Calendar and Materials

Each session includes discussion of the weekly research, led by an MIT faculty guest lecturer, and discussion of the non–research topic relevant to the professional development of the students.

Before each class session, students submitted answers to each of these questions about the readings:

  1. What is the primary motivation and overall aim of the study?
  2. What methods were used to investigate the problem, and what is / are one of two major limitation(s) of them?
  3. What is a principal result that you take away from the study?
  4. What future studies would you suggest as a follow up to the present work?

1 Dixon, Jesse R., et al. “Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions.” Nature 485 (2012): 376–80.

Becoming a Scientist

Giddings, Morgan C. “On the Process of Becoming a Great Scientist.” PLOS Computational Biology 4, no. 2 (2008): e33.

Erren, Thomas C., et al. “Ten Simple Rules for Doing Your Best Research, According to Hamming.” PLOS Computational Biology 3, no. 10 (2007): e213.

2 Alvarado, Jose, et al. “Molecular Motors Robustly Drive Active Gels to a Critically Connected State.” Nature Physics 9 (2013): 591–7.

Writing a Fellowship Proposal

Guidelines & Advice on Applying to Graduate Fellowships (PDF)
(Courtesy of Diana Chien and John Casey, Biological Engineering Communication Lab. Used with permission.)

3 Carnall, Jacqui M. A., et al. “Mechanosensitive Self–replication Driven by Self–organization.” Science 327, no. 5972 (2010): 1502–6.

Choosing a Research Problem

Alon, Uri. “How to Choose a Good Scientific Problem.” Molecular Cell 35, no. 6 (2009): 726–8.

4 Tavakoli Nia, et al. “Aggrecan Nanoscale Solid–fluid Interactions are a Primary Determinant of Cartilage Dynamic Mechanical Properties.” ACS Nano 9, no. 3 (2015): 2614–25.

Writing a Paper

Whitesides, George M. “Whitesides’ Group: Writing a Paper.” Advanced Materials 16, no. 15 (2004): 1375–7.

Doerr, Allison. “How to Write a Cover Letter.” Nature Methods (2013).

5 Macosko, Evan Z., et al. “Highly Parallel Genome–wide Expression Profiling of Individual Cells Using Nanoliter Droplets.” Cell 161, no. 5 (2015): 1202–14.

Reading Effectively

How to Navigate a Scientific Paper with Time Constraints: A Graphic Approach (PDF)

6 Yoshida, Takehito, et al. “Rapid Evolution Drives Ecological Dynamics in a Predator–prey System.” Nature 424 (2003): 303–6.

Peer Critique of Fellowship Proposals

There are no readings for this topic.

7 Koski, Kristie J., et al. “Non–invasive Etermination of the Complete Elastic Moduli of Spider Silks.” Nature Materials 12 (2013): 262–7.


Drubin, David G. “Any Jackass can Trash a Manuscript, but it Takes Good Scholarship to Create One (How MBoC Promotes Civil and Constructive Peer Review).” Molecular Biology of the Cell 22, no. 5 (2011): 525–7.

8 Scott, Mathew, et al. “[Interdependence of Cell Growth and Gene Expression: Origins and Consequences]( 10.1126/science.1192588).” Science 330, no. 6007 (2010): 1099–1102.

Making Figures

Wong, Bang. “Points of View: Gestalt Principles (Part 1).” Nature Methods 7, no. 11 (2010): 863.

———. “Points of View: Gestalt Principles (Part 2).” Nature Methods 7, no. 12 (2010): 941.

9 Meharenna, et al. “Crystallographic and Single–Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate.” Biochemistry 49 (2010): 2984.

Giving a Talk

McConnell, Susan. “Designing Effective Scientific Presentations.”

———. “The Importance of Giving a Good Talk.”

10 Zaks, Julia, et al. “A Kinetic Model of Rapidly Reversible Nonphotochemical Quenching.” Proceedings of the National Academy of Sciences 109, no. 39 (2015): 15757–62.

Scientific Ethics

Glass, Bentley. “The Ethical Basis of Science.” Science 150, no. 3701 (1965): 1254–61.

Engineering, and Public Policy Committee on Science, Institute of Medicine, et al. On Being a Scientist: A Guide to Responsible Conduct in Research. National Academies Press, 2009. ISBN: 9780309119702. [Preview with Google Books]

11 Hammar, Petter, et al. “[The Lac Repressor Displays Facilitated Diffusion in Living Cells]( 10.1126/science.1221648).” Science 336, no. 6088 (2012): 1595–8.

Curriculum Vitae

Resumes, CVs, Cover Letters, and LinkedIn

12 Campas, et al. “Quantifying Cell–generated Mechanical Forces within Living Embryonic Tissues.” Nature Methods 11 (2014): 183–9.

Life after the Ph.D.

Austin, Jim, and Bruce Alberts. “[Planning Career Paths for Ph.D.s]( 10.1126/science.1226552).” Science 337, no. 6099 (2012): 1149.

Course Info

Learning Resource Types

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