Year-2025

1              Zia, S. et al. Age-impaired remyelination is associated with dysregulated microglial transitions. Nature communications 16, 9951 (2025).

2              Zheng, J., Cardoen, B., Ortiz-Silva, M., Hamarneh, G. & Nabi, I. R. Comparative Analysis of SPLICS and MCS-DETECT for Detecting Mitochondria-ER Contact Sites (MERCs). Contact 8, 25152564251313721 (2025).

3              Yuan, Z. et al. A direct role for a mitochondrial targeting sequence in signalling stress. Nature, 1-10 (2025).

4              Yavarinasab, A. et al. Electrogenic dynamics of biofilm formation: Correlation between genetic expression and electrochemical activity in Bacillus subtilis. Biosens Bioelectron 276, 117218 (2025). https://doi.org/10.1016/j.bios.2025.117218

5              Wong, T. H. et al. SuperResNET–single-molecule network analysis detects changes to clathrin structure induced by small-molecule inhibitors. Journal of cell science 138, JCS263570 (2025).

6              Tretjakov, S., Palia, P. & Vogl, A. W. Myosin VI Is Associated With the Endoplasmic Reticulum in Regions of Sertoli Cells Containing Tubulobulbar Complexes. Cytoskeleton (Hoboken) 82, 333-343 (2025). https://doi.org/10.1002/cm.21949

7              Thoms, D. et al. A bacterial exotoxin-triggered plant immune response restricts pathogen growth. Cell Reports 44 (2025).

8              Suess, P. M., La, C. C., Vappala, S., Kizhakkedathu, J. N. & Morrissey, J. H. Platelet Polyphosphate Signals Through NFκB to Induce Myofibroblast Differentiation. Biomolecules 15, 1441 (2025).

9              Sperb, N. et al. The proto-oncogenic miR-106a-363 cluster enhances adverse risk acute myeloid leukemia through mitochondrial activation. Leukemia, 1-12 (2025).

10           Samudre, A. et al. nERdy: network analysis of endoplasmic reticulum dynamics. Communications Biology 8, 1529 (2025).

11           Qiu, X., Hu, P., Sevilla-Pym, A., Caine, J. R. & Hudson, Z. M. Supramolecular host-guest modulated thermally activated delayed fluorescence for photodynamic therapy. Chem Sci (2025). https://doi.org/10.1039/d5sc07827j

12           Paluri, S. & Auld, V. J. microRNA-184 distribution and consequences on glial septate junctions and the blood-brain barrier. PloS one 20, e0328862 (2025).

13           Murray, C. J., Tunderman, E. D., Vecchiarelli, H. A., Ibáñez, F. G. & Tremblay, M.-È. A comparison of microglial morphological complexity in adult mouse brain samples using 2-dimensional and 3-dimensional image analysis tools. Glial Health Research, 100007 (2025).

14           Masvikeni, T. R., Primrose, W. L., Mikulin, S. & Hudson, Z. M. Water-Dispersible Glassy Organic Dots Exhibiting Near-Infrared Delayed Emission for Bioimaging. ACS Applied Nano Materials (2025).

15           Li, Y. L. et al. SuperResNET: Model‐Free Single‐Molecule Network Analysis Software Achieves Molecular Resolution of Nup96. Advanced Intelligent Systems 7, 2400521 (2025).

16           Kincross, H. et al. Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1. J Clin Invest (2025). https://doi.org/10.1172/JCI181943

17           Hu, P., Primrose, W. L. & Hudson, Z. M. Polymer Dots Exhibiting Multi‐Resonant Thermally Activated Delayed Fluorescence for Cellular Imaging. Advanced Optical Materials, 2403409 (2025).

18           Hosseini-Farahabadi, S. et al. Advancing Esophageal Disease Modeling: Microfluidic Platforms for Adult Tissue-Resident Stem Cell Culture and Differentiation. Gastro Hep Advances, 100837 (2025).

19           Holme, S., Sapia, J., Davey, M., Vanni, S. & Conibear, E. An S-acylated N-terminus and a conserved loop regulate the activity of the ABHD17 deacylase. Journal of Cell Biology 224, e202405042 (2025).

20           Fairlie, G. M. J. et al. Biochemical and structural characterization of Rab3GAP reveals insights into Rab18 nucleotide exchange activity. Nature communications 16, 479 (2025). https://doi.org/10.1038/s41467-025-55828-8

21           Fairlie, G. M. et al. Biochemical and structural characterization of Rab3GAP reveals insights into Rab18 nucleotide exchange activity. Nature communications 16, 479 (2025).

22           Donald, K. et al. Human milk IgA promotes normal immune development by limiting Th17-inducing Erysipelatoclostridium ramosum in the infant gut. Proceedings of the National Academy of Sciences 122, e2501030122 (2025).

23           Deng, W. & Tanentzapf, G. Defining the role of integrins in melanoblast migration in vivo. Molecular biology of the cell 36, ar139 (2025).

24           Deng, W. et al. Consolidation of cell-ECM adhesion through direct talin-mediated actin linkage is essential for mouse embryonic morphogenesis. Communications Biology 8, 948 (2025).

25           Dean, P. A. et al. Abstract C108: The therapeutic candidate antibody PODO447 recognizes a glycopeptide on podocalyxin-expressing tumor cells that have undergone a partial epithelial-mesenchymal transition. Molecular Cancer Therapeutics 24, C108-C108 (2025).

26           Cui, J. H., Kwan, J. Z., Faghihi, A., Nguyen, T. F. & Teves, S. S. Functional divergence of TBP homologs through distinct DNA-binding dynamics. Nucleic Acids Research 53, gkaf436 (2025).

27           Clayworth, K. V. & Auld, V. J. Dystroglycan mediates polarized deposition of laminin and axon ensheathment by wrapping glia. Development 152, dev204391 (2025).

28           Chu, C. M. et al. Signal transduction pathways controlling Ins2 gene activity and beta cell state transitions. iScience 28 (2025).

29           Brown, J. A., Ling, M. Y., Ausió, J. & Howe, L. J. Human MeCP2 binds to promoters and inhibits transcription in an unmethylated yeast genome. Genetics, iyaf043 (2025).

30           Biswas, P. et al. Insulin/insulin-like growth factor signaling pathway promotes higher fat storage in Drosophila females. Cell reports 44 (2025).

31           Bhangu, K. S., Yang, C., Illing, H. J. & Brown, C. J. Impact of somatic XIST deletions on ongoing XIST expression and inactive X silencing and heterochromatin. Hum Mol Genet 34, 2027-2041 (2025). https://doi.org/10.1093/hmg/ddaf160

32           Bhangu, K. S., Yang, C., Illing, H. J. & Brown, C. J. Impact of somatic XIST deletions on ongoing XIST expression and inactive X silencing and heterochromatin. Human Molecular Genetics, ddaf160 (2025).

33           Bedi, A., Choi, K., Iskierski, A. & Gold, M. R. The tropomyosin 3.1/3.2 inhibitor ATM-3507 alters B-cell actin dynamics and impairs the growth and motility of diffuse large B-cell lymphoma cell lines. Frontiers in Immunology 16, 1668379 (2025).

34           Andrew, L. J. et al. High‐Resolution AFM Visualization of Nanocellulose Surface Grafting with Small Molecules. Small 21, e01435 (2025).

35           Abbasi, U. et al. Investigation on Active and Rapid Hepatobiliary Excretion of Triantennary N-Acetyl Galactosamine Conjugated Polymeric Nanoparticles. Biomacromolecules 26, 6282-6296 (2025).

Years before 2025

1              Zhao, J. et al. PDX1+ cell budding morphogenesis in a stem cell-derived islet spheroid system. Nature communications 15, 5894 (2024). https://doi.org/10.1038/s41467-024-50109-2

2              Ye, H. et al. Cost-Effective and Wireless Portable Device for Rapid and Sensitive Quantification of Micro/Nanoplastics. ACS Sens 9, 4662-4670 (2024). https://doi.org/10.1021/acssensors.4c00957

3              Ye, H. et al. Quantitative and rapid detection of nanoplastics labeled by luminescent metal phenolic networks using surface-enhanced Raman scattering. J Hazard Mater 470, 134194 (2024). https://doi.org/10.1016/j.jhazmat.2024.134194

4              Timmins, L. R. et al. Caveolin‐1 promotes mitochondrial health and limits mitochondrial ROS through ROCK/AMPK regulation of basal mitophagic flux. The FASEB Journal 38, e23343 (2024).

5              Sevilla-Pym, A., Primrose, W. L., Luppi, B. T., Bergmann, K. & Hudson, Z. M. Organelle-Targeting Polymer Dots Exhibiting Thermally Activated Delayed Fluorescence for Subcellular Imaging. ACS Appl Mater Interfaces 16, 46133-46144 (2024). https://doi.org/10.1021/acsami.4c10311

6              Quintard, C. et al. A microfluidic platform integrating functional vascularized organoids-on-chip. Nature communications 15, 1452 (2024). https://doi.org/10.1038/s41467-024-45710-4

7              Perez-Vargas, J. et al. Nanomolar anti-SARS-CoV-2 Omicron activity of the host-directed TMPRSS2 inhibitor N-0385 and synergistic action with direct-acting antivirals. Antiviral Res 225, 105869 (2024). https://doi.org/10.1016/j.antiviral.2024.105869

8              Nabi, I. R. et al. AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. Journal of Cell Biology 223, e202311073 (2024).

9              Lim, J. E., Bernatchez, P. & Nabi, I. R. Scaffolds and the scaffolding domain: an alternative paradigm for caveolin-1 signaling. Biochemical Society Transactions 52, 947-959 (2024).

10           Liao, S. et al. Transfection Potency of Lipid Nanoparticles Containing mRNA Depends on Relative Loading Levels. ACS Applied Materials & Interfaces 17, 3097-3105 (2024).

11           Holani, R. et al. Bile acid-induced metabolic changes in the colon promote Enterobacteriaceae expansion and associate with dysbiosis in Crohn’s disease. Sci Signal 17, eadl1786 (2024). https://doi.org/10.1126/scisignal.adl1786

12           Fleck, S. A. et al. Auxin exposure disrupts feeding behavior and fatty acid metabolism in adult Drosophila. eLife 12 (2024). https://doi.org/10.7554/eLife.91953

13           Donald, K. et al. Secretory IgA in breast milk protects against asthma through modulation of the gut microbiota. Cell Rep 43, 114835 (2024). https://doi.org/10.1016/j.celrep.2024.114835

14           Delhaye, M. et al. Adaptation of Magnified Analysis of the Proteome for Excitatory Synaptic Proteins in Varied Samples and Evaluation of Cell Type-Specific Distributions. J Neurosci 44 (2024). https://doi.org/10.1523/JNEUROSCI.1291-23.2024

15           Chao, C. F. et al. An important role for triglyceride in regulating spermatogenesis. eLife 12 (2024). https://doi.org/10.7554/eLife.87523

16           Cardoen, B. et al. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts. J Cell Biol 223 (2024). https://doi.org/10.1083/jcb.202206109

17           Alsouri, S. et al. Actinin-4 controls survival signaling in B cells by limiting the lateral mobility of B-cell antigen receptors. Eur J Immunol 54, e2350774 (2024). https://doi.org/10.1002/eji.202350774

18           Sadasivan, J., Hyrina, A., DaSilva, R. & Jan, E. An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells. J Mol Biol, 168042 (2023). https://doi.org/10.1016/j.jmb.2023.168042

19           Price, R. M. et al. Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes. Nucleic Acids Res (2023). https://doi.org/10.1093/nar/gkad304

20           Perez-Vargas, J. et al. Discovery of lead natural products for developing pan-SARS-CoV-2 therapeutics. Antiviral Res 209, 105484 (2023). https://doi.org/10.1016/j.antiviral.2022.105484

21           Paul, M., Golla, K. & Kim, H. Gelsolin Modulates Platelet Dense Granule Secretion and Hemostasis via the Actin Cytoskeleton. Thromb Haemost 123, 219-230 (2023). https://doi.org/10.1055/s-0042-1758800

22           Niu, X. et al. Structured Emulgels by Interfacial Assembly of Terpenes and Nanochitin. ACS Nano 17, 25542-25551 (2023). https://doi.org/10.1021/acsnano.3c09533

23           Guo, S. et al. All-Aqueous Bicontinuous Structured Liquid Crystal Emulsion through Intraphase Trapping of Cellulose Nanoparticles. Biomacromolecules 24, 367-376 (2023). https://doi.org/10.1021/acs.biomac.2c01177

24           Bedi, A. et al. WAVE2 Regulates Actin-Dependent Processes Induced by the B Cell Antigen Receptor and Integrins. Cells 12 (2023). https://doi.org/10.3390/cells12232704

25           Shapira, T. et al. A TMPRSS2 inhibitor acts as a pan-SARS-CoV-2 prophylactic and therapeutic. Nature 605, 340-348 (2022). https://doi.org/10.1038/s41586-022-04661-w

26           Sadasivan, J. et al. Targeting Nup358/RanBP2 by a viral protein disrupts stress granule formation. PLoS Pathog 18, e1010598 (2022). https://doi.org/10.1371/journal.ppat.1010598

27           Peters, V., Deretic, N., Choi, K. & Gold, M. R. ERK contributes to B cell receptor-induced cell spreading in the A20 mouse B cell line. MicroPubl Biol 2022 (2022). https://doi.org/10.17912/micropub.biology.000665

28           Dixon-McDougall, T. & Brown, C. J. Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation. Epigenetics Chromatin 15, 6 (2022). https://doi.org/10.1186/s13072-022-00438-7

29           Alan, P. et al. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS. Cell Mol Life Sci 79, 565 (2022). https://doi.org/10.1007/s00018-022-04585-8

30           Wong, T. H. et al. Single molecule network analysis identifies structural changes to caveolae and scaffolds due to mutation of the caveolin-1 scaffolding domain. Scientific reports 11, 7810 (2021). https://doi.org/10.1038/s41598-021-86770-6

31           Wong, A. K. O., Young, B. P. & Loewen, C. J. R. Ist2 recruits the lipid transporters Osh6/7 to ER-PM contacts to maintain phospholipid metabolism. J Cell Biol 220 (2021). https://doi.org/10.1083/jcb.201910161

32           Wat, L. W., Chowdhury, Z. S., Millington, J. W., Biswas, P. & Rideout, E. J. Sex determination gene transformer regulates the male-female difference in Drosophila fat storage via the adipokinetic hormone pathway. eLife 10 (2021). https://doi.org/10.7554/eLife.72350

33           Siren, E. M. J. et al. Prevention of vascular-allograft rejection by protecting the endothelial glycocalyx with immunosuppressive polymers. Nat Biomed Eng (2021). https://doi.org/10.1038/s41551-021-00777-y

34           Palia, P., Adams, A., Sriram, A. & Vogl, A. W. Cortactin knockdown results in disruption of basal TBCs and alters turnover of Sertoli cell ESs in R. norvegicus. Biology of reproduction (2021). https://doi.org/10.1093/biolre/ioab161

35           Dixon-McDougall, T. & Brown, C. J. Independent domains for recruitment of PRC1 and PRC2 by human XIST. PLoS Genet 17, e1009123 (2021). https://doi.org/10.1371/journal.pgen.1009123

36           Bolger-Munro, M. et al. The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse. Front Cell Dev Biol 9, 649433 (2021). https://doi.org/10.3389/fcell.2021.649433

37           Wat, L. W. et al. A role for triglyceride lipase brummer in the regulation of sex differences in Drosophila fat storage and breakdown. PLoS biology 18, e3000595 (2020). https://doi.org/10.1371/journal.pbio.3000595

38           Pournia, F. et al. Identification of serine residues in the Connexin43 carboxyl tail important for BCR-mediated spreading of B-lymphocytes. Journal of cell science (2020). https://doi.org/10.1242/jcs.237925

39           Long, R. K. M. et al. Super resolution microscopy and deep learning identify Zika virus reorganization of the endoplasmic reticulum. Scientific reports 10, 20937 (2020). https://doi.org/10.1038/s41598-020-77170-3

40           Cardoen, B. et al. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE transactions on medical imaging 39, 1942-1956 (2020). https://doi.org/10.1109/TMI.2019.2962361

41           Bai, L. et al. All-Aqueous Liquid Crystal Nanocellulose Emulsions with Permeable Interfacial Assembly. ACS Nano 14, 13380-13390 (2020). https://doi.org/10.1021/acsnano.0c05251

42           Adams, A. & Vogl, W. Knockdown of IP3R1 Disrupts TBC-ER Contact Sites and the Morphology of Apical Processes Encapsulating Late Spermatids. Biology of reproduction (2020). https://doi.org/10.1093/biolre/ioaa074

43           Abbina, S. et al. Blood circulation of soft nanomaterials is governed by dynamic remodeling of protein opsonins at nano-biointerface. Nature communications 11, 3048 (2020). https://doi.org/10.1038/s41467-020-16772-x

44           Khater, I. M., Meng, F., Nabi, I. R. & Hamarneh, G. Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data. Bioinformatics 35, 3468-3475 (2019). https://doi.org/10.1093/bioinformatics/btz113

45           Khater, I. M., Liu, Q., Chou, K. C., Hamarneh, G. & Nabi, I. R. Super-resolution modularity analysis shows polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Scientific reports 9, 9888 (2019). https://doi.org/10.1038/s41598-019-46174-z

46           Khater, I. M., Aroca-Ouellette, S. T., Meng, F., Nabi, I. R. & Hamarneh, G. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PloS one 14, e0211659 (2019). https://doi.org/10.1371/journal.pone.0211659

47           Khater, I. M., Aroca-Ouellette, S. T., Meng, F., *Nabi, I. R. & *Hamarneh, G. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PloS one 14, e0211659 (2019).

48           Gao, G., Zhu, C., Liu, E. & Nabi, I. R. Reticulon and CLIMP-63 regulate nanodomain organization of peripheral ER tubules. PLoS biology 17, e3000355 (2019). https://doi.org/10.1371/journal.pbio.3000355

49           Cardoen, B. et al. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE transactions on medical imaging (2019). https://doi.org/10.1109/TMI.2019.2962361

50           Bolger-Munro, M. et al. Arp2/3 complex-driven spatial patterning of the BCR enhances immune synapse formation, BCR signaling and B cell activation. eLife 8 (2019). https://doi.org/10.7554/eLife.44574

51           Wang, J. C., Bolger-Munro, M. & Gold, M. R. Imaging the Interactions Between B Cells and Antigen-Presenting Cells. Methods Mol Biol 1707, 131-161 (2018). https://doi.org/10.1007/978-1-4939-7474-0_10

52           Wang, J. C., Bolger-Munro, M. & Gold, M. R. Visualizing the Actin and Microtubule Cytoskeletons at the B-cell Immune Synapse Using Stimulated Emission Depletion (STED) Microscopy. J Vis Exp (2018). https://doi.org/10.3791/57028

53           Liu, Q., Chen, L., Aguilar, H. C. & Chou, K. C. A stochastic assembly model for Nipah virus revealed by super-resolution microscopy. Nature communications 9, 3050 (2018). https://doi.org/10.1038/s41467-018-05480-2

54           Khater, I. M., Meng, F., Wong, T. H., Nabi, I. R. & Hamarneh, G. Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds. Scientific reports 8, 9009 (2018). https://doi.org/10.1038/s41598-018-27216-4

55           Wang, J. C. et al. The Rap1-cofilin-1 pathway coordinates actin reorganization and MTOC polarization at the B cell immune synapse. Journal of cell science 130, 1094-1109 (2017). https://doi.org/10.1242/jcs.191858

56           Swayampakula, M. et al. The interactome of metabolic enzyme carbonic anhydrase IX reveals novel roles in tumor cell migration and invadopodia/MMP14-mediated invasion. Oncogene 36, 6244-6261 (2017). https://doi.org/10.1038/onc.2017.219

57           Meng, F. et al. The phospho-caveolin-1 scaffolding domain dampens force fluctuations in focal adhesions and promotes cancer cell migration. Molecular biology of the cell 28, 2190-2201 (2017). https://doi.org/10.1091/mbc.E17-05-0278

58           Freeman, S. A. et al. Applied stretch initiates directional invasion through the action of Rap1 GTPase as a tension sensor. Journal of cell science 130, 152-163 (2017). https://doi.org/10.1242/jcs.180612

59           Meng, F., Joshi, B. & Nabi, I. R. Galectin-3 Overrides PTRF/Cavin-1 Reduction of PC3 Prostate Cancer Cell Migration. PloS one 10, e0126056 (2015). https://doi.org/10.1371/journal.pone.0126056

60           Li, L. et al. p38 MAP kinase-dependent phosphorylation of the Gp78 E3 ubiquitin ligase controls ER-mitochondria association and mitochondria motility. Molecular biology of the cell 26, 3828-3840 (2015). https://doi.org/10.1091/mbc.E15-02-0120

61           Freeman, S. A. et al. Erratum: Toll-like receptor ligands sensitize B-cell receptor signalling by reducing actin-dependent spatial confinement of the receptor. Nature communications 6, 7015 (2015). https://doi.org/10.1038/ncomms8015

62           Zhou, L. et al. Microenvironmental regulation of BRCA1 gene expression by c-Jun and Fra2 in premalignant human ovarian surface epithelial cells. Mol Cancer Res 11, 272-281 (2013). https://doi.org/10.1158/1541-7786.MCR-12-0395

63           Shankar, J. et al. Raft endocytosis of AMF regulates mitochondrial dynamics through Rac1 signaling and the Gp78 ubiquitin ligase. Journal of cell science 126, 3295-3304 (2013). https://doi.org/10.1242/jcs.120162

64           Fu, M. et al. Regulation of mitophagy by the Gp78 E3 ubiquitin ligase. Molecular biology of the cell 24, 1153-1162 (2013). https://doi.org/10.1091/mbc.E12-08-0607

65           Austin, P. et al. The invasion inhibitor sarasinoside A1 reverses mesenchymal tumor transformation in an E-cadherin-independent manner. Mol Cancer Res 11, 530-540 (2013). https://doi.org/10.1158/1541-7786.MCR-12-0385

66           St-Pierre, P., Dang, T., Joshi, B. & Nabi, I. R. Peripheral endoplasmic reticulum localization of the Gp78 ubiquitin ligase activity. Journal of cell science 125, 1727-1737 (2012). https://doi.org/10.1242/jcs.096396

67           Joshi, B. et al. Phosphocaveolin-1 is a mechanotransducer that induces caveola biogenesis via Egr1 transcriptional regulation. J Cell Biol 199, 425-435 (2012). https://doi.org/10.1083/jcb.201207089

68           Boscher, C. et al. Galectin-3 protein regulates mobility of N-cadherin and GM1 ganglioside at cell-cell junctions of mammary carcinoma cells. The Journal of biological chemistry 287, 32940-32952 (2012). https://doi.org/10.1074/jbc.M112.353334