Alex Westman

Full-time collector of part-time hobbies | long-read sequencing enthusiast @pacbio | All opinions are my own

[Jake @jjminich]

Super stoked to be attending and presenting updates on our #longread #metagenomics work at @PacBio #PacBioPRISM

[Danilo Dubocanin @DubocDan]

I’m excited to share the first manuscript out of my PhD work with @NAltemose, in which we describe FiberFold: a deep learning tool that predicts cell-type-specific and haplotype-specific 3D genome organization from a single experiment!
https://t.co/FwJldYnCGe 1/

[Sam Modlin @sam_modlin]

1/ 🎉 Excited to share our lab’s latest work: “Intercellular mosaic methylation in fast-growing Mycobacterium tuberculosis clinical isolates,” now published in @NAR_Open Molecular Medicine: https://t.co/eGuEUbYLrZ

Huge thanks to my co-first author, Maryam Ahmadi Jeshvaghane!

[Luis E. Valentín-Alvarado @luisarchaeota]

If you're at #ASMicrobe, don't miss the poster from Dan on high-quality MAGs from wetland soil. Collaboration between @PacBio and @BanfieldLab . Stop by to learn more!

[bioRxiv Bioinfo @biorxiv_bioinfo]

Standardized Nomenclature and Reporting for PacBio HiFi Sequencing and Analysis of rAAV Gene Therapy Vectors https://t.co/E6LPeNLkJm #biorxiv_bioinfo

[Adam Ameur @_adameur]

Wow.. 55.4 million full-length reads from our first Kinnex bulk RNA run! This is from just one @PacBio Revio SMRT cell. What kind of throughput are others seeing?

[Lili Milani @MilaniLili]

We are so excited to start exploring #longread sequencing of 10,000 Estonian genomes with @PacBio
🧬improved genotype imputation reference panel
🧬more precise #pharmacogenetics
🧬actionable genetic findings for #personalizedmedicine @ESTbiobank
https://t.co/s92iLj59c8

[Alex Westman @AlexWestman4]

@jewilki How much for one of those cows?

[Lior Pachter @lpachter]

@mbeisen Why did you stop at PCA? This is much better visualized with UMAP.

[Javier Santoyo @jsantoyo]

🔥 Incredible results from our @PacBio #Revio🧬🙌!
📢4 SMRT cells with over 100 Gb of #HiFi reads, totaling 438 Gb!
Kudos to Caitlin, Helen, and Rob for this amazing achievement! 🎉
Get in touch with @edgenome for groundbreaking Long-Read Sequencing! 🚀🧬
@SBSatEd @UoETechnicians

[Liz Tseng @Magdoll]

Spatial transcriptomics at isoform resolution reveals isoform switching events in heart tissue post myocardial infarction - here's a use case of combining 10x Visium with the @PacBio MAS-Seq single-cell kit. No short reads needed. If you missed the story - the webinar recording is now up! https://t.co/Pj7b9KzbiS

[Alex Westman @AlexWestman4]

@jewilki I learn so much about Rhode Island from your run posts

[Iceland 🇮🇸  @todayiniceland]

A second Sundhnúkagígaröðin eruption that occurred at 06:05am yesterday morning (8th February 2024) 🌋

[GenomeWeb @GenomeWeb]

Germany's Bioscientia Launches Clinical PacBio HiFi WGS Test to Diagnose Sensory Disorders. Currently being offered to patients with certain sensory disorders as a routine clinical test, the company plans to expand the assay to other genetic disorders. https://t.co/SyKXsPaArW

[Kevin Kocot @kmkocot]

Interested in low-input genomics? @RNickellaus et al. posted a pre-print showing a simple MDA-based method to get HiFi reads and nice assemblies from e.g., 1/2 C. elegans with negligible coverage bias or chimeras. @fez_nhm @UaDeptBSC @QIAGEN @PacBio
https://t.co/DqoQMo9FcW

[Alex Westman @AlexWestman4]

@jewilki @PacBio That’s a fun 9 hole track

[Alex Westman @AlexWestman4]

MAGnificent!!

[Zymo Research @ZymoResearch]

Zymo Research has introduced its Metagenome Assembly Service, leveraging @PacBio HiFi sequencing to enable precise analysis and reconstruction of metagenomes from assembled genomes or genome bins.

Read the PR: https://t.co/Z4A4CLN2oP

Learn more: https://t.co/VUj7NnBQpv

[Alex Westman @AlexWestman4]

This is so cool. Anyone who’s been in my earshot the last two years has heard me rant about a spatially resolved isoform study.

Excited to see this out in the literature, and see what the field can do with these two techniques

[Camilla Engblom @camillaengblom]

And Spatial VDJ is out! More to follow, but for now, joy and gratitude for the privilege to work with the wonderful @thrane_kim @Qirongliiin @Jeff_Mold @FrisenJonas @joalunatkthse and many more collaborators. @karolinskainst @scilifelab @KTHuniversity https://t.co/3LujYGsCUA

[Alex Westman @AlexWestman4]

One cord of wood for those cold San Diego winters

[Alex Westman @AlexWestman4]

This paper 💯

"the ability to detect genetic and non-genetic sources of heterogeneity in cancer subclones using only one data modality is just too good"

[Arthur Dondi @ArthurDondi]

Delighted to present our full-length scRNA-seq study on ovarian cancer patients, in collaboration with the University Hospital Basel @labfranz ! https://t.co/I7LnLDd2gr

Can we simultaneously detect isoform-level gene expression, mutations and gene fusions in cancer cells? 1/