Newest journal articles by subject

Subjects > Biology

A Validated Regulatory Network for Th17 Cell Specification.
M. Ciofani;Aviv MadarC. GalanMaclean C SellarsK. MaceFlorencia PauliA. AgarwalW. HuangChristopher N. ParkurstM. MuratetKimberly M. NewberrySarah K. MeadowsAlex GreenfieldYi YangPreti JainFrancis K. KiriginC. BirchmeierE. WagnerK. MurphyR. MyersRichard BonneauD. Littman
Cell Published 2025/09/01

Summary:

This work aims to demonstrate the importance of knowing the carrier and removal status of canine coronavirus, as a source of infection for other animals, not necessarily belonging to the same breeds.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.
Hui Zhang;Tao LiuZhen ZhangS. PayneBai-meng ZhangJ. McdermottJianying ZhouV. PetyukLi ChenDebjit RayShisheng SunFeng YangLijun ChenJing WangPunit ShahS. ChaP. AiyetanSunghee WooYuan TianM. GritsenkoT. ClaussCaitlin H. ChoiM. MonroeStefani N. ThomasS. NieChaochao WuRonald J. MooreKun-Hsing YuD. TabbD. FenyöV. BafnaYue WangH. RodriguezEmily BojaTara HiltkeRobert C. RiversL. SokollHeng ZhuI. ShihL. CopeA. PandeyBing ZhangMichael SnyderD. LevineRichard D. SmithD. ChanK. Rodland
Cell Published 2025/11/01
Cancer Exosomes Perform Cell-Independent MicroRNA Biogenesis and Promote Tumorigenesis.
S. Melo;H. SugimotoJoyce T. O’ConnellNoritoshi KatoA. VillanuevaA. VidalLe QiuE. VitkinL. PerelmanC. A. MeloA. LucciC. IvanG. CalinR. Kalluri
Cancer cell Published 2025/08/01

Summary:

This data indicates that RNA Interference and Non-coding RNAs in Surgical Oncology and Experimental Therapeutics, as well as RNA Interference and Non-coding RNAs in Gene Regulation, at the University of Texas MD Anderson Cancer Center are likely to be influenced by each other.

Accurate structure prediction of biomolecular interactions with AlphaFold 3
Josh Abramson;Jonas AdlerJack DungerRichard EvansTim GreenA. PritzelOlaf RonnebergerLindsay WillmoreAndrew J BallardJoshua BambrickSebastian BodensteinDavid A EvansChia-Chun HungMichael O’NeillD. ReimanKathryn TunyasuvunakoolZachary WuAkvile ZemgulyteEirini ArvanitiCharles BeattieOttavia BertolliAlex BridglandAlexey CherepanovMiles CongreveA. Cowen-RiversAndrew CowieMichael FigurnovFabian B FuchsHannah GladmanRishub JainYousuf A. KhanCaroline M R LowKuba PerlinAnna PotapenkoPascal SavySukhdeep SinghA. SteculaAshok ThillaisundaramCatherine TongSergei YakneenEllen D. ZhongMichal ZielinskiAugustin ŽídekV. BapstPushmeet KohliMax JaderbergD. HassabisJ. Jumper
Nature Published 2024/05/08

Summary:

The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein–ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein–nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody–antigen prediction accuracy.

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches
J. Welsh;D. GoberdhanLorraine O’DriscollE. BuzásCherie BlenkironB. BussolatiHoujian CaiD. Di VizioTom A P DriedonksU. ErdbrüggerJ. Falcón-PerezQ. FuAndrew F. HillMetka LenassiSai Kiang LimMỹ G. MahoneySujata MohantyAndreas MöllerR. NieuwlandTakahiro OchiyaSusmita SahooA. TorrecilhasLei ZhengA. ZijlstraSarah AbuelreichReem BagabasP. BergeseE. BridgesM. BrucaleDylan BurgerRandy P. CarneyE. CocucciFederico ColomboR. CrescitelliE. HanserA. HarrisNorman J. HaugheyAn HendrixAlexander R IvanovT. Jovanović-TalismanNicole A. Kruh-GarciaVroniqa Ku'ulei-Lyn FaustinoDiego KyburzCecilia LässerKathleen M LennonJan LötvallAdam L MaddoxE. Martens-UzunovaRachel R. MizenkoLauren A. NewmanA. RidolfiEva RohdeTatu RojalinAndrew RowlandAndras SafticsU. SandauJ. SaugstadFaezeh ShekariSimon SwiftDmitry Ter-OvanesyanJ. TosarZivile UseckaiteF. ValleZoltán VargaEdwin van der PolM. V. van HerwijnenM. WaubenA. WehmanSarah WilliamsAndrea ZendriniAlan J ZimmermanMakon-Sébastien NJOCKAndre GörgensClotilde ThéryKennith W. Witwer
Journal of Extracellular Vesicles Published 2024/02/01

Summary:

The goal of the current document is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues.

The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024
F. Madeira;Nandana MadhusoodananJoon LeeAlberto EusebiAnia NiewielskaA. TiveyRodrigo LopezSarah Butcher
Nucleic Acids Research Published 2024/04/10

Summary:

Recent improvements to Job Dispatcher are overviews, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low- and middle-income regions.

UniProt: the Universal Protein Knowledgebase in 2025
Alex Maria-Jesus Sandra Michele Aduragbemi Shadab Emily Bateman Martin Orchard Magrane Adesina Ahmad Bowle;Alex BatemanM. MartinSandra OrchardM. MagraneA. AdesinaShadab AhmadE. Bowler-BarnettHema Bye-A-JeeD. CarpentierPaulus DennyJun FanPenelope GarmiriLeonardo Jose da Costa GonzalesAbdulrahman HusseinAlexandr IgnatchenkoGiuseppe InsanaRizwan IshtiaqVishal JoshiDushyanth JyothiSwaathi KandasaamyA. LockAurélien LucianiJie LuoYvonne LussiJ. MarinPedro RaposoDan RiceRafael SantosElena SperettaJames L. StephensonPrabhat TotooNidhi TyagiNadya UrakovaPreethi VasudevKate WarnerSupun WijerathneConny Wing-Heng YuR. ZaruAlan J. BridgeL. AimoGhislaine Argoud-PuyA. AuchinclossK. AxelsenParit BansalDelphine BaratinTeresa M Batista NetoMarie-Claude BlatterJerven T. BollemanE. BoutetLionel BreuzaBlanca Cabrera GilCristina Casals-CasasKamal Chikh EchioukhE. CoudertB. CucheEdouard de CastroA. EstreicherM. FamigliettiM. FeuermannElisabeth GasteigerPascale GaudetS. GehantV. GerritsenA. GosNadine GruazC. HuloNevila Hyka-NouspikelF. JungoArnaud KerhornouP. MercierD. LieberherrP. MassonA. MorgatS. PaesanoI. PedruzziS. PilboutL. PourcelS. PouxM. PozzatoManuela PruessNicole RedaschiC. RivoireChristian J A SigristKarin SonessonS. SundaramAnastasia SveshnikovaCathy H. WuC. ArighiChuming ChenYongxing ChenHongzhan HuangK. LaihoMinna LehvaslaihoPeter B. McGarveyD. NataleKaren RossC. R. VinayakaYuqi WangJian Zhang
Nucleic Acids Research Published 2024/11/18
InterPro: the protein sequence classification resource in 2025
Matthias Blum;Antonina AndreevaLaise Cavalcanti FlorentinoS. ChuguranskyTiago GregoEmma E. M. HobbsBeatriz Lázaro PintoAilsa OrrT. Paysan-LafosseIrina PonamarevaGustavo A. SalazarNicola BordinP. BorkA. BridgeLucy J ColwellJulian GoughD. HaftIvica LetunicFelipe Llinares-LópezAron Marchler-BauerLaetitia Meng-PapaxanthosH. MiD. NataleChristine A OrengoA. P. PanduranganD. PiovesanC. RivoireChristian J. A. SigristN. ThankiF. Thibaud-NissenP. D. ThomasSilvio C. E. TosattoCathy H. WuA. Bateman
Nucleic Acids Research Published 2024/11/20

Summary:

The status of InterPro is reported on, detailing new developments in the database, associated web interface and software, including the increased integration of structures predicted by AlphaFold and the enhanced description of protein families using artificial intelligence.

Extracellular vesicles as tools and targets in therapy for diseases
Mudasir A Kumar;S. K. BabaHana Q. SadidaSara Al MarzooqiJ. JerobinFaisal H. AltemaniNaseh A AlgehainyMohammad A AlanaziAbdul-Badi Abou-SamraRakesh KumarA. AL-SHABEEB AKILM. MachaRashid MirAjaz A. Bhat
Signal Transduction and Targeted Therapy Published 2024/02/05

Summary:

The roles of EVs across various conditions, including cancers, neurodegenerative disorders, diabetes, viral infections, autoimmune and renal diseases, are discussed, emphasizing the potential advancements in molecular diagnostics and drug delivery.

Cellular and molecular mechanisms of skin wound healing
Oscar A. Peña;Paul Martin
Nature Reviews Molecular Cell Biology Published 2024/03/25

Summary:

This Review discusses the complex mechanisms of wound healing — cell migration, matrix remodelling, inflammation and angiogenesis — and the contributions of different cell types, including immune cells, to this process, and highlights new methodologies that could inform future therapies to prevent scarring and repair chronic wounds.

The cell biology of ferroptosis
Scott J. Dixon;James A. Olzmann
Nature Reviews Molecular Cell Biology Published 2024/02/16

Summary:

This Review considers how the accumulation of membrane lipid peroxides leads to the execution of ferroptosis by altering ion transport across the plasma membrane and highlights transcriptional master regulators that integrate the functions of different pathways and organelles to modulate ferroptosis sensitivity globally.

Solar Heating by Polyethylene Mulching for the Control of Diseases Caused by Soil-Borne Pathogens.
J. Katan;A. GreenbergerA. AlonA. GrinsteinH. AlonP. Greenberger
Phytopathology Published 2025/08/01
The Role of Microbial Activity in Suppression of Damping-Off Caused by Pythium ultimum.
Weidong Chen;A. HoitinkA. SchmitthennerOlli H. Tuovinen
Phytopathology Published 2025/08/01

Summary:

It was concluded that coexistence of large populations of mesophilic microorganisms, great microbial activity, low concentrations of available nutrients, and high degree of microbiostasis characterized container media suppressive to Pythium damping-off.

The wound microbiota: microbial mechanisms of impaired wound healing and infection
A. Uberoi;A. McCready-VangiElizabeth A. Grice
Nature Reviews Microbiology Published 2024/04/04

Summary:

The current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants is explored.

Towards an AI co-scientist
Juraj Gottweis;Wei-Hung WengAlexander DaryinTao TuAnil PalepuPetar SirkovicArtiom MyaskovskyFelix WeissenbergerKeran RongRyutaro TannoKhaled SaabD. PopoviciJacob BlumFan ZhangKatherine ChouAvinatan HassidimBurak GokturkAmin VahdatPushmeet KohliYossi MatiasA. CarrollKavita KulkarniNenad TomaševYuan GuanVikram DhillonE. D. VaishnavByron LeeTiago R D CostaJos'e R Penad'esGary PeltzYunhan XuAnnalisa PawloskyA. KarthikesalingamVivek Natarajan
ArXiv Published 2025/02/26

Summary:

An AI co-scientist is introduced, a multi-agent system built on Gemini 2.0 intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance.

Glioblastoma multiforme: insights into pathogenesis, key signaling pathways, and therapeutic strategies
Ashkan Pouyan;Masoud GhorbanloMasoud EslamiMajid JahanshahiEhsan ZiaeiA. SalamiKhatereh MokhtariKoorosh ShahpasandNajma FarahaniT. E. MeybodiM. EntezariA. TaheriazamK. HushmandiMehrdad Hashemi
Molecular Cancer Published 2025/02/26

Summary:

A review of the epidemiology, molecular mechanisms, and therapeutic prospects of targeting these pathways in GBM are examined, highlighting recent insights into pathway interactions and discovering new therapeutic targets to improve patient outcomes.

One-quarter of freshwater fauna threatened with extinction
Catherine A. Sayer;E. FernandoRandall R. JiménezNicholas B. W. MacfarlaneG. RapacciuoloM. BöhmThomas M. BrooksT. Contreras-MacBeathNeil A. CoxI. HarrisonMichael HoffmannRichard JenkinsKevin G. SmithJ. ViéJohn C. AbbottD. AllenGerald R. AllenV. BarriosJ. BoudotSavrina F. CarrizoPatricia CharvetV. ClausnitzerL. CongiuKeith A. CrandallN. CumberlidgeAnnabelle CuttelodJames DaltonAdam G. DanielsS. De GraveGeert De KnijfK. DijkstraR. DowJörg FreyhofNieves GarcíaJoern GessnerA. GetahunClaudine GibsonM. GollockMichael I. GrantA. GroomMichael P. HammerG. HammersonC. Hilton‐TaylorLaurel HodgkinsonRobert A. HollandR. JabadoDiego Juffe BignoliV. KalkmanB. KarimovJ. KippingM. KottelatP. LalèyèHelen K. LarsonM. LintermansFederico LozanoArne LudwigTimothy J. LyonsL. Máiz-ToméSanjay MolurH. NgC. NumaA. F. Palmer-NewtonCharlotte PikeH. PippardC. N. M. PolazCaroline M PollockR. RaghavanPeter S. RandTsilavina RavelomananaRoberto E. ReisCassandra L. RigbyJanet ScottP. SkeltonM. SloatJos SnoeksM. StiassnyHeok Hui TanYoshinori TaniguchiE. B. ThorstadM. TognelliArmi G. TorresY. TorresD. TweddleKatsutoshi WatanabeJames R. S. WestripEmma G. E. WrightE. ZhangW. Darwall
Nature Published 2025/01/08

Summary:

Although global priority regions identified for tetrapod conservation are broadly reflective of those for freshwater faunas, given differences in key threats and habitats, meeting the needs of tetrapods cannot be assumed sufficient to conserve freshwater species at local scales.

Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies
Mark J. Adams;F. StreitXiangrui MengS. AwasthiB. AdeyKarmel W. ChoiV. K. ChundruJonathan R. I. ColemanBart FerwerdaJ. FooZ. GerringO. GiannakopoulouP. GuptaAlisha S. M. HallA. HarderD. M. HowardChristopher HübelA. KwongD. LeveyBrittany L MitchellG. NiVanessa K. OtaOliver PainG. PathakE. SchulteXueyi ShenJackson G. ThorpAlicia WalkerS. YaoJ. ZengJohan ZvrskovecDag AarslandKy'Era V. ActkinsM. AdliE. AgerboM. AichholzerAllison E AielloTracy M. AirT. AlsEvelyn AnderssonTill F M AndlauerV. AroltH. AskJulia BäckmanS. BadolaC. BallardK. BanasikNicholas J. BassA. BeekmanS. BelangeroT. BigdeliE. BinderO. BjerkesetG. BjornsdottirS. BørteE. BrännA. BraunT. BrodersenTanja M. BrücklS. BrunakM. BruunMargit BurmeisterP. BuspavanichJ. Bybjerg-GrauholmE. ByrneJianwen CaiA. CampbellMegan L. CampbellA. CamposE. CastelaoJ. CervillaB. ChaumetteChia-Yen ChenHsi- ChenZhengmin ChenS. CichonL. Colodro-CondeA. CorbettElizabeth C. CorfieldB. Couvy-DuchesneN. CraddockU. DannlowskiG. DaviesE. D. GeusI. DearyFranziska DegenhardtAbbas DehghanJ. DePauloMichael DeuschleM. DidriksenK. M. DinhN. DirekS. DjurovicA. DochertyK. DomschkeJoseph DowsettO. K. DrangeErin C. DunnWilliam EatonG. EinarssonT. EleySamar S M ElsheikhJ. EngelmannM. BenrosC. ErikstrupV. Escott-PriceChiara FabbriYu FangS. FinerJ. FrankRobert C. FreeL. GalloHe GaoMichael GillMaria GillesF. GoesScott D. GordonJakob GroveD. GudbjartssonBlanca GutiérrezTim HahnL. HallT. HansenM. HaraldssonCatharina HartmanA. HavdahlCaroline HaywardS. Heilmann-HeimbachS. HermsIan B. HickieH. HjalgrimJens Hjerling-LefflerP. HoffmannG. HomuthCarsten HornJ. HottengaD. HougaardI. HovattaQ. HuangDonald HucksF. HuiderK. HuntNicholas S. IalongoM. IsingE. IsometsäR. JansenYunxuan JiangIan JonesLisa A JonesL. JonssonM. KanaiR. KarlssonS. KasperKenneth KendlerRonald C KesslerS. KloiberJames A KnowlesN. KoenJ. KraftH. KranzlerKristi KrebsT. KallakZ. KutalikE. LahtelaMarilyn LakeM. LarsenE. LenzeMelissa LewinsGlyn LewisLiming LiB. LinKuang LinP. LindYu-Li LiuD. MacintyreD. MacKinnonB. MaherWolfgang MaierV. MarsheG. Martínez-LevyKoichi MatsudaH. MbarekP. McGuffinS. MedlandS. MeinertChristina MikkelsenS. MikkelsenY. MilaneschiI. MillwoodE. MolinaFrancis M. MondimoreP. MortensenBenoit H. MulsantJ. NaamankaJake M. NajmanMatthias NauckIgor NenadićK. R. NielsenIlja M. NoltM. NordentoftM. NöthenM. NyegaardM. O’DonovanA. OddssonAdrielle M OliveiraC. OlsenH. OskarssonS. OstrowskiM. OwenR. PackerT. PalviainenP. M. PanC. PatoM. PatoNancy L. PedersenO. B. PedersenW. PeyrotJ. PotashM. PreisigMichael H. PreussJorge A. QuirozMiguel E. RenteríaCharles F. ReynoldsJohn P. RiceS. SakaueM. L. SantoroR. A. SchoeversA. SchorkThomas G SchulzeT. SendJianxin ShiE. SigurdssonKritika SinghGrant C. B. SinnamonL. SirignanoO. SmelandDaniel J. SmithT. SoferErik SørensenS. SrinivasanH. StefánssonK. StefanssonPeter StraubMei-Hsin SuA. TadićH. TeismannA. TeumerA. ThaparP. ThomsonL. ThørnerA. TopaloudiShih-Jen TsaiI. TzoulakiGeorge UhlA. UitterlindenH. UllumDaniel UmbrichtR. UrsanoS. AuweraA. M. HemertA. VeluchamyA. ViktorinH. VölzkeG. WaltersXiaotong WangAgaz H. WaniMyrna M WeissmanJ. WellmannD. WhitemanDerek WildmanG. WillemsenA. T. WilliamsB. WinsvoldS. WittY. XiongLea ZillichJ. ZwartTwenty-Three and Me Research TeamChina Kadoorie Biobank (CKB) Collab GroupEstonian Biobank Research TeamGenes Health Research TeamHunt All-In PsychiatryThe Biobank Japan ProjectV. M. V. ProgramOle A. AndreassenBernhard T. BauneKlaus BergerD. BoomsmaA. BørglumG. BreenNa CaiHilary CoonWilliam E. CopelandB. CreeseC. S. Cruz-FuentesD. CzamaraLea K. DavisE. DerksEnrico DomeniciP. ElliottA. ForstnerM. GawlikJ. GelernterH. J. GrabeSteven P. HamiltonK. HveemCatherine JohnJ. KaprioT. KircherMarie-Odile KrebsPo-Hsiu KuoM. LandénKelli LehtoD. LevinsonQingqin S LiK. LiebRuth J. F. LoosYi LuS. LucaeJ. LuykxHermine H. M. MaesP. MagnussonHilary C. MartinN. G. MartinA. McQuillinC. MiddeldorpL. MilaniOle MorsDaniel J. MüllerB. Müller-MyhsokYukinori OkadaA. OldehinkelS. PacigaColin N. A. PalmerP. PaschouB. PenninxR. PerlisRoseann E. PetersonG. PistisR. PolimantiD. PorteousD. PosthumaJill A. RabinowitzTed Reichborn-KjennerudA. ReifFrances RiceR. RickenMarcella RietschelM. RiveraChristian RückGiovanni SalumCatherine SchaeferSrijan SenA. SerrettiA. SkalkidouJ. SmollerD. J. SteinF. SteinMurray B. SteinPatrick F. SullivanM. TesliT. ThorgeirssonHenning TiemeierN. TimpsonMonica UddinR. UherD. V. HeelK. VerweijR. WaltersSylvia Wassertheil-SmollerJ. WendlandT. WergeA. ZwindermanKaroline KuchenbaeckerN. WrayS. RipkeC. LewisA. M. McIntosh
Cell Published 2025/01/01
Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics.
Yunhe Liu;Ansam SinjabJimin MinGuangchun HanFrancesca ParadisoYuanyuan ZhangRuiping WangGuangsheng PeiYibo DaiYang LiuK. S. ChoEnyu DaiAkshay V. BasiJared K. BurksK. RajapaksheYanshuo ChuJiahui JiangDaiwei ZhangXinmiao YanPaola A. GuerreroAlejandra G SerranoMingyao LiTae Hyun HwangAndrew FutrealJaffer A. AjaniLuisa M. Solis SotoA. JazaeriH. KadaraAnirban MaitraLinghua Wang
Cancer cell Published 2025/03/01

Summary:

Through integrative analyses of over 14 million cells from 10 cancer types across 7 spatial transcriptomics and proteomics platforms, four distinct spatial CAF subtypes are discovered, validated, and characterize.

Genomics yields biological and phenotypic insights into bipolar disorder
K. S. O’Connell;M. KorominaTracey van der VeenT. BoltzF. DavidJ. M. K. YangKeng-Han LinXin WangJonathan R. I. ColemanBrittany L MitchellC. McGroutherA. RanganP. LindE. KochA. HarderN. ParkerJ. BendlK. AdorjanE. AgerboD. AlbaniS. AlemanyN. Alliey-RodriguezT. AlsTill F M AndlauerA. AntoniouH. AskNicholas J. BassMichael BauerE. BeinsT. BigdeliC. B. PedersenM. BoksS. BørteRosa BoschM. BrumB. M. BrumptonN. Brunkhorst-KanaanM. BuddeJ. Bybjerg-GrauholmW. ByerleyJ. Cabana-DomínguezMurray J. CairnsB. CarpinielloM. CasasP. CervantesC. ChatzinakosHsi- ChenTereza ClarenceToni‐Kim ClarkeI. ClausBrandon J. CoombesElizabeth C. CorfieldC. CruceanuA. Cuellar-BarbozaP. CzerskiK. DafnasA. DaleN. DalknerFranziska DegenhardtJ. DePauloS. DjurovicO. K. DrangeV. Escott-PriceA. FanousF. FellendorfI. FerrierL. FortyJ. FrankO. FreiNelson B. FreimerJ. FullardJ. GarnhamI. GizerS. GordonK. Gordon-SmithTiffany A. GreenwoodJakob GroveJ. Guzmán-ParraTae Hyon HaTim HahnM. HaraldssonM. HautzingerA. HavdahlU. HeilbronnerDennis HellgrenS. HermsIan B. HickieP. HoffmannP. HolmansMing-Chyi HuangM. IkedaS. JamainJessica S. JohnsonL. JonssonJ. KalmanY. KamataniJames L KennedyEuitae KimJaeyoung KimS. Kittel-SchneiderJames A KnowlesManolis KogevinasT. KranzKristi KrebsSteven A. KushnerC. LavebrattJ. LawrenceM. LeberHeon-Jeong LeeCalwing LiaoS. LucaeM. LundbergD. MacintyreW. MaierA. MaihoferDolores MalaspinaM. ManchiaE. MaratouL. MartinssonM. MattheisenN. McGregorMelvin G. McInnisJames D. MckayH. MedeirosAndreas Meyer-LindenbergV. MillischerDerek W. MorrisP. MoutsatsouThomas W. MühleisenC. O’DonovanC. OlsenGeorgia PanagiotaropoulouS. PapiolA. PardiñasH. ParkA. PerryAndrea PfennigC. PisanuJ. PotashDigby QuestedMark H RapaportE. J. RegeerJohn P. RiceM. RiveraEva C. SchulteF. SennerA. ShadrinP. ShillingE. SigurdssonL. SindermannL. SirignanoD. SiskindC. SlaneyLaura G. SloofmanO. SmelandDaniel J SmithJ. SobellM. Soler ArtigasD. J. SteinF. SteinMei-Hsin SuHeejong SungB. ŚwiątkowskaC. TeraoMarkos TesfayeM. TesliT. ThorgeirssonJackson G. ThorpClaudio TomaL. TondoP. TooneyShih-Jen TsaiE. TsermpiniM. VawterH. VedderA. VreekerJames T. R. WaltersB. WinsvoldS. WittHong-Hee WonRobert YeAllan H. YoungP. ZandiLea ZillichByung LeeJi-Woong KimYoung Kee LeeJoon Ho KangM. CheonDong Jun KimMihaela AslanPhilip D HarveyGrant D. HuangR. AdolfssonM. AldaLars AlfredssonL. BacklundB. T. BauneF. BellivierS. BengesserW. BerrettiniJ. BiernackaM. BoehnkeA. BørglumG. BreenV. CarrS. CattsS. CichonA. CorvinN. CraddockU. DannlowskiD. DikeosB. ÉtainP. FerentinosM. FryeJ. FullertonM. GawlikE. GershonF. GoesM. GreenM. Grigoroiu-SerbanescuJoanna HauserF. HenskensJ. Hjerling-LefflerD. HougaardK. HveemNakao IwataIan R. JonesLisa A JonesRené S KahnJ. KelsoeT. KircherG. KirovPo-Hsiu KuoM. LandénM. LeboyerQingqin S LiJ. LissowskaC. LochnerC. LoughlandJ. LuykxNicholas G. MartinC. MathewsF. MayoralSusan L. McElroyAndrew M. McIntoshF. McMahonS. MedlandI. MelleL. MilaniP. MitchellG. MorkenOle MorsP. MortensenB. Müller-MyhsokRichard M. MyersW. MyungB. NealeC. NievergeltM. NordentoftM. NöthenJ. NurnbergerM. O’DonovanK. OedegaardTomas OlssonM. OwenS. PacigaC. PantelisC. PatoM. PatoG. PatrinosJoanna M PawlakJ. Ramos-QuirogaA. ReifE. ReininghausM. RibasésMarcella RietschelS. RipkeGuy A RouleauP. RoussosTakeo SaitoU. SchallM. SchallingP. R. SchofieldT. G. SchulzeLaura J. ScottRodney J. ScottA. SerrettiJ. SmollerA. SquassinaE. StahlH. StefánssonKári StefánssonE. StordalF. StreitP. SullivanG. TureckiA. VaalerEduard VietaJohn B. VincentIrwin D. WaldmanC. WeickertT. WeickertT. WergeD. C. WhitemanJ. ZwartH. EdenbergA. McQuillinA. ForstnerN. MullinsA. Di FlorioR. OphoffO. Andreassen
Nature Published 2025/01/22

Summary:

Several analyses implicate specific cell types in the pathophysiology of bipolar disorder, including GABAergic interneurons and medium spiny neurons, and provide additional insights into the genetic architecture and biological underpinnings of bipolar disorder.

A neoantigen vaccine generates antitumour immunity in renal cell carcinoma
David A. Braun;Giorgia MoranzoniVipheaviny CheaB. McGregorEryn BlassChloe R. TuAllison P. VanasseCleo FormanJ. FormanAlexander B. AfeyanN. SchindlerYiwen LiuShuqiang LiJackson SouthardS. ChangM. HirschN. LeBoeufOriol OliveAmbica MehndirattaHaley GreensladeKeerthi ShettySusan KlaegerSiranush SarkizovaC. B. PedersenM. MossanenIsabel CarulliAnna Y TarrenJoseph E. Duke-CohanAlexis A. HowardJ. IorgulescuBohoon ShimJeremy M. SimonS. SignorettiJon C. AsterLiudmila ElaginaSteve CarrI. LeshchinerG. GetzS. GabrielN. HacohenL. R. OlsenG. OliveiraD. NeubergK. LivakS. ShuklaE. FritschCatherine J WuDerin B. KeskinP. OttT. Choueiri
Nature Published 2025/02/05

Summary:

Results demonstrate that neoantigen-targeting PCVs in high-risk RCC are highly immunogenic, capable of targeting key driver mutations and can induce antitumour immunity, and highlights the promise of PCVs as effective adjuvant therapy in RCC.

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
Rodrigo V. Honorato;M. TrelletBrian Jiménez-GarcíaJörg SchaarschmidtMarco GiuliniVictor ReysPanagiotis I. KoukosJ. RodriguesE. KaracaG. V. van ZundertJorge Roel‐TourisCharlotte van NoortZuzana JandovaA. MelquiondA. Bonvin
Nature Protocols Published 2024/06/17

Summary:

This new version of the HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types and supports various experimental data, including mutagenesis, NMR and cryo-EM data.

One-shot design of functional protein binders with BindCraft
Martin Pacesa;Lennart NickelChristian SchellhaasJoseph SchmidtEkaterina PyatovaLucas KisslingPatrick BarendseJagrity ChoudhurySrajan KapoorA. Alcaraz-SernaYehlin ChoKourosh H. GhamaryLaura VinuéB. YachninAndrew M. WollacottStephen BuckleyA. WestphalS. LindhoudS. GeorgeonCasper A. GoverdeG. HatzopoulosP. GönczyY. MullerGerald SchwankD. C. SwartsA. VecchioBernard L. SchneiderSergey OvchinnikovBruno E. Correia
Nature Published 2025/08/27

Summary:

BindCraft, an open-source and automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.

Complete sequencing of ape genomes
DongAhn Yoo;A. RhiePrajna HebbarF. AntonacciGlennis A. LogsdonSteven J. SolarD. AntipovBrandon D. PickettYana SafonovaFrancesco MontinaroYanting LuoJoanna MalukiewiczJessica M. StorerJiadong LinAbigail N SequeiraRiley J. ManganG. HickeyGraciela Monfort AnezParithi BalachandranAnton BankevichChristine R. BeckArjun BiddandaM. BorchersG. BouffardEmry BrannanShelise Y. BrooksLucia CarboneLaura CarrelAgnes P. ChanJuyun CrawfordM. DiekhansEric EngelbrechtCédric FeschotteG. FormentiGage H. GarciaLuciana de GennaroDavid M. GilbertRichard E. GreenAndrea GuarracinoIshaan GuptaDiana HaddadJunmin HanRobert S. HarrisGabrielle HartleyWilliam T. HarveyMichael HillerKendra HoekzemaM. HouckHyeonsoo JeongKaivan KamaliM. KellisBryce KilleChul LeeYoungho LeeWilliam D LeesAlexandra P. LewisQiuhui LiMark LoftusYong-Hwee E LohHailey LoucksJian MaYafei MaoJuan F. I. MartinezP. MastersonR. McCoyBarbara McGrathSean McKinneyBritta S. MeyerK. MigaS. MohantyKatherine M. MunsonKarol PálMatt PennellPavel A. PevznerDavid PorubskyT. PotapovaF. R. RingelingJoana L. RochaOliver A. RyderS. SaccoSwati SahaTakayo SasakiMichael C. SchatzNicholas J. SchorkCole ShanksLinnéa SmedsD. SonCynthia SteinerAlex SweetenMichael G. TassiaF. Thibaud-NissenEdmundo Torres-GonzálezMihir TrivediWenjie WeiJulie WertzMuyu YangPanpan ZhangShilong ZhangYang ZhangZhenmiao ZhangSarah A. ZhaoYixin ZhuErich D. JarvisJ. GertonIker Rivas-GonzálezBenedict PatenZachary A. SzpiechC. HuberTobias L. LenzMiriam K. KonkelSoojin V YiS. CanzarCorey T. WatsonPeter H. SudmantErin K. MolloyErik GarrisonCraig B. LoweMario VenturaRachel J. O’NeillS. KorenKateryna D. MakovaA. PhillippyE. Eichler
Nature Published 2025/04/09

Summary:

Complete sequences of chromosomes telomere-to-telomere from chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang provide a comprehensive and valuable resource for future evolutionary comparisons.

Medicinal plants: bioactive compounds, biological activities, combating multidrug-resistant microorganisms, and human health benefits - a comprehensive review
M. El‐Saadony;A. SaadD. M. MohammedSameh A. KormaM. AlshahraniA. E. AhmedEssam H. IbrahimHeba M. SalemS. S. AlkafaasAbdullah M. SaifS. S. ElkafasMohamed A. FahmyTaia A. Abd El-MageedMariam M. AbadyHanya Y. AssalMarawan K. El-TarabilyBetty T. MathewSynan F. AbuQamarKhaled A. El-TarabilySalam A. Ibrahim
Frontiers in Immunology Published 2025/04/28

Summary:

This current review aims to identify the most common pathogens threatening human health, analyze the factors contributing to the rise of drug-resistant microorganisms, and evaluate the widespread use of medicinal plants across various countries as alternative antibiotics, highlighting their unique mechanisms of antimicrobial resistance.

Genetic drivers of heterogeneity in type 2 diabetes pathophysiology
Ken Suzuki;K. HatzikotoulasL. SouthamHenry J. TaylorXianyong YinKimberly M. LorenzRavi MandlaA. Huerta-ChagoyaGiorgio E. M. MelloniS. KanoniN. W. RaynerO. BocherA. ArrudaK. SoneharaS. NambaSimon LeeMichael H. PreussLauren E. PettyPhilip H. SchroederBrett R. VanderwerffM. KalsF. BraggKuang LinXiuqing GuoWeihua ZhangJie YaoYoung Jin KimM. GraffF. TakeuchiJ. NanoA. LamriM. NakatochiSanghoon MoonRobert A. ScottJ. CookJung-Jin LeeIan PanD. TaliunE. ParraJin-Fang ChaiL. BielakY. TabaraY. HaiG. ThorleifssonN. GrarupT. SoferM. WuttkeC. SarnowskiC. GiegerDarryl NousomeS. TrompetS. KwakJ. LongMeng SunL. TongWei-Min ChenSuraj S NongmaithemR. NoordamV. J. LimC. H. TamYoonjung Yoonie JooChien-Hsiun ChenL. RaffieldB. PrinsA. NicolasL. YanekGuanjie ChenJ. BrodyE. KabagambePing AnAnny H. XiangHyeok Sun ChoiB. CadeJingyi TanK. BroadawayA. WilliamsonZoha KamaliJ. CuiManonanthini ThangamLinda S. AdairA. AdeyemoC. Aguilar-SalinasT. AhluwaliaS. AnandAlain G. BertoniJ. Bork-JensenIvan BrandslundThomas A. BuchananC. BurantA. ButterworthM. CanouilJuliana C N ChanLi ChangM. CheeJi ChenShyh-Huei ChenYuan-Tsong ChenZhengmin ChenLee-Ming ChuangMary CushmanJ. DaneshSwapan K. DasH. J. de SilvaG. DedoussisLatchezar DimitrovA. DoumateyS. DuQing DuanK.-U. EckardtL. EmeryDaniel S. EvansM. EvansK. FischerJames S FloydIan FordO. FrancoT. FraylingB. FreedmanP. GenterH. GersteinV. GiedraitisC. González‐VillalpandoM. González-VillalpandoP. Gordon-LarsenMyron GrossLindsay A GuareS. HackingerL. HakasteSohee HanA. HattersleyC. HerderM. HorikoshiA. HowardWilla A. HsuehMengna HuangWei HuangY. HungM. Y. HwangC. HwuS. IchiharaM. IkramM. IngelssonMd. Tariqul IslamM. IsonoHye-Mi JangF. JasmineGuozhi JiangJ. JonasT. JørgensenFrederick K. KamanuFouad R. KandeelA. KasturiratneTomohiro KatsuyaV. KaurT. KawaguchiJacob M. KeatonAbel N. KhoC. KhorM. KibriyaDuk-Hwan KimF. KronenbergJ. KuusistoKristi LällLeslie A. LangeK. LeeMyung-Shik LeeN. LeeAaron LeongLiming LiYun LiR. Li-GaoSymen LigthartCecilia M. LindgrenA. LinnebergChing-Ti LiuJianjun LiuA. LockeT. LouieJ. LuanA. LukXi LuoJun LvJ. LynchV. LyssenkoShiro MaedaVasiliki MamakouS. R. MansuriKoichi MatsudaT. MeitingerOlle MelanderA. MetspaluHuan MoA. D. MorrisFilipe A. MouraJerry L. NadlerMichael A. NallsUma NayakI. NtallaY. OkadaL. OrozcoSanjay R. PatelSnehal PatilP. PeiMark A. PereiraA. PetersF. PirieH. PolikowskyBianca C. PornealaGauri PrasadL. Rasmussen-TorvikAlexander P. ReinerM. RodenRebecca R. RohdeK. RollC. SabanayagamK. SandowA. SankareswaranNaveed SattarS. SchönherrM. ShahriarBotong ShenJinxiu ShiDong Mun ShinN. ShojimaJennifer A. SmithW. SoA. StančákováV. SteinthorsdottirA. StilpK. StrauchK. TaylorBarbara ThorandU. ThorsteinsdóttirB. TomlinsonTam C. TranF. TsaiJaakko TuomilehtoTeresa Tusié-LunaM. UdlerA. Valladares-SalgadoRob M. van DamJ. V. van KlinkenRohit VarmaNiels Wacher-RodarteEleanor WheelerA. R. WickremasingheKo Willems van DijkDaniel WitteC. YajnikKenichi YamamotoKenichi YamamotoKyungheon YoonCanqing YuJian-Min YuanSalim YusufM. ZawistowskiLiang ZhangWei ZhengL. RaffelM. IgaseEli IppS. RedlineYoon Shin ChoL. LindM. ProvinceM. FornageC. HanisE. IngelssonA. ZondermanB. PsatyYa-Xing WangC. RotimiDiane M. BeckerFumihiko MatsudaYongmei LiuM. YokotaS. KardiaP. PeyserJ. PankowJ. EngertA. BonnefondP. FroguelJames G WilsonW. H. SheuJer-Yuarn WuM. HayesR. MaTien Y. WongD. Mook-KanamoriT. TuomiG. ChandakF. CollinsD. BharadwajGuillaume ParéM. SaleH. AhsanA. MotalaX. ShuK. ParkJ. JukemaM. CruzYii-DerIda ChenS. RichR. Mckean-CowdinH. GrallertChing-Yu ChengM. GhanbariE. TaiJosé DupuisNorihiro KatoM. LaaksoA. KöttgenWoon-Puay KohD. BowdenColin N. A. PalmerJ. KoonerC. KooperbergSimin LiuKari E. NorthD. SaleheenT. HansenO. PedersenN. WarehamJuyoung LeeBong-Jo KimI. MillwoodR. WaltersK. StefánssonE. AhlqvistM. GoodarziK. MohlkeC. LangenbergC. HaimanRuth J. F. LoosJ. C. FlorezDaniel J. RaderMarylyn D. RitchieSebastian ZöllnerR. MägiN. MarstonC. RuffD. V. van HeelS. FinerJoshua C. DennyT. YamauchiTakashi KadowakiJ. C. ChambersM. NgXueling SimJ. BelowP. TsaoKyong-Mi ChangM. McCarthyJames B. MeigsA. MahajanCassandra N. SpracklenJosep M. MercaderM. BoehnkeJ. RotterM. VujkovićB. VoightA. P. MorrisE. Zeggini
Nature Published 2024/02/19

Summary:

A meta-analysis of genome-wide association studies of type 2 diabetes (T2D) identifies more than 600 T2D-associated loci; integrating physiological trait and single-cell chromatin accessibility data at these loci sheds light on heterogeneity within the T2D phenotype.

Human lifespan changes in the brain’s functional connectome
Lianglong Sun;Tengda ZhaoXinyuan LiangMingrui XiaQiongling LiXuhong LiaoGaolang GongQian WangChenxuan PangQian YuYanchao BiPindong ChenRui ChenYuan-Hui ChenTaolin ChenJingliang ChengYuqi ChengZaixu CuiZhengjia DaiYao DengYuyin DingQi DongDingna DuanJiahong GaoQiyong GongYing HanZaizhu HanChu-Chung HuangRuiwang HuangRan HuoLingjiang LiC. LinQixiang LinBangshan LiuChao LiuNingyu LiuYing LiuYong LiuJing LuLeilei MaWeiwei MenShaozheng QinJiang QiuShijun QiuT. SiShuping TanYanqing TangS. TaoDawei WangFei WangJiali WangPan WangXiaoqin WangYanpei WangDongtao WeiYan-Kun WuPeng XieXiufeng XuYuehua XuZhilei XuLiyuan YangHui-zong YuanZilong ZengHaibo ZhangXi ZhangGai ZhaoYanting ZhengSuyu ZhongMichael Paul Ronald Clifford R. William John Q. Arthur W. Weiner Aisen Petersen Jack Jagust Trojanowki Toga Michael W. WeinerP. AisenRon PetersenClifford R. JackW. JagustJ. TrojanowkiArthur W TogaL. BeckettRobert C. GreenA. SaykinJohn C. MorrisL. ShawEnchi LiuT. MontineR. ThomasMichael C. DonohueSarah WalterD. GessertT. SatherG. JiminezDanielle J HarveyM. BernsteinNick FoxPaul ThompsonN. SchuffC. DeCarliBret J. BorowskiJ. GunterM. SenjemP. VemuriDavid JonesK. KantarciC. WardR. KoeppeNormal L. FosterE. ReimanKewei ChenC. MathisSusan LandauN. CairnsE. HouseholderLisa Taylor ReinwaldV. LeeM. KoreckaM. FigurskiK. CrawfordS. NeuT. ForoudS. PotkinL. ShenFaber KelleySungeun KimK. NhoZaven KachaturianRichard FrankPeter J. SnyderS. MolchanJ. KayeJoseph QuinnB. LindR. CarterS. DolenLon S. SchneiderS. PawluczykMauricio BecceraL. TeodoroBryan M. SpannJ. BrewerH. VanderswagA. FleisherJ. HeidebrinkJ. LordS. MasonC. AlbersD. KnopmanK. JohnsonRachelle S. DoodyJavier Villanueva MeyerM. ChowdhuryS. RountreeM. DangY. SternL. HonigKaren L. BellB. AncesJohn C. MorrisM. CarrollSue LeonM. MintunS. SchneiderA. OliverR. GriffithD. ClarkD. GeldmacherJ. BrockingtonErik RobersonH. GrossmanEffie M. MitsisL. deToledo‐MorrellR. ShahR. DuaraD. VaronMaria T. GreigPeggy RobertsMarilyn S. AlbertC. OnyikeD. D’AgostinoS. KielbJames E. GalvinD. PogorelecBrittany CerboneChristina A. MichelH. RusinekM. D. de LeonL. GlodzikS. SantiP. DoraiswamyJ. PetrellaT. WongS. ArnoldJ. KarlawishD. WolkCharles D. SmithG. JichaPeter HardyP. SinhaElizabeth OatesG. ConradOscar L. LopezM. OakleyD. SimpsonA. PorsteinssonB. GoldsteinK. MartinK. MakinoM. IsmailC. BrandR. MulnardG. ThaiC. OrtizKyle B. WomackD. MathewsM. QuicenoR. D. ArrastiaRichard D. KingMyron WeinerK. M. CookMichael D. DevousA. LeveyJ. LahJ. CellarJeffrey M. BurnsH. AndersonR. SwerdlowL. ApostolovaK. TingusEllen WooDaniel H. S. SilvermanPo H. LuG. BartzokisNeill R. Graff RadfordF. ParfittTracy KendallHeather K. JohnsonMartin R. FarlowA. HakeBrandy R. MatthewsS. HerringCynthia HuntC. V. van DyckRichard E. CarsonM. MacAvoyH. ChertkowH. BergmanC. HoseinSandra BlackB. StefanovicCurtis CaldwellG. HsiungH. FeldmanB. MudgeMichele Assaly PastA. KerteszJ. RogersD. TrostC. BernickD. MunicD. KerwinM. MesulamK. LipowskiChuang‐Kuo WuN. JohnsonC. SadowskyWalter MartínezTeresa VillenaR. S. TurnerK. JohnsonB. ReynoldsR. SperlingK. JohnsonG. MarshallMeghan T. FreyJ. YesavageJoy TaylorB. LaneA. RosenJared S. TinklenbergM. SabbaghC. BeldenS. JacobsonSherye A. SirrelNeil W. KowallR. KillianyA. BudsonAlexander NorbashP. L. JohnsonT. ObisesanS. WoldayJoanne S. AllardAlan J. LernerP. OgrockiLeon HudsonEvan F. FletcherO. CarmichaelJ. OlichneyC. DeCarliS. KitturM. BorrieT. LeeRob BarthaSterling C. JohnsonSanjay AsthanaC. CarlssonS. PotkinAdrian PredaD. NguyenP. TariotStephanie A. ReederV. BatesH. CapoteM. RainkaD. ScharreM. KatakiAnahita AdeliE. ZimmermanD. CelminsAlice D. BrownGodfrey D. PearlsonK. BlankK. AndersonR. SantulliT. KitzmillerE. SchwartzK. SinkJ. WilliamsonP. GargF. WatkinsBrian R. OttHenry QuerfurthG. TremontS. SallowayP. MalloyStephen CorreiaH. RosenBruce L. MillerJacobo MintzerK. SpicerDavid BachmanE. FingerS. PasternakI. RachinskyD. DrostN. PomaraR. HernandoA. SarraelSusan K. SchultzL. L. Boles PontoH. ShimK. SmithN. RelkinG. ChaingLisa RaudinAmanda G. SmithK. FargherB. A. RajYuying ZhouYong He
Nature Neuroscience Published 2025/04/01

Summary:

Human lifespan changes in the brain’s functional connectome in 33,250 individuals is reported, which highlights critical growth milestones and distinct maturation patterns and offers a normative reference for development, aging and diseases.

Database resources of the National Center for Biotechnology Information in 2025.
E. Sayers;J. BeckEvan E. BoltonJ. R. BristerJessica ChanRyan ConnorMichael FeldgardenAnna M FineKathryn FunkJ. HoffmanS. KannanChristopher KellyW. KlimkeSunghwan KimS. LathropAron Marchler-BauerTerence D MurphyChris O’SullivanErin SchmiederYuri SkripchenkoA. StineF. Thibaud-NissenJiyao WangJian YeErin ZellersValerie A SchneiderKim D. Pruitt
Nucleic acids research Published 2024/11/11
Phase I trial of hES cell-derived dopaminergic neurons for Parkinson’s disease
V. Tabar;H. SarvaA. LozanoA. FasanoS. KaliaK. YuC. BrennanY. MaS. PengD. EidelbergM. TomishimaS. IrionW. StempleN. AbidA. LampronL. StuderC. Henchcliffe
Nature Published 2025/04/16

Summary:

Bilateral grafts of cryopreserved human embryonic stem cell-derived dopaminergic neuron progenitor cells into the putamen of patients with Parkinson’s disease in a phase I clinical trial showed safety, improvements in off-drug motor function and graft survival at 18 months after transplant.

Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory.
Athanasios Ziogas;Boris NovakovicL. VentrigliaNoriko GalangKim A. TranWenchao LiV. MatzarakiNienke van UnenTitus SchlüterAnaísa V. FerreiraS. MoorlagV. KoekenMthabisi MoyoXiaoling LiMarijke P. A. BaltissenJ. H. MartensYang LiMaziar DivangahiL. JoostenM. MhlangaM. Netea
Cell Published 2025/04/25

Summary:

Long-term histone lactylation persisted in vivo 90 days after vaccination with BCG, highlighting H3K18la as an epigenetic mark of innate immune memory.

Global meta-analysis shows action is needed to halt genetic diversity loss
Robyn E. Shaw;K. FarquharsonM. BrufordDavid J CoatesCarole P. ElliottJ. MergeayK. OttewellG. SegelbacherSean HobanC. HvilsomS. Pérez-EsponaD. RuņģisF. AravanopoulosL. BertolaHelena CotrimKaren CoxV. Cubric-CurikR. EkblomJ. A. GodoyM. KonopińskiL. LaikreIsa-Rita M. RussoN. VeličkovićP. VergeerCarles VilàV. BrajkovicDavid L. FieldW. Goodall‐CopestakeFrank HailerTara HopleyF. ZachosP. C. AlvesA. BiedrzyckaR. BinksJ. BuiteveldE. BužanM. ByrneBarton HuntleyL. IacolinaN. KeehnenPeter KlingaAlexander KopatzSara KurlandJennifer A. LeonardC. ManfrinAlexis MarchesiniM. MillarP. Orozco‐terWengelJente OttenburghsDiana PosledovichP. B. SpencerN. TourvasTina Unuk NahbergerP. van HooftR. VerbylaitėCristiano VernesiC. Grueber
Nature Published 2025/01/29

Summary:

It is shown that within-population genetic diversity is being lost over timescales likely to have been impacted by human activities, and that some conservation actions may mitigate this loss.

Granzyme K activates the entire complement cascade
Carlos A Donado;Erin TheisenFan ZhangA. NathanM.L. FairfieldK. RupaniDominique JonesKellsey P. A. JohannesJ. AlbrechtJ. AnolikW. ApruzzeseJ. BarnasJ. BathonA. Ben-ArtziBrendan F BoyceDavid L. BoyleS. BridgesVivian P. BykerkDebbie CampbellArnoldas CeponisA. ChicoineMichelle CurtisKevin D. DeaneE. DiCarloL. DonlinPatrick DunnAndrew FilerHayley L. CarrGarry S. FiresteinLindsy J. ForbessL. Geraldino‐PardillaSusan M. GoodmanEllen M. GravalleseDeepak A. RaoPeter K. GregersenJ. GuthridgeM. Gutierrez-ArcelusV. HolersD. HorowitzLaura B. HughesLionel B. IvashkivK. IshigakiJ. JamesJoyce B. KangGregory KerasAmit LakhanpalJames A. LedererMiles J. LewisYuhong LiKatherine P. LiaoA. MandelinI. MantelK. MarksM. MayburyAndrew McDavidM. McGeachyJoseph R. MearsNida MeednuN. MillardL. MorelandS. NayarA. NervianiDana E. OrangeH. PerlmanC. PitzalisJ. Rangel-MorenoKarim RazaYakir A. ReshefChristopher T. RitchlinF. RivelleseWilliam H. RobinsonLaurie RumkerI. SahbudinS. SakaueJennifer A SeifertD. Scheel-ToellnerA. SingarajuKamil SlowikowskiMelanie H. SmithDarren TabechianP. UtzKathryn WeinandDana WeisenfeldMichael H. WeismanQian XiaoZhu ZhuZhihan J. LiAndrew CordleAaron WyseSoumya RaychaudhuriDaniel F. DwyerA. JonssonMichael B. Brenner
Nature Published 2025/02/06

Summary:

It is found that a protease called granzyme K can activate the entire complement cascade, explaining how it can drive destructive inflammation in inflammatory diseases such as rheumatoid arthritis.

Genomic data in the All of Us Research Program
Alexander G. Ginger A. Kelsey R. Lee Shimon Robert J. Anjene Bick Metcalf Mayo Lichtenstein Rura Carroll Musick;Alexander G. Ginger A. Kelsey R. Lee Shimon Robert J. Anjene Bick Metcalf Mayo Lichtenstein Rura Carroll MusickA. BickG. MetcalfKelsey MayoLee T LichtensteinS. RuraRobert J. CarrollA. MusickJ. LinderI. JordanS. NagarShivam SharmaRob MellerMelissa Eric Mine S. Kimberly F. Evan E. Stacey Richard A. Basford Boerwinkle Cicek Doheny Eichler Gabriel GiMelissa A. BasfordE. BoerwinkleMine S. CicekK. DohenyE. EichlerS. GabrielR. A. GibbsDavid GlazerPaul A. HarrisGail P. JarvikA. PhilippakisHeidi L. RehmDan M. RodenS. ThibodeauS. TopperAshley L. Samantha J. Victoria A. Jeffrey G. Mine S. Blegen Wirkus Wagner Meyer CicekAshley L. BlegenSamantha J. WirkusVictoria WagnerJeffrey G. MeyerDonna M. Eric Michelle Z. Sean M. L. Elvin Hua Marcia K. Muzny Venner Mawhinney Griffith Hsu Ling Adams WalD. MuznyE. VennerMichelle MawhinneySean GriffithE. HsuHua LingMarcia K. AdamsK. WalkerJianhong HuH. DoddapaneniC. KovarM. MuruganShannon P. DuganZiad M. KhanNiall J. Christina Eric Michael Namrata Emma Katie Sheli Lennon Austin-Tse Banks Gatzen Gupta Henricks LarsN. LennonC. Austin-TseE. BanksMichael GatzenNamrata GuptaEmma R. HenricksKatie LarssonSheli McDonoughS. HarrisonC. KachulisMatthew S. LeboC. NebenMarcie A. SteevesA. Y. ZhouJoshua D. Christian D. Colleen P. Karynne E. Marsha M. Se Smith Frazar Davis Patterson Wheeler McGee LockwooJosh SmithC. D. FrazarColleen P. DavisKarynne E. PattersonMarsha M. WheelerSean McgeeC. M. LockwoodB. ShirtsColin C. PritchardMitzi L. MurrayValeria VastaDru F. LeistritzMatthew RichardsonJillian G. BuchanA. RadhakrishnanNiklas KrummB. EhmenSophie M. Morgan T. Kristian Andrea Rebecca Aurora Kylee Schwartz Aster Cibulskis Haessly Asch Cremer DegatSophie SchwartzM. AsterK. CibulskisAndrea HaesslyR. AschAurora CremerKylee DegatanoA. ShergillL. GauthierSamuel K. LeeA. HatcherGeorge B. GrantG. BrandtMiguel CovarrubiasE. BanksAshley AbleA. GreenRobert J. CarrollJennifer ZhangH. CondonYuanyuan WangMoira K. DillonC. AlbachWail BaalawiSeung Hoan Xin Elisabeth A. Choi Wang RosenthalSeung Hoan ChoiXin WangE. RosenthalAndrea H. Sokny Siddhartha Bradley Anastasia L. Chris Geo Ramirez Lim Nambiar Ozenberger Wise Lunt Ginsburg Andrea RamirezSokny LimSiddhartha NambiarB. OzenbergerAnastasia WiseC. LuntGeoffrey S. GinsburgJ. Denny
Nature Published 2024/02/19

Summary:

The release of clinical-grade whole-genome sequence data for 245,388 diverse participants by the All of Us Research Program is described and it is anticipated that this diverse dataset will advance the promise of genomic medicine for all.

Ensembl 2025
Sarah Dyer;Olanrewaju Austine-OrimoloyeA. G. AzovMatthieu BarbaIf H. A. BarnesV. Barrera-EnríquezArne BeckerRuth BennettMartin BeracocheaAndrew E. BerryJyothish BhaiSimarpreet Kaur BhurjiSanjay BodduPaulo R Branco LinsLucy BrooksShashank Budhanuru RamarajuLahcen CampbellManuel Carbajo MartinezMehrnaz CharkhchiL. A. CortésC. DavidsonSukanya DenniK. DodiyaS. DonaldsonBilal El HoudaiguiTamara El NaboulsiOluwadamilare FalolaReham FatimaThiago GenezJ. G. MartinezTatiana A. GurbichMatthew HardyZoe HollisT. HuntM. KayVinay KaykalaDiana LemosDisha LodhaNourhen MathlouthiGabriela A. MerinoRyan MerrittLouisse Paola MirabuenoAleena MushtaqS. N. HossainJose Perez-SilvaMalcolm PerryIvana PilizotaDaniel PoppletonIrina ProsovetskaiaShriya RajA. I. A. SalamShradha SarafNuno Saraiva-AgostinhoSwati SinhaBotond SiposVasily SitnikEmily SteedM. SunerLikhitha SurapaneniKyösti SutinenF. F. TricomiIan TsangDavid Urbina-GómezA. VeidenbergThomas A WalshNatalie L. WillhoftJames E. AllenJorge Alvarez-JarretaMarc ChakiachviliJitender CheemaJorge E. B. da RochaNishadi H. De SilvaStefano GiorgettiLeanne HaggertyGarth R. IlsleyJ. KeatleyJ. LovelandB. MooreJonathan M. MudgeG. NaamatiJohn G. TateS. TrevanionAndrea WinterbottomBeth FlintA. FrankishSarah E. HuntRobert D. FinnM. FreebergPeter W. HarrisonFergal J. MartinAndrew D. Yates
Nucleic Acids Research Published 2024/12/04

Summary:

The new Ensembl site, currently in beta, has continued to develop, currently holding >2700 eukaryotic genome assemblies and will replace the current Rapid Release site, and represents a key step towards provision of a single integrated Ensembl site.

Oxidative stress and inflammation in the pathogenesis of neurological disorders: Mechanisms and implications
Umesh Chandra Dash;Nitish Kumar BholSandeep Kumar SwainRashmi Rekha SamalPrabhat Kumar NayakV. RainaSandeep Kumar PandaRout George KerryA. DuttaroyA. B. Jena
Acta Pharmaceutica Sinica. B Published 2024/10/01

Summary:

By understanding the intricate interplay between oxidative stress and neurological disorders, scientists hope to pave the way for innovative therapeutic and preventive approaches, ultimately improving individuals' living standards.

Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets
Nuala A O'Leary;Eric CoxJ. B. HolmesW. R. AndersonR. FalkVichet HemMirian T N TsuchiyaGregory D. SchulerXuan ZhangJohn P TorciviaAnne KetterLaurie BreenJonathan CothranH. BajwaJovany TinnePeter A. MericW. HlavinaValerie A Schneider
Scientific Data Published 2024/07/05

Summary:

The current scope of data accessible through NCBI Datasets is outlined and various options for exploring and downloading the data are explained, facilitating improved data retrieval, sharing, and usability in research.

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche
Martha A. Zepeda-Rivera;Samuel S. MinotHeather BouzekHanrui WuA. Blanco-MíguezPaolo ManghiDakota S. JonesKaitlyn D. LacourseYing WuElsa F. McMahonSoon‐Nang ParkY. K. LimAndrew G. KempchinskyAmy D. WillisSean CottonS. YostEwa T SicinskaJ. KookF. DewhirstN. SegataS. BullmanChristopher D. Johnston
Nature Published 2024/03/20

Summary:

The results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.

Embracing cancer complexity: Hallmarks of systemic disease.
C. Swanton;Elsa BernardChris AbboshF. AndréJohan AuwerxAllan BalmainDafna Bar-SagiRené BernardsSusan BullmanJames DeGregoriC. ElliottA. ErezGerard EvanM. FebbraioAndrés HidalgoM. Jamal-HanjaniJohanna A. JoyceMr. KaiserKatja A. LamiaJ. LocasaleS. LoiI. MalanchiM. MeradKathryn MusgraveKetan J. PatelSergio A. QuezadaJ. WargoA. WeeraratnaE. WhiteF. WinklerJohn N. WoodK. VousdenDouglas Hanahan
Cell Published 2024/03/01

Summary:

Complexes of cancer as a systemic disease are discussed, including tumor initiation and promotion, tumor micro- and immune macro-environments, aging, metabolism and obesity, cancer cachexia, circadian rhythms, nervous system interactions, tumor-related thrombosis, and the microbiome.

The pathophysiology of sepsis and precision-medicine-based immunotherapy
E. Giamarellos‐Bourboulis;A. AschenbrennerMichael BauerChristoph BockThierry CalandraIrit Gat-ViksE. KyriazopoulouM. LupșeG. MonneretP. PickkersJ. SchultzeT. van der PollF. L. van de VeerdonkA. VlaarSebastian WeisW. J. WiersingaM. Netea
Nature Immunology Published 2024/01/01

Summary:

The latest research that contributes to the understanding of the pathophysiology of sepsis is summarized, and how this contributes to a new treatment approach through personalized immunotherapy is summarized.

Phylogenomics and the rise of the angiosperms
A. Zuntini;Tom CarruthersOlivier MaurinP. BaileyKevin LeempoelG. BrewerNiroshini EpitawalageElaine FrançosoBerta Gallego-ParamoCatherine McGinnieR. NegrãoShyamali RoyLalita SimpsonEduardo Toledo RomeroV. BarberLaura R. BotiguéJ. J. ClarksonRobyn S. CowanS. DodsworthMatthew G. JohnsonJan T. KimL. PokornyN. WickettG. AntarLucinda DeBoltKarime GutierrezKasper P. HendriksAlina HoewenerAi-Qun HuE. JoyceI. KikuchiI. LarridonDrew A. LarsonElton John de LírioJing‐Xia LiuP. MalakasiNatalia A. S. PrzelomskaToral ShahJ. ViruelTheodore R. AllnuttG. AmekaRose L. AndrewM. AppelhansM. AristaMaría ArizaJuan ArroyoWatchara ArthanJ. BachelierC. BaileyH. F. BarnesM. BarrettR. BarrettR. J. BayerM. BaylyE. BiffinNicky BiggsJ. BirchD. BogarínRenata BorosovaAlexander M. C. BowlesPeter C. BoyceGemma BramleyMarie BriggsLinda BroadhurstGillian K. BrownJ. BruhlAnne BruneauS. BuerkiEdie BurnsM. ByrneS. CableAinsley CalladineM. CallmanderÁ. CanoD. CantrillWarren M. Cardinal-McTeagueM. CarlsenAbigail J A CarruthersAlejandra de Castro MateoMark W. ChaseL. ChatrouM. CheekShilin ChenMaarten J. M. ChristenhuszP. ChristinM. ClementsSkye C. CoffeyJ. ConranXavier CornejoT. CouvreurIan D CowieLaszlo CsibaI. DarbyshireG. DavidseNina M J DaviesA. DavisKor-jent van DijkS. R. DownieM. DurettoM. DuvallSara L. EdwardsUrs EggliR. ErkensMarcial EscuderoM. de la EstrellaFederico FabrianiMichael F. FayP. D. L. FerreiraSarah Z. FicinskiRachael M. FowlerS. FrisbyLin FuT. FulcherM. Galbany‐CasalsE. GardnerD. GermanAugusto GiarettaM. GibernauL. GillespieCynthia C. GonzálezD. GoyderSean W. GrahamA. GrallLaura GreenBee F. GunnDiego G. GutiérrezJan HackelThomas HaevermansA. HaighJ. C. HallT. HallMelissa J. HarrisonS. HattO. HidalgoT. HodkinsonG. HolmesH. HopkinsChristopher J JacksonShelley A. JamesR. JobsonG. KadereitImalka M. KahandawalaKent KainulainenMasahiro KatoElizabeth A. KelloggG. J. KingBeata KlejevskajaB. KlitgaardR. KlopperSandra KnappMarcus A. KochJames H. Leebens-MackF. LensC. LeonÉtienne Léveillé‐BourretG. LewisDe‐Zhu LiLan LiS. Liede‐SchumannTatyana LivshultzD. LorenceMeng LuPatricia Lu-IrvingJaquelini LuberEve J. LucasManuel LujánMabel LumT. MacfarlaneCarlos MagdalenaV. F. MansanoLizo E. MastersS. MayoK. MccollAngela J McDonnellAndrew E. McDougallT. McLayHannah McPhersonR. I. MenesesV. MerckxF. MichelangeliJ. MitchellAlexandre K. MonroMichael J. MooreTaryn L. MuellerK. MummenhoffJ. MunzingerPriscilla MurielDaniel J. MurphyKatharina NargarLars NauheimerF. J. NgeR. NyffelerAndrés OrejuelaEdgardo M. OrtizL. PalazzesiA. PeixotoS. PellJ. PellicerD. PenneysÓ. Pérez-EscobarC. PerssonMarc PignalY. PillonJ. PiraniG. PlunkettR. PowellG. PranceCarmen PuglisiMing QinR. RabelerPaul ReesMatthew A. M. RennerE. RoalsonM. RoddaZ. S. RogersS. RokniR. RutishauserM. D. DE SALASHanno SchaeferRowan J. SchleyA. Schmidt‐LebuhnA. ShapcottI. AL-SHEHBAZK. ShepherdMark P. SimmonsA. SimõesA. SimõesMichelle SirosE. SmidtJames F. SmithNeil W. SnowD. SoltisP. SoltisR. SorengC. SothersJ. StarrPeter F. StevensS. StraubL. StruweJennifer M. TaylorI. TelfordAndrew H. ThornhillIfeanna M. ToothA. Trias‐BlasiF. UdovicicT. UtteridgeJ. C. del ValleG. VerboomHelen P. VonowM. VorontsovaJ. D. de VosNoor Al-WattarM. WaycottC. A. WelkerAdam J WhiteJ. WieringaLuis T. WilliamsonTrevor C. WilsonS. WongLisa A WoodsR. WoodsS. WorboysMartin D. XanthosYa YangYu‐Xiao ZhangMeng‐Yuan ZhouS. ZmarztyF. ZuloagaA. AntonelliS. BellotD. CraynO. GracePaul J. KerseyI. LeitchH. SauquetStephen A. SmithW. EiserhardtF. ForestWilliam J. Baker
Nature Published 2024/04/24

Summary:

This work built an angiosperm tree of life dated with 200 fossil calibrations, providing key insights into evolutionary relationships and diversification and shows the deep history and full complexity in the evolution of a megadiverse clade.

Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program
Anurag Verma;Jennifer E. HuffmanAlex RodriguezMitchell ConeryMolei LiuY. HoYoungdae KimDavid HeiseLindsay A GuareV. PanickanH. GarconFranciel LinaresLauren CostaIan GoethertRyan TiptonJ. HonerlawLaura DaviesS. WhitbourneJeremy CohenD. PosnerRahul SangarMichael MurrayXuan WangD. DochtermannP. DevineniYunling ShiT. NandiT. AssimesCharles A. BrunetteRobert J. CarrollRoyce CliffordS. DuvallJ. GelernterA. HungSudha K. IyengarJacob JosephR. KemberH. KranzlerColleen M. KripkeD. LeveyS. LuohVictoria C. MerrittC. OverstreetJ. DeakStruan F. A. GrantR. PolimantiPanagiotis RoussosG. ShaktYan V. SunN. TsaoS. VenkateshG. VoloudakisAmy JusticeE. BegoliRachel RamoniGeorgia D. TourassiS. PyarajanPhil TsaoChristopher J. O’DonnellS. MuralidharJ. MoserJuan P. CasasA. BickWei ZhouTianxi CaiB. VoightKelly ChoJ. GazianoR. MadduriS. DamrauerKatherine P. Liao
Science (New York, N.Y.) Published 2024/07/19
SenNet recommendations for detecting senescent cells in different tissues
V. Suryadevara;Adam D. HudginsAdarsh RajeshA. PappalardoA. KarpovaAmit K DeyAnn M HertzelAnthony AgudeloAzucena RochaBikem SoygurB. SchillingChase M CarverC. Aguayo-MazzucatoDarren J. BakerD. BernlohrD. JurkD. MangarovaEllen M. QuardokusE. A. L. EnningaElizabeth L. SchmidtFeng ChenFrancesca E DuncanFrancesco CambuliG. KaurG. KuchelGung LeeH. Daldrup-LinkHélène MartiniHemali PhatnaniI. M. Al-NaggarIrfan RahmanJia NieJ. PassosJonathan C. SilversteinJudith CampisiJulia T. WangKanako IwasakiKarina BarbosaKay MétisKerem NernekliL. NiedernhoferLi DingLichao WangLisa C AdamsRui LiuMadison L. DoolittleM. TenecheMarissa J. SchaferMing XuMohammadjavad HajipourMozhgan BoroumandNathan BasistyNicholas SloanNikolai SlavovOlena KuksenkoPaul RobsonPaul T. GomezPeriklis VasilikosP. AdamsPriscila CarapetoQuan ZhuRamalakshmi RamasamyRolando Perez-LorenzoRong FanRunze DongR. MontgomeryS. ShaikhSanja VickovicShanshan YinShoukai KangSonja SuvakovSundeep KhoslaVesna D. GarovicVilas MenonYanxin XuYizhe SongYousin SuhZhixun DouN. Neretti
Nature Reviews Molecular Cell Biology Published 2024/06/03

Summary:

Recommendations for detecting senescent cells in different tissues based on a comprehensive analysis of existing literature reporting senescence markers in 14 tissues in mice and humans are provided.

Integrated multimodal cell atlas of Alzheimer’s disease
M. Gabitto;K. TravagliniV. RachleffE. KaplanBrian R. LongJeanelle ArizaYi DingJoseph T. MahoneyN. DeeJeff GoldyErica J. MeliefKrissy BrounerJazmin CamposJ. CamposAmbrose J. CarrTamara CasperRushil ChakrabartyMichael ClarkJ. CoolNasmil J. Valera CuevasR. DalleyMartin DarvasS. DingTim DolbeareChristine L. Mac DonaldTom EgdorfLuke EspositoR. FerrerRohan GalaA. GaryJessica GloeNathan GuilfordJunitta B. GuzmanDaniel HirschsteinWindy V. HoTim JarksyNelson J. JohansenB. KalmbachLisa M. KeeneSarah KhawandMitchell D KilgoreAmanda KirklandMichael KunstBrian R. LeeJocelin MaloneZoe MaltzerNaomi MartinRachel McCueD. McMillenEmma MeyerdierksKelly P. MeyersTyler MollenkopfMark MontineAmber L. NolanJ. NyhusP. OlsenMaiya I PaclebNicholas PeñaThanh PhamC. PomN. PostupnaAugustin RuizAimee M. SchantzN. ShapovalovaS. SorensenB. StaatsM. SullivanS. SunkinC. ThompsonMichael TieuJ. TingA. TorkelsonTracy TranMing‐Qiang (Michael) WangJack WatersAngela M. WilsonD. HaynorN. GattoS. JayadevS. MuftiLydia NgS. MukherjeeP. CraneCaitlin S. LatimerBoaz P. LeviKimberly A. SmithJennie L. CloseJeremy A. MillerR. HodgeEric B. LarsonT. GrabowskiM. HawrylyczC. Dirk KeeneE. Lein
Nature Neuroscience Published 2024/02/15

Summary:

The current study harnesses single cell and spatial genomics tools and knowledge from the BRAIN Initiative Cell Census Network to understand the impact of disease progression on middle temporal gyrus cell types and mapped single nuclei from each donor to a common cell type reference with unprecedented resolution.

De novo designed proteins neutralize lethal snake venom toxins
Susana Vázquez Torres;Melisa Benard ValleS. MackessyStefanie K. MenziesN. CasewellShirin AhmadiNick J. BurletEdin MuratspahićIsaac SappingtonMax D OverathE. Rivera-de-TorreJann LedergerberA. H. LaustsenKim BoddumA. BeraA. KangEvans BrackenbroughIara A. CardosoEdouard P. CrittendenRebecca EdgeJustin DecarreauRobert J. RagotteArvind S PillaiMohamad H. AbediHannah L. HanStacey R. GerbenAnalisa MurrayRebecca SkotheimL. StuartL. StewartThomas FryerT.P. JenkinsDavid Baker
Nature Published 2025/01/15

Summary:

Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible antivenom treatments.

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle
Thao-Quyen Nguyen;Carl R. HutterAlexey MarkinMegan N. ThomasKristina LantzM. KillianGarrett M. JanzenSriram VijendranSanket WagleBlake InderskiDrew R. MagstadtGanwu LiD. DielElisha A FryeK. DimitrovA. SwinfordAlexis C. ThompsonKevin R. SnevikD. L. SuarezE. SpackmanSteven M. LakinSara C. AholaKammy R. JohnsonA. BakerS. Robbe-AustermanMia K. TorchettiT. Anderson
bioRxiv Published 2024/05/01

Summary:

The genomic analysis and epidemiological investigation showed that a reassortment event in wild bird populations preceded a single wild bird-to-cattle transmission episode of H5N1 HPAI within dairy cattle, increasing the risk for infection and subsequent spread of the virus to human populations.

The nature of the last universal common ancestor and its impact on the early Earth system
E. R. Moody;Sandra Álvarez-CarreteroT. MahendrarajahJames W ClarkHolly C. BettsNina DombrowskiLénárd L. SzánthóRichard A. BoyleS. DainesXi ChenN. LaneZiheng YangGraham A. ShieldsG. SzöllősiA. SpangD. PisaniT. WilliamsT. LentonP. Donoghue
Nature Ecology & Evolution Published 2024/07/12
The Pfam protein families database: embracing AI/ML
T. Paysan-Lafosse;Antonina AndreevaMatthias BlumS. ChuguranskyTiago GregoBeatriz Lázaro PintoGustavo A. SalazarMaxwell L. BileschiFelipe Llinares-LópezLaetitia Meng-PapaxanthosLucy J ColwellNick V. GrishinR. D. SchaefferDamiano ClementelSilvio C. E. TosattoErik SonhammerV. WoodA. Bateman
Nucleic Acids Research Published 2024/11/14

Summary:

This update describes major developments in Pfam since 2020, including decommissioning the Pfam website and integration with InterPro, harmonization with the ECOD structural classification, and expanded curation of metagenomic, microprotein and repeat-containing families.

Whole-brain annotation and multi-connectome cell typing of Drosophila
P. Schlegel;Yijie YinA. S. BatesS. DorkenwaldK. EichlerPaul BrooksDaniel HanMarina GkantiaMárcia dos SantosE. MunnellyGriffin BadalamenteLaia Serratosa CapdevilaVarun A. SaneA. M. FragniereLadann KiassatM. W. PleijzierT. StürnerImaan F. M. TamimiChristopher R. DunneIrene SalgarellaA. JavierSiqi FangEric PerlmanTom KazimiersSridhar R. JagannathanArie MatsliahA. SterlingSzi-chieh YuClaire E. McKellarKrzysztof KrukDoug BlandZairene LenizoAustin BurkeK. WillieA. S. BatesNikitas SerafetinidisNashra HadjerolRyan WillieB. SilvermanJohn Anthony OchoJoshua BañezRey Adrian CandiladaJay GagerAnne KristiansenNelsie PanesArti YadavRemer TancontianShirleyjoy SeronaJet Ivan DolorosaKendrick Joules VinsonDustin GarnerRegine SalemAriel DagohoyJaime SkeltonMendell LopezThomas StocksAnjali PandeyDarrel Jay AkiatanJames HebditchCelia DavidD. SapkalShaina Mae MonungolhVarun A. SaneMark Lloyd PielagoMiguel AlberoJacquilyn LaudeMárcia dos SantosDavid S. DeutschZeba VohraKaiyu WangAllien Mae GogoEmil KindAlvin Josh MandahayChereb MartinezJohn David AsisChitra V NairDhwani PatelMarchan ManaytayC. LimPhilip Lenard AmpoMichelle Darapan PantujanDaril BautistaRashmita RanaJansen SeguidoBhargav ParmarJohn Clyde SaguimpaMerlin MooreM. W. PleijzierMark LarsonJoseph HsuItisha JoshiDhara KakadiyaAmalia BraunC. PilapilKaushik ParmarQuinn X. VanderbeckChristopher R. DunneE. MunnellyChan Hyuk KangLena LörschJin-Min LeeLucia KmecováGizem SancerChrista A BakerJenna JoroffSteven CalleYashvi PatelO. SatoJanice SalocotFarzaan SalmanSebastian Molina-ObandoMai BuiMatthew LichtenbergerEdmark TamboboyKatieanne MolloyAlexis Santana-CruzA. HernandezSeongbong YuMarissa SorekArzoo DiwanMonika PatelT. AikenSarah MorejohnSanna KoskelaTansy YangD. LehmannJonas ChojetzkiS. SisodiyaSelden KoolmanP. ShiuSky ChoAnnika BastBrian ReicherMarlon BlanquartLucy HoughtonHyungjun ChoiMaria IoannidouMatt CollieJoanna L EckhardtBenjamin GorkoLi GuoZhihao ZhengA. PohMarina LinIstván TaiszWes MurfinÁ. S. DíezNils ReinhardPeter W. GibbNidhi PatelSandeep KumarMinsik YunMegan WangDevon JonesLucas Encarnacion-RiveraA. OswaldAkanksha JadiaMert ErginkayaN. DrummondLeonie F. WalterI. TastekinX. ZhongYuta MabuchiFernando J. Figueroa SantiagoU. VermaNick ByrneEdda KunzeT. CrahanRyan MargossianHaein KimIliyan GeorgievFabianna SzorenyiAtsuko AdachiBenjamin BargeronTomke StürnerDamian D DemarestBurak GürAndreas BeckerR. TurnbullA. MorrenAndrea SandovalAnthony Moreno-SanchezDiego A. PachecoEleni SamaraHaley CrokeAlex G. ThomsonConnor W. LaughlandS. DuttaPaula Guiomar Alarcón de AntónBinglin HuangPatricia PujolsI. HaberAmanda J. González-SegarraAlbert LinDaniel T. ChoeVeronika LukyanovaNino ManciniZequan LiuTatsuo S OkuboMiriam A. FlynnGianna VitelliM. LaturneyFeng LiShuo CaoCarolina Manyari-DiazHyunsoo YimAnh Duc LeKate MaierSeungyun YuYeonju NamDaniel BąbaAmanda AbusaifAudrey FrancisJesse GaykSommer S. HuntressR. BarajasMindy KimXinyu CuiGabriella R. SterneAnna LiKeehyun ParkG. DempseyAlan MathewJinseong KimTaewan KimGuanhao WuSerene DhawanMargarida BrotasCheng ZhangShanice BaileyAlexander Del ToroKisuk LeeT. MacrinaC. Schneider-MizellS. PopovychOluwaseun OgedengbeRunzhe YangA. HalageriW. SilversmithStephan GerhardA. ChampionN. EcksteinDodam IhN. KemnitzM. CastroZ. JiaJingpeng WuEric MitchellBarak NehoranS. MuJ. BaeR. LuR. MoreyKai KuehnerD. BrittainC. JordanD. J. AndersonRudy BehniaSalil S. BidayeA. BorstEugenia ChiappeF. CollmanKenneth J. ColodnerAndrew M. DacksB. DicksonJan FunkeDenise GarciaStefanie HampelV. HartensteinBassem A. HassanCharlotte Helfrich-ForsterWolf HuetterothJinseop S. KimSung Soo KimYoung-Joon KimJae Young KwonW. LeeG. LinneweberGaby MaimonRichard S. MannS. NoselliMichael J PankratzL. Prieto-GodinoJ. ReadMichael B ReiserKatie von ReynC. RibeiroKristin ScottA. SeedsM. SelchoM. SiliesJulie H. SimpsonS. WaddellMathias F. WernetRachel I. WilsonFred W. WolfZepeng YaoNilay YapiciMeet ZandawalaMarta CostaH. S. SeungM. MurthyD. BockG. Jefferis
Nature Published 2024/10/01

Summary:

A consensus cell type atlas for the fly brain provides both an intellectual framework and open-source toolchains for brain-scale comparative connectomics and provides evidence for functional homeostasis in the mushroom body through adjustments of the absolute amount of excitatory input.

Human de novo mutation rates from a four-generation pedigree reference
David Porubsky;H. DashnowT. SasaniGlennis A. LogsdonP. HallastMichelle D NoyesZ. KronenbergT. MokveldNidhi KoundinyaCillian NolanCody J. SteelyAndrea GuarracinoE. DolzhenkoWilliam T. HarveyW. RowellKirill A GrigorevT. J. NicholasMichael E. GoldbergKeisuke K. OshimaJiadong LinPeter EbertW. S. WatkinsTiffany Y. LeungVincent C. T. HanlonSean McgeeB. PedersenHannah C. HappHyeonsoo JeongKatherine M. MunsonKendra HoekzemaDaniel D. ChanYanni WangJordan KnuthGage H. GarciaCairbre FanslowChristine LambertCharles LeeJosh SmithShawn LevyChristopher E. MasonErik GarrisonPeter M. LansdorpD. NeklasonLynn B. JordeAaron R. QuinlanM. EberleE. Eichler
Nature Published 2025/04/23

Summary:

Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set to understand the most fundamental processes underlying human genetic variation.

Genomic selection in plant breeding: key factors shaping two decades of progress.
A. Alemu;Johanna ÅstrandO. Montesinos-LópezJulio Isidro y SánchezJavier Fernández-GonzálezW. TadesseR. VetukuriAnders S. CarlssonAlf CeplitisJ. CrossaRodomiro OrtizA. Chawade
Molecular plant Published 2024/03/01

Summary:

It is hypothesized that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods, and support from other omics approaches, the boundaries of the current limitations could overcome the boundaries of the current limitations to achieve the highest possible prediction accuracy, making GS an effective tool in plant breeding.

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