biomolecules/genes/etc. parametrization. Reading the BETSE source code, the presentation [4], and some of the articles referred through the source code has been a rewarding endeavour. Some other books I consulted, somewhat beginner friendly were:

       2018, Amit Kessel, Introduction to Proteins. Structure, Function, and Motion, CRC Press
       2019, Noor Ahmad Shaik, Essentials of Bioinformatics, Volume I. Understanding Bioinformatics. Genes to Proteins, Springer
       2019, Noor Ahmad Shaik, Essentials of Bioinformatics, Volume II. In Silico Life Sciences. Medicine, Springer — less basics, more protocol-oriented
       2021, Karthik Raman, An Introduction to Computational Systems Biology. Systems-Level Modelling of Cellular Networks, Chapman and Hall
       2022, Tiago Antao, Bioinformatics with Python Cookbook. Use modern Python libraries and applications to solve real-world computational biology problems, Packt
       2023, Metzger R.M., The Physical Chemist's Toolbox, Wiley — a beautiful story of mathematics, physics, chemistry, biology; gradually rising in complexity as the universe itself, from the whatever (data) structure the universe was before the Big Bang to us, today.
   
       somewhat more technical:
       2014, Wendell Lim, Cell Signaling. Principles and Mechanisms, Routledge
       2021, Mo R. Ebrahimkhani, Programmed Morphogenesis. Methods and Protocols, Humana
       2022, Ki-Taek Lim, Nanorobotics and Nanodiagnostics in Integrative Biology and Biomedicine, Springer
   

   In video format I particularly watched Kevin Ahern's Biochemistry courses BB 350/2017 [5], BB 451/2018 [6], Problem Solving Videos [7].

   [1] https://www.youtube.com/watch?v=gm7VDk8kxOw

   [2] not functional yet, https://github.com/daysful/beso

   [3] https://github.com/betsee/betse

   [4] BETSE 1.0, https://www.dropbox.com/s/3rsbrjq2ljal8dl/BETSE_Documentatio...

   [5] https://youtu.be/JSntf0iKMfM?list=PLlnFrNM93wqz37TUabcXFSNX2...

   [6] https://youtu.be/SAIFs_Mx8D8?list=PLlnFrNM93wqyay92Mi49rXZKs...

   [7] https://youtu.be/e9khXFSU6r4?list=PLlnFrNM93wqzeZvsE_GKes91C...

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3. Dn_AbJun 2012
   I too was recently looking for how someone with good machine learning experience could contribute. I signed up for the pharma, neurobiology and genomics coursera courses.

   My research also pointed me to the following books. The first two I got because they were highly recommended and most fit my interests.

   Genes, Proteins and Computers

   A Practical Introduction to the Simulation of Molecular Systems

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   ##Ungot

   An Introduction to Bioinformatics Algorithms

   Bioinformatics : Machine learning approaches

   Computational Genome Analysis,

   Understanding Bioinformatics by Marketa Zvelebil

   Biological Sequence Analysis, Durbin et al

   Bioinformatics by David Mount :

   Statistical Methods in Bioinformatics Warren J. Ewens, Gregory R. Grant

   Bioinformatics Basics: Applications in Biological Science and Medicine

   Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison

   Understanding Bioinformatics

   Bioinformatics for Dummies

   Molecular Evolution

   Bioinformatics and Molecular Evolution

   Algorithms on Strings, Tree's and Sequences

   Bioinformatics - A Practical Guide to the analysis of Genes and Protein

   The Art of Molecular Dynamics Simulation

   Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis

   'Bioinformatics and Functional Genomics

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