The day’s most consequential preprints — curated, contextualized, and read by the field.
This Week
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83 papers curated for you today
Yuly, J. L.; Avallone, M.; Abad, L.; Wingreen, N. S.
These phages play the ultimate microbial sugar daddy, helping pricey plasmids survive by crashing bacterial parties in a quirky evolutionary bargain that blurs parasite and pet lines.
Hu, H.; Krah, D.; Ntolkeras, A.; Chanda, S.; Heimbrodt, A.; Mondal, M.; Altendorf, J.; Jing, B.; Berger, B.; Shaib, A. H.; Rizzoli, S.; Boyden, E. S.
In a mind-bending microscopic makeover, scientists crank expansion microscopy to a ridiculous 1,000x (that's billion-fold by volume!), turning tiny cell bits into Olympic-pool-sized wonders so even basic light microscopes can spy on amino-acid distances like nosy neighbors with super binoculars.
Klumpe, H.; Loshinsky, S.; Hart, D.; Tong, K.; Dunlop, M.; Khalil, A. S.
When synthetic biologists glue cells into multicellular clumps, it's like forcing introverts into a never-ending group project—this preprint hilariously probes how "sticking together" messes with their individual fitness and quirky group behaviors via reformable bonds and nutrient sharing.
Chaudhary, N.; Yang, W.; Kalamkar, D.; Zhou, J.; Ghosh, S.; Xia, L.; Tiwari, M.; Heinecke, A.; Kaul, B.; Misra, S.
In a cheeky tech rebellion, Intel researchers show humble Xeon CPUs can outpace fancy H100 GPUs at AlphaFold2 protein folding with a 1.76x speedup, flipping the "GPUs rule everything" script like an underdog CPU victory dance.
Behera, B. P.; panda, B.
Like herding 350k wild preprints into one searchable online rodeo, this new Preprint Commons platform unifies bioRxiv/medRxiv data for meta-researchers with quirky analytics tools that make tracking science trends feel like a delightful data playground.
Townley, J.; Kladwang, W.; Baker, D.; Blair, H. M.; Choe, C.; El Nesr, G.; Favor, A.; Fisker, E.; Haack, D. B.; He, S.; Hingey, J.; Huang, R.; Huang, P.-S.; Joshi, C. K.; Karagianes, T. G.; Kubaney, A.; Lio, P.; Mancino, A.; Romano, J.; Rudolfs, B.; Spellmon, N.; Toor, N.; Wu, V.; Yu, Z.; Eterna players, ; Das, R.
In a sci-fi lab twist, AI dreams up the first synthetic RNA that folds into a crisp, never-before-seen 3D atomic structure—like a digital origami master crafting a brand-new molecular ballerina that actually stands up straight in real life.
Cho, Y.; Tsuboyama, K.; Litberg, T. J.; Jung, M. D.; Obisesan, A.; Wang, Q.; Phoumyvong, C. M.; Thibeault, J.; Ovchinnikov, S.; Rocklin, G. J.
Scientists measured a whopping 1.8 million protein stabilities in a massive data bonanza, then built a predictor so sharp it turns tiny domain design into a reliable game—think of it as a quirky molecular fortune-teller that actually gets the folding future right most of the time.
Toghani, A.; Garro, M.; Frijters, R.; Kamoun, S.; Contreras, M. P.
AlphaFold 3 finally unmasks a slippery plant immune receptor handshake that dodged labs for years—like a molecular detective catching a fleeting high-five between sensor and helper proteins in a dramatic NLR family reunion.
Hulse, B. K.; Aneesh, P. B.; Romani, S.; Jayaraman, V.; Hermundstad, A. M.
Fly brains pull off elegant navigation with messy, uneven neural wiring instead of perfect symmetry— a quirky real-world hack that keeps their internal compass spinning smoothly like a wonky but reliable fidget spinner.
Zhao, F.; Inague, A.; Peters-Clarke, T. M.; Chen, Y.; Ganjave, S. D.; Zhang, Y.; Miao, K.; Yao, Z.; Wu, Y.; Seto, M. K. C.; Leung, K. K.; Olzmann, J.; Wells, J. A.
Biotech wizards craft sneaky bispecific "KineTACs" that hijack LRP8 (selenium delivery guy) for lysosomal trash disposal, starving cancer cells of their antioxidant armor and making ferroptosis the surprise party crasher they can't resist.
Wherry, E. J.; Ngiow, S. F.
In an immuno-oncology plot twist worthy of a sci-fi reboot, long-term PD-1 blockade turns out to exhaust the exhausted T cells' progenitors like overtraining a quirky gym bro, but a strategic "drug holiday" lets them bounce back stronger with fresh Tpex energy and even teams up with CD22 co-blockade for extra drama.
Bilbo, S.; Patton, M.; Sun, W.; Stanley, L.; Paredes, A.; Kang, J. Y.; Schettewi, Z.; Horvath, B.; Dziabis, J. E.; Devlin, B.; Vaidyanathan, T. V.
Mom's junk-food pregnancy remodels baby boy mouse brains like a mischievous microglia interior decorator gone wild—beefing up serotonin highways in the reward center for turbo-charged motivation, while girls dodge the dopamine drama entirely.
Rawoof, A.; Lin, Y. T.; Rajendran, S.; Antoine, G.; Jayasundara, S.; Cai, Y.; Singh, D.; Whitehead, P.; Dornberger, H.; Mall, S.; Alonso, A. P.; Carroll, M. C.; Skellam, E.; Chapman, K. D.
Plants go full pharma-factory mode as scientists cram seven fungal genes into Nicotiana benthamiana leaves, turning tobacco into a living penicillin G synthesizer—complete with perfect subcellular compartmentalization, no signal peptides needed, like Mother Nature suddenly moonlighting as a biotech wizard.
May, G. E.; McManus, J.
A clever new massively parallel reporter assay called IRES-TrAPPr catches sneaky Internal Ribosome Entry Sites in the act, revealing that many "IRESes" from old screens are duds while viral ones from warm-blooded hosts evolved extra structural toughness to fold properly at body temperature—like viral mRNAs wearing thermal jackets.
wu, Z.; D'Alba, L.; Chang-Fu, Z.; Clarke, J.; Li, J.; Shawkey, M.; Li, Q.
Fossilized pterosaur fluff reveals photonic melanosome nanostructures straight out of a disco ball—producing shimmering green-to-magenta iridescence in Sinopterus, proving these ancient flyers rocked flashy colors long before birds stole the spotlight.
Cai, T.; Cruz, N. M.; Basu, S.; White, R. M.; Mayr, C.
In a molecular matchmaking plot twist, long conserved 3′UTRs don’t just chit-chat—they physically link up like quirky RNA wingmen, coaxing transcription factors and β-catenin into co-folding protein complexes on the fly to turbocharge Wnt signaling during stem cell dances.
Vanderlinden, L. A.; Vargas, J.; Inamo, J.; Young, J.; Wang, C.; Zhang, F.
scLASER rides to the rescue like a time-traveling single-cell simulator, spotting sneaky longitudinal dynamics in rare cell types and messy clinical trajectories (think IBD stromal shifts and COVID T-cell rollercoasters) way better than old-school clustering.
Toghani, A.; Seager, B. A.; Sugihara, Y.; Roijen, L.-M.; Azcue, J. M.; Garro, M.; Sargolzaei, M.; Morianou, I.; Harant, A.; Gallop, S.; Kourelis, J.; MacLean, D.; Contreras, M. P.; Kamoun, S.; Lüdke, D.
AlphaFold gets an upgrade with the Structural Novelty Index (SNI) to hunt weird protein complexes, uncovering an 11-mer "undecameric" resistosome assembly that flips the usual hexamer script like a quirky oligomer surprise party.
Ji, P.; Ren, K.; Han, X.; Li, E.; Wang, P.; Bi, H.; Cai, W.; Aydemir, I.; Wai, C. M.; Niu, H.; Yang, J.; Liu, Y.; Vadasz, B.; Sukhanova, M.; Fang, D.; Cui, W.
In TET2-mutant bone marrow, stromal cells go full pyroptosis drama queen via Gasdermin D, recruiting quirky TFH-like CD4 T cells into a chaotic feed-forward loop that turbocharges myeloid disease—until you cut the CD40L gossip.
Robinson, N. E.; Paul, J.-S.; Zhang, W.; Zhang, H.; Wang, S.; Zhao, T.; Abraham, E.; Simpson, B.; Wang, K.
DNA synthesis goes mega-scale with Sidewinder tech turning oligo pools into complex constructs in one glorious pot like a molecular assembly line on steroids, supercharging AI-driven synthetic biology dreams with parallel wizardry.
YAMAMOTO, T.; Kawasaki, K.; Fukaya, T.
Transcriptional bursting gets a quirky polymer physics makeover where genes act like micelle-forming molecules in a bubbling cauldron of chromatin, neatly explaining noisy gene expression bursts through phase-like behaviors and local crowding antics.
Gutierrez, J. C.; Chen, Y.; Babaian, A.; Dhindsa, R. S.; Lareau, C. A.
In a massive data-mining detective story, scientists sift through petabytes of human genomes to catch HSV-1 quietly reactivating inside specific RORB+ neurons like a sneaky brain saboteur, linking viral hijinks to dementia risk with single-nucleus precision.
Sehgal, E.; Politanska, Y.; Mitra, R.; Kim, P. T.; Gonzalez Rodriguez, N.; Warrier, T.; Kubaney, A.; Morishita, A.; Quijano, R.; Butcher, J.; Krishna, R.; Pecoraro, R.; Belmont, B.; Roullier, N.; Goreshnik, I.; Vafeados, D. K.; Kwon, P.; Ramarao, R.; Taipale, J.; Glasscock, C. J.; Baker, D.
In a protein-design party gone wild, RFdiffusion3 and friends ditch the usual structure-first diffusion drama to whip up custom DNA-binding proteins with hilarious precision, turning abstract sequence dreams into reality like a molecular matchmaker on steroids.
Mies, G.; Mathieson, I.
Ancient DNA sleuths use clever local ancestry tricks to spot strong selection signals in Neolithic Europeans, revealing how our ancestors genetically adapted in quirky, population-specific ways during big farming transitions.
Khwanbua, E.; Lappe, R. R.; Bierl, A. A.; Whitham, S.
A plant virus turned CRISPR courier: engineered TuMV sneaks gRNAs into tobacco leaves for transformation-free editing, with Csy4 processing boosting efficiency dramatically—multiplexing genes like a viral pizza delivery service that actually works.
Guo, F.; Tong, K.; Yang, J.; Yuan, F.; Tang, M.; Gan, Y.; Wu, S.; Tong, X.; Luo, P.; Chen, S.; Ji, H.
Mice get a built-in hibernation button thanks to a newly mapped neural circuit that flips them into safe, long-term torpor mode—basically nature's quirky snooze feature for surviving tough times without the usual risks.
Clark, R.; Smith, L. G.; Leighton, M. P.; Szukalo, R. J.; Khalid, S.; Debenedetti, P. G.; Cossio, P.; Astore, M. A.; Hanson, S. M.
Cryo-EM's rapid plunge into ice gets a molecular dynamics reality check on whether it freezes proteins in their natural poses or creates cooling artifacts, with simulations revealing tricks to recover true equilibrium ensembles like a thermodynamic time-travel correction.
Tzalavras, A.; Osher, D. E.; Cocuzza, C. V.; Nallan Chakravarthula, L.; Mill, R. D.; Peterson, K. L.; Cole, M. W.
Neuroscientists built an openly playable "digital twin" of mouse retinal inputs to the superior colliculus, letting you virtually poke neurons with any stimulus (like looming threats) before wasting months in the lab—finally, hypothesis testing with zero mouse guilt.
Blattman, S. B.; Maslah, N.; Varela, A. A.; Kumpaitis, K.; Nalbant, B.; Snopkowski, C.; Mariani, M.; Kida, L. C.; Takizawa, M.; Ratnayeke, N.; Yu, K. K. H.; Fernandes, S.; Mousavi, N.; Borgstrom, E.; Vallejo, D.; Boghospor, L.; Xin, R.; Mignardi, M.; Wu, S.; Scarlott, N.; Delgado-Rivera, L.; Kumar, P.; Krishnan, S.; Giraudier, S.; Kiladjian, J.-J.; Howitt, B. E.; Kohlway, A.; Lund, P.; Pe'er, D.; Chaligne, R.; Lareau, C. A.
GIFT genotypes hundreds of mutations while reading the full transcriptome from fixed single cells. It's like giving old FFPE samples a high-tech DNA barcode upgrade, revealing how mutant clones drive inflammation in blood cancers.
Liu, J.; Ibarraran, S.; Hu, F.; Park, A.; Dunn, A.; Rotskoff, G.
While everyone obsesses over rigid protein structures, this team flips the script with language-model RL to design messy intrinsically disordered proteins, complete with a playful web demo that feels like AI mad-libs for molecular chaos.
Thompon, A.; Venter, C.; de Villiers, W. J.; De Swardt, D.; Laubscher, G. J.; Kell, D. B.; Pretorius, E.
A new high-res flow cytometry method detects sticky platelet-monocyte clumps that fuel clotting and inflammation in Long COVID. Broadly applicable to any post-viral thrombo-inflammatory condition.
Ushiki, A.; Kelman, G.; Sheng, R.; Murray, E.; Eckalbar, W.; Zhang, Y.; Nobuhara, M.; Rajani, R.; Friess, K.; Barskyi, V.; Ngo, K.; Kinoshita, S.; Schlebusch, S. A.; Mason, M.; Zhan, S.; Liang, M.; Fong, S.; Haider, M. Y.; Singhal, V.; Schountz, T.; Hockman, D.; Illing, N.; Kaplan, T.; Ahituv, N.
Enhancers and gene expression tweaks explain how tiny rodent limbs morph into bat wings. A developmental genetics crossover highlighting evolution's tinkering at the DNA level.
Lu, P.; Izzy, S.; Da Silva, P.; Imkamp, H. T.; Christenson, J. R.; Yahya, T.; Mansi, M. H. A.; Alawi, A.; Moreira, T. G.; Monje, M.; Weiner, H. L.; Iwasaki, A.
In a mouse model of Long COVID brain fog, a nasal squirt of anti-CD3 antibody acts like an immune reset button—even weeks after infection. It dampens cranky microglia, boosts neuron birth in the hippocampus, and sharpens memory.
Ishibashi, T.; Nishizawa, R.; Ogita, G.; Tokushige, N.; Shibata, T.
Cells decide their collective "lefty or righty" through a tug-of-war of forces at adhesions. Cell-cell and cell-substrate pulls together determine which way the whole tissue twists.
Amer, K.; Moustafa, A.; Hassan, W. A.; Adel, E.; AbdElaal, K. R.; Ghanim, T. A.; Abd El-Raouf, A.; El-Hosseiny, A.; El-Sayed, A. F.; Badr, A. H.; Hassan, A.; Kotb, A.; Ragheb, A.; Muhammad, A. M.; Ali, A.; Abdelaal, A.; Ramadan, E.; El-Garhy, F. M.; El Shehaby, H.; Ali, M. A.; Albarbary, M.; Zahra, M. A.; Amer, M.; Elmonem, M. A.; Fahmy, N. T.; Abdel-Haseeb, O. M.; Hassan, T. M.; Daoud, Y. A.; Howeedy, Y.; Farouk, Y. K.; Soror, S.; El-Feky, G.; Sakr, M.; Soliman, N. A.; Gad, Y. Z.; Abdel-Ghaffar, K. A.; Egypt Genome Consortium,
Sequencing over a thousand Egyptian genomes reveals the rich genetic tapestry of the region, painting a detailed picture of population structure and diversity that fills a major gap in North African genomics—like finally zooming in on a long-blurry part of the human family portrait.
Kojima, A.; Kawakami, K.; Kobayashi, N.; Kobayashi, K.; Matsui, T. E.; Uemoto, K.; Gu, Y.; Narita, T. J.; Kugawa, M.; Fukuda, M.; Kato, H. E.
GPCR structures used to be a nightmare of linker tweaks, but this pipeline uses in silico optimization and de novo design to crank out high-res antagonist-bound structures like a universal 3D-printing factory for tricky membrane proteins.
WP, S.; Liu, S.; Nguyen, T. P.; Mishra, P. K.; Pratiman, D.; Gupta, A. S.; Hirashima, T.
Jammed epithelial cells get a quirky blebbistatin chill pill on their contractility, flipping them into protrusion-happy movers that fluidize the tissue like a molecular rave turning stiff crowds into flowing, ERK-rewired party animals with boosted traction.
Lee, J.; Mantri, M.; Murthy, K.; Seeker, L. A.; Crowley, G.; Jones, R. C.; Tabula Sapiens Consortium, ; Quake, S. R.
The Tabula Sapiens sequel goes rogue on non-coding RNAs via total RNA-seq, exposing cell-type-specific tRNA drama, nuclear-cytoplasmic hide-and-seek, and senescence plot twists that make protein-coding genes look like the boring straight men in the transcriptome comedy.
Lucarelli, D.; Parikh, S.; Jimenez, S.; Schneeweis, C.; Ngandiri, D. A.; Putze, P.; Kos, T.; Wellappili, D.; Goelling, V.; Kuerbanjiang, M.; Shull, C.; Litwinski, M. R.; Handschuh, T. B.; Dabiri, Y.; Zukowska, M.; Seidler, B.; Kfuri-Rubens, R.; Baerthel, S.; Halle, L.; Arbesfeld-Qiu, J. M.; Gong, D.; Schneider, G.; Rad, R.; Falcomata, C.; Schmidt-Supprian, M.; Hwang, W. L.; Theis, F. J.; Saur, D.
In a massive 1.6-million-cell nanoscale PDAC spy novel, human and mouse tumors swap notes on progression and radiotherapy's sneaky EMT-persistent villainy, with orthotopic models hilariously stealing the show as the most faithful mimics while rare double-positive T cells crash the immune party.
Wang, C.; Karimzadeh, M.; Ravindra, N. G.; Bounds, L. R.; Alerasool, N.; Huang, A. C.; Ma, S.; Gulbranson, D. R.; Cui, H.; Lee, Y.; Arjavalingam, A.; MacKrell, E. J.; Wilken, M. S.; Chen, J.; Herken, B. W.; Weber, J. A.; Onesto, M. M.; Gonzalez-Teran, B.; Leung, N. F.; Shi, S. Y.; Smith, B. J.; Lam, S. K.; Barner, A.; Wright, P.; Rumsey, E. M.; Kim, S.; Sit, R. V.; Litterman, A. J.; Chu, C.; Wang, B.
Xaira’s massive 4.9B-parameter “virtual cell” acts like a diffusion-language fortune teller, zero-shot predicting gene expression chaos from CRISPR hits across unseen cell types using a whopping 25M+ perturbed transcriptomes in pure LLM power-law style.
Pai, V. P.; Traer, J. A.; Sperry, M. M.; Zeng, Y.; Levin, M.
Imagine a blob of frog skin with no brain that can still "remember" things. These "xenobots" use weird calcium waves to store memories of chemical hits for days. It’s basically a biological hard drive made of lab-grown slime—proving you don't actually need a brain to have a memory.
Shi, T.; Korshunova, M.; Kim, S.; DeTomaso, D.; Zheng, X.; Vishvanath, L.; Nyasulu, T.; Huynh, N.; Sun, A.; Thompson, P. C.; Zhang, Y.; Wigdor, E. M.; Rohani, N.; Ali, S.; Qiu, H.; Geralt, M.; Zhao, Z.; Rabhi, S.; Yao, Z.; van Velthoven, C. T.; Nery, J. R.; Castanon, R. G.; Dicks, S.; Chen, T. J.; Ecker, J. R.; Zeng, H.; Zheng, G. X.; Sanders, S. J.; Sundaram, L.; Jin, X.
A 7.7-million-cell brain heist where 1,947 disease genes get CRISPR-mugged in living mice, revealing cell-type-specific plot twists—like NMDA subunits throwing opposing transcriptional tantrums—while turning the whole mouse brain into a living "virtual cell" atlas for neuro quirks.
Nener, J.; Selvamani, P.; Badarinarayan, S. S.; Chandramohan, N.; Grzybowski, A. T.
TRAILBLAZER is a transformer that models entire multicellular neighborhoods at once, predicting how patient cell populations will react to drugs in zero-shot—think a hyperspherical crystal ball that ranks immunomodulators like a quirky matchmaker for your immune system.
Zeng, Z.; Wang, X.; Luo, Z.; Zheng, Y.; Hu, L.; Xing, C.; Du, H.
Forget wrestling with code—OmicClaw lets you boss around massive multi-omics datasets using plain English, turning your wildest analysis dreams into traceable, reproducible workflows that even AI agents can execute without going rogue.
Seidel, Z. P.; Assad-Garcia, N.; Paralanov, V.; Wu, F.; Chao, O.; Strychalski, E. A.; Romantseva, E. F.; Goshia, T.; Venter, J. C.; Glass, J. I.
In a zombie-synth-bio heist straight out of a mad-scientist flick, the Venter crew chemically “kills” Mycoplasma cells with Mitomycin C crosslinks, then stuffs their empty shells with synthetic genomes via whole-genome transplantation—reviving them as fully functional synthetic bacteria with zero selection-marker drama, like the ultimate microbial resurrection hack.
Abraham Soria, S.; Peterson, P.; VanElzakker, M. B.; Tankelevich, M.; Mehandru, S.; Proal, A.; Putrino, D.; Freire, M.
Long COVID's pesky SARS-CoV-2 Spike protein crashes the gut party, cranking up Crohn’s-esque genes and muting immune traffic cops in a bizarre pro-inflammatory tango, turning the colon into a dysfunctional disco where the virus refuses to leave the dance floor.
Roa-Eguiara, A.; Marin-Arraiza, L.; Klein-Sousa, V.; Santiveri, M.; Rutbeek, N. R.; Piel, D.; Pape, T.; Sofos, N.; Hendriks, I. A.; Nielsen, M. L.; Hu, H.; Harms, A.; Taylor, N. M. I.
In a nanoscale espionage saga, bacteriophage T4 deploys its genome into E. coli with a tape measure protein pulling the strings like a quirky puppet master, while the Imm protein acts as a viral bouncer, hilariously slamming the door on unwanted phage crashers.
Lala, J.; Agrawal, H.; Dong, F.; Wells, J.; Angioletti-Uberti, S.
This AI tool acts like a shrink ray for proteins. It takes bulky, complex enzymes and designs "Mini-Me" versions that are tiny but still work perfectly. These pocket-sized enzymes are way easier to handle in the lab and are now available for anyone to download and test.
Caskey, M.; Rich, J.; Weber, R.; Mortazavi, A.; Pachter, L.; Hallgrimsdottir, I. B.
Single-cell data is usually full of "background noise"—like trying to hear a conversation in a loud stadium. CellSweep acts like a high-powered vacuum cleaner, sucking up all the digital gunk and ambient "ghost" RNA so that scientists can actually see what the cells are doing.
Melsted, P.; Guthnyjarson, E. M.; Nordal, J.
Bioinformatics just got a nitro boost. An Icelandic team rebuilt the industry-standard software to run on high-powered GPUs. Now, a massive data crunch that used to take a 40-minute lunch break is finished in 50 seconds. It’s "blink-and-it’s-done" wizardry for genomic data.
Schmitt, M. S.; Lee, K.; Bunbury, F.; Landsittel, J. A.; Vitelli, V.; Kuehn, S.
From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains…
Chuai, G.; Chen, X.; Yang, X.; Zhang, C.; Qu, K.; Wang, Y.; Li, W.; Yang, J.; Si, D.; Xing, F.; Gao, Y.; Wu, S.; Fu, S.; He, B.; Liu, Q.
Think of this as "The Sims" but for real biology. AlphaCell treats the inside of a cell like a video game physics engine. It can predict exactly how a cell will freak out when you hit it with a drug or a mutation—allowing scientists to run experiments in a digital world without ever touching a pipette.
Aranguren, M.; Doyon-Laliberte, K.; Boncheva, I.; Villard, A.; Desjardins, A.; Darbinian, E.; Patel, S.; DuSablon, C.; Rivera Conde, E.; Cabrera Munoz, D.; Purchase, L.; Piscopo, V. E. C.; Alluli, A.; Benaliouad, F.; Sirois, J.; Durcan, T.; Masse, C.; Mlaga, K. D.; Chandrasekaran, P.; Poudrier, J.; Falcone, E. L.
Post COVID-19 condition (Long COVID, LC) is frequently accompanied by persistent neurological symptoms, but the mechanisms linking intestinal dysbiosis to neuroinflammation remain unclear. Here we ide…
Hackett, S. F.; Boniface, C. T.; Fonseca, A. V. A.; Ramos-Yamasaki, A. D.; Watson, C.; Bazin, H. M. L.; Tan, A. B.; Lee Yu, H.; Hanssen, L. L. P.; Dev, H.; Apostolidou, S.; Gentry-Maharaj, A.; Esener, S.; Menon, U.; Blundell, J. R.
Hijacking the brain's quirky protocadherin methylation for a full-body barcode bash, this method tracks clonal expansions like a sneaky cellular detective, spotting hidden growths in blood and organs that traditional mutation sleuths miss with epimutation flair.
Zhang, H. G.; Eckmann, P.; Miao, J.; Mahon, A. B.; Zou, J.
Picture a squad of AI agents cosplaying as a biotech startup, zipping through mountains of clinical trials and genomics data like overcaffeinated interns, uncovering that cell-specific targets make drugs 40-48% more successful while dodging side effects with sassy precision.
Wirthlin, M. E.; Hunker, A. C.; Somasundaram, S.; Lerma, M. N.; Laird, W. D.; Omstead, V.; Taskin, N.; Kempynck, N.; Schmitz, M. T.; Gao, Y.; Thomas, E.; Hooper, M.; Ben-Simon, Y.; Martinez, R. A.; Opitz-Araya, X.; Mich, J. K.; Oster, A.; Dwivedi, D.; Groce, E.; Roth, J.; Thyagarajan, B.; Way, S.; Amaya, A.; Ayala, A.; Barta, S.; Bertagnolli, D.; Bixby, M.; Cardenas, T.; Casper, T.; Clark, M.; Donadio, N.; Dotson, N. I.; Egdorf, T.; Peterson, E. L.; Gloe, J.; Goldy, J.; Grasso, C.; Han, W.; Hastings, S. D.; Hewitt, M.; Hirschstein, D.; Ho, W.; Huang, A.; Johnson, T.; Jones, D.; Jordan, A.; Jun
The mammalian basal ganglia (BG) orchestrate motor, cognitive, and affective functions, yet cell type-specific genetic access remains limited, especially beyond rodents. Key structures implicated in m…
Pachter, L.
Lior Pachter, with a sprinkle of AI wizardry from Claude and Codex, teleports the venerable edgeR from R to Python in a mere week, birthing edgePython that jazzes up single-cell analysis with Empirical Bayes flair, leaving bioinformatic glitches in the dust.
Bakker, L.; Caganek, T.; Rooprai, A.; Hume, S.
Systematic reviews are used in academia, biotechnology, pharmaceutical companies and government to synthesise and appraise large numbers of publications. The current (largely manual) workflow takes an…
Xiao, W.; Zhang, Y.; Gong, C.; Zhang, H.; Ma, W.; Liu, Z.; Chen, X.; Guan, J.; Wang, L.
We introduce Protenix-v1 (PX-v1), the first open-source structure prediction model to attain superior performance to AlphaFold3 while strictly adhering to the same training data cutoff, model size, an…
Smith, A. A.; Wong, E. L.; Donovan, R. C.; Chapman, B. A.; Harry, R.; Tirandazi, P.; Kanigowska, P.; Gendreau, E. A.; Dahl, R. H.; Jastrzebski, M.; Cortez, J. E.; Bremner, C. J.; Hemuda, J. C. M.; Dooner, J.; Graves, I.; Karandikar, R.; Lionetti, C.; Christopher, K.; Consiglio, A. L.; Tran, A.; McCusker, W.; Nguyen, D. X.; Nunes da Silva, I. B.; Bautista-Ayala, A. R.; McNerney, M. P.; Atkins, S.; McDuffie, M.; Serber, W.; Barber, B. P.; Thanongsinh, T.; Nesson, A.; Lama, B.; Nichols, B.; LaFrance, C.; Nyima, T.; Byrn, A.; Thornhill, R.; Cai, B.; Ayala-Valdez, L.; Wong, A.; Che, A. J.; Thavaraj
We used an autonomous lab, comprising a large language model (LLM) and a fully automated cloud laboratory, to optimize the cost efficiency of cell-free protein synthesis (CFPS). By conducting iterativ…
Dibaeinia, P.; Babu, S.; Knudson, M.; ElSheikh, A.; Wen, Y.; Liu, H.; Perera, J.; Khan, A. A.
The intersection of AI and biology has entered a phase of explosive growth, driven by the ambition to build "Virtual Cells" or computational models capable of predicting cellular responses to any pert…
Zhang, Y.; Mead, E. A.; Ni, M.; Ksiezarek, M.; Liu, Y.; Cao, L.; Chen, H.; Fan, Y.; Qiao, W.; Li, Y.; Zuluaga, L.; Deikus, G.; Sebra, R.; Brody, R.; Yong, R. L.; Badani, K. K.; Zhang, X.-S.; Fang, G.
The detection of low-biomass microbial DNA in human tissues is often confounded by contamination, as demonstrated in the debates over the existence of microbiomes in the placenta, brain, blood, and tu…
Shi, P.; Yang, F.; FNU, T.; Huang, W.; Aparicio, A. O.; Kalicki, C. H.; Trehan, A.; Murphy, M. R.; Rotlevi, E. R.; Xing, L.; Reilly, M. P.; Que, J.; Wu, X.
The human genome is dominated by noncoding sequences, most of which are poorly conserved across species. How genetic information is distributed between coding and noncoding regions remains a fundament…
Heffel, M. G.; Xu, H.; Pastor-Alonso, O.; Li, X.; Baig, M. S.; Irfan Ghoor, R.; Li, R.; Kern, C.; Kum, J.; Zhang, Y.; Paino, J.; Tsai, M. J.; Tai, C.-Y.; Tucker, G.; Zhao, Z.; Hou, A.; von Behren, Z.; Bhade, M.; Li, S.; Sandoval, K.; Scholes, J.; Codrea, F.; Calimlim, J.; Liao, E. K.; Leung, G.; Kim, J.; Eskin, E.; Flint, J.; Cotter, J. A.; Pasaniuc, B.; Bintu, B.; Zhu, Q.; Mukamel, E. A.; Ernst, J.; Paredes, M. F.; Luo, C.
The human basal ganglia (BG), subcortical nuclei fundamental to motor regulation and cognitive modulation, is constructed from neurons produced during gestation in the adjacent ganglionic eminences (G…
Romanni-Klein, R.; Hendrix, N.; DeBacker, J.; Evans, R.
Biological aging imposes significant socio-economic costs, increasing health expenses, reducing productivity, stalling population growth and straining social systems, culminating in reduced economic a…
Teyssier, N.; Dobin, A.
Single-cell genomics is rapidly scaling toward billion-cell atlases, but computational analysis has become a critical bottleneck. Processing multiplexed datasets with existing tools requires substanti…
Rancati, S.; Arozarena Donelli, P.; Nicora, G.; Bergomi, L.; Buonocore, T.; Sy, M. A.; Pandey, S.; Prosperi, M.; Salemi, M.; Bellazzi, R.; Boucher, C.; Parimbelli, E.; Marini, S.
Genomic language models (gLMs) have recently emerged as powerful numerical surrogates for DNA, but existing architectures are largely focused on human DNA or trained on limited viral references, and n…
Cassidy, A. C.; Burnette, D. T.; Zanic, M.
Microtubule dynamics change during cell division to enable rapid microtubule network remodeling. The switching from microtubule growth to shrinkage is attributed to the loss of a stabilizing GTP-cap s…
Agamia, J.; Zacharias, M.
MotivationThe rational design of chemical compounds that bind to a desired protein target molecule is a major goal of drug discovery. Most current molecular docking but also fragment-based build-up or…
Seiser, T.; Porri, A.; Johnen, P.; Zeyer, S.; Wahrheit, J.; Betz, M.; Vandenberghe, B.; Asher, S.; Parra, L.
BackgroundFendioxypyracil is a novel protoporphyrinogen oxidase (PPO)-inhibiting herbicide (HRAC Group 14) developed to address the increasing prevalence of herbicide-resistant weeds and to expand ava…
Huang, K.; Zhou, Y.; Wang, T.; Li, X.; Zhao, X.; Liu, X.; Huang, L.; Zhou, X.; Liu, J.
RNA velocity is a computational framework for single-cell RNA sequencing (scRNA-seq) that estimates the future transcriptional state of individual cells, thereby capturing the direction and rate of ce…
Zhang, Y.; Tang, S.; Chen, T.; Mahood, E.; Vincoff, S.; Chatterjee, P.
Therapeutic peptides combine the advantages of small molecules and antibodies, offering target flexibility and low immunogenicity, yet their successful translation requires careful evaluation of multi…
Jang, Y.; Qin, Q.-Q.; Wang, J.-L.; Kornmann, B.
Remarkable progress has been achieved by machine learning, particularly in accurate prediction of protein tertiary structures. Despite these advances, accurately annotating protein functions through m…
Davis, M. T.; Busse, B. L.; Arabi, S.; Meyer, P.; Hoppe, T. A.; Meseroll, R. A.; Hutchins, B. I.; Willis, K. A.; Santangelo, G. M.
The ability to predict scientific breakthroughs at scale would accelerate the pace of discovery and improve the efficiency of research investments. Recent advances in artificial intelligence, graph th…
Gupta, S.; Romero, S.; Cai, J. J.
Gene knockout experiments are essential for dissecting gene function, and CRISPR has made targeted gene disruption more accessible than ever. Single-cell CRISPR screening enables the construction of r…
Kalfon, J.; Peyre, G.; Cantini, L.
Cell biology has been booming with foundation models trained on large single-cell RNA-seq databases, but benchmarks and capabilities remain unclear. We propose an additive benchmark across a gymnasium…
Maeda, G. P.; Xue, A. Z.; Smith, T. E.; Sundar, A.; Powell, J. E.; Yu, E. W.; Moran, N. A.
ABSTRACTIntracellular bacterial symbioses have arisen myriad times in eukaryotes, with dozens known from insects alone1,2. Beginning with Buchnera, the obligate endosymbiont of aphids, genomes of endo…
Sun, E. D.; Buendia, A.; Brunet, A.; Zou, J.
Perturbational studies are the gold standard for identifying causal relationships between components of biological systems. Recent technological advances, including Perturb-seq and related assays, hav…
Reifenrath, L.; van Kempen, M.; Kim, G.; Kim, S. H.; Radnezhad, M.; Mirdita, M.; Steinegger, M.; Söding, J.
The ubiquitous availability of protein structures permits replacing sequence alignment with more accurate and sensitive structure alignment algorithms. LoL-align maximizes a local log-odds score for p…
Fang, T.; Wang, X.; Xiao, Z.; Hang, S.; Murtaza, G.; Yang, J.; Xu, H.; Jha, A.; Noble, W. S.; Wang, S.
Understanding how genomic sequences shape three-dimensional (3D) genome architecture is funda-mental to interpreting diverse biological processes. Although previous studies have shown that sequence in…
Lanna, A.; Valvo, S.; Dustin, M.; Rinaldi, F.
The role of the immune system in regulating organismal lifespan remains poorly understood. Here, we show that CD4 T cells release "telomere Rivers" into circulation after acquiring telomeres from anti…
LeRoy, N. J.; Zheng, G.; Khoroshevskyi, O.; Campbell, D. R.; Zhang, A.; Sheffield, N. C.
IntroductionChromatin accessibility profiling is an important tool for understanding gene regulation and cellular function. While public repositories house nearly 10,000 scATAC-seq experiments, unifyi…
Kern, C.; Zhang, Q.; Lu, Y.; Eschbach, J.; Zeng, Z.; Farah, E. N.; Tai, C.-Y.; Yang, K.; Jenie, I.; Yao, F.; Zhao, Z.; Ma, Q.; Padilla, C. G.; Monell, A.; Moghadami, S.; Zhu, F.; Li, B.; Hou, A.; Tucker, G.; Ellison, D.; Chi, N. C.; Qiu, X.; Zhu, Q.; Bintu, B.
Hybridization-based spatial transcriptomics technologies have advanced our ability to map cellular and subcellular organization in complex tissues. However, existing methods remain constrained in gene…