Jing Yu

[Heng Li @lh3lh3]

Blog post on "The AI Rewrite Dilemma": https://t.co/4NxIpNbYzR

[Jing Yu @logust79]

@dennisconrad @AdamJSchwarz For the record, people on work / settlement visa can’t bring their parents in. Their parents have to apply for a regular visiting visa that only allows them to stay in the UK 6 months per year.

[Jing Yu @logust79]

@williameijer It’s akin to do biological analyses of “left vs. right”, “well educated vs. poorly educated”. What good do they lead us?

[Jing Yu @logust79]

@bettykamar @DrNeilStone Wanna try some Norovirus?

[Jing Yu @logust79]

@NurseMicheleRN @mcfunny @outbreakupdates @grok Nonetheless from the paper the data demonstrated excellent effectiveness of vaccine in infection protection. Those breakthroughs are likely a result of non-responders, and identifying them early can be helpful in preventing such breakthroughs.

[Heng Li @lh3lh3]

Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB https://t.co/DiRwZNHVVa

[Charlie Marsh @charliermarsh]

Today, we're shipping a series of features that move uv beyond a pip alternative, and into an end-to-end solution for managing Python projects, command-line tools, single-file scripts, and even Python itself.

A single, unified tool. Like Cargo, for Python.

It's very fast.

[Evan Floden @EvanFloden]

🚀 Big news in Nextflow! The latest 24.04 release is packed with genuinely groundbreaking features and enhancements that transform your pipelines. From job arrays to new resource limits and Seqera Containers, new "topic channels" and a workflow output definition (adios publishDir!). This release has it all. Let's jump into the details!

[Lior Alexander @LiorOnAI]

NVIDIA just made Pandas 150x faster with zero code changes.

It is now directly integrated in Google Colab.

All you have to do is:
%load_ext cudf.pandas
import pandas as pd

Their RAPIDS library will automatically know if you're running on GPU or CPU and speed up your processing.

You can try it here: https://t.co/oq7qkVWztY

[Jing Yu @logust79]

@quenchentin This is no luck! Huge congratulations on the quality research!

[Genomics England @GenomicsEngland]

Registration is open! 📣

Join us on 9 July for the Genomics England Research Summit. Our speakers will share valuable insights on genomics and cancer, rare conditions, emerging technologies & healthcare innovations 🧬 #GERS2024

Secure your spot for free: https://t.co/hHeZ1pWfHo

[Jing Yu @logust79]

@10DowningStreet This is as wrong as it gets. Immigrants on a work visa typically pay a huge sum for visa application (now over £1k), and over £600 per year on NHS surchange, and are NOT eligible for any public funds, including child benefit. They already bring so much and get so little in return

[Yoseph Barash @YosephBarash]

Assessing detection of deep intronic variants that affec #RNA splicing from @MCarmoFonseca and colleagues - nice to see this work finally out! 😀👏 https://t.co/QdVujoTqXr

[Edoardo Giacopuzzi @Supergecko]

The CHARR method paper is out in AJHG. It allows fast and sensitive quantification of sample contamination directly from VCF and scalable to population-scale projects thanks to Hail implementation. Great collaboration with @lu_wenhan @konradjk and others. https://t.co/wks3cKo5Ps

[Sasha Gusev @SashaGusevPosts]

Really cool paper that investigates (primarily mental health) phenotype imputation for GWAS as a trade-off between increased power versus decreased specificity. This gets at the broader conceptual question of what is a phenotype for? A few intriguing results/directions. 🧵:

[Retina UK @RetinaUK]

Join our next Webinar on Thursday 7 Dec to hear from Dr Nikolas Pontikos about the ways in which computer power can be used to tackle medical research challenges, including using AI to identify the genetic cause of a condition from scans. Register now: https://t.co/M3fLTP5eWV

[bioRxiv Genomics @biorxiv_genomic]

An encyclopedia of enhancer-gene regulatory interactions in the human genome https://t.co/sZt64JQZmH #biorxiv_genomic

[antisense. @razoralign]

SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes https://t.co/RI3Omf66jt

[Bo Wang @BoWang87]

Interested in LLMs for genomic research but don't know where to start? looking for a review/survey to get started in this field? 👇👇😀

I am very excited to share that our review paper titled "To Transformers and Beyond: Large Language Models for the Genome" is now available as a preprint (https://t.co/U24TUSseNr)! Our review unveils a revolution in genomics analysis with Genome LLMs. 🧬

🔍 What's Inside:
✅ The power & challenges of transformers in genomics.

✅ Cutting-edge models like HeynaDNA and scGPT & their impact.

✅ Deep dives into Enformer, DNABERT, and other Genome LLMs.

🌍 Why it Matters:
1. GPT-4's influence reshapes AI in genomics.
Unmatched insights into transformers' role in genomics.

2. Critical analysis of new models, addressing interpretability, privacy, & computational needs.

3. Essential for computational biologists & computer scientists to navigate the future of genomic data analysis.

This is a work led by the amazing PhD student, Mica Consens, in the lab! Also, a huge collaborative work with lots of field leaders @fabian_theis @genophoria @MKarimzade @michaelwainberg and Alan Moses!

@UofT @VectorInst @UofTCompSci @UofT_LMP @UHN @pmcc_ai @UHNAIHUB

[Erik Garrison @erikgarrison]

A basic biological discovery based on the human pangenome! The short arms of acrocentric chromosomes include regions where heterologous chromosomes pair up and recombine as if they were homologs: pseudo-homologous regions (PHRs) https://t.co/1Y5YA5HNkZ https://t.co/vF0aaT5vWc