AIM Resource Publications

A lipid cue drives the subcellular localization of a self-inserting bacterial transmembrane protein.

Pande VUpdegrove TBAnantharaman VBae AChen JAravind LRamamurthi KS

bioRxiv

2026 May 29

Efficient spatio-angular reconstruction enables high-fidelity mapping of six-dimensional structures and dynamics with polarized fluorescence microscopy.

Liu JChandler TLi YAgashe AWei MSu YWu YBaskin TIJaumouillé VChen JXu PYe HZhu WFischer RSSwaminathan VNain ASMehta SBRiviere PJShroff HLiu HGuo M

Res Sq

2026 Mar 04

U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs.

Garcia GRPalangat MMoraly JDonovan BTWang BPhadke ISturgill DChen JZhang GHolewinski RJShort BRivero GASwoboda DMTaylor NMcGraw KLarson DR

Mol Cell

2026 Apr 02

Intravital single-molecule imaging reveals cytoskeletal turnover as a driver of membrane remodeling in live animals.

Heydecker MChen DMasedunskas AMikolaj MNarayan KChen JVishwasrao HMeckel THardeman EGunning PWeigert R

bioRxiv

2026 Feb 25

Highly dynamic dural sinuses support meningeal immunity.

Monaghan KLZanluqui NGSu YRiggle BAPeterkin NJohnson KRRosenblum JSPetersen JDLiu JWang XVishwasrao HDLatour LLMcGavern DB

Nature

2026 Apr

[Identification of Nitrate Sources in Groundwater Based on Multiple Qualitative and Quantitative Statistical Analysis Methods].

Xi YXu SSChen JJTao LJing HWGuo JTian YShen XEChen Q

Huan Jing Ke Xue

2026 Feb 08

Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy.

Liu JChandler TLi YAgashe AWei MSu YWu YBaskin TIJaumouillé VChen JXu PYe HZhu WFischer RSSwaminathan VNain ASMehta SBLa Riviere PJShroff HLiu HGuo M

bioRxiv

2025 Sep 25

The CENP-A chaperone complex spatially organizes centromeres.

Gupta HHaase JWu YChen JKaradimov GShroff HKelly AE

bioRxiv

2025 Nov 09

Single-molecule fluorescence microscopy reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of live inner ear hair cells.

Miyoshi TVishwasrao HDBelyantseva IAMiyoshi JSajeevadathan MIshibashi YAdadey SMHarada NShroff HFriedman TB

Nat Commun

2025 Sep 01

Modeling neurotropic virus infection with functional human neural spheroids as a platform for high-throughput antiviral screening and pathogenesis.

Medina AChen YCZhang JOgden SCCotsmire SVishwasrao HDFerrer MLee EM

Antiviral Res

2025 Oct

Study on Liver Sinusoidal Endothelial Cell Fenestrations Based on Cellular Omics-Structure Integration Technology and Its Application in Metabolic Diseases.

Wei ZChen JLeapman RD

bioRxiv

2025 May 19

Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope.

Chandler TGuo MSu YChen JWu YLiu JAgashe AFischer RSMehta SBKumar ABaskin TIJaumouillé VLiu HSwaminathan VNain ASOldenbourg RLa Riviere PJShroff H

Proc Natl Acad Sci U S A

2025 Feb 25

[Hydrochemical Characteristics and Mechanism Analysis of Shallow Groundwater in Beijing Plain Area].

Wang SYMa ZHChang MChen YYXi YChen JJCui DTao LJing HWLu HFShen XELiu BX

Huan Jing Ke Xue

2025 Feb 08

Effect of exposure to environmental phenols and parabens on folate concentrations among 3-19 years old children and adolescents: A cross-sectional study in NHANES 2005-2016.

Ni MLin ZChen ZXu ZZhang QZhao JLi WTang YCao ZLi BYao DCheng CHu YLiu XChen JLiu Z

Ecotoxicol Environ Saf

2025 Jan 01

Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity.

Updegrove TBDelerue TAnantharaman VCho HChan CNipper TChoo-Wosoba HJenkins LMZhang LSu YShroff HChen JBewley CAAravind LRamamurthi KS

Sci Adv

2024 Oct 18

A Type I Photosensitizer-Polymersome Boosts Reactive Oxygen Species Generation by Forcing H-Aggregation for Amplifying STING Immunotherapy.

Wang ZMa WYang ZKiesewetter DOWu YLang LZhang GNakuchima SChen JSu YHan SWu LGJin AJHuang W

J Am Chem Soc

2024 Oct 23

Convolutional neural network transformer (CNNT) for fluorescence microscopy image denoising with improved generalization and fast adaptation.

Rehman AZhovmer ASato RMukouyama YSChen JRissone APuertollano RLiu JVishwasrao HDShroff HCombs CAXue H

Sci Rep

2024 Aug 06

Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2.

Nguyen AZhao HMyagmarsuren DSrinivasan SWu DChen JPiszczek GSchuck P

Elife

2024 Jun 28

Convolutional Neural Network Transformer (CNNT) for Fluorescence Microscopy image Denoising with Improved Generalization and Fast Adaptation.

Rehman AZhovmer ASato RMukoyama YChen JRissone APuertollano RVishwasrao HShroff HCombs CAXue H

ArXiv

2024 Apr 06

Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity.

Updegrove TBDelerue TAnantharaman VCho HChan CNipper TChoo-Wosoba HJenkins LMZhang LSu YShroff HChen JBewley CAAravind LRamamurthi KS

bioRxiv

2024 Mar 27

Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells.

Miyoshi TVishwasrao HBelyantseva ISajeevadathan MIshibashi YAdadey SHarada NShroff HFriedman T

Res Sq

2024 May 21

Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells.

Miyoshi TVishwasrao HDBelyantseva IASajeevadathan MIshibashi YAdadey SMHarada NShroff HFriedman TB

bioRxiv

2024 May 07

Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM).

Chandler TGuo MSu YChen JWu YLiu JAgashe AFischer RSMehta SBKumar ABaskin TIJamouillé VLiu HSwaminathan VNain AOldenbourg RRiviére PShroff H

bioRxiv

2024 Mar 12

Cell division machinery drives cell-specific gene activation during differentiation in .

Chareyre SLi XAnjuwon-Foster BRUpdegrove TBClifford SBrogan APSu YZhang LChen JShroff HRamamurthi KS

Proc Natl Acad Sci U S A

2024 Mar 26

Transgenic Tg(Kcnj10-ZsGreen) fluorescent reporter mice allow visualization of intermediate cells in the stria vascularis.

Strepay DOlszewski RTNixon SKorrapati SAdadey SGriffith AJSu YLiu JVishwasrao HGu SSaunders TRoux IHoa M

Sci Rep

2024 Feb 06

Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2.

Nguyen AZhao HMyagmarsuren DSrinivasan SWu DChen JPiszczek GSchuck P

bioRxiv

2024 Mar 22

Pro-regenerative biomaterials recruit immunoregulatory dendritic cells after traumatic injury.

Lokwani RJosyula ANgo TBDeStefano SFertil DFaust MAdusei KMBhuiyan MLin AKarkanitsa MMaclean EFathi PSu YLiu JVishwasrao HDSadtler K

Nat Mater

2024 Jan

Author Correction: Experimental and theoretical model for the origin of coiling of cellular protrusions around fibers.

Sadhu RKHernandez-Padilla CEisenbach YEPenič SZhang LVishwasrao HDBehkam BKonstantopoulos KShroff HIglič APeles ENain ASGov NS

Nat Commun

2023 Dec 21

Functional brain region-specific neural spheroids for modeling neurological diseases and therapeutics screening.

Strong CEZhang JCarrasco MKundu SBoutin MVishwasrao HDLiu JMedina AChen YCWilson KLee EMFerrer M

Commun Biol

2023 Nov 28

Transgenic Tg(Kcnj10-ZsGreen) Fluorescent Reporter Mice Allow Visualization of Intermediate Cells in the Stria Vascularis.

Strepay DOlszewski RTNixon SKorrapati SAdadey SGriffith AJSu YLiu JVishwasrao HGu SSaunders TRoux IHoa M

Res Sq

2023 Oct 04

Experimental and theoretical model for the origin of coiling of cellular protrusions around fibers.

Sadhu RKHernandez-Padilla CEisenbach YEPenič SZhang LVishwasrao HDBehkam BKonstantopoulos KShroff HIglič APeles ENain ASGov NS

Nat Commun

2023 Sep 12

Real-time imaging of drug-induced trapping of cellular topoisomerases and poly(ADP-ribose) polymerase 1 at the single-molecule level.

Sun YChen JPommier Y

Nucleic Acids Res

2023 Oct 13

Dendritic distribution of autophagosomes underlies pathway-selective induction of LTD.

Keary KMGu QHChen JLi Z

Cell Rep

2023 Aug 29

Targeting neddylation sensitizes colorectal cancer to topoisomerase I inhibitors by inactivating the DCAF13-CRL4 ubiquitin ligase complex.

Sun YBaechler SAZhang XKumar SFactor VMArakawa YChau CHOkamoto KParikh AWalker BSu YPChen JTing THuang SNBeck EItkin ZMcKnight CXie CRoper NNijhawan DFigg WDMeltzer PSYang JCThomas CJPommier Y

Nat Commun

2023 Jun 23

Targeting N-linked Glycosylation for the Therapy of Aggressive Lymphomas.

Scheich SChen JLiu JSchnütgen FEnssle JCCeribelli MThomas CJChoi JMorris VHsiao TNguyen HWang BBolomsky APhelan JDCorcoran SUrlaub HYoung RMHäupl BWright GWHuang DWJi YYu XXu WYang YZhao HMuppidi JPan KTOellerich TStaudt LM

Cancer Discov

2023 Aug 04

A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins.

Zhao HWu DHassan SANguyen AChen JPiszczek GSchuck P

Sci Adv

2023 Apr 05

Label-free cleared tissue microscopy and machine learning for 3D histopathology of biomaterial implants.

Ngo TBDeStefano SLiu JSu YShroff HVishwasrao HDSadtler K

J Biomed Mater Res A

2023 Jun

Three-dimensional structured illumination microscopy with enhanced axial resolution.

Li XWu YSu YRey-Suarez IMatthaeus CUpdegrove TBWei ZZhang LSasaki HLi YGuo MGiannini JPVishwasrao HDChen JLee SJShao LLiu HRamamurthi KSTaraska JWUpadhyaya ALa Riviere PShroff H

Nat Biotechnol

2023 Sep

Incorporating the image formation process into deep learning improves network performance.

Li YSu YGuo MHan XLiu JVishwasrao HDLi XChristensen RSengupta TMoyle MWRey-Suarez IChen JUpadhyaya AUsdin TBColón-Ramos DALiu HWu YShroff H

Nat Methods

2022 Nov

Practical considerations for quantitative light sheet fluorescence microscopy.

Hobson CMGuo MVishwasrao HDWu YShroff HChew TL

Nat Methods

2022 Dec

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein.

Zhao HNguyen AWu DLi YHassan SAChen JShroff HPiszczek GSchuck P

PNAS Nexus

2022 May

[Analysis of Pollution Characteristics and Sources of Rainfall Runoff from Roofs in the Central District of Beijing].

Xi YGuo JTao LTian YChen JJWu YXu SSJing HWLiu BX

Huan Jing Ke Xue

2022 Jun 08

The HIV-1 Viral Protease Is Activated during Assembly and Budding Prior to Particle Release.

Tabler COWegman SJChen JShroff HAlhusaini NTilton JC

J Virol

2022 May 11

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein.

Zhao HNguyen AWu DLi YHassan SAChen JShroff HPiszczek GSchuck P

bioRxiv

2022 Feb 09

Multiview confocal super-resolution microscopy.

Wu YHan XSu YGlidewell MDaniels JSLiu JSengupta TRey-Suarez IFischer RPatel ACombs CSun JWu XChristensen RSmith CBao LSun YDuncan LHChen JPommier YShi YBMurphy ERoy SUpadhyaya AColón-Ramos DLa Riviere PShroff H

Nature

2021 Dec

PARylation prevents the proteasomal degradation of topoisomerase I DNA-protein crosslinks and induces their deubiquitylation.

Sun YChen JHuang SNSu YPWang WAgama KSaha SJenkins LMPascal JMPommier Y

Nat Commun

2021 Aug 18

Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes.

Chen JSasaki HLai HSu YLiu JWu YZhovmer ACombs CARey-Suarez IChang HYHuang CCLi XGuo MNizambad SUpadhyaya ALee SJLucas LAGShroff H

Nat Methods

2021 Jun

A polymer index-matched to water enables diverse applications in fluorescence microscopy.

Han XSu YWhite HO'Neill KMMorgan NYChristensen RPotarazu DVishwasrao HDXu SSun YHuang SYMoyle MWDai QPommier YGiniger EAlbrecht DRProbst RShroff H

Lab Chip

2021 Apr 20

Semi-automated single-molecule microscopy screening of fast-dissociating specific antibodies directly from hybridoma cultures.

Miyoshi TZhang QMiyake TWatanabe SOhnishi HChen JVishwasrao HDChakraborty OBelyantseva IAPerrin BJShroff HFriedman TBOmori KWatanabe N

Cell Rep

2021 Feb 02

Zebrafish Posterior Lateral Line primordium migration requires interactions between a superficial sheath of motile cells and the skin.

Dalle Nogare DENatesh NVishwasrao HDShroff HChitnis AB

Elife

2020 Nov 25

[Concentration and Carbon Isotope Composition of DOC and DIC in the Miyun Reservoir Watershed in Summer].

Chen JJGuo JXu SSTao LJing HW

Huan Jing Ke Xue

2020 Nov 08

Quantum Dot-Conjugated SARS-CoV-2 Spike Pseudo-Virions Enable Tracking of Angiotensin Converting Enzyme 2 Binding and Endocytosis.

Gorshkov KSusumu KChen JXu MPradhan MZhu WHu XBreger JCWolak MOh E

ACS Nano

2020 Sep 22

Rapid image deconvolution and multiview fusion for optical microscopy.

Guo MLi YSu YLambert TNogare DDMoyle MWDuncan LHIkegami RSantella ARey-Suarez IGreen DBeiriger AChen JVishwasrao HGanesan SPrince VWaters JCAnnunziata CMHafner MMohler WAChitnis ABUpadhyaya AUsdin TBBao ZColón-Ramos DLa Riviere PLiu HWu YShroff H

Nat Biotechnol

2020 Nov

Visualizing the translation and packaging of HIV-1 full-length RNA.

Chen JLiu YWu BNikolaitchik OAMohan PRChen JPathak VKHu WS

Proc Natl Acad Sci U S A

2020 Mar 17

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

Gryder BEPomella SSayers CWu XSSong YChiarella AMBagchi SChou HCSinniah RSWalton AWen XRota RHathaway NAZhao KChen JVakoc CRShern JFStanton BZKhan J

Nat Genet

2019 Dec

A 2-dimensional ratchet model describes assembly initiation of a specialized bacterial cell surface.

Peluso EAUpdegrove TBChen JShroff HRamamurthi KS

Proc Natl Acad Sci U S A

2019 Oct 22

In situ polymerization on nanoscale metal-organic frameworks for enhanced physiological stability and stimulus-responsive intracellular drug delivery.

Liu YGong CSDai YYang ZYu GLiu YZhang MLin LTang WZhou ZZhu GChen JJacobson OKiesewetter DOWang ZChen X

Biomaterials

2019 Oct

Gas chromatography-mass spectrometry based metabolomics profile of hippocampus and cerebellum in mice after chronic arsenic exposure.

Mo TTDai HDu HZhang RYChai KPAn YChen JJWang JKChen ZJChen CZJiang XJTang RWang LPTan QTang PMiao XYMeng PZhang LBCheng SQPeng BTu BJHan TLXia YYBaker PN

Environ Toxicol

2019 Feb

[Nitrous Oxide Production in Response to Oxygen in a Solar Greenhouse Vegetable Soil].

Chen JJSong HCao WCWang YRWang JG

Huan Jing Ke Xue

2018 Aug 08

Single-shot super-resolution total internal reflection fluorescence microscopy.

Guo MChandris PGiannini JPTrexler AJFischer RChen JVishwasrao HDRey-Suarez IWu YWu XWaterman CMPatterson GHUpadhyaya ATaraska JWShroff H

Nat Methods

2018 Jun

A RAS-CaMKKβ-AMPKα2 pathway promotes senescence by licensing post-translational activation of C/EBPβ through a novel 3'UTR mechanism.

Basu SKGonit MSalotti JChen JBhat AGorospe MViollet BClaffey KPJohnson PF

Oncogene

2018 Jun

Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy.

Zhu GLynn GMJacobson OChen KLiu YZhang HMa YZhang FTian RNi QCheng SWang ZLu NYung BCWang ZLang LFu XJin AWeiss IDVishwasrao HNiu GShroff HKlinman DMSeder RAChen X

Nat Commun

2017 Dec 05

Intertwining DNA-RNA nanocapsules loaded with tumor neoantigens as synergistic nanovaccines for cancer immunotherapy.

Zhu GMei LVishwasrao HDJacobson OWang ZLiu YYung BCFu XJin ANiu GWang QZhang FShroff HChen X

Nat Commun

2017 Nov 14

Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy.

Wu YKumar ASmith CArdiel EChandris PChristensen RRey-Suarez IGuo MVishwasrao HDChen JTang JUpadhyaya ALa Riviere PJShroff H

Nat Commun

2017 Nov 13

DNA-RNA interactions are critical for chromosome condensation in .

Qian ZZhurkin VBAdhya S

Proc Natl Acad Sci U S A

2017 Nov 14

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.

Kieffer-Kwon KRNimura KRao SSPXu JJung SPekowska ADose MStevens EMathe EDong PHuang SCRicci MABaranello LZheng YTomassoni Ardori FResch WStavreva DNelson SMcAndrew MCasellas AFinn EGregory CSt Hilaire BGJohnson SMDubois WCosma MPBatchelor ELevens DPhair RDMisteli TTessarollo LHager GLakadamyali MLiu ZFloer MShroff HAiden ELCasellas R

Mol Cell

2017 Aug 17

Real-time visualization of chromatin modification in isolated nuclei.

Sardo LLin AKhakhina SBeckman LRicon LElbezanti WJaison TVishwasrao HShroff HJanetopoulos CKlase ZA

J Cell Sci

2017 Sep 01

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher.

Normanno DBoudarène LDugast-Darzacq CChen JRichter CProux FBénichou OVoituriez RDarzacq XDahan M

Nat Commun

2015 Jul 07

A general method to improve fluorophores for live-cell and single-molecule microscopy.

Grimm JBEnglish BPChen JSlaughter JPZhang ZRevyakin APatel RMacklin JJNormanno DSinger RHLionnet TLavis LD