• Keep your eyes on the prize, by Ron Vale
• A Critique of the Hypothesis, and a Defense of the Question, as a Framework for Experimentation, by David Glass. A good explanation of why model-building, not hypothesis-testing, is the most productive form of science

     
Two papers on choosing projects. Together, these papers offer an incredibly valuable perspective on how to do science.

• How to choose a good scientific problem, by Uri Alon
• Problem choice and decision trees in science and engineering, by Michael Fischbach

• A wake-up call: How failing a PhD led to a strategy for a successful scientific career, by Bruce Alberts. I love this piece because it emphasizes the value of good scientific questions and practical approaches rather than specific hypotheses.
• How to do great work, by Paul Graham. This is targeted at a broad audience of young people. I think this contains tons of great advice for young scientists.
• You and Your Research (1986), by Richard Hamming. This is a bit dated and somewhat intentionally provocative, but I think there's lots of very sound advice in here about how to do really important research. I don't devote my entire life to research and I don't expect my lab members to devote their entire lives either, but I think this is great to read and learn from.
• Understanding Academic Medical Centers: Simone's Maxims, by Joseph Simone. An interesting perspective on academic medical centers. I am too new to say whether I agree or not ;)

• Our lab's Mentoring Plan Template
• How to be a graduate advisee, by Indira Raman at Northwestern. This is incredibly valuable and correct advice that everyone should re-read every year!
• 7 Tips for making presentations, by Ruthie Johnson
• Fantastic advice on overcoming uncertainty in your career, and the importance of professional growth, by Jen Heemstra
• What to bring to a meeting with your advisor, by Prachee Avasthi
• Resources for new PhD students, by Matt Hauer (but talk to me about learning Python, not R!)
• Seven steps toward health and happiness in the lab, by Fernando Maestre
• You do not need to work 80 hours a week to succeed in academia, by Meghan Duffy
• How to find and apply for a postdoc position, by Guy Tanentzapf

On scientific writing:

• Incredible resources on grant writing from Northwestern's CLIMB office. I especially recommend "5 Principles for Writing Readable Sentences" and "Creating Coherent Paragraphs: Topic Sentences, Echo Words, Transitions". 
• Simple rules for concise scientific writing, by Scott Hotaling
• The art of writing science, by Kevin Plaxco
• Friends Don't Let Friends Make Bad Graphs (some short and very good advice!), by Chenxin Li

This is not exhaustive, but a starting point for educating our lab members and others.

• What Happens Before? A Field Experiment Exploring How Pay and Representation Differentially Shape Bias on the Pathway Into Organizations. Katherine L. Milkman et al, J App Psychol. 2015
• How Gender and Race Stereotypes Impact the Advancement of Scholars in STEM: Professors' Biased Evaluations of Physics and Biology Post-Doctoral Candidates. Asia A. Eaton et al, Sex Roles 2020
• Race, Ethnicity, and NIH Research Awards. Donna K. Ginther et al., Science 2011. See also commentaries here, here, and here (of many) by Drugmonkey (Blog, Twitter) 
• Equity, Diversity, and Inclusion: Racial inequity in grant funding from the US National Institutes of Health. Michael A Taffe and Nicholas Gilpin, eLife 2021 (related to the above).
• Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms. Daniel Z. Grunspan et al. PLoS One 2016
• Science faculty's subtle gender biases favor male students. Corinne A. Moss-Racusin et al. PNAS 2012
• Quality of evidence revealing subtle gender biases in science is in the eye of the beholder. Ian M. Handley PNAS 2015
• The Myth That Academic Science Isn't Biased Against Women, by Joan Williams and Jessi L. Smith. A rebuttal to Williams and Ceci 2015, National hiring experiments reveal 2:1 faculty preference for women on STEM tenure track. There's a lot to learn from thinking about the findings of Williams and Ceci, the media response, and the critique.