Running a research laboratory as a worker cooperative

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A cooperative or co-op is “a jointly owned enterprise engaging in the production or distribution of goods or the supplying of services, operated by its members for their mutual benefit.” A worker cooperative is a co-op owned and self-managed by its workers. The primary difference between traditional businesses and cooperatives is that the first emphasizes

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What is the point of gene set or pathway enrichment analysis?

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Gene set or pathway enrichment analysis is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. There are many different ways to perform gene set or pathway enrichment analysis, from hypergeometric distribution tests to bootstrap based approaches. Gene set or pathway enrichment

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Letter to Gaby

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I received an email from a 7th grader named Gaby (through her teacher, Rhea). Gaby was in the middle of a project that examined bias and stereotyping in past and present-day science. Rhea encouraged her students to reach out to local “real-life” STEM professionals with the goal of profiling a diverse range of scientists in

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Introduction to CyTOF

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Motivation: Characterizing large quantities of single cells is important to address clinically and biologically relevant questions. Traditionally, bulk measurements have been used to characterize the functional states of diseased vs. normal immune cells, livers, brains, and tissues or organs of interest to identify various interesting mechanistic differences. However, these bulk measurements average information across many

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Criticize me like a scientist

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Criticism is essential to science. Criticism is the vehicle by which science moves forward. We investigate, present our findings, and subject these findings to peer review – to criticism. If such findings are convincing to a qualified panel of our peers, we are granted permission to share these findings with a broader audience – to

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