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abess

Fast Best-Subset Selection Library

adhoc_covid

alcon.coevolution

Host-parasite coevolutionary simulation model based on the Alcon blue (Phengaris Alcon) and its two obligatory hosts (Gentiana pneumonanthe & a Myrmica sp.)

ants-task-partitioning-abm

assemblies-of-putative-sars-cov2-spike-encoding-mrna-sequences-for-vaccines-bnt-162b2-and-mrna-1273

RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.

best-subset

Comparisons between best subset selection and other popular estimators for sparse regression

covid-19

Covid-19 epidemiology - data and analysis

covid-19-excess-deaths-tracker

Source code and data for The Economist's covid-19 excess deaths tracker

covid-19-the-economist-global-excess-deaths-model

The Economist's model to estimate excess deaths to the covid-19 pandemic

covid19.sgene.utla.rt

Local area reproduction numbers and S-gene target failure.

covidbe_analysis

Descriptive summaries of covid data for Belgium

emmeans

Estimated marginal means

epi-mcmc

Scripts for estimating and visualizing epidemiological modeling of an epidemic (developed for COVID-19)

export

R package for streamlined export of graphs and data tables.

gcmspro

R package for processing GCMS data

glmnet-benchmark

gpumagic

An R interface to write OpenCL functions

huanan-environmental

Fork of original repository with some binomial GLMM tensor spline fits added + heatmap & biplot of metagenomic reads

insight

:crystal_ball: Easy access to model information for various model objects

introduction-to-machine-learning

A document covering machine learning basics. 🤖📊

l0adri

R package to fit L0 penalized GLM models via an iterative adaptive ridge regression procedure

l0ara

Sparse Generalized Linear Models with L0 Approximation for Feature Selection

labelpepmatch.r

labelpepmatch

lineageexplorer

Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline fits

mandelexplorer

Interactive Shiny Mandelbrot set explorer in R & Rcpp with fast animated zooms

marginaleffects

An R package to compute marginal effects, adjusted predictions, contrasts, and marginal means for a wide variety of models

mocy

MOCY Mortality Cycles: Timeseries of weekly death counts and covariates by country, sex and age

nnet2

Fork of the nnet CRAN repository, with faster calculation of Hessian via Kronecker products & some Rcpp code — Feed-Forward Neural Networks and Multinomial Log-Linear Models. Homepage: http://www.stats.ox.ac.uk/pub/MASS4/

parent_of_origin_expression_bumblebee

parglm

R package that provides a parallel estimation method for generalized linear models