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Alexis Lomakin, Ph.D.

@alexis-lomakin.bsky.social
314 followers 621 following 146 posts

Fascinated by the regulatory logic behind cell phenotype-environment interactions: How biological cells leverage the structural information encoded in protein molecules to morph themselves into shapes and sizes conferring environmental stress resistance.

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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 20h
www.nature.com/articles/s41...
nature.com
Bacteria regulate collective behaviour by mechanosensing cell–cell collisions - Nature Microbiology
Density-dependent regulation of collective order through collision sensing and collision-induced reversals provides a navigational advantage to Pseudomonas aeruginosa during surface colonization and n...
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Reposted by Alexis Lomakin, Ph.D.
Nature Ecology & Evolution @natecoevo.nature.com · 01/10/2026
A comparative analysis of multiomics data from embryonic and adult tissues of Atlantic salmon and rainbow trout reveals developmental and tissue-specific constraints shaping regulatory evolution following whole genome duplication 🧪 www.nature.com/articles/s41...
nature.com
Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids - Nature Ecology & Evolution
A comparative analysis of multiomics data from embryonic and adult tissues of Atlantic salmon and rainbow trout reveals developmental and tissue-specific constraints shaping regulatory evolution follo...
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Reposted by Alexis Lomakin, Ph.D.
Nature Biotechnology @natbiotech.nature.com · 30/09/2026
Stem cell differentiation is controlled by manipulating RNA condensates go.nature.com/3X215du rdcu.be/QMNfdKz92Ypa
go.nature.com
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
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Reposted by Alexis Lomakin, Ph.D.
Snezhka Oliferenko @alebenoit.bsky.social · 27/09/2026
People!!! This workshop will be ACE - please share, please apply!
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Reposted by Alexis Lomakin, Ph.D.
Nature Cell Biology @natcellbio.nature.com · 28/09/2026
☕Meiring, Mahapatra et al. show that expanded microtubule lattice conformations, such as those induced by small-molecule taxanes, can lead to the release of GEF-H1 and thus induce RhoA activation. www.nature.com/articles/s41...
nature.com
Taxane-induced conformational changes in the microtubule lattice activate GEF-H1-dependent RhoA signalling - Nature Cell Biology
Meiring, Mahapatra et al. show that expanded microtubule lattice conformations, such as those induced by small-molecule taxanes, can lead to the release of GEF-H1 and thus induce RhoA activation.
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Reposted by Alexis Lomakin, Ph.D.
Melanie D. White @melaniedwhite.bsky.social · 27/09/2026
The Nikon Small World AI controversy has me worried. AI is transforming science, but what happens once it can generate “raw data” indistinguishable from real data? How do we embrace AI without losing confidence in the data underpinning scientific discovery? www.the-scientist.com/allegations-...
the-scientist.com
Allegations of AI Use in Nikon Competition Spark Controversy | The Scientist
Microscopists raise concerns about inappropriate AI usage in Nikon's microscopy contest-winning video. Nikon stands their ground, citing no policy breach.
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Reposted by Alexis Lomakin, Ph.D.
John Tuthill @tuthill.bsky.social · 26/09/2026
this story about @couchmicroscopy.bsky.social captures science at its best: a scrappy team, a homemade microscope in a motel room, working under funding duress, pursuing a fundamental question about the evolution of photosynthetic organelles. www.nytimes.com/2026/09/26/s...
nytimes.com
In an $80 Motel Room, a Discovery to Shed Light on the Origins of Life
A scrappy science project led to a significant discovery: two new species of a rare organism that could elucidate a fundamental transition in the history of life on our planet.
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Reposted by Alexis Lomakin, Ph.D.
Mia Konjikusic, PhD @konjikusicmia.bsky.social · 25/09/2026
To add to all the lovely videos of non-AI processes multicilia beating: ctenophore multiciliated cells! They can reach up to 1mm long, causing a rainbow light refraction effect with the correct light positioning! Taken by myself at MBL in 2019 embryology. Realtime frame-rate!
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Reposted by Alexis Lomakin, Ph.D.
Journal of Cell Biology @jcb.org · 25/09/2026
Sydir, Lee, Pellman et al. @harvard.edu @danafarber.bsky.social identify an #ESCRT-independent pathway for #NuclearEnvelope assembly in S. japonicus that involves the conserved proteins, Vid27 and Alx1. rupress.org/jcb/article/... #CellCycle #CellDivision #Genetics #Biochemistry #Membrane #lipid
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Reposted by Alexis Lomakin, Ph.D.
PLOS Biology @plosbiology.org · 25/09/2026
A long-standing mystery in #neuroscience is how the length of myelin sheaths are matched to the axons they wrap. Marie Bechler &co show that #oligodendrocytes use Piezo1 to sense axon diameter and locally control sheath elongation 🧪 #NeuroSky buff.ly/9HdgiHt
This image depicts a single oligodendrocyte cell myelinating mixed diameter synthetic axons. The myelin basic protein immunofluorescence image has been colorized by confocal z-plane and modified with edge detection to highlight numerous myelin sheaths of different lengths formed by a single oligodendrocyte.  The longer myelin sheath formed on a larger diameter synthetic axon stands out in blue-green. Image credit: Marie E. Bechler
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Reposted by Alexis Lomakin, Ph.D.
Genes & Development @genesdev.bsky.social · 24/09/2026
🆕 ADVANCE ONLINE 🆕 RESEARCH PAPER: Temporal gating dictates stress-induced transcript export from the nucleus By Helton et al. and Stephanie Moon ➡️ ow.ly/Q5mn50ZR8fg Stephanie Moon #mRNA #stress #RNAexport
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Reposted by Alexis Lomakin, Ph.D.
Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026
🔬🚀 Out now in Communications AI & Computing: mAIcrobe, our open-source napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇 doi.org/10.1038/s44488-026-00022-y
Screenshot of the published article page. Software, Open access, published 15 September 2026. Title: mAIcrobe, an open-source framework for high-throughput bacterial image analysis. Authors: António D. Brito, Dominik Alwardt, Beatriz de P. Mariz, Sérgio R. Filipe, Mariana G. Pinho, Bruno M. Saraiva and Ricardo Henriques. Communications AI & Computing 1, article number 16 (2026), followed by the abstract.Diagram of the mAIcrobe workflow. Acquisition feeds into segmentation with StarDist, Cellpose and community models, then into morphological profiling and a three-class cell cycle classifier, ending in a feature-space scatter plot with three separated clusters.
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Reposted by Alexis Lomakin, Ph.D.
Joyce Meiring @joycemeiri.bsky.social · 24/09/2026
Excited to share that our latest story on #microtubule conformation controlling cell #signaling is now out in NCB! We show that microtubule expansion by taxane chemotherapeutics releases microtubule bound GEF-H1 which in turn activates RhoA/ROCK signaling. ✨ www.nature.com/articles/s41...
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Reposted by Alexis Lomakin, Ph.D.
Gautam Dey @gautamdey.bsky.social · 24/09/2026
Proud to contribute the World’s Hottest Mitotic Spindle™️ to this incredible study @fmikus.bsky.social @dudinlab.bsky.social #ProtistsOnSky
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Reposted by Alexis Lomakin, Ph.D.
Agathe Chaigne @agathechaigne.bsky.social · 24/09/2026
I'm super proud of this review written (mostly) by Zoé Ducarne and @myanhtruong.bsky.social about the extraordinary genomic features of the placenta. Such a crazy organ! journals.biologists.com/dev/article/...
journals.biologists.com
The curious case of the placental genome
Summary: The placenta is the only mammalian organ that harbors a cancer-like genome while remaining functional and healthy. This Review highlights its high mutational load, structural variants, aneupl...
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Reposted by Alexis Lomakin, Ph.D.
Proceedings of the National Academy of Sciences @pnas.org · 24/09/2026
Biology textbook descriptions of #chromosomes may fall short. The cellular structures aren’t composed of carefully folded #DNA, a recent study shows. Instead, they’re dual-phase gels. In PNAS Journal Club: ow.ly/jgBI50ZR52R #IonicHydrogel #histones #protein
The behavior of chromosomes matches that of an ionic hydrogel, which can exist in a decondensed or condensed phase. 
Image credit: Shutterstock / CHIARI VFX.
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Reposted by Alexis Lomakin, Ph.D.
Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...
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Reposted by Alexis Lomakin, Ph.D.
Manuel Mendoza @longchrom.bsky.social · 24/09/2026
Biophysics, membranes, evolution, yeast 🙌 @alebenoit.bsky.social does it again! www.cell.com/biophysrepor...
cell.com
Cellular membranes of the related fission yeast species differ in their dipole potential
The dielectric environment and membrane dipole potential are key electrostatic properties of biological membranes, which modulate the function of membrane-associated proteins. If and how these propert...
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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 23/09/2026
Meet the ‘fire amoeba,’ a record-breaking survivor of extreme heat share.google/Ry5i59a0Zr3L...
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Meet the ‘fire amoeba,’ a record-breaking survivor of extreme heat
Incendiamoeba cascadensis can replicate at 145° F, breaking the heat tolerance record for eukaryotes, a domain of life that includes plants and animals.
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Reposted by Alexis Lomakin, Ph.D.
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 18/09/2026
Fluorescence imaging-induced phospholipid oxidation drives membrane phase separation by shifting miscibility boundaries www.biorxiv.org/content/10.64898/20…
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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 12/09/2026
Microbial adhesion promotes Piezo1 activation to initiate innate immunity | Nature Immunology share.google/0BBvJ4eBz6kc...
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Reposted by Alexis Lomakin, Ph.D.
PLOS Biology @plosbiology.org · 03/09/2026
#Fungi must sense and prioritize nutrients to compete with microbes and form relationships with plants and animals. This study by @cornellcals.bsky.social shows that the regulator Cbr1 coordinates nutrient use and supports stable access to food sources. 🧪 #AcademicSky plos.io/4gt8htU
Cells of the fungus Rhodotorula toruloides expressing a fluorescently tagged citrate transporter (red). The cell walls (cyan) are fluorescently labeled using calcofluor white and the mitochondria (yellow) were fluorescently labeled using MitoTracker Green. 

Image credit: Joshua D. Kerkaert
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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 03/09/2026
Under deadly conditions, these sea creatures can age in reverse | Science | AAAS www.science.org/content/arti...
science.org
Under deadly conditions, these sea creatures can age in reverse
When stressed, this comb jelly reverts to a larval form, then matures again when favorable conditions return
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Reposted by Alexis Lomakin, Ph.D.
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 03/09/2026
Starvation improves epithelial fitness by selectively extruding DNA damaged cells www.biorxiv.org/content/10.64898/20…
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Reposted by Alexis Lomakin, Ph.D.
Thibaut Brunet @thibautbrunet.bsky.social · 02/09/2026
🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️
biorxiv.org
Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals
Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...
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Reposted by Alexis Lomakin, Ph.D.
Proceedings of the National Academy of Sciences @pnas.org · 01/09/2026
A review of antimicrobial resistance calls for AI-powered platforms to support and accelerate drug development alongside a community-driven approach that engages scientists, policymakers, health economists, clinicians, and patients. In PNAS Nexus: ow.ly/gwLt50ZHm7z
 A conceptual illustration of an inclusive, community-driven approach to address antimicrobial resistance.
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Reposted by Alexis Lomakin, Ph.D.
Itai Yanai @itaiyanai.bsky.social · 31/08/2026
Nobel Prize winner Ada Yonath sadly passed away today. She was a legend for her pioneering work on the structure of ribosomes.
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Reposted by Alexis Lomakin, Ph.D.
Molecular Cell @cp-molcell.bsky.social · 28/08/2026
Online Now: Intragenomic homologs with distinct phase behaviors broaden the range of cellular stress responses Online now:
dlvr.it
Intragenomic homologs with distinct phase behaviors broaden the range of cellular stress responses
Guan et al. show that bacteria use protein homologs with different material properties to regulate biomolecular condensates. By tuning the abundance of these proteins in heterotypic assemblies, bacteria balance condensate dynamics and stability, thereby maintaining fitness during stress.
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Reposted by Alexis Lomakin, Ph.D.
Genes & Development @genesdev.bsky.social · 27/08/2026
🆕 ADVANCE ONLINE 🆕 RESEARCH PAPER: Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes By Gomez-Gil et al., and Snezhana Oliferenko ➡️ ow.ly/VfIS50ZFkK4 Snezhka Oliferenko The Francis Crick Institute King's Faculty of Life Sciences & Medicine
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Reposted by Alexis Lomakin, Ph.D.
Journal of Cell Biology @jcb.org · 27/08/2026
Importin-9 and a TPR domain protein MpH drive periodic patterning of ciliary arrays in #Tetrahymena. From Anushi Suwaneththiya Deraniyagala, Wolfgang Maier, Jacek Gaertig and colleagues: rupress.org/jcb/article/... 📕 Part of #Centrosomes and #Cilia 2026: rupress.org/jcb/collecti...
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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 27/08/2026
Dry seeds preserve fully formed mitochondria, unlocking rapid energy at germination share.google/YhigOTa7kIkh...
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Dry seeds preserve fully formed mitochondria, unlocking rapid energy at germination
The majority of plant seeds have the special ability to almost completely dry out and yet remain viable. While most living cells die with a 90% loss of water, cells in seeds enter a biological state o...
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Reposted by Alexis Lomakin, Ph.D.
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 27/08/2026
Nuclear size is genetically controlled and influences cell fate www.biorxiv.org/content/10.64898/20…
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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 26/08/2026
Dolly Parton dies aged 80 – researchers celebrate her contributions to science www.nature.com/articles/d41...
nature.com
Dolly Parton dies aged 80 – researchers celebrate her contributions to science
The country singer was an advocate for vaccines, public health, literacy and marginalized communities.
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Reposted by Alexis Lomakin, Ph.D.
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 25/08/2026
Inflammatory restraint and membrane lipid integrity protect hematopoietic stem cells under stress www.biorxiv.org/content/10.64898/20…
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Reposted by Alexis Lomakin, Ph.D.
Cell Reports @cp-cellreports.bsky.social · 25/08/2026
Intermembrane coupling between Bcl-xL and the IP3 receptor supports local Ca2+ transfer at ER-mitochondrial contacts
dlvr.it
Intermembrane coupling between Bcl-xL and the IP3 receptor supports local Ca2+ transfer at ER-mitochondrial contacts
Ghosh et al. report that the anti-apoptotic Bcl2 family protein, Bcl-xL, primarily found in the outer mitochondrial membrane, interacts with endoplasmic reticulum resident protein inositol 1,4,5-trisphosphate receptors. This interaction facilitates local calcium transfer at the ER-mitochondria contacts but does not impact mitochondrial calcium transfer due to global changes in cellular calcium.
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Reposted by Alexis Lomakin, Ph.D.
Jan Lammerding - Lab @lammerdinglab.bsky.social · 26/08/2026
Interested in nuclear mechanobiology and want to know what some of the big open questions are in the field? Read our recent editorial with input from >15 leading experts in the field, along with a list of review articles on nuclear mechanobiology: www.tandfonline.com/doi/full/10....
tandfonline.com
Nuclear mechanobiology: a brief history and five unresolved questions
Published in Nucleus (Vol. 17, No. 1, 2026)
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Kate Cavanaugh @katecavanaugh.bsky.social · 25/08/2026
🧵 What if one reason fertility declines with age isn’t just genetic-but mechanical? Thrilled to share our new paper in @NatureCellBio : Elevated contractility drives implantation failure in mouse embryos from aged females… here’s what we found 👇 www.nature.com/articles/s41... 1/11
nature.com
Elevated contractility drives implantation failure in mouse embryos from aged females - Nature Cell Biology
Cavanaugh et al. show that embryos from aged mice have increased contractility and tissue viscosity on embryonic day 4.5, which leads to poor spreading and attachment. Similar age-associated mechanica...
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Reposted by Alexis Lomakin, Ph.D.
bioRxiv Genetics @biorxiv-genetic.bsky.social · 24/08/2026
The C. elegans endonuclease NUC-1 acts in engulfing cells to degrade the apoptotic cell DNA www.biorxiv.org/content/10.64898/20…
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Reposted by Alexis Lomakin, Ph.D.
eLife @elife.bsky.social · 23/08/2026
Lipid packing contributes to the confinement of caveolae to the plasma membrane
buff.ly
Lipid packing contributes to the confinement of caveolae to the plasma membrane
Membrane insertion of Dyngo-4a results in a dynamin-independent inhibition of caveola dynamics, revealing that outer leaflet lipid packing in the plasma membrane contributes to the confinement of caveolae.
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Reposted by Alexis Lomakin, Ph.D.
Andrea Musacchio @andrea-musacchio.bsky.social · 23/08/2026
www.science.org/doi/10.1126/... “MPIs operate on the Harnack principle: build an institute around a small group of exceptional scientists granted near-absolute autonomy. On paper, scientific paradise; in practice, junior scientists live entirely at the director’s pleasure.” Tranchant…
science.org
In (qualified) defense of the research project grant
In a debate that has been building for years, a growing coalition of reformers has concluded that the research project grant (RPG) approach used by many science funders in the United States and based ...
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Reposted by Alexis Lomakin, Ph.D.
Cell Reports @cp-cellreports.bsky.social · 23/08/2026
Organelle proteomics of human, neonatal pig, healthy and diabetic mouse islets
dlvr.it
Organelle proteomics of human, neonatal pig, healthy and diabetic mouse islets
Caliskan, Haas et al. present a cross-species subcellular proteomic atlas of pancreatic islets, revealing conserved organelle organization across human, pig, and mouse. The study uncovers disease-associated remodeling of vesicular trafficking, granule acidification machinery, and mitochondrial metabolism in a mouse model of type 2 diabetes.
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Reposted by Alexis Lomakin, Ph.D.
Nature Metabolism @natmetabolism.nature.com · 23/08/2026
COMMENT | R Khandelwal & AK Sharma (Imperial College London): How tissue-specific somatic mutations drive adaptive metabolism across the lifespan. 🧪
dlvr.it
Understanding the somatic evolution of metabolic traits - Nature Metabolism
Somatic mutations are linked to diseases, yet their prevalence and relevance in health remain poorly defined. Technological advancements now enable us to delineate how tissue-specific somatic mutations drive adaptive metabolism across the lifespan and uncover hidden determinants of health and drivers of diseases.
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Reposted by Alexis Lomakin, Ph.D.
Robert Arkowitz @robertarkowitz.bsky.social · 23/08/2026
www.aipoch.com/blog/claude-...
aipoch.com
Claude Science Review: Testing AI on a Full Bioinformatics Paper Reproduction Task
Claude Science reproduced Figures 1–14 of a breast cancer bioinformatics paper using Opus alone — 2 skills, 0 MCP calls. Here's what worked, what didn't, and why it matters.
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Reposted by Alexis Lomakin, Ph.D.
Robert Arkowitz @robertarkowitz.bsky.social · 21/08/2026
A bacterial metabolite rewires fungal metabolism, triggering the hyphae-to-yeast transition: Current Biology www.cell.com/current-biol...
cell.com
A bacterial metabolite rewires fungal metabolism, triggering the hyphae-to-yeast transition
The hyphae-to-yeast morphological transition promotes dissemination of the pathogen Candida albicans, but the mechanisms underlying this process are poorly defined. By identifying a bacterial metaboli...
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Reposted by Alexis Lomakin, Ph.D.
bioRxiv Developmental Biology @biorxiv-devbio.bsky.social · 21/08/2026
Loss of cohesin subunit Stag1 in zebrafish limits cell cycle progression and is compensated by altered BMP signalling and metabolic pathways www.biorxiv.org/content/10.64898/20…
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Robert Arkowitz @robertarkowitz.bsky.social · 21/08/2026
RAD51 stabilizes neutrophil extracellular traps to compartmentalize inflammation | Science www.science.org/doi/10.1126/...
science.org
RAD51 stabilizes neutrophil extracellular traps to compartmentalize inflammation
Neutrophil extracellular traps (NETs) feature a branched chromatin architecture whose origin and function remain unknown. We found that NET branching is mediated by RAD51, a protein generating DNA jun...
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Alexis Lomakin, Ph.D. @alexis-lomakin.bsky.social · 17/08/2026
phys.org/news/2026-07...
phys.org
Life speaks one universal language to activate genes: It speaks many more to silence them
The signals that cells use to switch genes on have remained almost unchanged across 2 billion years of evolution, but the ones used to switch genes off vary dramatically from one branch of life to ano...
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Reposted by Alexis Lomakin, Ph.D.
Yves Van de Peer @yvdp.bsky.social · 10/08/2026
Polyploidy: A macromutational force pushing bioeconomic developments | PNAS www.pnas.org/doi/abs/10.1...
pnas.org
Polyploidy: A macromutational force pushing bioeconomic developments | PNAS
Polyploidization, the consequence of genome doubling, is a macromutation that reshapes genomes, phenotypes, and ecological interactions. Polyploidi...
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Kutay lab @kutaylab.bsky.social · 09/08/2026
We are excited by the publication of our work on Torsin1A, its interaction partner CLCC1, and their role in membrane fusion during NPC biogenesis! A fantastic collaboration with @jagannathan-lab.bsky.social @labvanni.bsky.social @gautamdey.bsky.social and the Korkhov and Antonin labs!
cell.com
The dystonia-associated Torsin1A sustains CLCC1 function in membrane fusion of the nuclear envelope for NPC biogenesis
Maslennikova et al. identify the ER membrane protein CLCC1 as an interaction partner of the dystonia-linked AAA+ ATPase Torsin1A. Torsin1A sustains the function of CLCC1, which is proposed to facilitate fusion of the nuclear envelope during NPC biogenesis by forming an oligomer that promotes lipid bilayer approach and remodeling.
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Reposted by Alexis Lomakin, Ph.D.
Nature @nature.com · 30/07/2026
Nature research paper: Intestinal stem cells count self-renewal divisions to switch multipotency go.nature.com/45uYCwn
go.nature.com
Intestinal stem cells count self-renewal divisions to switch multipotency - Nature
In Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing an enteroendocrine mother cell every ninth division.
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