Biology subjects

Murray, D.

Publications and source records attributed to Murray, D..

3 recordsLinked to original sources

bioRxiv2018

Gender and international diversity improves equity in peer review

The fairness of scholarly peer review has been challenged by evidence of disparities in publication outcomes based on author demographic characteristics. To assess this, we conducted an exploratory analysis of peer review outcomes of 23,876 initial submissions and 7,192 full submissions that were submitted to the biosciences journal eLife between 2012 and 2017. Women and authors from nations outside of North America and Europe were underrepresented both as gatekeepers (editors and peer reviewers) and authors. We found evidence of a homophilic relationship between the demographics of the gatekeepers and authors and the outcome of peer review; that is, there were higher rates of acceptance in the case of gender and country homophily. The acceptance rate for manuscripts with male last authors was seven percent, or 3.5 percentage points, greater than for female last authors (95% CI = [0.5, 6.4]); this gender inequity was greatest, at nine percent or about 4.8 percentage points (95% CI = [0.3, 9.1]), when the team of reviewers was all male; this difference was smaller and not significantly different for mixed-gender reviewer teams. Homogeny between countries of the gatekeeper and the corresponding author was also associated with higher acceptance rates for many countries. To test for the persistence of these effects after controlling for potentially confounding variables, we conducted a logistic regression including document and author metadata. Disparities in acceptance rates associated with gender and country of affiliation and the homophilic associations remained. We conclude with a discussion of mechanisms that could contribute to this effect, directions for future research, and policy implications. Code and anonymized data have been made available at https://github.com/murrayds/elife-analysis\n\nAuthor summaryPeer review, the primary method by which scientific work is evaluated, is ideally a fair and equitable process in which scientific work is judged solely on its own merit. However, the integrity of peer review has been called into question based on evidence that outcomes often differ between male and female authors, and for authors in different countries. We investigated such disparities at the biosciences journal eLife by analyzing the demographics of authors and gatekeepers (editors and peer reviewers), and peer review outcomes of all submissions between 2012 and 2017. Outcomes were more favorable for male authors and those affiliated with institutions in North America and Europe; these groups were also over-represented among gatekeepers. There was evidence that peer review outcomes were influenced by homophily --a preference of gatekeepers for manuscripts from authors with shared characteristics. We discuss mechanisms that could contribute to this effect, directions for future research, and policy implications.

scientific communication and education↗

bioRxiv2018

Systematic Elucidation and Validation of OncoProtein-Centric Molecular Interaction Maps

The largely incomplete and tissue-independent nature of cancer pathways represents a key limitation to the ability to elucidate mechanistic determinants of cancer phenotypes and to predict adaptive response to targeted therapy. To address these challenges, we propose replacing canonical cancer pathways with a more accurate, comprehensive, and context-specific architecture - dubbed a Protein-Centric molecular interaction Map (PC-Map) - representing modulators, effectors, and cognate binding-partners of any oncoprotein of interest. To reconstruct these complex molecular architectures de novo, we introduce a novel OncoSig algorithm. Validation of a lung adenocarcinoma specific (LUAD) KRAS-centric PC-Map recapitulated known KRAS biology and, more critically, identified a novel repertoire of proteins eliciting synthetic lethality in KRASG12D LUAD organoid cultures. Showing the generalizable nature of the algorithm, we elucidated PC-Maps for ten recurrently mutated oncoproteins, including KRAS, in distinct tumor contexts. This revealed a highly context-specific nature of cancers regulatory and signaling architectures to an unprecedented degree of resolution.

systems biology↗

bioRxiv2016

THE IDENTIFICATION OF SOURCE AND VECTOR OF A PROLIFIC MARINE INVADER

The source and vector of an introduced species inform its ecological and evolutionary history and may guide management that seeks to prevent future introductions. Surprisingly, few studies have successfully used genetic tools to independently inform the specific source and pathway of biological invasions. The ecological history of many introduced species, including their origins and vectors, is often based on suppositions or educated guesses. Here, we used mitochondrial and microsatellite genotyping to trace the invasion of the Asian seaweed Gracilaria vermiculophylla (Rhodophyta) along the three coastlines of the Northern Hemisphere to which it has been introduced: the western coast of North America, eastern coast of the United States and the coasts of Europe and northwest Africa. Analyzing 37 native and 53 introduced sites, we identified the Pacific coastline of northeastern Japan as the ultimate source of the Northern Hemisphere invasion. Coincidentally, most exports of the oyster Crassostrea gigas historically originated from this region and both species often grow in close proximity. Based on genetic signatures, each of the three coastlines likely received thalli directly from Japan, as well as material from another introduced coastline (i.e., a secondary invasion). Our ability to document a source region, which was enabled by a robust sampling of locations and loci that previous studies lacked, reflected strong phylogeographic structure along native coastlines. We suggest Gracilaria vermiculophylla is an important representative example of many species likely exported out of Japan by the oyster trade and its genetic signatures that may be a hallmark of oyster introduction legacies.

evolutionary biology↗