# single cell (blogs) — RSS Amplifier Recent posts from the 5 feeds in the RSS Amplifier directory that cover single cell. Page: Feed: --- ## [Discovery proteomics with O-Link reveals new HCC markers?](https://proteomicsnews.blogspot.com/2026/08/discovery-proteomics-with-o-link.html) _2026-08-20 · Unknown · News in Proteomics Research_ When I think of proximity extension assays (PEA) which is either famous because of O-Link - or is? O-Link, I think of purely using it for large population studies or for validating discoveries by high depth mass spectrometry based proteomics. But...could you use it in place of mass spec proteomics? Because that is basically what this group did here. Now...if your protein or proteoform isn't in… ## [Lyse your cells in 100% formic acid to get 40% more membrane proteins??](https://proteomicsnews.blogspot.com/2026/08/lyse-your-cells-in-100-formic-acid-to.html) _2026-08-19 · Unknown · News in Proteomics Research_ Okay. Chemically I do not understand why this would work. That's okay, I don't understand how a lot of things work.... They start out by laser capture microdissecting a pretty big area of cells. Something like 500 micron x 500 in 15 micron cuts. And you stop wondering why the cut is that big when you see the digests are loaded on a Q Exactive Classic. Man, I love those old things, but proteomics… ## [Multi-omics day on-site at Waters corporation!](https://proteomicsnews.blogspot.com/2026/08/multi-omics-day-on-site-at-waters.html) _2026-08-18 · Unknown · News in Proteomics Research_ Hey proteomics people! Did you know that Waters makes mass spectrometers? They totally do and, while I'm not at all sure how this happened, I got invited to drop in and meet scientists and see some talks and touch some instruments. I'm pretty sure I got to visit because of some impressive numbers out of the P10 instrument which looks like a compelling piece of proteomics hardware. I'm trying to… ## [AI in Drug Discovery: Data Quality, Not Quantity, Is the Bottleneck](https://divingintogeneticsandgenomics.com/post/ai-drug-discovery-data-quality-not-quantity/) _2026-08-17 · Chatomics on Chatomics_ Two important essays on AI in drug discovery landed in August. Both are worth your time. Both have the right intuitions. And one of them is subtly framing the wrong problem, in my opinion. The first is the Nature Reviews Drug Discovery review by Andreas Bender, Morgan Thomas, Jack Scannell, David Shaywitz, Gian Marco Ghiandoni, Joe Greener, and colleagues: "Artificial intelligence in drug… ## [Wait. Are we doing this wrong? An argument for SUPER MASS SPECTROMETRY!](https://proteomicsnews.blogspot.com/2026/08/wait-are-we-doing-this-wrong-argument.html) _2026-08-10 · Unknown · News in Proteomics Research_ This is an interesting one. What if it wasn't the most efficient to have proteomics mass spec instruments EVERYWHERE? Rather, what if mass spectrometry proteomics was, instead, a fully centralized system where each sample could be measured comprehensively on multi-capacity hardware without all the compromises that come with solo 150kg - 400 kg vacuum chambers? In the simulations presented here it… ## [Evolution is Complex](https://cstein.xyz/posts/2026/8/10/evolution.html) _2026-08-10 · Connor Stein_ As someone who never seriously studied life sciences, I've always thought that the story with evolution was basically one of "random mutations can sometimes increase the likelihood of reproduction." A bird who happens to get a genetic mutation for, say, a longer beak may have an easier time feeding, ## [The biggest proteomic human atlas yet should reduce our reliance on transcripts to determine specificity!](https://proteomicsnews.blogspot.com/2026/08/the-biggest-proteomic-human-atlas-yet.html) _2026-08-09 · Unknown · News in Proteomics Research_ I won't like that picture freaks me out a little, but here we are. 2,800 human samples analyzed at incredible depth. You have to be asking yourself that with a dataset this large and comprehensive, clearly we'll know for sure that the correlation is between transcript abundance from GTEX and this, right? Uuuuummmm..... yeah, it's...the same....though that 0.105 from the pancreas is....special....… ## [Bruker is boosting customer support and hiring.](https://proteomicsnews.blogspot.com/2026/08/bruker-is-boosting-customer-support-and.html) _2026-08-07 · Unknown · News in Proteomics Research_ Today I had the privilege of meeting with some fancy people from all over the place to discuss some concerns I have voiced and/or amplified about Bruker Daltronics support system. My concerns largely centered on what looked like a model I've seen before where an LCMS business is the cash cow (wtf is a cash cow?) for a big company to buy a lot of dumb shit. Who cares if a company uses their profits… ## [Defining quality standards for single cell proteomics OR Astral vs TIMSTOF Ultra2](https://proteomicsnews.blogspot.com/2026/08/defining-quality-standards-for-single.html) _2026-08-06 · Unknown · News in Proteomics Research_ Okay. So what if you sent the same single cells out to a whole bunch of labs that agreed to send the data back? Obviously no one would want to play unless they had the very best stuff, right? Or maybe you had to have the stuff to play? I don't know but this is super cool. Now....I am a little confused about the HPLC setup. It looks like they used a bunch of instruments but there is exactly one… ## [NanoLC dead volume calculator since I can't find the MSBioworks one!](https://proteomicsnews.blogspot.com/2026/08/nanolc-dead-volume-calculator-since-i.html) _2026-08-05 · Unknown · News in Proteomics Research_ nanoLC System Volume — Flow Path Calculator This is a nanoLC volume calculator inspired by the AMAZING (but dead?) MSBioWorks phone application I miss a lot and made with the frustrating assistance of some AI thing my university lets me use. It's honestly pretty good at color palettes, even if it's bad at math and confident/arrogant about it. nanoLC System Volume To use this, I've assumed some… ## [Generate Viral Hot Takes (Sponsored)](https://crawlproof.com/a/CQeKibpundmH) _2026-08-05 · **Sponsored**_ Get platform-optimized hot takes and rebuttals to spark debate and engagement ## [Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes](https://divingintogeneticsandgenomics.com/publication/2026-08-04-chromatin-landscape-cancer-cell-lines/) _2026-08-04 · Chatomics on Chatomics_ ## [AI in proteomics - from protein identification to virtual cells!](https://proteomicsnews.blogspot.com/2026/08/ai-in-proteomics-from-protein.html) _2026-08-03 · Unknown · News in Proteomics Research_ Man, I need to start being more collaborative so I can get on these gigantic papers that are going to get a billion lazy citations (that's where you use the title and abstract to make a citation without ever reading the paper). This new one is definitely going to get cited like crazy and since there are people out there who judge you by how many citations you have, each of these people are going… ## [Proteome Discoverer 3.3 has a DIA-NN (commercial license required) node!](https://proteomicsnews.blogspot.com/2026/08/proteome-discoverer-33-has-dia-nn.html) _2026-08-02 · LCMSmethodAdmin · News in Proteomics Research_ I was trying to help someone out who, due to the fact the US government is working great, has instruments but can't pay their annual license fee to use the DIA cloud nodes. I was like - how hard could it be to link PD through the node maker things to DIA-NN and then integrate the whole thing. Up until the .parquet thing appears it looked pretty straight-forward if you're smart, but I'm not and it… ## [Intro to Single Cell RNA Sequencing](https://cstein.xyz/posts/2026/7/23/scrna-seq.html) _2026-07-23 · Connor Stein_ Single cell RNA sequencing, known as scRNA-seq, is the process of determining the level of gene expression across individual cells. Before it, we could only measure average gene expression across many cell types in a sample, hiding cell-type-specific responses. In the mid-2010s, special "droplet" ma ## [$6/mo Agent-Friendly Side Project Stack](https://cstein.xyz/posts/2026/6/5/6_mo_agent_friendly_side_project_stack.html) _2026-06-05 · Connor Stein_ I recently found myself with some time on my hands, so I built a news filtering service for myself with Claude. I didn't like scrolling through multiple apps on my phone or newsletters in my email, subject to the whims of each news source's algorithm, and the solutions out there charge outrageous su ## [Is Truth Absolutely Necessary for Science?](https://homolog.us/blogs/biology/2026/05/27/is-truth-absolutely-necessary-science/) _2026-05-27 · Homolog.us – frontier in bioinformatics_ These days, corporate entities are increasingly dominating research in basic science. This essay looks into how this will change the most cherised convention of science. Researchers follow many conventions. In the short term, graduate students learn these conventions from their seniors and follow them without question. Over time, those students grow up as senior researchers and modify the… ## [Etherean to Crypto Moderate, Part 4: Equilibrium](https://cstein.xyz/posts/2026/5/27/crypto_evolution_part4.html) _2026-05-27 · Connor Stein_ 2025/early 2026 was a pivotal time for crypto. I was not the only one for whom these core crypto questions bubbled to the surface. The announcement of EVM-based Tempo and Arc in mid-2025 as regulator-compliant, whitelisted validator chains with native privacy features was met with a lot of pushback ## [Batch Effect: To Correct or Not for Bulk RNA-seq Data](https://divingintogeneticsandgenomics.com/post/batch-effect-correct-or-not-bulk-rnaseq/) _2026-05-22 · Chatomics on Chatomics_ A colleague sent me a PCA plot last week. Three replicates per condition, control vs KO of a gene. PC1 cleanly separated replicate 1 from replicate 2 from replicate 3. PC2 separated control vs KO. The question that followed: should we run limma::removeBatchEffect() before differential expression? The answer is “it depends,” and most of the time the answer is “no, do not… ## [Biology is Messy, Because Physicists Failed](https://homolog.us/blogs/biology/2026/05/21/biology-messy-because-physicists-failed/) _2026-05-21 · Homolog.us – frontier in bioinformatics_ I came across an interesting blog post titled Biology is Messy . The main argument is that biology is not built on top of reductionist theories, and the current push to collect large amount of data and use “AI” to “solve” biology is not likely to lead to finding reductionist theories either. Instead we will get a bunch of overfitted models hyped up as “solutions” by corporate entities. I agree… ## [Mathematical Side of AI and Its Applications in Biology](https://homolog.us/blogs/bioinfo/2026/05/20/mathematical-side-ai-applications-biology/) _2026-05-20 · Homolog.us – frontier in bioinformatics_ Right now everyone is either enamored of or is completely turned off by AI. Speaking of being fed up, please check the students at University of Florida booing at this commencement event . Much of their reactions comes from intense hype generated by the tech-bros of Silly Con valley to increase stock prices of their companies. Instead of emotionally swayed by hyped-up projections, let us learn the… ## [Play Both Sides Of The Lie (Sponsored)](https://crawlproof.com/a/i95OMgWzVmaM) _2026-05-20 · **Sponsored**_ Two operatives, one manufactured war — uncover the Complete Truth after both campaigns. ## [Etherean to Crypto Moderate, Part 3: Doubt](https://cstein.xyz/posts/2026/5/16/crypto_evolution_part3.html) _2026-05-16 · Connor Stein_ As part of the 2020 DeFi wave there was also a big rise in NFT usage. I never saw enormous value in NFTs. Most of the utility is similar to people trading baseball/pokemon cards or gaming skins, which just is not a big priority for me personally. Some people argued that ENS or other kinds of naming ## [Gene Regulatory Network Reconstruction with Single-cell Data](https://homolog.us/blogs/biology/2026/05/14/gene-regulatory-network-single-cell-multiomics/) _2026-05-14 · Homolog.us – frontier in bioinformatics_ On the subject of reconstructing gene regulatory networks (GRNs) from RNAseq and scRNAseq data, I am working through a number of review papers and the techniques described therein. Gene Regulatory Network Inference in the Era of Single-cell Multi-omics - review paper published in 2023. Gene Regulatory Network Reconstruction: Harnessing the Power of Single-cell Multi-omic Data - published in 2023.… ## [Scientific Questions (and Maybe Answers) for 2021-2038](https://homolog.us/blogs/biology/2026/05/11/questions-for-2021-2038/) _2026-05-11 · Homolog.us – frontier in bioinformatics_ In an earlier post , I divided the modern era of genetics into 18-year periods (eras). The discoveries of each era opened new questions and provided fuel for the next era. In the most recent era (2003-2020), biologists moved from working on individual genes to whole genome experiments, performing single-cell experiments instead of measuring gene expressions in many cells in aggregate and also… ## [Etherean to Crypto Moderate, Part 2: Building](https://cstein.xyz/posts/2026/5/10/crypto_evolution_part2.html) _2026-05-10 · Connor Stein_ After RC, I took a job at Paxos because, aside from practical reasons like it let me stay in NYC, I interviewed with some engineers who seemed to share this "World Computer" vision. ## [Three Layers of AI with an Analogy](https://homolog.us/blogs/bioinfo/2026/05/08/three-layers-ai-analogy/) _2026-05-08 · Homolog.us – frontier in bioinformatics_ In my earlier post , I mentioned about three distinct activities described under the broad term “AI”. They are - (i) using web-based text engines like Chatgpt, Claude or Gemini and their extensions as coding tools, (ii) downloading numerical models directly from Huggingface and building applications on top of them, and (iii) developing and training mathematical models for new applications. Maybe… ## [History of Genetics from 1949 to Today](https://homolog.us/blogs/biology/2026/05/08/history-genetics-1949-today/) _2026-05-08 · Homolog.us – frontier in bioinformatics_ I have decided to divide the last 70-80 years of genetics into different eras. Each period started with a set of burning questions, which were resolved by the end of the era. However, those answers created another set of burning questions to be resolved by the newcomers to the field. Please tell me whether you agree my classifications, and what you expect the current era to be like. 1949-1966 -… ## [Bioinformatics in the AI-era](https://homolog.us/blogs/bioinfo/2026/05/05/bioinformatics-ai-era/) _2026-05-05 · Homolog.us – frontier in bioinformatics_ In 2011, I wrote two articles ( here and here ) providing beginners’ guides to bioinformatics. Eight years later (2019), I posted an updated guide here . Now that AI has become a powerful tool, it is time to discuss how the work of bioinformatics and computational biology is changing. Before continuing, I will mention that three distinct activities fall under the broad term “AI”. They are - (i)… ## [In Data Analysis We Trust](https://divingintogeneticsandgenomics.com/talk/2026-nextflow-summit-boston/) _2026-04-29 · Chatomics on Chatomics_ ## [Etherean to Crypto Moderate, Part 1: Excitement](https://cstein.xyz/posts/2026/4/28/crypto_evolution_part1.html) _2026-04-28 · Connor Stein_ I spent around 8 years in crypto as an engineer and I'm now exploring other areas of technology. Over the years, my views on the industry evolved into what I'd call a "crypto moderate." This series of posts documents how I came to that position and what it comprises. ## [Has AI Changed the Course of Drug Development? Three Years Later](https://divingintogeneticsandgenomics.com/post/has-ai-changed-drug-development-3-years-later/) _2026-04-24 · Chatomics on Chatomics_ Almost three years ago I wrote Has AI Changed the Course of Drug Development? . The post was cautiously skeptical. AlphaFold was the headline. BenevolentAI had just flopped a Phase 2a in atopic dermatitis. Verge Genomics’ VRG50635 was about to enter the clinic. I argued that data quality was the real bottleneck, not algorithms. Time to revisit that. I now lead epigenomics bioinformatics at… ## [Code Faster with Clear Tutorials (Sponsored)](https://crawlproof.com/a/2JAFVNB2bn6w) _2026-04-23 · **Sponsored**_ Short, step-by-step coding videos you can follow along ## [Coding with AI - It Speeds You Up and Then Slows You Down](https://homolog.us/blogs/bioinfo/2026/04/22/coding-with-ai-speeds-up-then-slows-down/) _2026-04-22 · Homolog.us – frontier in bioinformatics_ I have been coding with AI assistance for about six months now and more actively since late December 2025. If I had to compress the entire experience into a single sentence, it would be this: AI made me faster first and then it made me slower. Let me explain. How I Started Like most people, I began small. I needed a specific customization in a plot generated by ggplot. Instead of going through… ## [I Built a Personal AI Assistant on a Mac Mini](https://divingintogeneticsandgenomics.com/post/openclaw-ai-assistant-mac-mini-setup/) _2026-04-06 · Chatomics on Chatomics_ My first blog post in a long time! I wanted an AI assistant that knew me. Knew my research. Knew my content calendar. Knew that when I say “write a thread about batch effects,” I mean single-cell RNA-seq batch effects with Harmony and Seurat code, for an audience of computational biologists who already know what a UMAP is. So I built Helix. An OpenClaw agent running on a Mac Mini in my… ## [Targeting the chromatin modifying enzyme, KDM5C, enhances AKT inhibition response in ER+ breast cancer](https://divingintogeneticsandgenomics.com/publication/2026-03-15-kdm5c-akt-breast-cancer/) _2026-03-15 · Chatomics on Chatomics_ ## [Computational Analyses and Challenges of Single-cell ATAC-seq](https://divingintogeneticsandgenomics.com/publication/2025-12-01-scatac-seq-review/) _2025-12-01 · Chatomics on Chatomics_ ## [Reviving BETA for Python 3: Integrating ChIP-seq and RNA-seq to Predict TF Targets](https://divingintogeneticsandgenomics.com/post/reviving-beta-chip-seq-rna-seq-integration-python3/) _2025-11-09 · Chatomics on Chatomics_ I started to learn bioinformatics because I needed to analyze public ChIP-seq data in 2012. That’s how I got to know Shirley Liu’s lab at Dana-Farber Cancer Institute. And God knows that I would join her group in 2020 for a staff scientist position to lead the CIDC bioinformatic project . I witnessed the development of many groundbreaking computational tools for genomics in… ## [Understanding prcomp() center and scale Arguments for Single-Cell RNA-seq PCA](https://divingintogeneticsandgenomics.com/post/understanding-prcomp-center-scale-arguments/) _2025-10-29 · Chatomics on Chatomics_ During my work with single-cell RNA-seq data, I’ve often encountered confusion about PCA and specifically when to use the center and scale arguments in R’s prcomp() function. While tools like Seurat’s RunPCA() abstract away these details, understanding what happens under the hood is crucial for proper analysis and troubleshooting. In this post, I’ll show you exactly what center and scale do, why… ## [Do not repeat yourself: List column to do RNAseq differential expression analysis](https://divingintogeneticsandgenomics.com/post/list-column-rnaseq/) _2025-09-23 · Chatomics on Chatomics_ To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. In this blog post, I am going to show you how to use list column and purrr::map() , a powerful toolkit in your belt to avoid repetition in your bioinformatics analysis. To demonstrate the usage, We will use RNAseq differential expression analysis and pathway enrichment analysis as an example.… ## [Reproducible Computing in Bioinformatics: Lessons from My Latest Talk](https://divingintogeneticsandgenomics.com/post/repro-comp/) _2025-08-17 · Chatomics on Chatomics_ Hey everyone, it’s Tommy here. If you’ve been following my blog or my Twitter/X ( @tangming2005 ), you know I love diving into the practical side of bioinformatics and genomics. Recently, I gave a talk titled “Good Enough Practices for Reproducible Computing” at Moderna, where I spent a good chunk of time chatting about reproducible computing. Why? Because in our field, where data is exploding and… ## [Crashing Excel to Curing Cancer: How AI and Open Science Transformed One Scientist’s Path](https://divingintogeneticsandgenomics.com/talk/2025-ai-on-the-hill-podcast/) _2025-08-01 · Chatomics on Chatomics_ We’re bringing a podcast to the conversation: AI on the Hill — and our very first episode is now live! In this show, host René Bastón sits down with 🎯 Ming “Tommy” Tang, a first-gen PhD who arrived in the U.S. with just $2,000 and a dream. Through grit, coding, and a passion for open science, he transformed his career — and became a voice for how AI is reshaping drug discovery. They… ## [Panel discussion: From Physics-Based Modeling to AI-driven Drug Discovery](https://divingintogeneticsandgenomics.com/talk/2025-atombeat-panel/) _2025-07-18 · Chatomics on Chatomics_ ## [Fuzzy Sequencing: Sometimes close enough is good enough](https://www.omic.ly/fuzzy-sequencing-sometimes-close-enough-is-good-enough/) _2025-07-15 · Brian Krueger · Omic.ly_ DNA is coded by 4 bases, but no one said that's how we have to sequence it. Ready to have your mind bent? ## [How to create a GenomicRanges object in Bioconductor using canonical transcripts](https://divingintogeneticsandgenomics.com/post/canonical-tx/) _2025-07-15 · Chatomics on Chatomics_ To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. Introduction to Annotation Data Packages in Bioconductor Accurate gene and transcript annotation is the foundation of many bioinformatics workflows, including RNA-seq analysis, functional genomics, and variant annotation. In the R/Bioconductor ecosystem, dedicated annotation data packages… ## [Nerve cells transfer their mitochondria to cancer cells](https://www.omic.ly/nerve-cells-transfer-their-mitochondria-to-cancer-cells/) _2025-07-08 · Brian Krueger · Omic.ly_ Just when you thought cancer couldn't get any crazier...neurons can directly transfer their power producing mitochondria to tumor cells ## [The microbiome has more to do with traditional ecology than you might think](https://www.omic.ly/the-microbiome-has-more-to-do-with-traditional-ecology-than-you-might-think/) _2025-07-08 · Brian Krueger · Omic.ly_ Studying the microbiome is really just a lesson in ecology! ## [The most beautiful experiment in biology](https://www.omic.ly/the-most-beautiful-experiment-in-biology-2/) _2025-07-08 · Brian Krueger · Omic.ly_ Watson and Crick solved the structure of DNA and everyone lived happily ever after, right? Wrong. That was just the opening argument. ## [Weekly Reading List: July 7, 2025](https://www.omic.ly/weekly-reading-list-26/) _2025-07-08 · Brian Krueger · Omic.ly_ ’We couldn’t live without it’: the UCSC Genome Browser turns 25 After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact. The Percentage of Tasks AI Agents Are Currently Failing At May ## [Mastering Bioinformatics in the Age of AI: Foundational Skills for the Modern Scientist](https://divingintogeneticsandgenomics.com/post/ai-bioinformatics/) _2025-07-04 · Chatomics on Chatomics_ To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. AI is transforming every field — and bioinformatics is no exception. From designing drug molecules in minutes to writing entire pipelines, generative AI is making it faster than ever to process biological data. But here’s the truth: AI doesn’t understand biology — you do. That’s why, in this… ## [STAMP brings us non-destructive single-cell profiling without the sequencing](https://www.omic.ly/stamp-brings-us-non-destructive-single-cell-profiling-without-the-sequencing/) _2025-07-01 · Brian Krueger · Omic.ly_ No sequencer needed: Imaging based single-cell multiomics ## [So, you want to learn more about your microbiome?](https://www.omic.ly/so-you-want-to-learn-more-about-your-microbiome/) _2025-07-01 · Brian Krueger · Omic.ly_ Microbiomes are complicated and if you want to understand them you better start with good data ## [What did Watson and Crick actually discover?](https://www.omic.ly/what-did-watson-and-crick-actually-discover/) _2025-07-01 · Brian Krueger · Omic.ly_ History is written by victors, and that statement couldn't be more true than it is in the case of Watson and Crick's 'discovery' of the DNA double helix.