Open collaborative writing with Manubot

Himmelstein, Daniel S.; Rubinetti, Vincent; Slochower, David R.; Hu, Dongbo; Malladi, Venkat S.; Greene, Casey S.; Gitter, Anthony

doi:10.1371/journal.pcbi.1007128

Cited by 60 publications

(56 citation statements)

References 69 publications

(69 reference statements)

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“…We conducted our analyses using the R language (version 4.0.1), the cmprsk (version 2.2-10) package 66 implementation of the Fine-Gray model, MySQL version 5.6, and tidyverse meta-package version 1.1.2. The manuscript was written openly on GitHub using Manubot 67 .…”

Section: Methodsmentioning

confidence: 99%

Associations between blood type and COVID-19 infection, intubation, and death

2020

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The rapid global spread of the novel coronavirus SARS-CoV-2 has strained healthcare and testing resources, making the identification and prioritization of individuals most at-risk a critical challenge. Recent evidence suggests blood type may affect risk of severe COVID-19. Here, we use observational healthcare data on 14,112 individuals tested for SARS-CoV-2 with known blood type in the New York Presbyterian (NYP) hospital system to assess the association between ABO and Rh blood types and infection, intubation, and death. We find slightly increased infection prevalence among non-O types. Risk of intubation was decreased among A and increased among AB and B types, compared with type O, while risk of death was increased for type AB and decreased for types A and B. We estimate Rh-negative blood type to have a protective effect for all three outcomes. Our results add to the growing body of evidence suggesting blood type may play a role in COVID-19.

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Section: Methodsmentioning

confidence: 99%

Associations between blood type and COVID-19 infection, intubation, and death

2020

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“…Specifically, the race categories include White, Black or African American, American Indian or Alaska Native, Asian, Native Hawaiian or Other Pacific Islander, Other race, and Two or more races [34], and ethnicity categories include Hispanic/Latino or Not Hispanic/Latino [35]. We made race and ethnicity predictions of the surnames of US-affiliated authors and honorees using the R package wru, which implements methods described in Imai and Khanna [36]. wru uses similar race/ethnicity categories as in the Census but groups American Indian or Alaska Native and Native Hawaiian or Other Pacific Islander to form the Other category.…”

Section: Methodsmentioning

confidence: 99%

Analysis of ISCB honorees and keynotes reveals disparities

Himmelstein

Hippen

et al. 2020

Preprint

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Professional societies and their conferences provide an important venue for disseminating scienti c knowledge. Delivering a keynote for or being named a fellow by an international society is a major recognition. Do such recognitions re ect the composition of the eld of bioinformatics? We compiled a list of 412 International Society for Computational Biology honorees (75 fellows and 337 keynote speakers). To assess the composition of senior researchers in the eld, we analyze the names and a liations of corresponding authors in leading bioinformatics journals. Comparing to the distribution based on names and a liations of honorees, we looked for disparities in gender, country of a liation, race, and name-origin. Name-origin predictions were created using a neural network trained on 700,000 name-nationality pairs mined from Wikipedia. The proportion of female honorees has kept pace with increasing levels of female authorship, but neither has yet to reach gender parity. However, we noticed a striking geographic disparity where the proportion of honorees with an a liation in the United States was 1.6-fold greater compared to eld-speci c senior authors. In total, we estimate the U.S. received 85 more honorees than would be expected from randomly selecting honorees from senior authors. Almost half of the excess in U.S. honorees was accounted for by a de cit of 41 honoree slots from China, France, and Italy. Furthermore, within the U.S., we identify racial disparities with an excess of white honorees and a depletion of Asian honorees. This pattern replicated globally, where we nd names of East Asian origin have been persistently underrepresented among ISCB honorees. Early indications suggest the ICSB has taken note of our ndings by selecting more diverse honorees.

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“…This paper was collaboratively written with Manubot [87], and supplementary information including demonstration and benchmarking environments descriptions and walk-through can be seen on GitHub at https://github.com/apeltzer/eager2-paper/ and the directory.…”

Section: Data and Software Availabilitymentioning

confidence: 99%

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

Yates

Lamnidis

Borry

et al. 2020

Preprint

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The broadening utilisation of ancient DNA (aDNA) to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned pipeline for the analysis of ancient genomic data. nf-core/eager builds on existing ideas and concepts introduced in the original EAGER pipeline, and improves various aspects of the analysis procedure by employing computational frameworks such as Next ow and nfcore. The pipeline aims to address three main themes: accessibility and adaptability to di erent research groups and their computing con gurations, reproducibility to ensure robust analytical standards in the eld, and updating the EAGER pipeline to the latest routine ancient genomic practises. This new version of EAGER has been developed within the nf-core initiative, to ensure high quality software development and maintenance support; contributing to a long-term lifecycle for the pipeline. nf-core/eager will assist in ensuring that ancient DNA sequencing data can be used by a diverse range of research groups and elds.

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Open collaborative writing with Manubot

Cited by 60 publications

References 69 publications

Associations between blood type and COVID-19 infection, intubation, and death

Associations between blood type and COVID-19 infection, intubation, and death

Analysis of ISCB honorees and keynotes reveals disparities

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

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