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Teif Lab@TeifLab·6 Eyl

My first interview in a major podcast :) Quite an interesting experience! Thank you very much for inviting @epigenetics_pod

Epigenetics Podcast@epigenetics_pod

In this episode we talked to @TeifLab from the University of Essex about his work on nucleosome positioning in #cancer #diagnsotics. #podcast #Epigenetics Listen here: activemotif.com/podcasts-vladi…

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Teif Lab@TeifLab·6 Mar

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/54… A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy! #nucleosomics #nucleosome #chromatin #cfDNA

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Teif Lab@TeifLab·14 Oca

Congratulations to Negin Behboodi on successfully passing your PhD viva! We are so proud of you! Keep an eye out for Negin's upcoming big papers! And thank you to the kind examiners @mikhailspivakov and @amarcobio!

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Teif Lab@TeifLab·31 Ara

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Teif Lab@TeifLab·24 Kas

Some refs on nucleosome-mediated cooperativity in TF binding: ▶️Concept suggested by Polach & Widom, 1996: sciencedirect.com/science/articl… ▶️Our first single-bp resolution model, 2010: cell.com/biophysj/fullt… ▶️Its application to TFs at enhancers, 2011: iopscience.iop.org/article/10.108…

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Teif Lab@TeifLab·19 Kas

Congratulations to Amishasingh Beeharry for successfully passing the MSD viva! You are the best, Amisha! Thank you very much to the examiners, Abdenour Soufi and Toni Marco!

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Teif Lab@TeifLab·16 Kas

@SylvanBacaLab @jberchuck @manoliskellis Congratulations on your preprint! You may be also interested in this one: x.com/TeifLab/status…

Teif Lab@TeifLab

Great to see that this preprint used our software NucTools to calculate NRL, and reached conclusions confirming our previous paper, which reported effect of linker histones H1 on cfDNA fragmentation patterns and nucleosome spacing in cancer tissues/cfDNA link.springer.com/article/10.118…

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Sylvan Baca MD PhD (Hiring!)@SylvanBacaLab·12 Kas

Much more in the preprint! Looking forward to translational applications to study cancer evolution and guide treatment selection. Grateful to @jberchuck, @manoliskellis, and our other collaborators who made this happen!

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Sylvan Baca MD PhD (Hiring!)@SylvanBacaLab·12 Kas

Excited to share our latest preprint by Alexis Yang and Gary Lee, in collab with the @jberchuck lab: biorxiv.org/content/10.110…. We found that transcription of enhancers (a mark of activation) causes distinct fragmentation patterns in #cfDNA.

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Teif Lab@TeifLab·16 Kas

Great to see that this preprint used our software NucTools to calculate NRL, and reached conclusions confirming our previous paper, which reported effect of linker histones H1 on cfDNA fragmentation patterns and nucleosome spacing in cancer tissues/cfDNA link.springer.com/article/10.118…

Sylvan Baca MD PhD (Hiring!)@SylvanBacaLab

Excited to share our latest preprint by Alexis Yang and Gary Lee, in collab with the @jberchuck lab: biorxiv.org/content/10.110…. We found that transcription of enhancers (a mark of activation) causes distinct fragmentation patterns in #cfDNA.

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Teif Lab@TeifLab·15 Eyl

Happy to announce that our department (School of Life Sciences at the University of Essex) is upgraded to number 6th out of 91 UK universities in the subject area Biology according to the Guardian University Guide 2026. theguardian.com/education/ng-i…

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Teif Lab@TeifLab·8 Tem

Very happy to contribute to this CTCF-nucleosome paper by @ElenaPugachev12 &Co. Exciting science and a cool journal cover!

Elena Pugacheva@ElenaPugachev12

Excited to share our latest study published in Nucleic Acids Research: academic.oup.com/nar/article/53… It’s the cover story for Issue #12! We drew inspiration from Greek mythology to illustrate CTCF’s constant struggle in shaping the 3D genome architecture.

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Elena Pugacheva@ElenaPugachev12·8 Tem

Excited to share our latest study published in Nucleic Acids Research: academic.oup.com/nar/article/53… It’s the cover story for Issue #12! We drew inspiration from Greek mythology to illustrate CTCF’s constant struggle in shaping the 3D genome architecture.

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Teif Lab@TeifLab·1 Haz

NHS announced that it will start offering first liquid biopsy tests for diagnostics of lung and breast cancer; also planning expansion to pancreatic and gallbladder cancers england.nhs.uk/2025/05/nhs-fi…

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Teif Lab@TeifLab·27 Mar

We have a postdoctoral opening for a researcher with experience in bioinformatics of DNA sequencing and machine learning to work on the development of new methods for cancer diagnostics related to nucleosomes, chromatin and more jobs.ac.uk/job/DMK060/sen…. Apply by 21st April 2025!

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Teif Lab@TeifLab·6 Mar

Very happy to contribute to this paper about cfDNA in SCLC, led by the team of Anish Thomas. It's already online in Genome Medicine: Takahashi et al., Genomic alterations and transcriptional phenotypes in circulating free DNA and matched metastatic tumor genomemedicine.biomedcentral.com/articles/10.11…

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Pancreatic Cancer UK@PancreaticCanUK·6 Mar

Early detection of #PancreaticCancer saves lives. @TeifLab @EssexLifeSci are using cutting-edge technology to measure fragments of tumour DNA in the blood. This "liquid biopsy" could provide an accurate & affordable new test for pancreatic cancer: bit.ly/3F3vXF1

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IsabellaC@isabella_ciu·31 Oca

2nd time at #FOG2025 (1st time presenting!), it never disappoints!✨ Great talks, groundbreaking research and good times with old&new friends Huge thanks to everyone who stopped by my poster, truly grateful for the interest & discussions Already looking forward to next year!🙌

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IsabellaC@isabella_ciu·17 Oca

So excited for the festival and this great opportunity to present my research 😄

Front Line Genomics@FLGenomics

We're pleased to share that @isabella_ciu (PhD Student, University of Essex) will be sharing her research in the #FOG2025 Poster Zone! Register now: hubs.la/Q032Q75f0

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Teif Lab@TeifLab·10 Oca

@vitaliikl @StevenSalzberg1 @DaveJuergens The paper actually says they use ATAC-seq as input. It's not just from sequence

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Vitalii Kleshchevnikov, PhD@vitaliikl·10 Oca

@StevenSalzberg1 @DaveJuergens I agree with the point about impossibility to predict from sequence alone - but it’s a problem with how people communicate what these models do - models that use only DNA sequence as input (like Enformer) introduce sample/cell type-specific latent variables in the last layer.

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Steven Salzberg 💙💛@StevenSalzberg1·9 Oca

Is this real, or is it excessive AI hype? New paper claims that an AI foundation model achieves experimental-level accuracy in predicting gene expression even in previously unseen cell types." I'll read the paper, but don't believe it for a second nature.com/articles/s4158…

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IsabellaC@isabella_ciu·7 Oca

Low quality picture but… Had to show the matching glasses 🤭🤓

Teif Lab@TeifLab

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Teif Lab@TeifLab·6 Oca

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Teif Lab@TeifLab·2 Oca

Interestingly, the BBC coverage attributed this success to NHS testing vans stationed in busy areas where any person can walk-in without referral. Probably technological genomics developments also contributed to this improvement, in any case these are set to help going forward

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Teif Lab@TeifLab·2 Oca

Encouraging news to start the new year: NHS reports 2.7% improvement in early cancer diagnostics in comparison to pre-pandemic levels. An estimated additional 7,000 patients diagnosed at an early stage.

NHS England@NHSEngland

Latest NHS data shows that the proportion of patients being diagnosed with cancer at an early stage in England has risen to its highest ever level. Find out more about the latest data. ➡️ england.nhs.uk/2025/01/early-…

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