Bedford, MA
Joined May 2008
B. Arman Aksoy retweeted
Half the battle in helping cancer patients involves just being a dog on a bone operationally, and having a maniacal ops team. We're working with a young adult patient whose samples had failed sequencing three times before we met them. We tried 4 more times, and failed every time. Tumor content too low. Necrosis. DNA / RNA extraction failed. Finally, we managed to get some results on single cell RNA sequencing. Tumor cells were only 9% of the total, but they were present. When looking at those tumor cells, we saw clear signs of enrichment in a T-cell therapy target. But we also needed to know their HLA type, and we couldn't infer that from our single cell assay. So we did a Guardant 360 blood test, and fortunately, got the exact HLA type we were hoping for. A few days ago, we got the terrible news that the patient progressed. Now, this therapy might be the best option. Our ops team works with feral persistence for exactly these situations, even before it's urgent. In cases of recurrence, we want all the data to be on the table, so patients and physicians can make the best possible decisions. @Valius_Sciences
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We (@Valius_Sciences) have recently open-sourced two tools we developed in-house to address common pain points for single-cell sequencing analysis: annotating cell types and calling copy-number alterations.
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kopya assesses copy-number alterations across the cells in your single-cell data. Drawing on best practices established by our team and past learnings from other tools, it provides a resource-efficient implementation that allows you to analyze hundreds of thousands of cells on a laptop within minutes. kopya has allowed our team to efficiently evaluate different analysis settings without worrying about long run times. With the help of this tool, we are better able to distinguish tumor cells from normal cells for challenging cancer types (e.g., glioblastomas): github.com/valiussciences/ko…
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Both tools are early-stage but stable. We highly encourage checking out the repositories for technical details, example use cases, installation instructions, and evaluations. Don't hesitate to reach out of if you hit any issues or if you have any ideas on how to improve them.
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B. Arman Aksoy retweeted
At Valius, we think a lot about what the most important oncology diagnostics will be 5 years from now. We're excited about single cell RNA sequencing as a future diagnostic modality, and we're working to bring it to the clinic. This case study of a myxofibrosarcoma patient illustrates why.
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B. Arman Aksoy retweeted
It's amazing how often you find actionable targets in tough cancers when you look hard enough. We're working with a leiomyosarcoma patient, a rare abdominal cancer. This one was considered inoperable.
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“Can Atalay’a Özgürlük” demek ve yakın tarihe Amerika’dan bir not düşmek adına, 15 Mart Pazar günü Nebil Özgentürk’ün de katılımıyla NYC’de buluşuyoruz… ✌️🌿 Yer: Drom NYC, 85 Avenue A, NYC Saat:15.00 Ücretsiz biletinizi hemen alın. @dromnyc dromnyc.com @ankahabera
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ICYMI: All ~6,500 abstracts from #ASH2025 #ASH25 are available at abstract.plus and ready to be exported, filtered, and annotated with the help of AI. If you are looking for the abstract spreadsheets for earlier conferences or would like to serve your own instance due to privacy concerns, the tool and the past archives are all available at github.com/armish/abstract.p…
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3 aylık olduk 🎉
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Okumaya üşenenler için, son 1 aydır gündemi 3-5 dakikalık mini kayıtlar halinde Spotify'da da yayınlamaya başladım: open.spotify.com/show/4VXeLU…
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I recently (and unexpectedly) received $1,000 credits for Claude Code on the web from @AnthropicAI so I put those credits to good use for the R community. Happy to announce two new R packages that were both vibe-coded: 1️⃣ {plumber2mcp} turns any plumber R API into an MCP server. 2️⃣ {hgnc.mcp} brings HGNC gene data (aliases, IDs, families) directly into LLM workflows via MCP + Docker. Below is a video of {hgnc.mcp} in action within Claude Desktop.
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We now have 1286 #SITC25 abstracts up on abstract.plus for AI-assisted mining/exploration 📰
Quite a few of you have reached out to me after I posted the abstract browsing and annotation tool that I prototyped for #asco25 in May and sorry if I wasn't able to get back to you with a private copy of it in a timely manner. This time I am making the tool publicly available right away. abstract.plus now runs an updated version that works against the recently released ESMO 2025 abstracts. In the video below, you can see how I quickly filter >2500 abstracts with a keyword ("bispecific") and ask a scientific question ("what are the targets of the bispecific") against the abstracts to annotate them with the help of the OpenAI service. For those of you who want to use this, feel free to head over to the website (abstract.plus) and browse/filter abstracts right away. You can copy/paste your OpenAI API key under the Advanced Setting to start annotating abstracts on your own as well. For those of you who don't feel comfortable with this, I have also decided to release the source code (feel free to reach out to your IT to help with the setup): github.com/armish/abstract.p… Hope this tool helps make the best out of thousands of abstracts in an easy way. #esmo2025 #esmo25
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Did you know that most biotech start-ups undergo a "reverse stock split" right before IPO to stay within the $10-$15 listing range (so the stocks look more appealing)? Until a few years ago, I did not. Talking to other people, I now realize that most people also do not know about this common practice; but talking about these things is such a taboo that nobody wants to dig into the details due to shame. There is also not much on the Google about pre-IPO splits as post-IPO reverse splits are more common.
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