Iana V. Kim
@ianakim.bsky.social
Postdoctoral researcher in the Sebe-Pedros and Marti-Renom Labs at CRG. Transposable elements enthusiast, passionate about piRNAs, 3D genomes, and Star Trek 🖖
Reposted by Iana V. Kim
Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.
January 9, 2026 at 11:44 AM
Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.
Reposted by Iana V. Kim
Nature research paper: An expanded registry of candidate cis-regulatory elements
go.nature.com/4pAbARf
go.nature.com/4pAbARf
An expanded registry of candidate cis-regulatory elements - Nature
The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types.
go.nature.com
January 9, 2026 at 4:25 PM
Nature research paper: An expanded registry of candidate cis-regulatory elements
go.nature.com/4pAbARf
go.nature.com/4pAbARf
Huge congrats, Dr. Alberti 🎉!
November 14, 2025 at 7:28 AM
Huge congrats, Dr. Alberti 🎉!
Check out this beautiful work from our lab and discover how some corals adapted to live without symbionts 🪸https://www.nature.com/articles/s41586-025-09623-6 !!! Huge congratulations to Shani Levy and @xgrau.bsky.social. It was a privilege for me to contribute to your project 🙏
October 27, 2025 at 10:06 AM
Check out this beautiful work from our lab and discover how some corals adapted to live without symbionts 🪸https://www.nature.com/articles/s41586-025-09623-6 !!! Huge congratulations to Shani Levy and @xgrau.bsky.social. It was a privilege for me to contribute to your project 🙏
Congratulations, Alex 👏👏👏
October 9, 2025 at 5:04 AM
Congratulations, Alex 👏👏👏
Really grateful to see our work featured by @quantamagazine.bsky.social in this piece on the evolution of genome regulation. Huge thanks to @philipcball.bsky.social for such a beautifully written article.
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
October 8, 2025 at 8:49 PM
Really grateful to see our work featured by @quantamagazine.bsky.social in this piece on the evolution of genome regulation. Huge thanks to @philipcball.bsky.social for such a beautifully written article.
Reposted by Iana V. Kim
A thoughtful and beautifully written @quantamagazine.bsky.social article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to @philipcball.bsky.social for this fantastic piece.
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
October 8, 2025 at 7:04 PM
A thoughtful and beautifully written @quantamagazine.bsky.social article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to @philipcball.bsky.social for this fantastic piece.
Reposted by Iana V. Kim
🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
May 13, 2025 at 7:55 PM
🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
Reposted by Iana V. Kim
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
The genomic origin of the unique chaetognath body plan - Nature
Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...
www.nature.com
August 13, 2025 at 4:38 PM
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
Reposted by Iana V. Kim
Updating my intro slides with this fantastic figure now! (And maybe I'll add an extra dashed line for my beloved bryophytes)
Happy to have contributed to this great article: #Protist genomics: key to understanding eukaryotic evolution. Congrats Alexandra Schoenle et al. #ProtistsOnSky
authors.elsevier.com/sd/article/S...
authors.elsevier.com/sd/article/S...
June 13, 2025 at 7:47 AM
Updating my intro slides with this fantastic figure now! (And maybe I'll add an extra dashed line for my beloved bryophytes)
Reposted by Iana V. Kim
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...
rdcu.be
May 27, 2025 at 12:19 PM
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Reposted by Iana V. Kim
Our new paper is out@ScienceAdvances👇
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2
March 29, 2025 at 1:06 AM
Our new paper is out@ScienceAdvances👇
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2
Thank you so much, Lorenza :)
May 11, 2025 at 5:54 PM
Thank you so much, Lorenza :)
Thank you very much, Thibaut!
May 7, 2025 at 9:58 PM
Thank you very much, Thibaut!
thanks a lot, Claus! :)
May 7, 2025 at 4:14 PM
thanks a lot, Claus! :)
There’s much more to explore in the paper—so dive in! It also opens exciting questions for future research: What is the role (if any) of loop extrusion in the formation of these structures? Are these loops dynamic across development/cell types? When did insulating sequence elements evolved?
May 7, 2025 at 3:23 PM
There’s much more to explore in the paper—so dive in! It also opens exciting questions for future research: What is the role (if any) of loop extrusion in the formation of these structures? Are these loops dynamic across development/cell types? When did insulating sequence elements evolved?
This is our (current/tentative) model for the early evolution of animal chromatin architecture.
May 7, 2025 at 3:23 PM
This is our (current/tentative) model for the early evolution of animal chromatin architecture.
Finally, in unicellulars, chromatin architecture is “passively” defined by active/repressive chromatin states, without evidence of sequence elements or specific factor binding. See for example co-segregating repressive domains in Sphaeroforma, highly enriched in TEs:
May 7, 2025 at 3:23 PM
Finally, in unicellulars, chromatin architecture is “passively” defined by active/repressive chromatin states, without evidence of sequence elements or specific factor binding. See for example co-segregating repressive domains in Sphaeroforma, highly enriched in TEs:
In sponges we do not identify loops, despite the existence of distal enhancers. We hypothesize this could be explained by the relative proximity (<10Kb) of these enhancers to the closest TSS. What we do observe are prominent chromatin jets/fountains, as also recently described in other species.
May 7, 2025 at 3:23 PM
In sponges we do not identify loops, despite the existence of distal enhancers. We hypothesize this could be explained by the relative proximity (<10Kb) of these enhancers to the closest TSS. What we do observe are prominent chromatin jets/fountains, as also recently described in other species.
In the cnidarian Nematostella, we observe multiple enhancer-promoter loops, including some very distal ones (1Mb). Interestingly, here loops show a characteristic one-sided stripe, which may suggest active extrusion (?).
May 7, 2025 at 3:23 PM
In the cnidarian Nematostella, we observe multiple enhancer-promoter loops, including some very distal ones (1Mb). Interestingly, here loops show a characteristic one-sided stripe, which may suggest active extrusion (?).