Bioinformatics Resources

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Revision as of 17:22, 6 August 2025 by Mazumder (talk | contribs) (Created page with "Bioinformatics and Biochemistry MS and PhD Student Resources = Contacts = MS Program Director, Anelia Horvath - horvatha@gwu.edu Bioinformatics Program Co-Director, Raja Mazumder -  mazumder_lab@gwu.edu = Recommendations: = * Consider purchasing Bioinformatics Data Skills (<nowiki>https://vincebuffalo.com/book/</nowiki>) and go over Part I and Part II before the first day of class. For those interested, GW's digital library has a copy of Bioinformatics Data Skills:...")
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Bioinformatics and Biochemistry MS and PhD Student Resources

Contacts

MS Program Director, Anelia Horvath - horvatha@gwu.edu

Bioinformatics Program Co-Director, Raja Mazumder -  mazumder_lab@gwu.edu

Recommendations:

  • Consider purchasing Bioinformatics Data Skills (https://vincebuffalo.com/book/) and go over Part I and Part II before the first day of class. For those interested, GW's digital library has a copy of Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools available. Use the following link and sign in with GW credentials to access the ebook. https://ebookcentral.proquest.com/lib/gwu/reader.action?docID=3564550
  • Harper's Illustrated Biochemistry: Please read Sections I, II, VII and Chapters 46, 56, 57, 58. GW students have free access at - https://accessmedicine.mhmedical.com/content.aspx?bookid=3220&sectionid=268299968

Important Links & Information

All BMM students are strongly encouraged to join Linkedin group: https://www.linkedin.com/groups/8313079/

To join make sure your profile says MS in Bioinformatics and Molecular Biochemistry at GW.

Overview

Please see the tutorials section below to brush up on skills, programming languages, and analysis tools.

Useful tutorials

Use the resources below to learn data analysis and visualization skills.

GW Workshops/Support

  • Take GW Library sponsored Python, R, JavaScript, Tableau, OpenRefine Workshops. This is really important for all bioinformatics students (especially python, R, JavaScript).
  • Free one-on-one Coding Consultations to anyone at GW who would like to meet with to discuss a particular coding topic or problem, including JavaScript:   https://calendly.com/gwul-coding/
  • Students wanting to learn about coding are also invited to join the GW Coders group (https://gwcoders.github.io/) this fall.

CFDE Bioinformatics workshops

  • CFDE provides training for various bioinformatics tools and analysis including basic unix and linux commands. Students are encouraged to join these workshops throughout the year: https://training.nih-cfde.org/en/latest/

Learning programming languages

  • Take online python, R, JavaScript (key skills to have as a bioinformatician) courses at CodeAcademy (https://www.codecademy.com), freeCodeCamp (https://www.freecodecamp.org/) or JavaScript for Data Science (https://js4ds.org/)

Additional resources

  • Python courses for beginners (free):
    • https://www.youtube.com/watch?v=rfscVS0vtbw
    • https://www.youtube.com/watch?v=_uQrJ0TkZlc
    • https://www.udacity.com/course/introduction-to-python--ud1110
    • https://www.learnpython.org/ (https://www.datacamp.com/courses/intro-to-python-for-data-science?utm_source=learnpython_com&utm_campaign=learnpython_tutorials)
    • https://www.codecademy.com/catalog/language/python (https://www.codecademy.com/learn/learn-python-3)
  • Python courses for (beginner/intermediate) (free/paid):
    • https://www.codecademy.com/catalog/language/python
    • https://www.udemy.com/course/complete-python-bootcamp/ (comprehensive course)
    • https://www.edx.org/professional-certificate/introduction-to-python-programming?index=product&queryID=6c3afa69576b337f9baf146031185fe1&position=3
  • UCR R tutorial
  • Computational Genomics in R - Computational Genomics with R (compgenomr.github.io)
  • Bioinformatics and computational biology
    • Harvard's STAT115 class by X. Shirley Liu is a great grad-level class for bioinformatics
    • https://www.mathworks.com/matlabcentral/discussions/distance-learning/132907-teaching-learning-deep-learning-and-machine-learning-videos-and-content/?s_tid=mlc_lp_leaf MATLAB is a course to take over the summer or winter break to learn how to use Artificial Intelligence, Machine Learning, and Neural Networks

Bioinformatics Projects

https://hivelab.biochemistry.gwu.edu/wiki/Volunteership_Fall_2025  

Linux basics

  • Online course on Linux, Bash, Scripting and R: https://dmtrk.net/2SUU-14DIB-4F53EA044DAF46CB3X0082B0D42B4F1461C8BC/cr.aspx
  • Linux for beginners: https://ubuntu.com/tutorials/command-line-for-beginners#1-overview
  • Command Line Crash Course: https://www.youtube.com/playlist?list=PLCHnubFzFwjLDKwWQhH3BlGA9OasLKIFl%0AW
  • Windows User - Set up Linux Virtual Machine: https://www.windowscentral.com/how-run-linux-distros-windows-10-using-hyper-v
  • Linux Cheat Sheet: https://ryanstutorials.net/linuxtutorial/cheatsheet.php
  • Shell scripting tutorial: https://youtu.be/GtovwKDemnI

Open Opportunities

Subscribe to linkedin group (https://www.linkedin.com/groups/8313079/) to learn about open opportunities. To join make sure your profile says MS in Bioinformatics and Molecular Biochemistry at GW.

Past/Potential Mentors

Mentors might have spots available and are looking for students: Please use links below to contact potential mentors:

GW Mentors: https://apps.smhs.gwu.edu/smhs/facultydirectory/biochemistry/faculty.cfm

Rong Li - Breast cancer research

Raja Mazumder - GWU HIVE-Lab - Bioinformatics

Brett Shook - Shook Lab - Immune Response

Anelia Horvath - MGPC - scRNA-seq

Wei Li - Children’s Hospital - Genome engineering, single cell genomics

Kazue Hashimoto-Torii - Children’s Hospital - Neurobiology

Vittorio Gallo - Children’s Hospital - Children’s Hospital - Neuroscience Research

Deepa Rastogi - Children’s Hospital - Obesity-related asthma

Inhee Chung -  Anatomy and Regenerative Biology

Kathryn King - US Food and Drug Administration  - Cancer Biology

Sabyasachi Sen, Medical Faculty Associates, Diabetes and HIV

Sydney Fu - GW Cancer Center, Cancer Biology

Daoud Meerzaman - NIH NCI

Vahan Simonyan - DNA-HIVE

Ilya Mazo - Argentys

Also see https://hivelab.biochemistry.gwu.edu/wiki/GW_Bioinformatics_Network

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