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Article
| Open AccessMYADM binds human parechovirus 1 and is essential for viral entry
Host factors required for parechovirus entry are not well understood. Here, the authors identify MYADM as an essential host entry factor that directly binds human parechovirus 1 and that is required for PeV-A infection in cell lines and human gastrointestinal epithelial organoids.
- Wenjie Qiao
- , Christopher M. Richards
- & Jan E. Carette
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Article
| Open AccessPrecise prediction of phase-separation key residues by machine learning
Understanding intracellular phase separation is essential for transcriptional control, cell fate, and disease. Here the authors report PSPHunter which accurately predicts key residues, aiding in disease-associated protein identification and mechanistic insights.
- Jun Sun
- , Jiale Qu
- & Junjun Ding
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Article
| Open AccessFunctional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair
Here the authors describe a functional screening platform in human stem cells to identify and optimize protein-based gene editing additives that increase homologous directed recombination and have potential to improve gene therapy workflows.
- Juan A. Perez-Bermejo
- , Oghene Efagene
- & Kristen L. Seim
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Article
| Open AccessGAS41 modulates ferroptosis by anchoring NRF2 on chromatin
GAS41 is recognized as a histone reader and oncogene, but the mechanism by which GAS41 contributes to tumorigenesis is not well understood. Here, the authors discover that GAS41 is a ferroptosis repressor that anchors NRF2 to chromatin, promoting tumor growth.
- Zhe Wang
- , Xin Yang
- & Wei Gu
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Article
| Open AccessA universal system for boosting gene expression in eukaryotic cell-lines
Production of proteins at scale and affordable cost has been a major need of the biotech sector for the last several decades. Here the authors present a design algorithm called UNILIB for boosting gene expression in eukaryotic cells developed using an oligo-library and machine learning approach, validated in both yeast and mammalian cells using unseen sequences.
- Inbal Vaknin
- , Or Willinger
- & Roee Amit
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Perspective
| Open AccessCellular reprogramming as a tool to model human aging in a dish
The development of human cellular models of aging that surpass the limitations of animal models of aging is urgent. Here, the authors explore the opportunities and limitations of cellular reprogramming to create reliable aging in vitro models and their potential for the discovery of anti-aging compounds.
- Patricia R. Pitrez
- , Luis M. Monteiro
- & Lino Ferreira
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Article
| Open AccessMirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins
Mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders but is hindered by the optimization required for D-protein chemical synthesis. Here, the authors report a general mirror-image phage display pipeline based on automated flow peptide synthesis and use it to prepare and characterize 12 L/D-protein pairs.
- Alex J. Callahan
- , Satish Gandhesiri
- & Bradley L. Pentelute
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Article
| Open AccessProtein design using structure-based residue preferences
Recent protein design methods rely on large neural networks, yet it is unclear which dependencies are critical for determining function. Here, authors show that learning the per residue mutation preferences, without considering interactions, enables design of functional and diverse protein variants.
- David Ding
- , Ada Y. Shaw
- & Debora S. Marks
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Article
| Open AccessEfficient encoding of large antigenic spaces by epitope prioritization with Dolphyn
Profiling antibody responses to vast antigenic spaces has been challenging using programmable phage display (PhIP-Seq). Here, authors develop a methodology for compressing large proteomic spaces and have discovered human antibodies targeting gut bacteria-infecting phages.
- Anna-Maria Liebhoff
- , Thiagarajan Venkataraman
- & H. Benjamin Larman
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Article
| Open AccessGenome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover
Mechanisms regulating collagen clearance may be useful for treating fibrosis. Here, the authors conducted functional genome-wide screens and found that collagen biosynthesis directly regulates collagen clearance via a noncanonical function of SEL1L.
- Michael J. Podolsky
- , Benjamin Kheyfets
- & Kamran Atabai
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Article
| Open AccessDrug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor
There is a need for effective antiviral drugs against RSV infection. Conducting an RSV repurposing screen using the ReFRAME library Sake et al. identify lonafarnib as an RSV fusion protein inhibitor, characterize its binding site within the viral protein and show its antiviral effects in a mouse model.
- Svenja M. Sake
- , Xiaoyu Zhang
- & Thomas Pietschmann
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Article
| Open AccessNanoparticle-based DNA vaccine protects against SARS-CoV-2 variants in female preclinical models
Here the authors screen different lipid nanoparticle (LNP) formulations for intramuscular delivery of plasmid DNA and uptake by antigen-presenting cells. The lead LNP exhibits immunogenicity and protection in small animal models that is comparable to approved SARS-CoV-2 mRNA vaccine formulations.
- Lays Cordeiro Guimaraes
- , Pedro Augusto Carvalho Costa
- & Pedro Pires Goulart Guimaraes
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Article
| Open AccessHigh-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia
Using an unbiased phenotypic cell-based high-throughput screen, the authors identify and characterize a small molecule, BCH-HSP-C01, that restores aberrant protein trafficking in neuronal models of adapter protein complex 4 deficiency.
- Afshin Saffari
- , Barbara Brechmann
- & Mustafa Sahin
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Article
| Open AccessMultiplexed multicolor antiviral assay amenable for high-throughput research
Antiviral approaches against entire genera or families of viruses need to be constantly developed and innovated. Focusing on several distantly-related orthoflaviviruses, the authors develop a cell-based multiplex antiviral assay for high-throughput screening against multiple viruses at once.
- Li-Hsin Li
- , Winston Chiu
- & Kai Dallmeier
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Article
| Open AccessMolecular basis of human trace amine-associated receptor 1 activation
hTA1 is a drug target for several neuropsychiatric disorders. Using cryo-EM and pharmacological assays, the authors illuminate hTA1’s similarity to neurotransmitter receptors and discover that the antipsychotic asenapine potently activates the receptor.
- Gregory Zilberg
- , Alexandra K. Parpounas
- & Daniel Wacker
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Article
| Open AccessIntegrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection
Amnesic screening methods are useful to discover host factors that are important for SARS-CoV2 infection. Here the authors use a CRISPR screen to identify three anti-viral factors, which are associated with the coagulation system, and two pro-viral candidates and then use individual genetic deletion experiments to characterise their effect.
- Jiakai Hou
- , Yanjun Wei
- & Weiyi Peng
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Article
| Open AccessHigh-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos
Computational methods to analyse 3D organoids in high-throughput and with high cellular resolution remain scarce. Here, the authors propose Cellos, a high-throughput pipeline for 3D organoid segmentation using classical algorithms and a trained convolutional neural network.
- Patience Mukashyaka
- , Pooja Kumar
- & Jeffrey H. Chuang
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Article
| Open AccessMapping combinatorial drug effects to DNA damage response kinase inhibitors
DNA damage is a key component of many cancer therapies. Here, the authors utilised a dose-response combination screen of ATR, ATM and DNA-PK inhibitors, and identified combination treatments that achieves high combinatorial efficacy and synergy.
- Hanrui Zhang
- , Julian Kreis
- & Yuanfang Guan
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Article
| Open AccessCurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves
Dose-response curves are ubiquitous in pharmacology and biology, yet potency and effect size are often estimated even when there is no response. Here, authors present a statistical framework to assess curve significance and demonstrate how this aids drug mode of action analysis in large public datasets.
- Florian P. Bayer
- , Manuel Gander
- & Matthew The
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Article
| Open AccessDiscovery of a novel cardiac-specific myosin modulator using artificial intelligence-based virtual screening
Modulation of the myosin molecular motor has emerged as a potential therapeutic target for both heart disease and heart failure. Here, the authors use AI-based virtual high throughput screening to identify compounds that acts as a cardiac-specific myosin modulators.
- Priyanka Parijat
- , Seetharamaiah Attili
- & Thomas Kampourakis
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Article
| Open AccessSmall molecule regulators of microRNAs identified by high-throughput screen coupled with high-throughput sequencing
Regulatory miRNAs have significant therapeutic potential. Here the authors developed a screen to identify small molecule drugs that modulate miRNome profiles in human neurons and validated cardiac glycosides as inducers of the neuroprotective miR-132.
- Lien D. Nguyen
- , Zhiyun Wei
- & Anna M. Krichevsky
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Article
| Open AccessSimultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment
INSPIREseq discovers accessible epitopes in complex environments and leads to nanobodies targeting thousands of epitopes. This in vivo diversity selection identifies selective nanobodies, potentially expediting target discovery and drug development.
- Thillai V. Sekar
- , Eslam A. Elghonaimy
- & Todd A. Aguilera
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Article
| Open AccessCLOOME: contrastive learning unlocks bioimaging databases for queries with chemical structures
Artificial intelligence can assist in obtaining knowledge from bioimaging data, but need human annotation. Here the authors use multimodal contrastive learning to link chemical structures and cell phenotypes, which can lead to foundation models for microscopy images.
- Ana Sanchez-Fernandez
- , Elisabeth Rumetshofer
- & Günter Klambauer
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Article
| Open AccessRecognition and reprogramming of E3 ubiquitin ligase surfaces by α-helical peptides
Identification of molecules that induce novel interactions between proteins has been limited by the complexity of rationally designing interactions. The authors report a method to discover molecular glue-like “trimerizers” based on α-helically constrained peptides that can co-opt the surfaces of E3 ubiquitin ligases to bind therapeutically important proteins.
- Olena S. Tokareva
- , Kunhua Li
- & John H. McGee
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Article
| Open AccessCyclic fasting bolsters cholesterol biosynthesis inhibitors’ anticancer activity
Nutritional stress induced by short-term dietary restriction has been shown to alter the activity of some anti-tumour drugs. Here, the authors demonstrate that periodic fasting enhances the anti-tumour effect of cholesterol biosynthesis inhibitors via decreased AKT-STAT3 signaling and oxidative phosphorylation.
- Amr Khalifa
- , Ana Guijarro
- & Alessio Nencioni
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Article
| Open AccessGenome-wide association analysis of plasma lipidome identifies 495 genetic associations
The human plasma lipidome captures risk for cardiometabolic diseases. Here, the authors perform univariate and multivariate genome-wide analyses of 179 lipid species in 7174 Finnish individuals, revealing genetic links between diseases and lipid species beyond the standard lipids HDL-Cholesterol, LDL-Cholesterol, Triglycerides, and total Cholesterol.
- Linda Ottensmann
- , Rubina Tabassum
- & Matti Pirinen
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Article
| Open AccessDynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet
Predicting dynamic RNA-RBP interactions in diverse cell lines is an important challenge in unravelling RNA function and post-transcriptional regulatory mechanisms. Here, authors develop HDRNet, an end-to-end deep-learning-based framework for accurately predicting dynamic RBP binding events across various cellular conditions.
- Haoran Zhu
- , Yuning Yang
- & Xiangtao Li
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Article
| Open AccessRepurposing conformational changes in ANL superfamily enzymes to rapidly generate biosensors for organic and amino acids
Biosensors have a wide number of potential applications, but rapidly constructing genetically encoded biosensors remains challenging. Here, authors report a method for rapidly converting ANL superfamily enzymes into biosensors for organic acids, based on their conformational changes upon binding.
- Jin Wang
- , Ning Xue
- & Meng Wang
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Article
| Open AccessAn automated single-molecule FRET platform for high-content, multiwell plate screening of biomolecular conformations and dynamics
Single-molecule FRET (smFRET) studies often struggle with large parameter spaces. Here, the authors introduce an automated smFRET platform for multiwell plate screening of biomolecular conformations and dynamics.
- Andreas Hartmann
- , Koushik Sreenivasa
- & Michael Schlierf
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Article
| Open AccessWidefield imaging of rapid pan-cortical voltage dynamics with an indicator evolved for one-photon microscopy
Genetically encoded voltage indicators need fast and large signals to allow widefield imaging of rapid neuronal activity. Here, the authors develop the indicator JEDI-1P and demonstrate pan-cortical voltage imaging and gamma-frequency tracking in awake mice in single trials.
- Xiaoyu Lu
- , Yunmiao Wang
- & François St-Pierre
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Article
| Open AccessHigh-throughput screening of BAM inhibitors in native membrane environment
The bacterial insertase BAM is a key target for novel antibiotics that are urgently needed. Here, we describe the implementation of an assay that allows screening for BAM inhibitors in the native membrane in high-throughput format.
- Parthasarathi Rath
- , Adrian Hermann
- & Sebastian Hiller
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Article
| Open AccessSHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
Chromatin boundary elements are hard to define and characterize. Here the authors report Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains (SHIELD) for high-throughput screening of barrier-type DNA elements in human cells.
- Meng Zhang
- , Mary Elisabeth Ehmann
- & Huimin Zhao
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Article
| Open AccessFine-scale collective movements reveal present, past and future dynamics of a multilevel society in Przewalski’s horses
High resolution tracking is providing new opportunities to understand the social dynamics of wild animals. Here, the authors track individual wild horses with drones and link their movement patterns to long-term population monitoring to reveal the structure of their society.
- Katalin Ozogány
- , Viola Kerekes
- & Máté Nagy
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Article
| Open AccessPharmacological perturbation of the phase-separating protein SMNDC1
SMNDC1 is a splicing factor that binds arginine methylation with its Tudor domain. Here, the authors study the protein’s phase-separating behavior and develop small-molecule Tudor domain inhibitors that perturb SMNDC1 function.
- Lennart Enders
- , Marton Siklos
- & Stefan Kubicek
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Article
| Open AccessspinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
Droplet microfluidics enables high-throughput single-cell sequencing, but often with increased noise. Here the authors report spinDrop (sorting picoinjection inDrop) to increase gene detection and reduce noise; they use this to generate a high-quality molecular atlas of mouse brain development.
- Joachim De Jonghe
- , Tomasz S. Kaminski
- & Florian Hollfelder
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Article
| Open AccessLiver lipophagy ameliorates nonalcoholic steatohepatitis through extracellular lipid secretion
Nonalcoholic steatohepatitis (NASH) starts with lipid droplet accumulation in the liver that eventually causes inflammation and fibrosis. Here, authors use lipophagy activators to limit the accumulation of lipids in the liver and show that this can prevent disease progression in a mouse model of nonalcoholic steatohepatitis.
- Yoshito Minami
- , Atsushi Hoshino
- & Satoaki Matoba
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Article
| Open AccessMultiomics analysis of naturally efficacious lipid nanoparticle coronas reveals high-density lipoprotein is necessary for their function
ApoE is known to be important for lipid nanoparticle function. Here, the authors shows that efficacious coronal ApoE originates from high-density lipoprotein (HDL) particles and, enhances hepatic delivery, making HDL a superior biomarker for lipid nanoparticle potency.
- Kai Liu
- , Ralf Nilsson
- & Alan Sabirsh
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Article
| Open AccessProfiling of basal and ligand-dependent GPCR activities by means of a polyvalent cell-based high-throughput platform
Interrogating the dynamic and functionally diverse signaling of GPCRs requires comprehensive cellular tools. Here Zeghal et al. develop Tango-Trio, a screening platform capable of profiling basal and drug-activated activities at hundreds of GPCRs.
- Manel Zeghal
- , Geneviève Laroche
- & Patrick M. Giguère
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Article
| Open AccessA rapid cell-free expression and screening platform for antibody discovery
Antibody discovery is bottlenecked by the individual expression and evaluation of antigen specific hits. Here, the authors build an antibody screening workflow leveraging cell-free protein synthesis that enables expression and evaluation of hundreds of antibody fragments in less than 24 h.
- Andrew C. Hunt
- , Bastian Vögeli
- & Michael C. Jewett
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Article
| Open AccessA landscape of response to drug combinations in non-small cell lung cancer
Combination of drugs within cancer treatment is a popular way to overcome resistance and increase efficacy. Here, the authors analyse over 5000 targeted agent combinations in non-small cell lung cancer to identify potentially effective drug strategies.
- Nishanth Ulhas Nair
- , Patricia Greninger
- & Cyril H. Benes
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Article
| Open AccessSystematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq
Compact RNA structural motifs control many aspects of gene expression, but methods for their identification are lacking. Here the authors present a sequencing-based terbium probing approach to detect complex 3D structural elements, which can be used to pinpoint potential riboregulatory elements.
- Shivali Patel
- , Alec N. Sexton
- & Anna Marie Pyle
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Article
| Open AccessLight-switchable transcription factors obtained by direct screening in mammalian cells
Light-switchable variants are only available for a limited subset of proteins and pathways. Here the authors adapt strategies for protein domain insertion and mammalian-cell expression to generate and screen a library of potential optogenetic tools directly in mammalian cells.
- Liyuan Zhu
- , Harold M. McNamara
- & Jared E. Toettcher
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Article
| Open AccessNewborn metabolomic signatures of maternal per- and polyfluoroalkyl substance exposure and reduced length of gestation
Mechanisms of the impact of PFAS (also known as forever chemicals) on adverse birth outcomes remain largely unknown. Here, authors identified tissue neogenesis, neuroendocrine function, and redox homeostasis as imprints of prenatal PFAS exposures and reduced gestational age in the newborn metabolome.
- Kaitlin R. Taibl
- , Anne L. Dunlop
- & Donghai Liang
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Article
| Open AccessDesigned active-site library reveals thousands of functional GFP variants
Mutations in a protein active site can alter function in useful ways, but the active site is sensitive to changes. Here the authors present a general strategy to design combinatorial mutation libraries. Applied to GFP, the authors isolate thousands of fluorescent designs that exhibit large and useful changes in spectral properties.
- Jonathan Yaacov Weinstein
- , Carlos Martí-Gómez
- & Sarel J. Fleishman
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Article
| Open AccessSingularity response reveals entrainment properties in mammalian circadian clock
Current methods to assess circadian biological parameters can be labor intensive. Here, the authors establish a method for estimating circadian entrainment characteristics using simple experiments and mathematical modeling, revealing the responsiveness of circadian rhythms to diverse stimuli in the mammalian circadian clock.
- Kosaku Masuda
- , Naohiro Kon
- & Arisa Hirano
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Article
| Open AccessHigh-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing
Long-read single-cell RNA isoform sequencing can elucidate the intricate landscape of alternative RNA splicing in individual cells, but it suffers from a low read throughput. Here, the authors develop circular consensus sequencing methods to allow high-throughput and high-accuracy single-cell RNA isoform sequencing.
- Zhuo-Xing Shi
- , Zhi-Chao Chen
- & Yi-Zhi Liu
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Article
| Open AccessRAD-TGTs: high-throughput measurement of cellular mechanotype via rupture and delivery of DNA tension probes
Mechanical forces drive critical cellular processes, but methods to study such cellular forces are typically low-throughput. Here the authors present a method using “Rupture And Deliver” Tension Gauge Tethers, where flow cytometry or sequencing can be used to record the mechanical history of thousands of individual cells.
- Matthew R. Pawlak
- , Adam T. Smiley
- & Wendy R. Gordon
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Article
| Open AccessA massively parallel screening platform for converting aptamers into molecular switches
Efforts to convert aptamers into molecular switches using rational design are often unsuccessful. Here the authors describe a massively parallel screening-based strategy whereby millions of potential aptamer switches are synthesised, sequenced and screened directly on a flow-cell.
- Alex M. Yoshikawa
- , Alexandra E. Rangel
- & H. Tom Soh
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Article
| Open AccessHigh-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike
Designing vaccine immunogens is often a tedious process. Here the authors develop a deep mutational scanning-based method to rapidly and comprehensively identify prefusion stabilizing mutations of SARS-CoV-2 spike as a vaccine immunogen.
- Timothy J. C. Tan
- , Zongjun Mou
- & Nicholas C. Wu