Richard N. Merkin Institute for Translational Research

https://merkin.caltech.edu/

combined from CaltechAUTHORS

• Cervantes Rincón, Tomás; Kapoor, Tania; et al. (2024) Human antibodies in Mexico and Brazil neutralizing tick-borne flaviviruses; Cell Reports; Vol. 43; No. 6; 114298; 10.1016/j.celrep.2024.114298
• Li, Hongyi R.; Harb, Manwal; et al. (2024) Engineering viral vectors for acoustically targeted gene delivery; Nature Communications; Vol. 15; 4924; 10.1038/s41467-024-48974-y
• Ramadan, Sherif; Mayieka, Morgan; et al. (2024) Recent advances in the synthesis of extensive libraries of heparan sulfate oligosaccharides for structure–activity relationship studies; Current Opinion in Chemical Biology; Vol. 80; 102455; 10.1016/j.cbpa.2024.102455
• Hills, Rory A.; Tan, Tiong Kit; et al. (2024) Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses; Nature Nanotechnology; 10.1038/s41565-024-01655-9
• Griffiths, Jessica A.; Yoo, Bryan B.; et al. (2024) Peripheral neuronal activation shapes the microbiome and alters gut physiology; Cell Reports; Vol. 43; No. 4; 113953; PMCID PMC11132177; 10.1016/j.celrep.2024.113953
• Ding, Xiaozhe; Chen, Xinhong; et al. (2024) Fast, accurate ranking of engineered proteins by target-binding propensity using structure modeling; Molecular Therapy; 10.1016/j.ymthe.2024.04.003
• Guo, Jimmy K.; Blanco, Mario R.; et al. (2024) Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo; Molecular Cell; Vol. 84; No. 7; 1271-1289.e12; PMCID PMC10997485; 10.1016/j.molcel.2024.01.026
• Chong, Shasha and Yoshida, Shawn (2024) How transcription factor binding controls transcriptional bursting dynamics: A single-molecule view; Molecular Cell; Vol. 84; No. 6; 997-999; 10.1016/j.molcel.2024.02.027
• Ling, Bill; Gungoren, Bilge; et al. (2024) Truly Tiny Acoustic Biomolecules for Ultrasound Imaging and Therapy; Advanced Materials; 2307106; 10.1002/adma.202307106
• Flynn, Michael James; Mayfield, Acacia M.; et al. (2024) Synthetic dosage-compensating miRNA circuits allow precision gene therapy for Rett syndrome; bioRxiv; 2024.03.13.584179; PMCID PMC10980028; 10.1101/2024.03.13.584179
• Kubinski, Hannah C.; Despres, Hannah W.; et al. (2024) Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation; bioRxiv; 53; PMCID PMC10979914; 10.1101/2024.03.08.584120
• Wang, Eric; Cohen, Alexander A.; et al. (2024) Designed mosaic nanoparticles enhance cross-reactive immune responses in mice; PMCID PMC10925254; 10.1101/2024.02.28.582544
• Schulte, Samuel J.; Shin, Boyoung; et al. (2024) Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction; ACS Chemical Biology; Vol. 19; No. 2; 280-288; PMCID PMC10877569; 10.1021/acschembio.3c00431
• Cohen, Alexander A.; Keeffe, Jennifer R.; et al. (2024) Mosaic sarbecovirus vaccination elicits cross-reactive responses in pre-immunized animals; PMCID PMC10871317; 10.1101/2024.02.08.576722
• Dam, Kim-Marie A.; Fan, Chengcheng; et al. (2024) Publisher Correction: Intermediate conformations of CD4-bound HIV-1 Env heterotrimers; Nature; Vol. 627; E7; 10.1038/s41586-024-07082-z
• Schulte, Samuel J.; Fornace, Mark E.; et al. (2024) HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples; Development; Vol. 151; No. 4; dev202307; PMCID PMC10941662; 10.1242/dev.202307
• de Araujo, William Reis; Lukas, Heather; et al. (2024) Low-Cost Biosensor Technologies for Rapid Detection of COVID-19 and Future Pandemics; ACS Nano; Vol. 18; No. 3; 1757-1777; 10.1021/acsnano.3c01629
• Yao, Yuxing and Shapiro, Mikhail G. (2023) Using ultrasound to 3D-print materials; Science; Vol. 382; No. 6675; 1126; 10.1126/science.adl5887
• Moyers, Belle A.; Partridge, E. Christopher; et al. (2023) Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells; Genome Research; Vol. 33; No. 11; 1879-1892; PMCID PMC10760452; 10.1101/gr.278205.123
• Cohen, Alexander A.; van Doremalen, Neeltje; et al. (2023) Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models; PMCID PMC8978945; 10.1101/2022.03.25.485875
• Chen, Lizhen; Zhang, Zhao; et al. (2023) Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions; Molecular Cell; Vol. 83; No. 19; 3438-3456.e12; PMCID PMC10592010; 10.1016/j.molcel.2023.08.027
• Papini, Santiago; López-Castro, Teresa; et al. (2023) Alcohol, cannabis, and nicotine use have distinct associations with COVID-19 pandemic-related experiences: An exploratory Bayesian network analysis across two timepoints; Drug and Alcohol Dependence; Vol. 248; Art. No. 109929; PMCID PMC10186931; 10.1016/j.drugalcdep.2023.109929
• Jiang, Jialong; Chen, Sisi; et al. (2023) D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response; PMCID PMC10153191; 10.1101/2023.04.19.537364
• Griffin, Matthew E.; Thompson, John W.; et al. (2023) Functional glycoproteomics by integrated network assembly and partitioning; PMCID PMC10312638; 10.1101/2023.06.13.541482
• Hoffmann, Magnus A. G.; Yang, Zhi; et al. (2023) ESCRT recruitment to SARS-CoV-2 spike induces virus-like particles that improve mRNA vaccines; Cell; Vol. 186; No. 11; 2380-2391; PMCID PMC10121106; 10.1016/j.cell.2023.04.024
• Yoshida, Shawn R.; Maity, Barun K.; et al. (2023) Visualizing Protein Localizations in Fixed Cells: Caveats and the Underlying Mechanisms; Journal of Physical Chemistry B; Vol. 127; No. 19; 4165-4173; PMCID PMC10201523; 10.1021/acs.jpcb.3c01658
• Shen, Cheng; Rawal, Siddarth; et al. (2023) Automatic detection of circulating tumor cells and cancer associated fibroblasts using deep learning; Scientific Reports; Vol. 13; 5708; PMCID PMC10082202; 10.1038/s41598-023-32955-0
• Rand, Alexander W.; Gonzalez, Kevin J.; et al. (2023) Total Synthesis of Strempeliopidine and Non-Natural Stereoisomers through a Convergent Petasis Borono-Mannich Reaction; Journal of the American Chemical Society; Vol. 145; No. 13; 7278-7287; PMCID PMC10281614; 10.1021/jacs.2c13146
• Wise, Toby; Zbozinek, Tomislav D.; et al. (2023) Computationally-defined markers of uncertainty aversion predict emotional responses during a global pandemic; Emotion; Vol. 23; No. 3; 722-736; 10.1037/emo0001088
• Schulte, Samuel J.; Huang, Jining; et al. (2023) HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing; 10.1101/2022.09.18.508442
• Chen, Lizhen; Zhang, Zhao; et al. (2023) Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions; 10.1101/2022.10.28.514297
• Hills, Rory A.; Tan, Tiong Kit; et al. (2023) Multiviral Quartet Nanocages Elicit Broad Anti-Coronavirus Responses for Proactive Vaccinology; PMCID PMC9980174; 10.1101/2023.02.24.529520
• Haloi, Nandan; Huang, Shan; et al. (2023) Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids; 10.1101/2023.01.16.524298
• Hoffmann, Magnus A. G.; Yang, Zhi; et al. (2023) ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses; PMCID PMC9810232; 10.1101/2022.12.26.521940
• Schulte, Samuel J.; Huang, Jining; et al. (2023) Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing; ACS Infectious Diseases; Vol. 9; No. 3; 450-458; PMCID PMC9924079; 10.1021/acsinfecdis.2c00472
• Moestopo, Widianto P.; Shaker, Sammy; et al. (2023) Knots are not for naught: Design, properties, and topology of hierarchical intertwined microarchitected materials; Science Advances; Vol. 9; No. 10; eade6725; PMCID PMC9995035; 10.1126/sciadv.ade6725
• Boeynaems, Steven; Chong, Shasha; et al. (2023) Phase Separation in Biology and Disease; Current Perspectives and Open Questions; Journal of Molecular Biology; Vol. 435; No. 5; Art. No. 167971; PMCID PMC9970028; 10.1016/j.jmb.2023.167971
• Wang, Xue Qing David; Fan, Dandan; et al. (2023) Mutant NPM1 Hijacks Transcriptional Hubs to Maintain Pathogenic Gene Programs in Acute Myeloid Leukemia; Cancer Discovery; Vol. 13; No. 3; 724-745; PMCID PMC9975662; 10.1158/2159-8290.cd-22-0424
• Rusch, Tessa; Han, Yanting; et al. (2023) COVID-Dynamic: a large-scale longitudinal study of socioemotional and behavioral change across the pandemic; Scientific Data; Vol. 10; Art. No. 71; PMCID PMC9897616; 10.1038/s41597-022-01901-6
• López-Castro, Teresa; Papini, Santiago; et al. (2023) Posttraumatic stress disorder symptom trajectories in a 16-month COVID-19 pandemic period; Journal of Traumatic Stress; Vol. 36; No. 1; 180-192; PMCID PMC9880687; 10.1002/jts.22899
• Huang, Kuan-Ying A.; Chen, Xiaorui; et al. (2023) Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2; Nature Communications; Vol. 14; Art. No. 311; PMCID PMC9852238; 10.1038/s41467-023-35949-8
• Fan, Chengcheng; Cohen, Alexander A.; et al. (2022) Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes; Immunity; Vol. 55; No. 12; 2419-2435.e10; PMCID PMC9606073; 10.1016/j.immuni.2022.10.019
• Irgen-Gioro, Shawn; Yoshida, Shawn; et al. (2022) Fixation can change the appearance of phase separation in living cells; eLife; Vol. 11; Art. No. e79903; PMCID PMC9817179; 10.7554/elife.79903
• Cohen, Alexander A.; van Doremalen, Neeltje; et al. (2022) Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models; Science; Vol. 377; No. 6606; Art. No. eabq0839; PMCID PMC9273039; 10.1126/science.abq0839
• Fan, Chengcheng; Cohen, Alexander A.; et al. (2022) Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes; 10.1101/2022.06.28.497989
• Liang, Mingshu and Yang, Changhuei (2022) Implementation of free-space Fourier Ptychography with near maximum system numerical aperture; Optics Express; Vol. 30; No. 12; 20321-20332; PMCID PMC9363023; 10.1364/oe.459833
• Li, Shan; Wang, Feng; et al. (2022) NMS-873 Leads to Dysfunctional Glycometabolism in A p97-Independent Manner in HCT116 Colon Cancer Cells; Pharmaceutics; Vol. 14; No. 4; 764; PMCID PMC9024726; 10.3390/pharmaceutics14040764
• Tanaka, Shiho; Olson, C. Anders; et al. (2022) Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display; Cell Reports; Vol. 38; No. 6; Art. No. 110348; PMCID PMC8769934; 10.1016/j.celrep.2022.110348
• Wang, Feng; Li, Shan; et al. (2022) The p97 Inhibitor UPCDC-30245 Blocks Endo-Lysosomal Degradation; Pharmaceuticals; Vol. 15; No. 2; Art. No. 204; PMCID PMC8880557; 10.3390/ph15020204
• Brune, Karl D.; Liekniņa, Ilva; et al. (2021) N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone; ChemBioChem; Vol. 22; No. 22; 3199-3207; 10.1002/cbic.202100381
• Cheng, Kai-Wen; Li, Shan; et al. (2021) Impacts of p97 on Proteome Changes in Human Cells during Coronaviral Replication; Cells; Vol. 10; No. 11; Art. No. 2953; PMCID PMC8616207; 10.3390/cells10112953
• Abernathy, Morgan E.; Dam, Kim-Marie A.; et al. (2021) How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika; Viruses; Vol. 13; No. 10; Art. No. 2106; PMCID PMC8537525; 10.3390/v13102106
• Shahrestani, Shane; Chou, Tzu-Chieh; et al. (2021) A wearable eddy current based pulmonary function sensor for continuous non-contact point-of-care monitoring during the COVID-19 pandemic; Scientific Reports; Vol. 11; Art. No. 20144; PMCID PMC8505507; 10.1038/s41598-021-99682-2
• Rusch, Tessa; Han, Yanting; et al. (2021) COVID-Dynamic: A large-scale multifaceted longitudinal study of socioemotional and behavioral change across the pandemic; 10.31234/osf.io/75eyx
• Jette, Claudia A.; Cohen, Alexander A.; et al. (2021) Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies; Cell Reports; Vol. 36; No. 13; Art. No. 109760; PMCID PMC8423902; 10.1016/j.celrep.2021.109760
• West, Anthony P., Jr.; Wertheim, Joel O.; et al. (2021) Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York; Nature Communications; Vol. 12; Art. No. 4886; PMCID PMC8352861; 10.1038/s41467-021-25168-4
• Greaney, Allison J.; Starr, Tyler N.; et al. (2021) Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies; Nature Communications; Vol. 12; Art. No. 4196; PMCID PMC8263750; 10.1038/s41467-021-24435-8
• Scheid, Johannes F.; Barnes, Christopher O.; et al. (2021) B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV; Cell; Vol. 184; No. 12; 3205-3221; PMCID PMC8064835; 10.1016/j.cell.2021.04.032
• De Gasparo, Raoul; Pedotti, Mattia; et al. (2021) Bispecific IgG neutralizes SARS-CoV-2 variants and prevents escape in mice; Nature; Vol. 593; No. 7859; 424-428; PMCID PMC8330819; 10.1038/s41586-021-03461-y
• Wang, Zijun; Schmidt, Fabian; et al. (2021) mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants; Nature; Vol. 592; No. 7855; 616-622; PMCID PMC7836122; 10.1038/s41586-021-03324-6
• Gaebler, Christian; Wang, Zijun; et al. (2021) Evolution of antibody immunity to SARS-CoV-2; Nature; Vol. 591; No. 7851; 639-644; PMCID PMC8221082; 10.1038/s41586-021-03207-w
• Muecksch, Frauke; Weisblum, Yiska; et al. (2021) Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies; PMCID PMC7987023; 10.1101/2021.03.07.434227
• Cohen, Alexander A.; Gnanapragasam, Priyanthi N. P.; et al. (2021) Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice; Science; Vol. 371; No. 6530; 735-741; PMCID PMC7928838; 10.1126/science.abf6840
• Lukas, Heather; Xu, Changhao; et al. (2020) Emerging Telemedicine Tools for Remote COVID-19 Diagnosis, Monitoring, and Management; ACS Nano; Vol. 14; No. 12; 16180-16193; PMCID PMC7754783; 10.1021/acsnano.0c08494
• Linsky, Thomas W.; Vergara, Renan; et al. (2020) De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2; Science; Vol. 370; No. 6521; 1208-1214; PMCID PMC7920261; 10.1126/science.abe0075
• Torrente-Rodríguez, Rebeca M.; Lukas, Heather; et al. (2020) SARS-CoV-2 RapidPlex: A Graphene-Based Multiplexed Telemedicine Platform for Rapid and Low-Cost COVID-19 Diagnosis and Monitoring; Matter; Vol. 3; No. 6; 1981-1998; PMCID PMC7535803; 10.1016/j.matt.2020.09.027
• Flynn, Michael J.; Snitser, Olga; et al. (2020) A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic; 10.1101/2020.11.19.20234948
• Barnes, Christopher O.; Jette, Claudia A.; et al. (2020) Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies; 10.1101/2020.08.30.273920
• Wise, Toby; Zbozinek, Tomislav D.; et al. (2020) Changes in risk perception and self-reported protective behaviour during the first week of the COVID-19 pandemic in the United States; Royal Society Open Science; Vol. 7; No. 9; Art. No. 200742; PMCID PMC7540790; 10.1098/rsos.200742
• Robbiani, Davide F.; Gaebler, Christian; et al. (2020) Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals; Nature; Vol. 584; No. 7821; 437-442; PMCID PMC7263513; 10.1038/s41586-020-2456-9
• Barnes, Christopher O.; West, Anthony P., Jr.; et al. (2020) Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies; Cell; Vol. 182; No. 4; 828-842; PMCID PMC7311918; 10.1016/j.cell.2020.06.025