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1. iGenomics: Comprehensive DNA sequence analysis on your Smartphone

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   Palatnick, Aspyn; Zhou, Bin; Ghedin, Elodie; Schatz, Michael_C (December 2020, GigaScience)

   Abstract BackgroundFollowing the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is on a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available. ResultsiGenomics is the first comprehensive mobile genome analysis application, with capabilities to align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets of viral and bacterial genomes and show that iGenomics has performance comparable to the popular BWA-MEM/SAMtools/IGV suite, without necessitating a laptop or server cluster. ConclusionsiGenomics is available open source (https://github.com/stuckinaboot/iGenomics) and for free on Apple's App Store (https://apple.co/2HCplzr). 

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2. Double Your Variance, Dirtify Your Bayes, Devour Your Pufferfish, and Draw your Kidstrogram

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   Meng, Xiao-Li (October 2022, The New England Journal of Statistics in Data Science)

   This article expands upon my presentation to the panel on “The Radical Prescription for Change” at the 2017 ASA (American Statistical Association) symposium on A World Beyond $p<0.05$. It emphasizes that, to greatly enhance the reliability of—and hence public trust in—statistical and data scientific findings, we need to take a holistic approach. We need to lead by example, incentivize study quality, and inoculate future generations with profound appreciations for the world of uncertainty and the uncertainty world. The four “radical” proposals in the title—with all their inherent defects and trade-offs—are designed to provoke reactions and actions. First, research methodologies are trustworthy only if they deliver what they promise, even if this means that they have to be overly protective, a necessary trade-off for practicing quality-guaranteed statistics. This guiding principle may compel us to doubling variance in some situations, a strategy that also coincides with the call to raise the bar from $p<0.05$ to $p<0.005$ [3]. Second, teaching principled practicality or corner-cutting is a promising strategy to enhance the scientific community’s as well as the general public’s ability to spot—and hence to deter—flawed arguments or findings. A remarkable quick-and-dirty Bayes formula for rare events, which simply divides the prevalence by the sum of the prevalence and the false positive rate (or the total error rate), as featured by the popular radio show Car Talk, illustrates the effectiveness of this strategy. Third, it should be a routine mental exercise to put ourselves in the shoes of those who would be affected by our research finding, in order to combat the tendency of rushing to conclusions or overstating confidence in our findings. A pufferfish/selfish test can serve as an effective reminder, and can help to institute the mantra “Thou shalt not sell what thou refuseth to buy” as the most basic professional decency. Considering personal stakes in our statistical endeavors also points to the concept of behavioral statistics, in the spirit of behavioral economics. Fourth, the current mathematical education paradigm that puts “deterministic first, stochastic second” is likely responsible for the general difficulties with reasoning under uncertainty, a situation that can be improved by introducing the concept of histogram, or rather kidstogram, as early as the concept of counting. 

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3. Your peers are your pillars

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   Maisel, Katharina (October 2021, Science)
4. Individual Development Plans, your strengths, your career, and your professional identity

   Kuniyoshi, C.Y. (January 2021, 2929 SACNAS The National Diversity in STEM Virtual Conference)

   null (Ed.)

   Individual Development Plans (IDPs) have been used to support the career and professional development of graduate students across disciplines. This interactive session focuses on how IDPs can help you build your skills, form your professional identity, and take control of your career through an iterative process of self‐assessment, career exploration, decision making and goal setting. To provide an introduction to the IDP process attendees will be able to take a self‐assessment to learn about their particular strengths and begin to target their strengths toward their professional goals. Additionally a co‐developer and researcher of IDP platforms will highlight the aspects that can help your IDP be more effective than others. 

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5. Hide Your Distance: Privacy Risks and Protection in Spatial Accessibility Analysis

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   Fan, Liyue; Bonomi, Luca (November 2023, ACM)