• Interesting Papers

  • Cardiac Development and Therapy

    Stem cell, development, markers

    1. Palpant, N. J. et al. Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells. Nat Protoc 12, 15–31 (2017).

    Overall Cardiac Development

    1. Laflamme, M. A. & Murry, C. E. Heart regeneration. Nature 473, 326–335 (2011).

    Statistics on Cardiac Disease and Heart Failure

    1. Mozaffarian, D., et. al., (2016) Heart Disease and Stroke Statistics-2016 Update: A Report From the American Heart Association. Circulation. 133, e38–360

    2. CDC Stats on Heart Disease: https://www.cdc.gov/heartdisease/facts.htm

    Drug Testing and Analysis

    1. Sharma, A., McKeithan, W. L., Serrano, R., Kitani, T., Burridge, P. W., del Álamo, J. C., Mercola, M., and Wu, J. C. (2018) Use of human induced pluripotent stem cell-derived cardiomyocytes to assess drug cardiotoxicity. Nat Protoc. 13, 3018–3041

    2. Nair, A., and Jacob, S. (2016) A simple practice guide for dose conversion between animals and human. J Basic Clin Pharma. 7, 27

  • Anesthesia and Pain Medicine

    Drug Mechanisms

    1. Vutskits, L. & Xie, Z. Lasting impact of general anaesthesia on the brain: mechanisms and relevance. Nat. Rev. Neurosci. 17, 705–717 (2016).

    Review of Pediatric Pain Assessment

    1. Cohen, L. L., Lemanek, K., Blount, R. L., Dahlquist, L. M., Lim, C. S., Palermo, T. M., McKenna, K. D., and Weiss, K. E. (2008) Evidence-based assessment of pediatric pain. J Pediatr Psychol. 33, 939–55– discussion 956–7

  • Mitochondrial Analysis

    Shape Quantification

    • 1.    Koopman, W. J. H., Visch, H.-J., Smeitink, J. A. M. & Willems, P. H. G. M. Cytometry A 69, 1–12 (2006): description of which metrics best differentiate mitochondrial shapes.
    • 2.    Koopman, W. J. H., Visch, H.-J., Smeitink, J. A. M. & Willems, P. H. G. M. Simultaneous quantitative measurement and automated analysis of mitochondrial morphology, mass, potential, and motility in living human skin fibroblasts. Cytometry A 69, 1–12 (2006).

    Membrane Potential Analysis

    • 1. Cottet-Rousselle, C., Ronot, X., Leverve, X., and Mayol, J.-F. (2011) Cytometric assessment of mitochondria using fluorescent probes. Cytometry A. 79, 405–425
    • 2. Acin‐Perez, R., Benador, I. Y., Petcherski, A., Veliova, M., Benavides, G. A., Lagarrigue, S., Caudal, A., Vergnes, L., Murphy, A. N., Karamanlidis, G., Tian, R., Reue, K., Wanagat, J., Sacks, H., Amati, F., Darley‐Usmar, V. M., Liesa, M., Divakaruni, A. S., Stiles, L., and Shirihai, O. S. (2020) A novel approach to measure mitochondrial respiration in frozen biological samples. EMBO J. 10.15252/embj.2019104073

    Measuring Cellular ROS

    • 1. Murphy, M. P., Bayir, H., Belousov, V., Chang, C. J., Davies, K. J. A., Davies, M. J., Dick, T. P., Finkel, T., Forman, H. J., Janssen-Heininger, Y., Gems, D., Kagan, V. E., Kalyanaraman, B., Larsson, N.-G., Milne, G. L., Nyström, T., Poulsen, H. E., Radi, R., Van Remmen, H., Schumacker, P. T., Thornalley, P. J., Toyokuni, S., Winterbourn, C. C., Yin, H., and Halliwell, B. (2022) Guidelines for measuring reactive oxygen species and oxidative damage in cells and in vivo. Nature Metabolism. 4, 651–662
  • Biological Data Interpretation/Networks


    1. Warde-Farley, D. et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38, W214–20 (2010).

    R Resources

    Notes from Ben Bolker (McMaster):


    GLMM Course material (more info also on Ben Bolker's github):


    R packages on CRAN (check out vignettes section for tutorials):


    Model fitting:


    Estimates and inference:


    Residuals for more complex models (glmer and heterogeneous variance fits):

  • Lab Methods

    Cancer/Focal Adhesion

    1. Chakraborty, S., Lakshmanan, M., Swa, H. L. F., Chen, J., Zhang, X., Ong, Y. S., Loo, L. S., Akıncılar, S. C., Gunaratne, J., Tergaonkar, V., Hui, K. M., and Hong, W. (2015) An oncogenic role of Agrin in regulating focal adhesion integrity in hepatocellular carcinoma. Nat Commun. 6, 6184

    Protein Proximity Labeling

    1. Bar, D. Z., Atkatsh, K., Tavarez, U., Erdos, M. R., Gruenbaum, Y., and Collins, F. S. (2018) Biotinylation by antibody recognition—a method for proximity labeling. Nat Methods. 15, 127–133

    Reproducible TAC

    1. Merino, D. et al. Experimental modelling of cardiac pressure overload hypertrophy: Modified technique for precise, reproducible, safe and easy aortic arch banding-debanding in mice. Sci Rep 8, 3167 (2018).
  • Data That Can (But Won't) Be Used by Hospital Administrators

    The Futility of Inane OR Dress Codes

    1. Farach, S. M., Kelly, K. N., Farkas, R. L., Ruan, D. T., Matroniano, A., Linehan, D. C., and Moalem, J. (2018) Have Recent Modifications of Operating Room Attire Policies Decreased Surgical Site Infections? An American College of Surgeons NSQIP Review of 6,517 Patients. J Am Coll Surg. 226, 804–813

    Why Checklists Shouldn't Be Followed Blindly and Aren't Always the Answer

    1. Tamburini, F. B., Andermann, T. M., Tkachenko, E., Senchyna, F., Banaei, N., and Bhatt, A. S. (2018) Precision identification of diverse bloodstream pathogens in the gut microbiome. Nat Med. 4, 278