Gene Regulation
@generegulation
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Gene regulation community. #chromatin #nucleosome #TFbinding #CTCF #cancer #epigenetics. Personal views do not represent @TeifLab. Mostly moved to 🦋 and 🐘
London, UK
Joined January 2013
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 https://t.co/eaPqOWINHN
Excited to share our latest preprint by Alexis Yang and Gary Lee, in collab with the @jberchuck lab: https://t.co/cb3pRjketO. We found that transcription of enhancers (a mark of activation) causes distinct fragmentation patterns in #cfDNA.
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10% of human transcription factors are oligomeric. Stoichiometry can be dialled to modulate transcription. We show CREB searches DNA mixtures as a dimer, and suggest this might be common amongst other members of the bZIP family which fold on binding DNA. https://t.co/4UZWB9Odaw
biorxiv.org
The operation of Eukaryotic transcription factors remains enigmatic. Cyclic AMP-responsive element-binding protein (CREB) is a member of the basic zipper family, a superfamily of transcription...
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Excited to share our latest study published in Nucleic Acids Research: https://t.co/ZSFQt4DI57 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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@sara_mostafavi (@genentech ) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
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Perspective on recent developments and challenges in regulatory and systems genomics https://t.co/dn8pts7diL is out, amazing to think about this with @JuliaZeitlinger, @ferhatay, @mahonylab, @AMathelier, @AleMedinaRivera, @jernst98!
academic.oup.com
Abstract. Summary: Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the
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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 https://t.co/7btyVTeDR8. Apply by 21st April 2025!
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I am so happy to see this work finally out 🎉 https://t.co/g157pqC1fz Thanks to all the authors for the incredible teamwork!!!
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❤️🔥 Passionate about gene regulation research, wet/dry lab? 🎡 Excited about London's vibrant research and social scene? 🔬 Looking for a funded postdoc position (+ ideally, have the CV & drive to apply for a fellowship in your 1st year)? Please DM/email me to discuss!
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My first, first author paper is now on bioRxiv! 🤩 Linker histone H1 is a liquid-like "glue" condensing chromatin, which revises textbooks! 📖✨ https://t.co/ASW9Vxxhro Huge thanks to my PI, @kazu_maeshima, for supervision. Amazing collab with @rcollepardo’s group!" (1/n)
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🚨 Registration for the Molecular Biosystems Conference is now OPEN! Join us to discuss cutting-edge research in gene regulation & functional genomics. 📅 Sep 29-Oct 3, 2025 📍 Puerto Varas, Chile 🔗 Register here: https://t.co/VyNn7FjUKL Register now—space is limited!
molbiosystems.com
Leading Latin American conference on Eukaryotic Gene Regulation & Functional Genomics.
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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
Background Profiling circulating cell-free DNA (cfDNA) has become a fundamental practice in cancer medicine, but the effectiveness of cfDNA at elucidating tumor-derived molecular features has not...
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Our latest preprint on emergent #3Dgenome reorganization from the stepwise assembly of the #transcriptional #condensates. Check it out! #GeneExpression #chromatin @generegulation @Pha_Tran_Papers @4DNucleome #cellularstress
biorxiv.org
Transcriptional condensates are clusters of transcription factors, coactivators, and RNA Pol II associated with high-level gene expression, yet how they assemble and function within the cell remains...
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New paper alert! The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and DNA repair efficiency https://t.co/uKPBE6QumT.
academic.oup.com
Abstract. Lung cancer sequencing efforts have uncovered mutational signatures that are attributed to exposure to the cigarette smoke carcinogen benzo[a]pyr
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We are looking to recruit a highly motivated postdoc with cell or molecular biology expertise. Excellent #epigenetics, #chromatin training & networking opportunities @qmulepigenetics DM me for inquiries pl apply/share https://t.co/hUEgP6fpMp
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IT'S HAPPENING! The Woodstock of Biology 2.0 meets Night Science @nightsciencepod 10-13 of June in Prague & the Woods of Bohemia... Be there or be REJECTED. #theconferencetoendallconferences
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Our new study shows in our that the fate of foreign DNA in a eukaryote depends on its GC content. It can either packaged into active or inactive chromatin. https://t.co/gcjPiGnv8F
science.org
In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and...
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Shifting the pitch and contours of Waddington’s valleys, putative enhancers, and transcription through H3K27me3 chromatin in the endoderm. Find it all here: https://t.co/3VUYiyOFlo. Fantastic collaboration with @josh_brickman and @wendy_bickmore. Well done Jurriaan and @djmbio.
journals.plos.org
Author summary Embryogenesis requires a tightly coordinated programme of cellular expansion and specialisation to gives rise to all of the cell- and tissue-types of the developing organism. In...
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Happy to contribute to this excellent story about heterochromatin role in centromere maintenance, led by @ben_carty93 ! Heterochrom. boundaries control centromere expansion, drift & number! Great usage of induced neocentromere model and modern epigenomics across the labs🥳
What is the molecular basis for maintaining centromere size and position? In a great collaboration with @NAltemose @GiuntaLab and @FachinettiLab labs, we investigate the long standing question of how heterochromatin maintains centromere size/position! https://t.co/I41gYDcL8B
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CPGE's most recent publication on cohesin function and chromatin domain organization is out now in Science Advances. This thread will take a look at some of the key observations from the paper! #chromatin #epigenetics #genomics #northwestern #dna
https://t.co/NYZ0lRNplh
science.org
RAD21 contributes to nascent packing domain formation, but maturation requires nucleosome posttranslational modifications.
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Transcription ahead of chromatin regulation? Activation in endoderm occurs prior to K27me3 removal, plus much more. A tribute to our collaborations with @wendy_bickmore and @RobertIllingwo7, who worked tirelessly to insure this data saw daylight! https://t.co/cS2fJWbdYr
journals.plos.org
Author summary Embryogenesis requires a tightly coordinated programme of cellular expansion and specialisation to gives rise to all of the cell- and tissue-types of the developing organism. In...
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