• https://cpb-us-e1.wpmucdn.com/sites.ucsc.edu/dist/4/216/files/2019/12/Thompson-On-being-a-successful-graduate-student-version-9-1.pdf

How to write a summary paragraph, and how it pertains to:

1) how to plan for a thesis project

2) how to approach writing Quals

3) how to plan work on a project at the data collection stage well in advance of the paper writing stage.

• Nature summary paragraph

• Article from Ben Barres

• How to be a successful PhD student

• Problem choice and decision trees in science and engineering

• https://www.nature.com/documents/nature-summary-paragraph.pdf

• AI and science: what 1,600 researchers think
• Is AI leading to a reproducibility crisis in science?
• Artificial Intelligence in Molecular Medicine
• Using AI in Peer Review Is a Breach of Confidentiality

• A Beginner's Guide to Conducting Reproducible Research
• Ten simple rules for implementing open and reproducible research practices after attending a training course
• Microarrays: retracing steps

• https://www.cell.com/neuron/pdf/S0896-6273(13)00907-0.pdf

• Stanford Daily and Science articles on MTL publications
• Some faculty urge caution about rushing to judgement
• Searchable PubPeer resource and examples
• Nature profile of image sleuth Elisabeth Bik
• On Academic Authorship (Stanford Research Handbook)
• A co-author’s tale (looking at data from collaborators)
• An editor’s tale (why do retractions sometimes take so long)

• Various tips and strategies amidst an ocean of information

• Ben Barres essay on importance of mentoring record, as well as research projects in faculty labs
• Faculty websites (including lab alumni and outcomes).
• Stanford Profiles that list both current PhD students as well as teaching and advising committees of faculty (search by faculty name, then look  under “Teaching” tab)
• NIH and NSF databases of current and past federal funding, searchable by faculty name

• geneticsdevbio.stanford.edu

• Academic postdoc and faculty track 
• Biotechnology and startups
• Biotech patent law 

Scientific, social, and ethical aspects of human-nonhuman chimeras

(discussion with Hiromitsu Nakauchi)

• Revisiting the Flight of Icarus: Making Human Organs from PSCs with Large Animal Chimeras”  (Rashid 2014)

• UK Academy of Medical Sciences Report

• COVID-19 Antibody Seroprevalence in Santa Clara County, CA” (Bendavid  2020)
• Questions about recruiting, methodology, funding, and objectivity of COVID study https://www.buzzfeednews.com/article/stephaniemlee/stanford-coronavirus-neeleman-ioannidis-whistleblower https://www.buzzfeednews.com/article/stephaniemlee/stanford-coronavirus-study-bhattacharya-email

• Pro:  “One Day Sooner” 
• Con: "For now, it's unethical” (Khan, 2020)
• WHO recommendations
• Survey of our training faculty & students

• "50 years of J.R. Platt’s Strong Inference” (Fudge, 2014)

• Advice from faculty and Dean of Graduate Studies
• Article by Ben Barres

• Essay by John Thompson
• Survey of advice from our own students, alumni and training faculty

Jason Buenrostro:   Alumni, Harvard 

• Buenrostro Lab
• Networking
• Career Path
• Q&A

Apr. 2020

What is a robust scientific result? 

• Problem solving skills
• Reproducibility
• Be Rigorous And Transparent
• Ten Simple Rules for Effective Statistical Practice

Mar. 2020

Ethics and Urgency in Emerging Epidemics

• Genomics-based discussions of coronoviral  transmission
• Ethics discussion

Feb. 2020

• Useful website for simple calculations
• Practical example from recent genetics/dev bio literature

Jan. 2020

Extreme Biology

• Symposium

Dec. 2019

Should we sequence everything?

• "The Earth BioGenome project: sequencing life for the future of life"

Nov. 2019

On becoming a better scientist

•  "Cynical and acynical advice for graduate students",  from Stearns and Huey.  

Oct. 2019

"Extreme Biology" planning

• Symposium flyer, schedule, and website.

May 2019

Planning a scientific symposium

• Topic and speaker discussion.

Apr. 2019

Authorship standards and case studies

• "Intellectual contributions meriting authorship: Survey results from the top cited authors across all science categories"

Mar. 2019

Choosing a thesis lab

• Schuldiner, "Choosing a thesis lab",
• IDP forms for guided thinking

Feb. 2019

Maintaining laboratory notebooks

• "NIH record keeping guidelines "(Intramural).
• "Keeping a lab notebook: Principles and Best practices" webinar.
• "Pocket Guide to Electronic Notebooks"

Dec. 2018

Ethics and human germline editing

• National Academy Consensus Study (2017)
• Nuffield Council on Bioethics Report (2018)
• Consent forms from Jiankui He human trial

Nov. 2018

Choosing a model organism

• "Why the fly?"
• "Biologists search for new model organisms"
• "Non-model model organisms"

Oct. 2018

How to succeed in graduate school

• Thompson, "On being a successful graduate student in the sciences"