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Fernando Bazan

@jfernandobazan.bsky.social
111 followers 229 following 5 posts

curious about all things bio & solving tricky structural puzzles / mlbio for protein design, engineering & drug disco / cytokine immunologist / stanfordberkelyucsf & dnaxgenentech / recovering twit

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Reposted by Fernando Bazan
Barbara Mellone 🇺🇦 @centromellone.bsky.social · 21/07/2026
America's R1 universities educate ~8–9 million students (undergraduate + graduate) -> more than 1/3 of U.S. college students (vs. the ~0.6% of Ivies). Undermining this system threatens the institutions that train our workforce and drive scientific innovation. www.science.org/doi/10.1126/...
science.org
An American research crisis with real human consequences
Ivy League universities have dominated recent news headlines, having become popular targets for critics of higher education. But the threats they face—cuts to federal research funding, assaults on aca...
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Ján Bíňovský @jbinovsky.bsky.social · 02/07/2026
🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...
nature.com
Why a synthetic human genome is still worth building
A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.
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Sorek Lab @soreklab.bsky.social · 03/06/2026
Our paper is out in Nature Microbiology: functional analysis of 80 phage sponges, revealing new sponges that inhibit bac immunity by binding the immune signals cCMP, cUMP and N7-cADPR Thanks to all coauthors and our collaborators at the Kranzusch Lab. Congrats Romi! www.nature.com/articles/s41...
nature.com
Functional diversity of phage sponge proteins that sequester host immune signals - Nature Microbiology
A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.
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Reposted by Fernando Bazan
Mann Lab @mannlab.bsky.social · 28/05/2026
1/5 Cell identity is written in the proteome, not in the DNA, and not always in the RNA. Out on bioRxiv today: The first cell type-resolved, MS-based proteomic atlas of the human body. www.biorxiv.org/content/10.6...
biorxiv.org
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Ryan Flynn @raflynn5.bsky.social · 28/05/2026
Happy to share a new review: Functional Inclusion of RNA Biology in the Tethered Extracellular Matrix We discuss the emerging interface of RNA biology and the ECM. The way biology solved protein-HS interactions is very similar to RNA-protein! wires.onlinelibrary.wiley.com/doi/10.1002/...
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Reposted by Fernando Bazan
Derek Lowe @dereklowe.bsky.social · 28/05/2026
An unapologetically angry post about what’s being done to US science:
science.org
The Current Crisis: What's Happening to Science in America
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pmamtraveller.bsky.social @pmamtraveller.bsky.social · 19/05/2026
Artist Riccardo Albiero "Quiet the Room" Oil and Watercolour on Board (2025)
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Nick Loman @pathogenomenick.bsky.social · 08/05/2026
First genome sequence from Andes hantavirus strain from ongoing ship outbreak posted on Virological: virological.org/t/complete-s... courtesy Swiss National Reference Centre for Emerging Viral Infections, Geneva University Hospitals, University of Zurich
virological.org
Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026
Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 04/05/2026
Shelduck And Coot, 2024 by Joseph Lynch. UK contemporary artist. Acrylic on canvas | 50 x 50 cm. #art #painting #artist #BlueSkyArt
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Richard Morris @ahistoryinart.bsky.social · 01/05/2026
'Sun, Sea and Sky: a Summer Phantasy,' (1892) is unique in John Atkinson Grimshaw’s body of work. It's remarkable in its minute Boudin-like detail with each grouping of figures given characterisation and individuality, location: Scarborough in Yorkshire.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 30/04/2026
"Toward life with a 19–amino acid alphabet through generative artificial intelligence design" www.science.org/doi/10.1126/... Turns out isoleucine isn't essential
Tasting notes for isoleucine ("This is a weak, tasteless compound with a flat, dry consistency...)

Taken from: "Taste of nutrients: Amino acids, vitamins, and fatty acids"
https://doi.org/10.3758/BF03203878
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Derek Lowe @dereklowe.bsky.social · 01/05/2026
Let’s see how this goes over:
science.org
An Open Letter to Jay Bhattacharya
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Rabih Alameddine @rabihalameddine.bsky.social · 02/05/2026
Dmitri Cavender "Very Steep Hill," 2007 Oil on canvas 24 x 24 in
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Pedro Beltrao @pedrobeltrao.bsky.social · 22/04/2026
"A minimal, pedagogical PyTorch reimplementation of AlphaFold2" github.com/ChrisHayduk/...
github.com
GitHub - ChrisHayduk/minAlphaFold2: A minimal PyTorch re-implementation of AlphaFold2's model & training
A minimal PyTorch re-implementation of AlphaFold2's model & training - ChrisHayduk/minAlphaFold2
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marzzistar.bsky.social @marzzistar.bsky.social · 16/04/2026
🎨 David Hockney
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BejaLabTechnion @bejalab.bsky.social · 13/04/2026
Cryo-EM structure of a photosystem I supercomplex from Euglena gracilis containing pentameric LHCE and dimeric LHCII www.nature.com/articles/s41...
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Sorek Lab @soreklab.bsky.social · 07/04/2026
Our current understanding of the Metis defense system - carved in wood By @naamalila.bsky.social www.biorxiv.org/content/10.1...
Would carving of the mechanism of Metis antiphage defense
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Alexey Amunts @amunts.bsky.social · 07/04/2026
65 years after Peter Mitchell’s chemiosmotic theory, we report an association between ATP synthase and the electron transport chain. In the preprint led by @longzhou88.bsky.social, we describe a large supercomplex and show how the supramolecular organization contribute to oxidative phosphorylation 🧵
langtaosha.org.cn
A Supercomplex Incorporating Both Electron Transport Chain and ATP Synthase
The mitochondrial oxidative phosphorylation system powering most aerobic organisms is typically depicted as two spatially segregated machineries(1): electron transport chain complexes I-IV (ETC CI-CIV
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 07/04/2026
Johannes Müller-Franken (German, born 1960) "Woman Carrying a Bicycle", 1989. Acrylic, Oil on Canvas, 47.24 × 31.5 inches. Private Collection #art #painting #artist #BlueSkyArt
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 31/03/2026
Cori Lee Marvin (Canadian Artist, born 1980) "The Penguin", 2021. Watercolor, 14 × 14 inches. Private Collection. #art #painting #artist #BlueSkyArt
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Pedro Beltrao @pedrobeltrao.bsky.social · 31/03/2026
We will probably stop in a few weeks and cover all-by-all for around 4200 ORFs. We are around 80% of this goal and we will try to work quickly through the analysis of this. We already have several interesting observations from doing this in a pool setting that go beyond predicting interactions.
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Clinton Lau @ckylau.bsky.social · 30/03/2026
Check out our first lab preprint: A real team effort to understand the Plasmodium GAPM proteins, which form part of a essential bridge between the parasite's cytoskeleton and motility apparatus. Below is a sneak peek of some beautiful microscopy - light and electron! www.biorxiv.org/content/10.6...
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Joost Snijder @joostsnijder.bsky.social · 30/03/2026
Structure of SARS-CoV-2 spike in complex with its co-receptor the neuronal cell adhesion protein contactin1 www.biorxiv.org/content/10.6... Check out our new preprint. Cool structure by Sabrina Krepel with Bert Janssen. Thanks to @danielhurdiss.bsky.social @utrechtvirology.bsky.social #covid #pais
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 29/03/2026
Leiko Tar (Japanese/Swiss Artist, born 1951) "Wait", 2026. Mixed Media, Oil and Acrylic. Digital Painting. #art #painting #artist #BlueSkyArt
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Joseph Lewczak (Truth Seeker) @truthseeker59.bsky.social · 27/03/2026
David Hockney
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FrancineNewYorkForever🏒🏀⚾️ @sportlover.bsky.social · 26/03/2026
Good morning all Piet Mondrian
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 14/03/2026
This is really nice work on conformational entropy of proteins by Kaitlin Trenfield. Check it out. Dihedral angle changes and distributions are key.
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 11/03/2026
Kate Jarvik Birch (American Artist, born 1977) "Red Cup of Espresso", 2025. Gouache on Paper, 6 × 6 inches. Private Collection. #art #painting #artist #BlueSkyArt
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Terre-Strial @terre-strial.bsky.social · 01/02/2026
“Minnesota's nickname is the North Star State due to its motto "L'Etoile du Nord," which was adopted in 1861. Minnesota is the North Star State. ✨ Consider this fact whenever you're feeling despair at what's happening in our country right now. Follow our North Star.” - Mari Talkin
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 01/02/2026
Peter Eugén (Sweden Artist, born 1978) "Tree and Boat in Lake", 2024. Watercolor, 30 × 40 cm. Private Collection. #art #painting #artist #BlueSkyArt
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 30/01/2026
Follow up to Doug Hanahan’s visionary article about the stages of cancer development from back in the 1990s www.cell.com/cell/fulltex...
cell.com
Hallmarks of cancer—Then and now, and beyond
Hanahan revisits the evolving framework of cancer hallmarks, synthesizing 25 years of conceptual refinement into a multidimensional view of tumor biology. This review highlights how aberrant capabilit...
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The EMBO Journal @embojournal.org · 28/01/2026
See also the great News&Views comment by Monica Gobran and @plenart.bsky.social - highlighting all three papers! link.springer.com/article/10.1...
link.springer.com
Mitotic entry: Bora takes Polo to Aurora, and gives them a hug - The EMBO Journal
The EMBO Journal - Cell division involves the complete reorganization of the cellular architecture, requiring precise coordination of cellular processes in space and time, but how does this control...
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Milot Mirdita @milot.bsky.social · 20/01/2026
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
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Rabih Alameddine @rabihalameddine.bsky.social · 20/01/2026
Tomás Sánchez, Ojo de aguas Tempera on paper, 2005 22,5 x 30 cm | 8 ³/₄ x 11 ¹³/₁₆ in
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Edward Marcotte @edwardmarcotte.bsky.social · 16/01/2026
Very sad to hear about the passing of Peer Bork, one of true giants of computational biology www.embl.org/news/embl-an...
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 12/01/2026
Happy to finally share the amazing results of our long-term collaboration with Karin Reinisch’s lab on how bridge lipid-transfer proteins (BLTPs) cooperate with partner proteins to orchestrate lipid delivery. A quick thread (1/7) www.biorxiv.org/content/10.6...
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Eugene Serebryany @eserebry.bsky.social · 09/01/2026
Proud to share our newest preprint. We introduced conformational constraints (disulfides) into alpha-synclein and measured effects on aggregation. There were surprises, including a possible new amyloid polymorph and a substoichiometric chaperone-like aggregation inhibitor. doi.org/10.64898/202...
doi.org
Disulfide engineering reveals unexpected pro- and anti-aggregation conformers of human α-synuclein
Intrinsically disordered proteins can aggregate in many distinct conformations (polymorphs). Polymorphs are a striking example of fold-switching: one primary structure able to form distinct tertiary s...
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Jim Musil Painter @jimmusilpainter.bsky.social · 07/01/2026
My painting DARK STORM
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Jakob Farnung @jakobfarnung.bsky.social · 06/01/2026
When RNA Degradation 🤝 meets 🤝 Protein Degradation! tinyurl.com/E3TDMD In a collaboration of @bartellab.bsky.social and Schulman lab, we show that, in target-directed microRNA degradation (TDMD), 2-RNA-factors recruit an E3 ligase and induce the degradation of not only a protein but also RNA (1/5).
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Erika Lee Sears @erikaleesears.bsky.social · 07/01/2026
Orange slices #oilpainting #art
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/01/2026
Nice description of ipTM problems & how actifPTM, LIS, & ipSAE fix those for scoring protein-protein interactions. New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.
af2rechain.py

Takes input legacy-PDB format file and splits single chain AF2 model into separate chains given starting residue numbers for domains/regions.

Output pdb file can then be input into ipsae.py to calculate intraprotein ipSAE values between domains.

Example:
   python3 af2rechain.py AGC_AKT1_model.pdb 123 141 409

will create output PDB file named "AGC_AKT1_model_rechain.pdb" with
     chain A: residues 1-122
     chain B: residues 123-140
     chain C: residues 141-408
     chain D: residues 409-480 (end of original chain A)

Note: by default, first chain begins on residue 1 and last chain ends on last residue of input chain A

Then run ipsae.py on json file and PDB file to get intraprotein ipSAE values:
       python3 ipsae.py AGC_AKT1_model.json AGC_AKT1_model_rechain.pdb 10 15
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Rabih Alameddine @rabihalameddine.bsky.social · 31/12/2025
László Moholy-Nagy. 7am, New Year’s Morning, Berlin, 1930
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 24/12/2025
Franco Matticchio (Italian Artist, born 1957) "The Pillow and surroundings", 2016. Illustration. #art #painting #artist #BlueSkyArt
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Cell Chemical Biology @cp-cellchembiol.bsky.social · 15/12/2025
Online now! Online now! Single-cell glycome and transcriptome profiling enabled by a library of anti-glycan antibodies #chembiol
dlvr.it
Single-cell glycome and transcriptome profiling enabled by a library of anti-glycan antibodies
Marglous et al. generated a database of anti-glycan antibody sequences, expressed and characterized a library of 154 antibodies, and generated DNA-barcoded antibodies for single-cell transcriptome and glycome profiling. Glycans associated with cancer stem cells and metastasis were uncovered, demonstrating utility for basic and clinical research.
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 06/12/2025
Hiroo Isono ( 1945-2013) japanese painter and illustrator, known for his intricate and fantastical scenes of tropical jungles and animals. #art #painting #artist #BlueSkyArt
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ΜΑΝΟΣ ΤΡΑΧΙΑΣ™ @trahias.bsky.social · 06/12/2025
Pablo Picasso 1881-1973. Rafael Nogueras and a Friend at Els Quatre Gats Barscelona, 1899-1900. Oil on canvas. Tel Aviv Museum of Art. #art #painting #artist #BlueSkyArt
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Waggoner Lab @labwaggoner.bsky.social · 05/12/2025
Extrusive and cohesive cohesin cooperate to repair double-strand breaks in DNA @science.org @albertomarin.bsky.social @gerlichlab.bsky.social @imbavienna.bsky.social www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...
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