Keith Siklenka

Postdoc in the Reddy lab at DukeU. Interested in genomics. Study how regulatory elements contribute to gene expression and cell fate

[Keith Siklenka @siklenkak]

Excited to see our preprint made it into QED's top 1%. Combining STARR-seq with CRISPRi and high-res 3D chromatin capture, we identify multi-enhancer hubs critical for Th17 cell identity, a step towards linking regulatory function to specific physical interactions.

Read their summary here - https://t.co/IxloWPbgCi

[Oded Rechavi @OdedRechavi]

Gloves are off!

TODAY WE RELEASE THE 1%

A list of the year’s very best papers.

When we launched QED a little over half a year ago, I told you that our mission is to revolutionize scientific publishing. Revolutions don’t happen overnight… or maybe they do? When new technologies enable it? Time to put the power back in the scientists’ hands, not the journals’. Many scientists are depressed, and think journals will stay the same forever, no matter how dysfunctional, but no, it’s happening. Sooner than most people (or committees, or universities) can imagine. Check this out:

When we released our AI review platform, it started a whole debate (and social media storm) on what it is that human reviewers can do that AI review still can’t. There are such things (and I’m happy about it), but the list is getting shorter and shorter. Numerous scientists already use QED to find gaps in their manuscripts and grants and to get constructive feedback that improves their experiments. And now, with your help, we take it to the next level.

Today we release reviews and scores for all the experimental Life Science pre-prints that came out last year: 57,455 manuscripts!! If we are being conservative, and estimate that it takes a minimum of 8 hours to review a paper (it takes longer), and if we agree that 3 reviewers are typically required to review every submission, then reviewing this amount of manuscripts would take human experts >1 MILLION REVIEWER HOURS… Assuming you can find so many experts (not going to happen!), and assuming the experts who agree would have no conflict of interest (ha!!).

QED did it. Then, we chose the best papers in every field (you can browse and search for key words), based on the originality and validity of the claims being made. We benchmarked our reviews not only using eventual journal selections but also by comparing our evaluations to those of human experts. When there were disagreements between the QED score and journal rank, we asked domain experts to judge who’s right (blindly), and they overwhelmingly sided with QED. No need to rely on glam journals anymore. No need to wait for two years to get their stamp of approval. No need to beg the reviewers, or worse, to write less ambitious papers, so no one would be upset. Want to find the most interesting papers in your field? Want to see where your paper stands? (“What’s your QED SCORE?”) Just visit https://t.co/hLxNq9nDMc!

One last thing: We want good science to be seen (you can read the winners’ comments about their selection and the stories behind their discoveries on our website). We plan to organize a conference where the first authors (yes, the first authors, not the PIs) will present their work. We are not here to shame anyone (papers that got low scores). The reviews of the best papers that we selected explain why QED’s AI thought these papers are especially good - what’s unique about them, what their strengths are, which conceptual leaps were made, and what cutting-edge tools were developed. However, on the QED Science site you can analyze any paper in private, it’s fully transparent, and see if there are any gaps and what’s missing. Run your paper to see how it can improve, and maybe next time your paper will reach the top (if it’s not there already).

Whether you’re on the 1% list of just have a good score that you want to share, on our website you can download the report and share it, for example with your tenure, promotion, or hiring committee, or with your university PR department. Forget about journal embargoes and waiting for it to be “accepted”. Improve your work until it’s good enough for YOU. You decide.

[Keith Siklenka @siklenkak]

Our preprint "Enhancer hubs govern chromatin topology and Th17 cell identity" is now up on BioRxiv! We welcome your feedback https://t.co/ii6sPoyGee

[Nature Methods @naturemethods]

An Analysis presents a collection of non-coding CRISPRi screens from the ENCODE4 Functional Characterization Centers and establishes experimental guidelines for future screens identifying cis-regulatory elements. @ReillyLikesIt
https://t.co/QYYpApqhDW

[Steve Reilly @ReillyLikesIt]

So you're thinking about doing a #CRISPR screen...
@ENCODE_NIH is here to help! The CRISPR group is proud to share:
“Multi-center integrated analysis of non-coding CRISPR screens”

Lotsa great stuff inside for newbies and experts, here's a quick tour
https://t.co/7sxxexmYmM

[Keith Siklenka @siklenkak]

@lough_kendall We are!

[Keith Siklenka @siklenkak]

Excited to share our mouse models for in vivo epigenome editing. Grateful to have been part of this awesome team. Can’t wait to see what discoveries come from using these tools.

[Charles Gersbach @cgersbach]

We're very happy to see this published with the hope that others will be able to use these models to study function and regulation of their favorite genes and noncoding elements. Mice are available at Jax: https://t.co/9ZqSHwaIsg https://t.co/8flLbT9MGj

[Keith Siklenka @siklenkak]

@ReillyLikesIt @YaleGenetics @YaleMed Congrats Steve. Great news!!

[Blanca Pijuan-Sala @BPijuanSala]

PAPER ALERT! Excited to share our work studying the chromatin accessibility landscape of early mouse organogenesis at the single-cell level, published today @NatureCellBio!! You can check it out here https://t.co/tazEMaOVja
Summary thread below:

[Victor Corces @CorcesVictor]

Our paper describing the epigenome of mouse germ cells is out @MolecularCell . We show that CTCF loops present in the gametes are inherited in a parent-of-origin specific manner and they become the same in both homologs by the 8-cell stage https://t.co/JTY98sLAnz

[Dewran Koçak @dewrankocak]

Our paper is finally out! We show that RNA secondary structure regulates the activity of diverse CRISPR systems. Easy enough to believe but give it a read:
https://t.co/VjwaJLLMit …
@NatureBiotech

[Keith Siklenka @siklenkak]

@timreddy Visual evidence of effective mentorship... or that there are only 2 stores in Durham.

[Keith Siklenka @siklenkak]

@AcademicsSay The PI Menace
Attack of the Undergrads
Revenge of the Postdoc

A New Manuscript
Reviewer 3 Strikes Back
Return of the Collaborator

The Last Submission
The Editor Awakens

Reviewer One
Solo: A Tenure Track Story
#academicMovieTitles

[Adam Chekroud @drchekkers]

our new @TheLancetPsych paper was the biggest ever study of exercise and mental health. it caused quite a stir! here's my guided tour of the paper, highlighting some of our excitements and apprehensions along the way [thread] 1/n https://t.co/hvlzstkISR

[Serge McGraw @McGraw_Lab]

We are hiring!
My lab is recruiting a #postdoc to study the impact of #Epigenetic dysfunction on cell lineage specification.

Help us spread the word!!

For more info : https://t.co/mmf9GAxbZ5

[Keith Siklenka @siklenkak]

@alexbortvinlab @KimminsSarah Thanks Alex. Nice to hear from you.

[Keith Siklenka @siklenkak]

@KimminsSarah Thanks everyone. Exciting times ahead!

[Bluma Lesch @ambystoma22]

Excited to be starting my lab at Yale in the fall! Looking for postdocs into evolution, reproduction, chromatin: https://t.co/XZRhoWfIOj

[Keith Siklenka @siklenkak]

@McGraw_Lab @virginie_b_l @ChuSteJustine congrats!! ✍️💰

[Keith Siklenka @siklenkak]

Thank a scientist for herd immunity. You can find them in droves today #MarchForScience #evidencebased #factsmatter https://t.co/RD09wgaau1

[Timothy Caulfield @CaulfieldTim]

"Canada eradicated measles in 1998 — so why is it making a comeback?" https://t.co/ywd7JFyCwu via @nationalpost