Marcus Fedarko

Please give this petition a read and sign it; this is an abhorrent situation at UCSD.

In case anyone still thought this was about "graffiti"—UC is clearly misusing their private police to target unions. Last night they searched a member’s home for: “Evidence of membership or affiliation with any university organization […] to include any reference to "UAW"

pre-print is on arxiv! 🥰 tl;dr there are ways in which people can be systematically, algorithmically blocked from achieving their desired predicted outcome (bad). soln? recourse and exploration methods as standard practice (good!) arxiv.org/abs/2305.09035

Our methods are contained in strainFlye (github.com/fedarko/strain…), an open-source Python pipeline. It's installable through bioconda, and we have a detailed tutorial up at nbviewer.org/github/fedarko…. Thank you to co-authors @MishaKolmogorov and Pavel Pevzner for their help! (3/3)

This is a chunky paper that details many new (and not-so-new!) approaches to the analysis of these mutations. For example, we propose the idea of performing FDR estimation on a set of mutation calls in a contig—done by borrowing the target-decoy approach from proteomics. (2/3)

Just before the end of 2022: we recently published a paper in @genomeresearch on some new methods for analyzing (calling, phasing, etc.) rare mutations in metagenomes assembled using long & accurate (e.g. PacBio HiFi) reads. Please check it out at genome.cshlp.org/content/32/11-…! (1/3)

Right now at UCSD, academic workers are rallying in support of Li Jiang, an international postdoc whose appointment is being terminated while she is 7 months pregnant, threatening her visa and her healthcare. We demand justice.

New Research: Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data frontiersin.org/articles/10.33… #Bioinformatics

A neural network method for rapid and accurate genotyping of variable number tandem repeats from large whole genome sequencing datasets. @mdbakhtiari @mgymrek @bvhalldorsson @ucsd_cse @UCSDJacobs nature.com/articles/s4146…

@BojingJia Thanks Blair!!! :D

@mwfedarko GO MARCUS

It's very exciting to see this work published, and it's been a lot of fun working on it! 🌲🌲🌲

@jongsanders @BananaWithACh @satriaphd Hi @BananaWithACh - I believe Kalen (whom I don't think is on twitter) put the bulk of the work into the shaders. The drawing code is up at github.com/biocore/empres…. I've found webglfundamentals.org to be really helpful; as a tutorial that might be a good place to start :)

A lot of people have contributed to this software/paper—the work's been led by Kalen Cantrell, with @yoshikivb, @gibsramen, @mcdonadt, Yimeng Yang, Thant Zaw, @MehrbodEstaki, @theladybeck, @zhuqiyun, @erfansayyari, @jamietmorton, @anupriya_trip, and a smorgasbord of other folks.

Source code, installation instructions, and docs are available at github.com/biocore/empress; visualizations of example trees shown in the paper available at github.com/knightlab-anal….

We just published a preprint on EMPress, a project ~3 years in the making! TLDR, it's another interactive tree viewer for web browsers—but with some useful new features for community data analysis, eg integration with ordinations. Plus it can handle trees with over 500k nodes. 🌳

Our paper on Compositional Tensor Factorization (CTF) an extension of Robust Aitchison PCA that allows for the factorization of repeated-measure data is out now in @NatureBiotech! nature.com/articles/s4158…

Bacteria modify mucosal layer glycans, altering the ability of SARS-CoV-2 to bind human cells. Mucosal glycan trimming bacteria may play a critical role in non-modifiable predisposing factors for COVID-19 such as age. Pre-print biorxiv.org/content/10.110…

I pledge to continue opposing racism and hate [and all forms of inequality]. We are all human and need and want the same things! I nominate 5 others to do the same. @JoshuaProfio @jamietmorton @gibsramen @bkell1123 @mwfedarko

Check out @mwfedarko 's awesome paper on visualizing differentially abundant microbes! @cameronmartino @lisa55asil @gibsramen @lisa55asil @jjminich @KnightLabNews academic.oup.com/nargab/article…

A preprint on Qurro, our new visualization tool for exploring 'omic datasets, is ready! Code/docs/demos at github.com/biocore/qurro. (Thanks to @cameronmartino @jamietmorton @gibsramen @lisa55asil @jjminich @KnightLabNews and a few other folks not on Twitter for help with this!)