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IT's OFFICIAL: Oracle Buys Cerner prn.to/33M1mcn "Oracle intends to maintain and grow Cerner's community presence, including in the Kansas City area, while utilizing Oracle's global footprint to reach new geographies faster."

PSA for everyone out there using Python 3 to help aggregate their final grades. 🚨🚨🚨 round() ROUNDS TO THE NEAREST EVEN NUMBER 🚨🚨🚨 If that doesn't mean anything to you, let me give some examples: round(1.5)==2 round(2.5)==2 round(3.5)==4 round(4.5)==4 🤬

Kelvin Liu and Michael Schatz touted HiFi at todays #BoG22 PacBio session - no Invitae update but Mike highlighted that "the new input for bioinformatics tools is a set of near-perfect genomes". He also showed a neat pangenome pipeline: wfmash -> OrthoFinder -> genespace -> clinker

So excited about our new Medications feature in iOS 16 and watchOS 9! Create a medications list, set up reminders, and receive critical interaction alerts. It’s even easier when you use the Health Records feature to connect to your health system to download your current med list!

In iOS 16 we're making it easier to export a copy of your health records to share with those you trust. From the Health app, simply go to the Health Records section of the Browse tab and tap on "All Records" and then "Export PDF"

We've made a draft human pangenome! 47 haplotype-resolved assemblies, two reference genomes, and five pangenome graphs!

A nice trick to convert nucleotide ASCII chars (A,C,G,T,a,c,g,t) to integers (0,1,2,3): 0b11 & (bp >> 2 ^ bp >> 1) vastly outperforms using char:int maps and very handy for some high-performance bioinformatics tasks.

A misleading paper in Science Magazine just came out talking about how a single gene can increase rice yield by 41-68%. As a (wanna-be) plant breeder, I’m here to tell you why this study is misleading, and we can’t “solve” yield through single genes 🧵 science.org/doi/10.1126/sc…

Figure 3 shows the example through the very complicated and undoubtedly very important but poorly understood HLA Class II region in MHC

We've released the ESM2 protein language models up to 15B parameters today. Available now at the FAIR/@MetaAI Protein Team ESM repo: github.com/facebookresear…

DeepConsensus is published! You can use this link if you need - rdcu.be/cUMIx Excited to see transformers used for DNA error correction, and scientists getting more out of their sequencing instruments.

Ragnar {Groot Koerkamp} 🦋 and I extended the seed heuristic to exact alignment of long (Mbps) erroneous (≤15%) sequences. The empyrical near-linear runtime makes our aligner A*PA 250x faster than Edlib and WFA on synthetic data, and looks promising on human data. biorxiv.org/cgi/content/sh…

Oh my god is this real

Minigraph-Cactus: Pangenome Graph Construction from Genome Alignment biorxiv.org/content/10.110…

I just completed all 25 days of Advent of Code 2022! adventofcode.com #AdventOfCode

Nice and hopefully NIH/NCBI can run annotation service as well - NIH software assembles complete genome sequences on-demand nih.gov/news-events/ne…

California’s second largest reservoir was down to its lowest levels ever recorded in September 2021 (628’). Incessant parades of atmospheric rivers have almost refilled the 3.5 million acre-foot reservoir by March 2023 (845’). Lake Oroville, CA recovered 217 FEET! 📸: California Department of Water Resources

Major, fatal errors found in the data and methods of a 2020 paper in nature, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. @abrahamgihawi Mihaela Pertea Yuchen Ge Jen Lu biorxiv.org/content/10.110…

I've posted the notes/slides for my computational biology class at github.com/pachterlab/Bi-… Topics were chosen based on appearing in >=3 bio areas, although for focus examples are all drawn from #scRNAseq. Homeworks include both theory and exploration of data (via Colaboratory).

In 2012 I gave a talk at a biology conference where I started by discussing the unexpected hanging paradox. Since then I have unexpectedly found the paradox popping up repeatedly, to the extent that it should probably become part of core curriculum.