Links to useful resources

Here, I list publicly available resources.

Genomics

• UCSC genome browser tutorial
  • Part One: Getting Around in the Browser
  • Part Two: Configuring the Browser
  • Part Three: Configuration + DNA Navigation
• Computational Biology Lectures by Prof. Manolis Kellis (my postdoc advisor):
  • Manolis Kellis Research Talks, Interviews, Course Lectures, and Outreach talks
  • Dr. Manolis Kellis on Lex Fridman Podcast
    • Human Genome and Evolutionary Dynamics, Lex Fridman Podcast #113
    • Origin of Life, Humans, Ideas, Suffering, and Happiness, Lex Fridman Podcast #123
    • Biology of Disease, Lex Fridman Podcast #133
• Dr. Rahul Satija on Single Cell Genomics
  • Single Cell Genomics Day
• Dr. Jay Shendure
  • The 2019 Jeffrey M. Trent Lecture in Cancer Research
  • What will the field of genomics look like in 5-10 years? How will it get there?

Statistical genetics

• Psychiatric Genomics Consortium (PGC) Video Textbook
• International Statistical Genetics Workshop
  • Workshop 2022 Syllabus
• Dr. Raymond Walters, Video recording lectures in Summer Institute in Social-Science Genomics
  • LD Score Regression, Part I: Heritability and Partitioning (2017)
  • LD Score Regression, Part II: Genetic Correlation (2017)
• Hilary Finucane, Identifying disease-related cell types from GWAS data (2017)

Computing

• The Missing Semester of Your CS Education
• H. Shi, Tips for Formatting A Lot of GWAS Summary Association Statistics Data, blog post, 2017
• H. Shi, Practical guidelines to save disk space, blog post, 2018

MIT Resources

• Luria computing environment
  • http://rous.mit.edu/index.php/Minicourse_ComputingIntro
  • http://rous.mit.edu/index.php/Introduction_to_UNIX_and_the_KI/BioMicro_Computational_Resources
• Access MIT (transportation)
• MIT’s Career Advising and Professional Development (CAPD)
  • Postdoc
• The MIT Center for Work-Life and Well-Being
• MIT Postdocs Slack Space
• Independent Activities Period (IAP)
• Domestic Ground Transportation
  • For Car Rentals, there are discount codes for Avis/Budget. Please see the links in the “4. Contact MIT Preferred car and truck rental agencies” section in the website
    • If you are using Avis, you can put the discount code in the AWD# field to book a car and bring your MIT ID at the counter.

Stanford Resources

• Stanford Splash
• Biomedical Informatics (BMI) Program
• Bechtel International Center
• Office of International Affairs
  • International travel registry
• Design your financial future seminar videos
• 1:1 Financial Coaching
• Emergency response guideline
• Booking rooms
  • 25live
  • Med Scheduler
• University IT password manager
• Career Guides from BEAM office
  • Career Guides section has two career guides (pdf)

Productivity tips

• How to get unstuck (Link to Prof. Takeshi Tokuyama’s page). (local copy)
• Mensh, B. & Kording, K. Ten simple rules for structuring papers. PLOS Computational Biology 13, e1005619 (2017)
• TeXclip

Carrier development

• U. Alon, How To Choose a Good Scientific Problem. Molecular Cell. 35, 726-728 (2009).
• K.-H. Yu, A survival guide for interdisciplinary PhD students. Nature Biotechnology 34, 993-994 (2016).
• Andrej Karpathy, A Survival Guide to a PhD

Graduate School Application

• Graduate School Personal Statement, MIT Biological Engineering Communication Lab
  • Find Communication Labs, MIT Biological Engineering Communication Lab page lists tips across disciplines.
• What faculty members are looking for in a grad school application essay, MIT EECS
• Career Guides from BEAM office, Stanford University
  • Career Guides section has two career guides (pdf)

Bioinformatics and computational biology resources in Japanese

バイオインフォマティクス解析、計算生物学を日本語で学ぶためのリソース集

• 参考図書, 日本バイオインフォマティクス学会
• 日本語総説誌『JSBi Bioinformatics Review』
• 遺伝統計学・夏の学校, 岡田随象先生
• バイオインフォマティクス: web連携テキスト基礎から応用
• 次世代シークエンサーDRY解析教本, 清水厚志先生 & 坊農秀雅先生
• バイオインフォマティクスのためのアルゴリズム入門
• ToGo TV, DBCLS

Fellowship

• Funai overseas scholarship program
  • 船井情報科学振興財団による Funai Overseas Scholarship