Associate Professor @CincyChildrens Epidemiology|Microbiome|Biostatistics|Predictive Modeling|Views are my own
Joined September 2011
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WHERE WILL HER GO? youtube.com/shorts/R_e3tsRsE… via @YouTubesqwssvz wet few 12222222222
Nicholas Ollberding retweeted
In mice, pups with a #microbiome fortified w/ #butyrate had reduced risk of #biliaryatresia Study @NatureComms nature.com/articles/s41467-0… Congrats @bezerratweet @DrRomesPhD @Nick10243 and team! View our blog: scienceblog.cincinnatichildr…
Nicholas Ollberding retweeted
Lots of #COVID19 cases in Greater #Cincinnati today - highest daily total since winter. Highest case rate (per 100,000 on a 7-day moving average) is now among youth 0-19yo. #GetVaccinatedNow & #MaskUp for yourself, your neighbors, and our children.
#DeltaVariant #schoolreopening
Nicholas Ollberding retweeted
What started as a 1 day side project turned into a nearly 3 year long lab analysis. "Microbiome differential abundance methods produce disturbingly different results across 38 datasets" biorxiv.org/content/10.1101/…
My lab is going to conduct a 1 day hackathon to compare methods for identifying differential abundances of microbes in microbiome studies: List of methods to test are: t-test, Wilcoxon-Mann-Whitney, ALDEx2, DeSeq2, LEFse, ANCOM, Gneiss, corncob, Maaslin. Did we miss any? #16S
Nicholas Ollberding retweeted
bioBakery 3 is out in @eLife! It describes our latest versions of MetaPhlAn 3, HUMAnN 3, StrainPhlAn 3, PanPhlAn 3 and more from @cibiocm and @hutlab ! Huge thanks to so many but especially to Francesco Beghini @chocophlan and Lauren McIver! elifesciences.org/articles/6…
Nicholas Ollberding retweeted
The latest mSystems brings to the public a new interactive web tool for visualizing large-scale phylogenetic trees - Read all about it:
jacobsschool.ucsd.edu/news/r…
@IBMResearch #mSystemsJ @ASMicrobiology #Phylogenetic @qiime2 #Python
Nicholas Ollberding retweeted
Submit your responses now for the National Microbiome Data Collaborative survey for users: bit.ly/nmdc_survey.
Nicholas Ollberding retweeted
#Statistics thought of the day: if you are not certain how to transform a continuous dependent variable to make assumptions work (e.g. normality of residuals) use a semiparametric method that is transformation-invariant, e.g. proportional odds/hazard model. #rmscourse #bbrcourse
Nicholas Ollberding retweeted
Metalign: efficient alignment-based metagenomic profiling via containment min hash genomebiology.biomedcentral.… github.com/nlapier2/Metalign
Nicholas Ollberding retweeted
New R package rmsb: Bayesian counterpart to the rms (regression modeling strategies) package now on CRAN. Uses pre-compiled @mcmc_stan code. Information including lots of examples at hbiostat.org/R/rmsb #rmscourse @vandy_biostat @VUDataScience
Nicholas Ollberding retweeted
In addition, you can now also set discrete colour/fill scale defaults via a vector (or list) of colour codes. Super useful for providing colour-blind safe defaults! #rstats
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Nicholas Ollberding retweeted
Woohoo -- I finally carved out some time today to make a Wiki to answer the most common questions I get about my #R #rstats package `breakaway` 🥳😻🎀
Check it out here:
github.com/adw96/breakaway/w…
#rstats #microbiome #microbialdiversity
Nicholas Ollberding retweeted
HUMAnN 3.0 (alpha) is out! Functionally profile #metagenomes or #metatranscriptomes at species-level resolution. Designed in tandem with MetaPhlAn 3.0, more options for fine-tuning tiered search, 2x the species #pangenomes and 3x the gene families. Enjoy!
huttenhower.sph.harvard.edu/…
Nicholas Ollberding retweeted
powmic: #Rstats pkg for power assessment in #microbiome case-control studies academic.oup.com/bioinformat… github.com/lichen-lab/powmic
Nicholas Ollberding retweeted
If you like using propensity matching, think again. See
pubmed.ncbi.nlm.nih.gov/1805… or proceedings.mlr.press/v9/guo… by @PhilDawid or gking.harvard.edu/publicatio… by @kinggary
Nicholas Ollberding retweeted
Got observational data with time-varying treatments and confounders?
Want to estimate the effects of sustained treatment
strategies?
Then you'll enjoy this gentle introduction to the gfoRmula package in #rstats.
Led by Sean McGrath & Victoria Lin
cell.com/patterns/pdf/S2666-…
Nicholas Ollberding retweeted
David is producing clean thorough tidyverse versions of my book exercises. Seems useful for you tibblers.
Week 5, part II: once we have HMC in our toolkit, we must take care of our chains. To get some practice doing it while plotting interaction effects, here it's Week 5 homework. As always, @rlmcelreath's metaphors and teaching creativity are amazing #rstats
david-salazar.github.io/2020…
Nicholas Ollberding retweeted
Question from our journal club today. Microbiome sequence data is widely accepted as compositional. So when does it become compositional? At post-extraction, post-PCR, or post-sequencing? #coda
Nicholas Ollberding retweeted
GraphBin: Refined binning of metagenomic contigs using assembly graphs academic.oup.com/bioinformat… github.com/Vini2/GraphBin
