- by /u/gwernsubmitted by /u/gwern [link] [comments]
- by /u/Holodoxasubmitted by /u/Holodoxa [link] [comments]
- by /u/ManyLine6397Hey everyone! đź‘‹ We just released LLM4Cell, a comprehensive survey exploring how large language models (LLMs) and agentic AI frameworks are being applied in single-cell biology — spanning RNA, ATAC, spatial, and multimodal data. 🔍 What’s inside: • 58 models across 5 major families • 40+ benchmark datasets • A new 10-dimension evaluation rubric (biological grounding, interpretability, fairness, scalability, etc.) • Gaps, challenges, and future research directions If you’re into AI for biology, multi-omics, or LLM applications beyond text, this might be worth a read. đź“„ Paper: https://arxiv.org/abs/2510.07793 Would love to hear thoughts, critiques, or ideas for what “LLM4Cell 2.0” […]
- by /u/Potential-Dish-6972So I have been on SSRIS 20 years since childhood, they constantly stopped working so I had about 20 drug switches/titrations/increases during this time. Unable to come off x6 attempts that have left me disabled with protracted withdrawal syndrome which I wouldn’t wish on my worst enemy. In trying to do some research to save my life I saw I have a few genetic mutations related to serotonin that I’m wondering if the SSRIs are making worse. Longterm use of SSRIs is associated with receptor downregulation and overall decreased serotonin levels due to adaptation. I have TPH2 homozygous, SLC6a4 homozygous, […]
- by /u/MaleficentOkra4047Hi all, I have been working on a gwas for continuous trait. My gwas retuning thousands of genome wide hits with small effects, without forming visible peaks with plink2. The qq plot looks okay and the λ is 1.025. I have also used regenie, but with regenie I do not see any genome wide hits. My question would be if it’s more possible a confounding issue, or an extremely polygenic trait with very small effects? submitted by /u/MaleficentOkra4047 [link] [comments]
- by /u/VariomeAnalyticsHey everyone, We just launched Pipette.bio – a conversational AI agent for running bioinformatics analyses without the usual scripting headaches. What it does: Run differential expression, single-cell, and multi-omics workflows through natural language Built on standard tools (R/Bioconductor + Python packages) Secure data handling – everything stays in your own workspace with version control and provenance tracking Auto-generates interactive reports, plots, and reproducible code Scalable backend on AWS so heavy jobs don't freeze your session Why we built this: The goal isn’t to replace existing workflows, but to lower the barrier to bioinformatics that lab biologists often face. We think […]
- by /u/LowerWillingness7178I have 200 SNP markers that I would like to use for genotyping. We wanted to do the genotyping in house, and we have funds available to buy the equipment. We will do the genotyping routinely. Can you please suggest some options for the equipment and methods (etc. microarray reader) or other options such as targeted genotyping by sequencing that can be done in house? For the number of samples, we were only looking at 300 samples per year, so just something small and not industrial scale. I am also open to explore any options, to efficiently and accurately genotype […]
- by /u/Dear_Raise_2073Hey folks, I’ve been working on a small ML project over the last month and thought it might interest some of you doing variant analysis or functional genomics. It’s a non-deep-learning model (Gradient Boosting / Random Forests) that predicts the functional impact of genetic variants (SNPs, indels) using public annotations like ClinVar, gnomAD, Ensembl, and UniProt features. The goal is to help filter or prioritize variants before downstream experiments — for example: ranking variants from a new sequencing project, triaging “variants of unknown significance,” or focusing on variants likely to alter protein function. The model uses features like: conservation scores […]
- by /u/ElefteriosteophilosHi! I am trying to isolate Genomic DNA from buccal swabs with the Genolution Nextractor NX-48s. I am using the GD-162 genomic kit. I do not have a DNA signal from the tested swabs in the PCR reaction. In the lab where I work, there isn't any kind of instrument for measuring DNA. The kit expired in 2021, but my colleague in the lab assured me that he previously used a similar GD-162 genomic kit with the same lot number and expiration date and it was functional. Swabs were put into NaCl 0.9% solution for half hour. That is the […]
- by /u/HolodoxaAbstract Quantification of the direct effect of genetic variation on human behavioural traits is important for understanding between-individual variation in socio-economic and health outcomes but estimates of their heritability can be biased by between-family indirect genetic effects. In contrast, using within-family variation in DNA sharing is robust to most confounding factors including shared environmental effects and population stratification. Yet, accurate estimates for most traits are not available using this design, and none for non-European ancestry populations. Here, we analyse approximately 500,000 sibling pairs with diverse ancestries and obtain robust and precise heritability estimates for 14 phenotypes, including two well-studied model […]
- by /u/ComprehensiveDot8287Hello Reddit, I just got into analyzing my DNA to look for genetic causes of disease and came across a huge amount of LOH mutations in my cnv.vcf file, spanning ~82Mb, ~67Mb and many others. Most of which are QUAL 40 PASS. Its a regular buccal swab. This seems to be associated with cancer, inbreeding or UPD. All of which make absolute no sense and UPD is very rare too. Does anyone know whats up? I feel like I just can't trust the entire file on anything now and need to redo it with a thorough blood test… submitted by […]
- by /u/Shockslayer_submitted by /u/Shockslayer_ [link] [comments]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
