Xin ZENG

Computational postdoc fellow at Siepel Lab @asiepel, Cold Spring Harbor Lab. Interested in modeling transcriptional regulation by machine learning methods.

[Xin ZENG @Shinzeng_Bio]

Excited to share the first paper from my postdoc! 🎉

Promoter-proximal Pol II pausing is usually summarized by a single number. But is that enough?

We find that pausing has distinct kinetic and spatial dimensions—and they do not always change together.

https://t.co/UE8SZe5ftw

[nature @Nature]

The most successful early-career researchers often rely on a network of mentors who each have different roles — from advising on research and grants to making professional introductions and providing emotional support
https://t.co/QpXeDxoufD

[Shilatifard Lab @ShilatifardLab]

We’ve been trying to crack locus-specific control of transcriptional regulation and the role of Pol II pause/release and transcriptional elongation control for years. Now, a new postdoctoral fellow in the lab, David Lowe, may have identified an exciting path forward. His analysis offers a provocative new way to think about how the extraordinary complexity and plasticity of human transcription can be regulated at specific genes and loci. Take a look at his work, and keep an eye out for his next few papers. I think they may change how we think about gene- and locus-specific transcriptional regulation @NU_BMG_SQE @MolecularCell @CellPressNews @ScienceMagazine @Nature @NatureGenet @theNASciences @NUFeinbergMed https://t.co/EV48q4fI10

[Ming "Tommy" Tang @tangming2005]

A nice python package for creating Publication-Ready Scientific Plots https://t.co/WX2kvXtzxU

if you use R, take a look at https://t.co/HgyiQA7CbA

[Ivan @chaperones4life]

The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation https://t.co/OeJ9XJ22RS

[Molecular Cell @MolecularCell]

Online Now: Genome-wide rotational and translational phasing of nucleosomes with human transcription factors https://t.co/bb5trMfJgN

[Jonathan Henninger @jehenninger]

Excited to share the first pre-print from our lab!!

Check it out here! https://t.co/N72qCF2V4c

We found that many RNA-binding proteins understood to regulate RNA processing can also function like transcription factors and cofactors to directly regulate transcription.

[Xin ZENG @Shinzeng_Bio]

https://t.co/8rJX9YFmDW

[antisense. @razoralign]

PoolParty: streamlined design of DNA sequence libraries in Python https://t.co/D8FaV6JV0k

[Nature Reviews Molecular Cell Biology @NatRevMCB]

New Online! Systemic epigenetic dysregulation as a driver of ageing and a therapeutic target https://t.co/kfDApyZZKS

[Taka Nojima @pol2rna]

当研究室と@STOPlabPIの共同研究がEMBO Repに出ました👏SETD2やH3K36me3が、「間接的に」転写終結を制御することを明らかにしました。大学院生２人（野島研中山千尋さんとKKG Lab のMagda）の研究成果です🎉https://t.co/1r9ODvDlyo

[Nature Reviews Drug Discovery @NatRevDrugDisc]

Epigenetic editing: from concept to clinic
https://t.co/O7Ps5IKptM
https://t.co/ZjO4C40MsD

This Review in the March issue covers approaches to reprogramme gene expression by rewriting epigenetic signatures, and discusses challenges including target specificity and delivery

[Trends in Genetics @TrendsGenetics]

RNA polymerase II: the elephant in the room https://t.co/lfPkAzd9r2

[Stephen Turner @strnr]

Gene regulatory networks: from correlative models to causal explanations https://t.co/avvT7Stc8R 🧬💻🧪 https://t.co/jjMg2zYXCA

[Peter Koo @pkoo562]

Excited to share new finetuning scripts for AlphaGenome in JAX! This was in collaboration with @anshulkundaje group.

As part of the initial release, we provide lightweight wrapper to finetune AlphaGenome on functional genomics (i.e. bigwig) tracks.

[Taka Nojima @pol2rna]

投稿から２年、大変な難産でしたが、大学院生の中山さんが頑張りました🙂NELFが転写終結を制御していること、その制御が破綻した際に、転写と複製のコンフリクトが起きることを明らかにした論文です。英米日の国際共同研究 @Michael_Tellier @DaigakuYasu @ShilatifardLab
https://t.co/0Od4kt92iD

[Peter Koo @pkoo562]

Excited to share a new Review: "Toward Interpretable and Generalizable AI in Regulatory Genomics" with @msyk_nagai @Al_Murphy_ @kae_rizzo

We lay out the landscape of AI x Genomics and offer an opinionated perspective on where the field should go!

https://t.co/gN0HjiJ3WG

[Shilatifard Lab @ShilatifardLab]

Aging through transcriptional elongation control: https://t.co/ZEdKIa02wC Pleased to share extraordinary findings led by Dr. Saeid Parast @SaeidMP (postdoctoral fellow in our lab), in collaboration with Dr. Vijay Ramani’s lab, identifying key roles for the transcriptional elongation factors NELF & ELOA in cellular senescence & aging. Our findings indicate that proper 3′-end processing during transcription elongation is a critical regulator of senescence & aging. Our lab’s complementary, unpublished animal studies further support an essential role for transcription elongation control in organismal aging. Take a look at this paper—and stay tuned for what’s next. Congratulations Saeid! @NU_BMG_SQE @NUFeinbergMed @UCSF @MolecularCell @CellPressNews @ScienceMagazine @Nature @NatureGenet @theNASciences @NatureAging @Aging_Cell @GeroScienceAGE

[細胞運命コード @EpicodeOfficial]

胡桃坂計画研究代表による成果が Science Advances 誌に掲載されました!
Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture
https://t.co/xEkXl3XCkI

[Ming "Tommy" Tang @tangming2005]

8 Resources to study Transcription factor binding, enhancers and histone modification distribution
 1. ENCODE https://t.co/N5hScyoAoP