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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Xie BMCBioinfo21 22.png|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Tomich Sustain23 15-8.png|260px]]</div>
'''"[[Journal:Popularity and performance of bioinformatics software: The case of gene set analysis|Popularity and performance of bioinformatics software: The case of gene set analysis]]"'''
'''"[[Journal:Why do we need food systems informatics? Introduction to this special collection on smart and connected regional food systems|Why do we need food systems informatics? Introduction to this special collection on smart and connected regional food systems]]"'''


Gene set analysis (GSA) is arguably the method of choice for the functional interpretation of omics results. This work explores the popularity and the performance of all the GSA methodologies and software published during the 20 years since its inception. "Popularity" is estimated according to each paper's citation counts, while "performance" is based on a comprehensive evaluation of the validation strategies used by papers in the field, as well as the consolidated results from the existing benchmark studies. Regarding popularity, data is collected into an online open database ("GSARefDB") which allows browsing bibliographic and method-descriptive [[information]] from 503 GSA paper references; regarding performance, we introduce a repository of [[Jupyter Notebook]] [[workflow]]s and Shiny apps for automated benchmarking of GSA methods (“GSA-BenchmarKING”). After comparing popularity versus performance, results show discrepancies between the most popular and the best performing GSA methods. ('''[[Journal:Popularity and performance of bioinformatics software: The case of gene set analysis|Full article...]]''')<br />
Public interest in where food comes from and how it is produced, processed, and distributed has increased over the last few decades, with even greater focus emerging during the [[COVID-19]] [[pandemic]]. Mounting evidence and experience point to disturbing weaknesses in our food systems’ abilities to support human livelihoods and wellbeing, and alarming long-term trends regarding both the environmental footprint of food systems and mounting vulnerabilities to shocks and stressors. How can we tackle the “wicked problems” embedded in a food system? More specifically, how can convergent research programs be designed and resulting knowledge implemented to increase inclusion, sustainability, and resilience within these complex systems ... ('''[[Journal:Why do we need food systems informatics? Introduction to this special collection on smart and connected regional food systems|Full article...]]''')<br />
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Revision as of 17:11, 22 April 2024

Fig1 Tomich Sustain23 15-8.png

"Why do we need food systems informatics? Introduction to this special collection on smart and connected regional food systems"

Public interest in where food comes from and how it is produced, processed, and distributed has increased over the last few decades, with even greater focus emerging during the COVID-19 pandemic. Mounting evidence and experience point to disturbing weaknesses in our food systems’ abilities to support human livelihoods and wellbeing, and alarming long-term trends regarding both the environmental footprint of food systems and mounting vulnerabilities to shocks and stressors. How can we tackle the “wicked problems” embedded in a food system? More specifically, how can convergent research programs be designed and resulting knowledge implemented to increase inclusion, sustainability, and resilience within these complex systems ... (Full article...)
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