Andrew Gross

Bioinformatics scientist working on clinical WGS. Avid eater of eats and see-er of sights. Opinions my own.

[Anne Carpenter, PhD @DrAnneCarpenter]

Students already have a PI and reviewers, do they really need another out of touch entity suggesting new experiments they should do? 😄

[Andrew Gross @GrossScientist]

@gsherloc https://t.co/vm22hpTf1J

[Fritz Sedlazeck @sedlazeck]

(4/4) Furthermore with @egor_dolzhenko & @PacBio we contributed to TRGT a new tandem repeat caller. Here we can characterize also pathogenic repeat lengths, visualize them and compare them with our generated DB (Adam E.). This should make TR calling easier and more reliable!

[Andrew Carroll @acarroll_ATG]

Excited to share this analysis of @ElemBio’s data (and their new Cloudbreak chemistry). We see accuracy advantages in Element data, especially at 20x-30x coverages and in homopolymers and repeats. Longer sequening inserts can further improve recall through hard genome regions.

[Fritz Sedlazeck @sedlazeck]

Finally, Structural Variation calls is available for TOPMed across 138,134 individuals is out. Huge work by so many! This allows the study of SV across tiny AF fractions, identifies new hotspots, & new associations are shown! @BCM_HGSC @BCMFromtheLabs
https://t.co/cbBwZKX4zJ

[Nils Homer @nilshomer]

2. At least two very senior ICs (10-20+ years in industry).

These folks have solved hard problems, maintained their own solutions for years, and have learned effective habits. Above all they are competent. Learn from them. Be skeptical like them.

[Element Biosciences @ElemBio]

Introducing a $200 genome on the AVITI™ Sequencing System, available today. We’re driving down costs and redefining what a benchtop sequencer can do. Element empowers labs everywhere to produce their own high-quality data. Read our press release: https://t.co/aC388jmsOa
#jpm2023

[Scripps Institution of Oceanography @Scripps_Ocean]

A study led by Scripps alum & @scripps_climate postdoc @MangroveMatt shows how stable organic matter stocks are in old, deep #mangrove peat deposits in Baja California Sur. Mangroves & coastal #BlueCarbon ecosystems sequester more carbon per unit area than most ecosystems🌎

[Sean J. Taylor @seanjtaylor]

I can’t understand how this can sound so ridiculous and yet be totally reasonable advice

Credit: https://t.co/I9bRJacEWe

[Andrew Gross @GrossScientist]

@sbarnettARK @arminscheben @AlbertVilella @igvteam Option 1) systematic benchmarking on multiple assays with fully transparent methods to avoid the appearance of manipulation in favor of your tech, Option 2) show an IGV shot and let people see the data. Not only is 1) more biased, but it takes a lot of time to do right.

[Olivier Harismendy @00livier]

Ever wondered if Polygenic Risk Scores can help predict outcome after a pre-cancer diagnosis ? Check out our new preprint at https://t.co/OuRKArXIJD. #AACR22

[Genomics Cow @GenomicsCow]

Software for clinical variant interpretation doesn’t scale globally. I don’t even know if it scales regionally either.

[Keith Robison @OmicsOmicsBlog]

Element Unveils AVITI https://t.co/ZhI0zLOUhr @ElemBio

[Reply All @replyall]

Morning! We have a new episode for you today. https://t.co/CtlwCEB8Nb

[Andrew Gross @GrossScientist]

SARS-CoV-2 monitoring at three sewersheds of different scales and comp... https://t.co/P6Rtx5LjDA

[Luis B Barreiro @LB_Barreiro]

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios | bioRxiv https://t.co/5rZuttd8kO

[Mike Eberle @MikeEberle]

If you are a user of ExpansionHunter and want to visualize the read alignments behind the genotype calls, check out this paper led by @egor_dolzhenko REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats https://t.co/4TPnqYpJAI

[Andrew Gross @GrossScientist]

@gabepratt Feel like I’m glass 10% full here and you are glass 90% empty. Rock bottom sucked but I still had plenty of good times there.

[Andrew Gross @GrossScientist]

😲 many good evenings started with “I guess we can just go to Rock Bottom”

[Michael A. Taffe @effatma]

End of an era for those who passed time at UCSD over the years.