Sina Nassiri

Principal Bioinformatics Scientist at Roche pRED

[Sina Nassiri @NassiriSina]

@3DiMMUNE @Nature Wait, centering data then clipping all negatives to zero? 🤨 That’s one way to force NMF to work, but you’re basically deleting half the variance just to keep the algorithm happy. It looks like the "few months" prophecy was a bit optimistic!

[Sina Nassiri @NassiriSina]

@tangming2005 @XShirleyLiu Hi Tommy. The TISMO portal has been down for a while. Do you know if a mirror or copy of the data is accessible elsewhere, or if you happen to know someone from the former Liu Lab who might be able to help revive the portal or share processed data with us?

[Sina Nassiri @NassiriSina]

@RiyueSunnyBao What’s the objective of such integration? To find commonalities between tumor cells, I suggest integrating them separately using an unsupervised approach if you need a joint embedding for downstream, or use NMF to dissect gene expression programs wo integration.

[Sina Nassiri @NassiriSina]

@LabWaggoner @NatImmunol @BSilva_Santos @NitalSumaria @GJ_Fiala @DanPennington1 This caught my eye, what's going on here?!

[Sina Nassiri @NassiriSina]

@maxim_artyomov @ImmunityCP My bad! I was looking for data in "Single-cell explorer". Found what I was looking for.

[Sina Nassiri @NassiriSina]

@maxim_artyomov @ImmunityCP Congratulations on this impressive effort and resource! Could you please check data availability? Synapse under accession code syn49637038 does not return anything.

[Sina Nassiri @NassiriSina]

@MHemingNeuro @tangming2005 @theHumanBorch @YosefLab recently presented MrVI at @SCG2023, which does exactly that. Multiscale PHATE and PhEMD from @KrishnaswamyLab are also relevant. Per cell type NMF-based analysis of transcriptional heterogeneity also seems to work well as mentioned previously.

[Sina Nassiri @NassiriSina]

@theHumanBorch @tangming2005 It’s back up now. Thanks!

[Sina Nassiri @NassiriSina]

@tangming2005 Hi Ming, do you happen to know any of the maintainers of TISCH2? The website seems to be down.

[Sina Nassiri @NassiriSina]

Hi @SwissEmbassyIr, are you aware that there is no availability for a VISITOR visa appointment at @VFSGlobal in Tehran until Jun 2024? How is this possible? Are we back to a black market situation like a few years ago? Please fix this!

[Sina Nassiri @NassiriSina]

Hi @vfsglobalcare , been having issues accessing the appointment booking system (applying from Iran, going to Switzerland) for the past few days. I get the same error in 🇨🇭 as family&friends in 🇮🇷 . Please advise.

[Sina Nassiri @NassiriSina]

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[Joshua Batson @thebasepoint]

Single-Cell RNA-seq data is notoriously noisy. There are dozens of methods for cleaning it, but how do you know when they’re working right?

How clean is too clean?

Presenting...Molecular Cross-Validation

https://t.co/5Qeu7jxo4i

[Sina Nassiri @NassiriSina]

@tangming2005 Most relevant messages are: 1) Multiple ML approaches failed to identify a baseline gene signature highly predictive of response across indications, 2) Signatures described previously failed to validate, and 3) need to consider indication-specific molecular contexts.

[Sina Nassiri @NassiriSina]

@tangming2005 https://t.co/Iwjbt9IFGA

[Sina Nassiri @NassiriSina]

@Mohlotf @BayerFoundation Congrats, well-deserved! 🥳

[Will Macnair @willmacnair]

¡𝗣𝗵𝗗 𝗜𝗻𝘁𝗲𝗿𝗻𝘀𝗵𝗶𝗽!

Give yourself the gift of a 9 month research internship in industry (much better than socks). Or pass it on to someone you know.

https://t.co/Jp1ZPmJnNm

[Sina Nassiri @NassiriSina]

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[Eytan Ruppin, MD, PhD @EytanRuppin]

Is chromosomal and/or focal copy number alterations predictive of patients’ survival following immunotherapy across all cancer types?

We answer this in our latest preprint, which contradicts major recently published claims about this relationship. https://t.co/NiriLgI4DJ

[Sina Nassiri @NassiriSina]

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[Eytan Ruppin, MD, PhD @EytanRuppin]

Drug target identification is at the heart of drug development, and we’ve been working to change how it’s been done.

We present DeepTarget: a new computational tool to characterize a drug’s mechanism of action in-depth beyond its primary target. 🧰🧵👇
https://t.co/MuNTjsiniI

[Sina Nassiri @NassiriSina]

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[𝐉𝐨𝐡𝐧-𝐖𝐢𝐥𝐥𝐢𝐚𝐦 𝐒𝐢𝐝𝐡𝐨𝐦, 𝐌𝐃, 𝐏𝐡𝐃 @John_Will_I_Am]

5 years ago, I proposed using #DeepLearning to predict response to immunotherapy in TCR-Seq.
🧬🧬🧬🧬
Last year, we published #DeepTCR. Today, I am proud to share its application in cancer immunology, now out in @ScienceAdvances #ScienceResearch
🔶🔷🔶🔷
https://t.co/VRxPqwZP5F

[Sina Nassiri @NassiriSina]

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[Aaron Wilk @wilk_aaronj]

Some time ago, @SherlockpHolmes told me: “Premature agglomeration is the root of all evil.” Those wise words inspired me to embark on a project I’m incredibly excited to share today. https://t.co/lOHlg3WPDq 1/