Han Altae-Tran @altaetran Twitter profile

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Han Altae-Tran

7 months

Our latest work exploring ultra rare CRISPR systems with new big data algorithms has been published by @ScienceMagazine ! @zhangf @soumya_kannan12 . This thread will unwrap how we found needles in a haystack of metagenomes. Let's dive in! (1/8)

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Han Altae-Tran

@altaetran

7 months

Our latest research, published in @PNASNews , identifies nearly 1 million OMEGA-TnpB & CRISPR-Cas12 genome editors. Key insights? RNA-guided activity is linked to more processes than we thought: transcription, transposition, motility and more! #CRISPR (1/3)

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Han Altae-Tran

@altaetran

7 months

Check out our latest work on a new algorithm for protein clustering and the discovery of new CRISPR systems! More on this soon. So grateful to have this work published by @ScienceMagazine !

Science Magazine

@ScienceMagazine

7 months

Using a new algorithm called FLSHclust, researchers have revealed rare and previously unknown #CRISPR -Cas systems. The approach and results provide novel opportunities for understanding the vast functional diversity of microbial proteins.

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Han Altae-Tran

@altaetran

7 months

CRISPR defense now known to target mRNAs in ribosomes - the source of all proteins in the cell - in order to prevent viruses from making proteins. Truly amazing!

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling

A prokaryotic antiviral CRISPR-Cas auxiliary effector cleaves ribosome-bound messenger RNAs to inhibit translation

www.science.org

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Han Altae-Tran

@altaetran

3 years

Excited to share our latest work uncovering new classes of RNA-guided systems! @soumya_kannan12 @zhangf

Feng Zhang

@zhangf

3 years

CRISPR technologies are powerful gene editing tools because they are programmable. We are excited to describe 3 new programmable systems, IscB, IsrB, and TnpB, some of the most abundant genes on the planet, with potential for gene editing. @ScienceMagazine

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Han Altae-Tran

@altaetran

7 months

🌐 With now over a billion sequenced known proteins, it has become challenging to analyze them all. So we developed FLSHclust, an algorithm that can deep cluster billions of proteins in nearly linear time. #BigData #Bioinformatics (2/8)

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Han Altae-Tran

@altaetran

7 months

🔍 Strikingly, a candidate Type VII CRISPR system emerged. We show that these are a new class of RNA editors that rely on a new effector, Cas14, which contains a β-CASP RNase domain and a domain distantly related to part of Cas10. (4/8)

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Han Altae-Tran

@altaetran

7 months

We're excited about the potential impact of our work and look forward to collaborating with the scientific community to explore these systems further. A huge thank you to our team and collaborators @rachel_oshiro @lkmoeller . Follow us for more updates #TeamScience (8/8)

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Han Altae-Tran

@altaetran

7 months

Navigating grad school apps? I've been there! Offering help for anyone diving into Bio, Bioengineering, and Bioinformatics PhD applications. Happy to share feedback & some much-needed moral support. Let's make this journey easier! #PhD #GradSchoolApps

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Han Altae-Tran

@altaetran

7 months

🧬 The remaining systems we identified include new CRISPR-linked transposon systems, CARF effectors, reverse-transcriptase associated acquisition modules, large ATPase systems, and more, highlighting the vast untapped natural diversity of CRISPR functions #CRISPR (7/8)

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Han Altae-Tran

@altaetran

7 months

🔍 The functions of type IV CRISPR systems have remained enigmatic for years. Our search unveiled a new subtype that uses an HNH nuclease domain, resulting in targeted processive degradation of DNA (5/8)

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Han Altae-Tran

@altaetran

7 months

🌐 We used FLSHclust to develop an ultra-sensitive CRISPR discovery pipeline, discovering 188 rare CRISPR-linked systems from ~8TB of genomic data. These systems we found have diverse biochemical functions. #GenomeMining #CRISPR (3/8)

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Han Altae-Tran

@altaetran

7 months

🔍We also uncovered new types of precise genome editors in which multi-component type I CRISPR systems naturally lost Cas3 and gained an HNH nuclease, resulting in newly evolved precise genome editors. #GenomeEditing (6/8)

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Han Altae-Tran

@altaetran

7 months

A new preprint from @shsternberg @SternbergLab shows that TnpB, the ancestor of CRISPR-Cas12, has been naturally co-opted for RNA-guided transcriptional regulation of bacterial flagellin systems!

Emergence of RNA-guided transcription factors via domestication of transposon-encoded TnpB nucleases

Transposon-encoded tnpB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination[1][1]–[4][2]. This widespread gene...

www.biorxiv.org

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Han Altae-Tran

@altaetran

3 years

So cool to see this structural model for IscB!

Michael Chambers

@greenkidneybean

3 years

@zhangf @ScienceMagazine @altaetran @soumya_kannan12 @eugene_koonin @Ivan_Bilinski @GCACTAATTGAGAAC just for giggles, #AlphaFold IscB (model confidence: 🔵high, 🟠low)

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Han Altae-Tran

@altaetran

7 months

We can also witness transformation of TnpB into Cas12. that likely took place over millions of years using #AlphaFold2 ! (3/3)

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Han Altae-Tran

@altaetran

2 years

Check out this amazing work from Sophia Liu using spatial sequencing to better understand T cell receptors!

Sophia Liu

@immunoliugy

2 years

Presenting Slide-TCR-seq: our method for measuring the transcriptomes of cells & T cell receptor (TCR) sequences in situ! This collaboration w/ Bryan Iorgulescu, Shuqiang Li, Catherine Wu, and @insitubiology led to some cool findings... 1/8

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Han Altae-Tran

@altaetran

7 months

@Kaju_Nut I tried to limit all my undergrad research to summers because it let me take lots of interesting classes to build foundations in many fields which is an investment in future research. I think we're now taking away this investment and just focusing on the short term. Sad

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Han Altae-Tran

@altaetran

7 months

So many cool systems to study further! Flagellin, DppD systems, sigma factors, SpoIIE, RHH! (2/3)

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Han Altae-Tran

@altaetran

2 years

Our work on compact Cas13s for AAV-deliverable RNA base editors is on the cover of NBT! This work aims to bring RNA editing closer to the clinic. RNA editing has distinct advantages from DNA editing, one of which is that it does not change a patient's genome sequence. #CRISPR

Nature Biotechnology

@NatureBiotech

2 years

The February issue is live Our cover features a rendering of the predicted structure of an RNA editor based on the compact Cas13bt enzyme presented by Kannan et al.

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Han Altae-Tran

@altaetran

7 months

@pdhsu @SKonermann Nice! I wonder if specificity models from large data collection could be used to engineer proteins

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Han Altae-Tran

@altaetran

11 months

@xinjin @rachel_oshiro Wow how worlds collide!! Wonderful to see both of you together! :)

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Han Altae-Tran

@altaetran

7 months

@shsternberg Awesome findings! Really excited to see what else these reprogrammable systems are capable of!

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Han Altae-Tran

@altaetran

7 months

@JasonSynaptic @neuromichael @AliciaRavens Epic idea

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Han Altae-Tran

@altaetran

7 months

@pdhsu @SKonermann Sure, some time in Jan? Lets DM to setup a time

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Han Altae-Tran

@altaetran

3 years

@SeanKuWang @soumya_kannan12 @zhangf Thank you! We had a picnic out in nature to express our gratitude for all of the biodiversity it provided for this study!

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Han Altae-Tran

@altaetran

7 months

DM me if there's anything you'd like to discuss!

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Han Altae-Tran

@altaetran

7 months

@Deconstructdog @Patrick18287926 I see your perspective, and I'd like to offer that scientific precedence is worth valuing. It helps keep scientists working on diverse problems. The number of views or citations is a metric of hotness rather than scientific contribution. Truth is truth, at least we hope.

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Han Altae-Tran

@altaetran

7 months

@MartinPacesa A timeless treasure never gets old :)

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Han Altae-Tran

@altaetran

7 months

@KimiChernoby What do you make of this? "The national average salary for a doctor is $239,408 per year, while the national average salary for a lawyer is $71,546 per year. Other factors, like location, can also affect their earnings" from

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Han Altae-Tran

@altaetran

7 months

@SashaGusevPosts @mattyglesias Is this undergrad, or grad? Academia/research is surprisingly high!

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Han Altae-Tran

@altaetran

1 year

@ZegarraRuizPhD @UVA_MIC @UVAimmunology @MedicineUVA @UVA Very cool! Congratulations! Excited to see your new work!

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Han Altae-Tran

@altaetran

7 months

@vijaypande Dang Vijay getting swole

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Han Altae-Tran

@altaetran

7 months

@jin69388522 @zhangf @soumya_kannan12 Keep studying! There's so much cool stuff to learn :)

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Han Altae-Tran

@altaetran

5 months

@ArlottaLab @HSCRB @broadinstitute Congrats!!

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Han Altae-Tran

@altaetran

4 months

@eigie111 @Nature Beautiful work!

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Han Altae-Tran

@altaetran

7 months

@evokerr @livkosterlitz @nate_grassi @baileymwerner @RS_McGee @EvaTop3 @MolBioEvol Wow that was so interesting and really refreshing to learn about!

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Han Altae-Tran

@altaetran

7 months

@irmantas_mogila I LOVE this paper, and the biological story it conveys. Inspiring!

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Han Altae-Tran

@altaetran

3 years

@draparente It's been so long since the Pande lab! :)

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Han Altae-Tran

@altaetran

1 year

@fmmartinz @Nature Wow that's really interesting!

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Han Altae-Tran

@altaetran

7 months

@kocalars #Team

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Han Altae-Tran

@altaetran

7 months

@sarilog @KostChristian @kiran_r_patil @JFriedman_micro @RalserLab @NatureMicrobiol Fascinating work!

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Han Altae-Tran

@altaetran

1 year

@UWMadisonRNA Just study group II introns, problem solved! :)

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Han Altae-Tran

@altaetran

7 months

@matthewherper Throwback memories

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Han Altae-Tran

@altaetran

7 months

@livangoP Possibly. The new sickle cell data looks very promising, but long term safety needs to be assessed still

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Han Altae-Tran

@altaetran

7 months

@julirsch @Nature @illumina @IBE_Barcelona @bcmhouston Amazing evolutionary work!

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Han Altae-Tran

@altaetran

7 months

@eigie111 @science Really interesting work! I'm so glad yall decided to study these systems!

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Han Altae-Tran

@altaetran

7 months

@daniel_s_oh @ScienceMagazine @zhangf @soumya_kannan12 Thanks man, hope you're doing well in NY!

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Han Altae-Tran

@altaetran

8 months

@CeeZeeH @BIG_CenterWashU @wusm_pathology Super cool! Congrats!

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Han Altae-Tran

@altaetran

7 months

@breakliquid Haha they didn't expect a scientifically astute researcher to notice

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Han Altae-Tran

@altaetran

7 months

@Jwestrob Dali is the most sensitive search you can do at scale using distance matrix alignment rather than 2D DL based sequence alignment. These repeats do seem structural though!

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Han Altae-Tran

@altaetran

7 months

@sytelus @sarahookr Why is it not required for researchers to provide what they say they provide at the time of publication?

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Han Altae-Tran

@altaetran

7 months

@pdhsu looks amazing yo

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Han Altae-Tran

@altaetran

7 months

@microlacie Best of luck!

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Han Altae-Tran

@altaetran

7 months

@ardemp Not sure if I agree that 60 citations a year is "not catching much attention", but congrats on the long term success!

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Han Altae-Tran

@altaetran

7 months

@ir_rizzle yesterday

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Han Altae-Tran

@altaetran

7 months

@neuromichael I wonder this too man... I only became very obsessed with rodents after becoming a scientist

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Han Altae-Tran

@altaetran

7 months

@neuromichael Question: as I have contemplated pet mice many times, I always wonder if it would make it harder for me to separate emotion when doing research involving mouse work. Did you ever experience anything like this? Thank you!

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Han Altae-Tran

@altaetran

7 months

@tzerhan29 @ScienceMagazine @zhangf @soumya_kannan12 Thank you! Also congrats on your appointment!

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Han Altae-Tran

@altaetran

7 months

@Jwestrob Wow that's so cool! Glad it helped. Looking forward to seeing more about these systems!

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