Updates in dplyr 1.1.0. Bye bye `group_by()`, hello `.by`:

Incredible! Kansas city, Missouri votes 11-1 to make the city a sanctuary city for gender affirming care. It has looked at the anti-trans laws passed in the legislature, and said, "enforce it yourself." These are some of the best protections of any city out there.

Do only pioneer TFs open chromatin? No! Does motif affinity affect how well pioneering TFs work? Yes! Learn more by checking out our manuscript, now out in Developmental Cell! sciencedirect.com/science/articl…

Perl, R, Python 😂

Please join us in congratulating Khyati Dalal (Khyati Dalal), @KUMedcenter #graduatestudent in the Julia Zeitlinger (@[email protected]) lab, on a successful #thesisdefense! 👏 Well done.

There is so much talk lately about #ArtificialIntelligence (#AI) – but what exactly is it? Melanie Weilert, Bioinformaticist in the ZeitlingerLab, explains what it is & how it's used at the Institute & in medical #research. #WorldAIWeek MORE: bit.ly/45zKorD

Happy to share my postdoc work about enhancer-enhancer cooperativity! Find out more at biorxiv.org/content/10.110…

Gorgeous paper, Surag Nair ! Fascinated by the nature of low-affinity OctSox enrichment across transient peaks during reprogramming. Very useful work! biorxiv.org/content/10.110…

Check out our latest work led by Surag Nair & Mo Ameen using neural nets to dissect the interplay of TF stoichiometry, motif affinity & syntax in fibroblast reprogramming to iPSCs. Several fascinating insights from the models. biorxiv.org/content/10.110… Tweetorial coming soon 1/

Excited to share work with co-first author Mo Ameen. Gene regulation is a delicate balance b/w cis-regulatory sequence & TF conc, but these components are often studied in isolation. Reprogramming is a fantastic system to study their interplay 1/16 biorxiv.org/content/10.110…

The sequence syntax that boosts TF binding also transfers to their signaling TF partners. Excellent work, Khyati Dalal !

Best fit imaginable #laboratory

The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ Joseph Rich et al. we take a close look. The results are 👀 1/🧵

Our latest - how does DNA sequence dictate the chromatin response to changing transcription factor levels? 1/n biorxiv.org/content/10.110…

Attributions are invaluable in genomics for identifying the drivers of model predictions, but it's easy to make a mistake WITHOUT REALIZING. Here is a short vignette describing the challenges you might encounter and how tangermeme makes it easier for you. github.com/jmschrei/tange…

Check out ProCapNet by Kelly Cochran, a robust, local sequence context deep learning model of base-resolution transcription initiation profiles (PRO-cap) that provides deep insights into the cis-regulatory code of initiation & more ... biorxiv.org/content/10.110… 1/

Last week we kicked off our first #OpenMicScience of the summer with presentations from Amanda Lawlor, A.J. Treichel, and Melanie Weilert. 👏 #science #biology

Excellent talk by Michael Hoffman @michaelhoffman.bsky.social predicting transcription factor binding. Old school motif-based approaches are not the answer, most TF binding sites lack TF’s sequence motifs. #ISMB2024 1/

It was an honor to defend my PhD thesis today Stowers Institute. I am so appreciative of my advisor Julia Zeitlinger (@[email protected]) for her guidance and mentorship, as well as my committee members Matt Gibson, BazziniLab , Jerry Workman, and Chris Rushlow for their support! What a terrific day!

🎉 Excited to share the peer-reviewed version of our manuscript describing COBIND, a tool for revealing TF co-binding patterns using non-negative matrix factorization. Great work led by Ieva Rauluševičiūtė NCMM Nordic EMBL P'ship UiO - Det medisinske fakultet Universitetet i Oslo academic.oup.com/nar/advance-ar… Nucleic Acids Res