Yun-Huai Kuo, Chloe N. Brown, Ece Akin, Yunxuan Xie, Peter M. Tessier
{"title":"Multi-objective antibody design and optimization using machine learning","authors":"Yun-Huai Kuo, Chloe N. Brown, Ece Akin, Yunxuan Xie, Peter M. Tessier","doi":"10.1038/s44222-026-00444-4","DOIUrl":"10.1038/s44222-026-00444-4","url":null,"abstract":"Antibodies, ranging from conventional immunoglobulins to single-domain and bispecific antibodies, are developed for a wide spectrum of therapeutic and diagnostic applications. However, lead antibodies are commonly engineered to optimize one or more key properties, including affinity, specificity, polyreactivity, stability, aggregation and immunogenicity, and trade-offs among these attributes frequently hinder the development of variants suitable for clinical use. Furthermore, identifying lead candidates with desirable properties typically requires multiple rounds of experimental screening and evaluation, particularly when targeting pre-selected epitopes or challenging, high-value targets such as G protein-coupled receptors (GPCRs), ion channels and multipass membrane proteins. Artificial intelligence (AI) and machine learning (ML) methods can streamline experimental screening and antibody generation methods. In this Review, we discuss both computational multi-objective optimization of existing antibodies and de novo antibody design. The application of AI and ML methods has the potential to overcome current bottlenecks in antibody development and accelerate the generation of improved therapeutics for human health. Antibodies are among the best-selling drugs and are crucial for numerous therapeutic and diagnostic purposes. However, optimizing antibodies for desirable drug-like properties has long been a hurdle, delaying or preventing promising drugs from reaching patients. Advances in computational methods, especially those using artificial intelligence and machine learning, can streamline and enhance conventional methods, enabling more efficient discovery and optimization of therapeutic antibodies.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"778-792"},"PeriodicalIF":42.7,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zixun Wang, Feng Guo, Hailiang Sun, Yutong Kong, Zhengyang Wang, Juan Tao, Mina Xu, Joe Yeong, Rong Fan, Peng Shi
{"title":"Clinical translation of spatial omics","authors":"Zixun Wang, Feng Guo, Hailiang Sun, Yutong Kong, Zhengyang Wang, Juan Tao, Mina Xu, Joe Yeong, Rong Fan, Peng Shi","doi":"10.1038/s44222-026-00458-y","DOIUrl":"10.1038/s44222-026-00458-y","url":null,"abstract":"Spatial omics is moving from atlas-building to clinical translation, with the potential to reshape diagnosis, prognosis and therapy selection. Realizing this promise now requires scalable assays, standardized workflows, rigorous validation and regulatory-ready integration to convert spatial biology into practical tools for precision medicine.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"699-701"},"PeriodicalIF":42.7,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mini human cervix-on-a-chip","authors":"Caroline Beyer","doi":"10.1038/s44222-026-00466-y","DOIUrl":"10.1038/s44222-026-00466-y","url":null,"abstract":"An article in Science Advances reports the development of a mini human cervix-on-a-chip. The model supports the growth of cervical cells and vaginal microbiota as well as inoculation with sexually transmitted infections, enabling investigation of complex host–microbiota–pathogen relationships.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 6","pages":"476-476"},"PeriodicalIF":42.7,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148262067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jennifer Lorimer, Robert McLachlan, Deirdre Zander-Fox, Moira K. O’Bryan, Reza Nosrati
{"title":"AI and automation in assisted reproduction","authors":"Jennifer Lorimer, Robert McLachlan, Deirdre Zander-Fox, Moira K. O’Bryan, Reza Nosrati","doi":"10.1038/s44222-026-00454-2","DOIUrl":"10.1038/s44222-026-00454-2","url":null,"abstract":"Infertility rates are rising globally, leading to increased reliance on assisted reproductive technologies (ART). Despite technological advances, many ART procedures remain highly manual and subjective, with few evidence-based tools available to guide protocols, evaluate and select gametes, or provide the necessary precision in a non-invasive manner. As a result, ART outcomes are often difficult to predict. Artificial intelligence (AI) and automation present promising opportunities to standardize and streamline processes. Some approaches, such as AI-driven embryo analysis and selection, and microfluidic-based semen processing, have already been adopted in clinical settings. However, the full potential of automation, computer vision and deep learning in ART has yet to be realized. This Review examines the development and application of AI and automation across the embryology laboratory, highlighting key innovations, clinical opportunities and ongoing challenges, including ethical and regulatory considerations. We conclude with a systems-level discussion of how these technologies could ultimately converge into an AI-integrated, closed-loop in vitro fertilization laboratory capable of adaptive, data-driven reproductive care. Rising infertility rates have increased reliance on assisted reproductive technologies, yet many such technologies remain manual, subjective and hard to standardize. This Review surveys advances in artificial intelligence and automation technologies across the embryology lab, highlighting emerging tools, clinical opportunities and challenges, and envisioning an integrated, adaptive, artificial intelligence-driven in vitro fertilization laboratory.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 9","pages":"818-839"},"PeriodicalIF":42.7,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giacomo Valle, Denise Oswalt, Robert A. Gaunt, Pieter Roelfsema, Charles M. Greenspon, Eduardo Fernandez
{"title":"Restoring vision and touch with cortical microstimulation","authors":"Giacomo Valle, Denise Oswalt, Robert A. Gaunt, Pieter Roelfsema, Charles M. Greenspon, Eduardo Fernandez","doi":"10.1038/s44222-026-00449-z","DOIUrl":"10.1038/s44222-026-00449-z","url":null,"abstract":"The restoration of sensory function following injury or disease represents a critical challenge in neuroengineering. Sensory neuroprostheses, particularly those targeting the primary visual (V1) and somatosensory (S1) cortices, promise to bypass damaged afferent pathways and reintroduce sensory percepts through direct cortical stimulation. Building on foundational insights from non-human primate research, epicortical and intracortical microstimulation has been used to evoke artificial visual and tactile experiences in early human trials. In this Review, we examine the state of cortical sensory prostheses, focusing on visual and somatosensory applications. We compare neural encoding strategies for touch and vision, discuss the technical and clinical requirements of cortical stimulation, and evaluate the qualitative advantages of these devices over conventional assistive technologies. We also highlight emerging directions, including biomimetic encoding, multisensory integration and alternative implant sites, that could enhance the fidelity and usability of future interfaces. Together, these developments mark a critical step towards clinically viable, high-resolution restoration of naturalistic sensation. Cortical sensory prostheses aim to restore vision and touch by stimulating primary visual and somatosensory cortices. This Review examines shared challenges and principles underlying visual and somatosensory restoration, comparing encoding strategies, technical and clinical requirements, and emerging approaches that advance high-fidelity, functional percepts across both modalities.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"713-732"},"PeriodicalIF":42.7,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Matthew Wester, Jongwon Lim, Mohammadreza Ghaderinia, Katherine Koprowski, An Bao Van, John Heredia, Karen White, James Kumar, Enrique Valera, Rashid Bashir
{"title":"Rapid diagnosis of sepsis and bloodstream infections","authors":"Matthew Wester, Jongwon Lim, Mohammadreza Ghaderinia, Katherine Koprowski, An Bao Van, John Heredia, Karen White, James Kumar, Enrique Valera, Rashid Bashir","doi":"10.1038/s44222-026-00446-2","DOIUrl":"10.1038/s44222-026-00446-2","url":null,"abstract":"Sepsis accounts for approximately 20% of global mortality and a substantial healthcare cost. Delayed or missed diagnoses of sepsis and poorly targeted treatment of sepsis-causing bloodstream infections are key contributors to this high mortality. Clinical diagnosis and monitoring of sepsis is based on several host-response measures related to organ system dysfunction. Owing to the low concentration of pathogens in bloodstream infections, identification of the causative pathogen generally requires blood culture over the course of hours to days. This necessitates the use of broad-spectrum antibiotics before culture results are available, which is a major risk factor for the development of antimicrobial resistance. In this Review, we describe the current standards for diagnosis of sepsis and summarize the technologies in use for detection of pathogens and host-response biomarkers in blood. We then identify key challenges in rapid diagnosis and discuss how ideal diagnostics for bloodstream infections could be achieved. Sepsis causes approximately 20% of global mortality and targeted treatment of causative bloodstream infection is limited by slow and insensitive pathogen detection, leading to delayed diagnosis and the overuse of broad-spectrum antibiotics that fuel antimicrobial resistance. This Review describes the measurement of host-response biomarkers for the detection and diagnosis of sepsis and addresses the need for sensitive and scalable approaches to bypass time-consuming blood culture.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"756-777"},"PeriodicalIF":42.7,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Applying therapeutic peptide design principles to agricultural peptides","authors":"Jack H. Cobon, David J. Craik, Conan K. Wang","doi":"10.1038/s44222-026-00461-3","DOIUrl":"10.1038/s44222-026-00461-3","url":null,"abstract":"Peptides offer a biodegradable, specific alternative to conventional pesticides, with the potential to address resistance and reduce harm to beneficial species. Here we argue that adopting the design playbook of peptide therapeutics, from library screening to de novo design strategies, could accelerate the development of precise, field-ready agricultural peptide products.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"705-707"},"PeriodicalIF":42.7,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
María Andrea Negret, Valentina Agudelo, David Grajales
{"title":"Portable breast cancer pre-screening device for equitable access","authors":"María Andrea Negret, Valentina Agudelo, David Grajales","doi":"10.1038/s44222-026-00457-z","DOIUrl":"10.1038/s44222-026-00457-z","url":null,"abstract":"Breast cancer disproportionately affects women in low- and middle-income countries, where barriers to diagnosis can delay detection and treatment. JULIETA, a portable bioimpedance device, supports triage and clinical prioritization, translating a bioengineering concept into a manufacturable and regulatorily viable tool to bridge detection gaps.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"708-709"},"PeriodicalIF":42.7,"publicationDate":"2026-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evan D. Groover, Flora Z. Wang, Amala John, Jianqiang Shen, Peggy G. Lemaux, David F. Savage, Krishna K. Niyogi
{"title":"Genome engineering of plant photosynthesis for carbon sequestration","authors":"Evan D. Groover, Flora Z. Wang, Amala John, Jianqiang Shen, Peggy G. Lemaux, David F. Savage, Krishna K. Niyogi","doi":"10.1038/s44222-026-00453-3","DOIUrl":"10.1038/s44222-026-00453-3","url":null,"abstract":"Anthropogenic carbon emissions have destabilized Earth’s carbon cycle, triggering cascading effects on climate and biodiversity. Plant-based carbon dioxide removal (CDR) presents a scalable, economically viable path to atmospheric carbon sequestration through soil carbon deposition, dedicated biomass cultivation and strategic agroforestry. Although photosynthesis drives terrestrial carbon capture, effective CDR strategies demand genetic optimization of carbon assimilation, retention and storage. The regulatory landscape is restrictive towards transgenic crops yet permissive of genome editing, creating a window for intervention. Advances in CRISPR-based editing, computational plant trait prediction and delivery systems for gene-editing tools in planta enable precision engineering of plant phenotypes to increase photosynthetic efficiency and carbon sequestration capacity. In this Review, we map the molecular and physiological innovations required to realize plant-based CDR at climate-relevant scales. Beyond optimizing carbon capture itself, we examine strategies to engineer enhanced biomass accumulation, improve nitrogen and water use efficiency, and stabilize carbon storage in plant and soil systems. We further assess the opportunities, implementation challenges and the potential of deploying genome-edited crops as a cornerstone of global carbon management. Gene editing to enhance photosynthesis in crop plants offers a strategy to boost plant carbon capture and mitigate climate change. This Review explores the agronomic, molecular and technical challenges in engineering photosynthesis for carbon sequestration as well as the genetic tools and editing technologies that can improve plant productivity and carbon storage.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 9","pages":"900-920"},"PeriodicalIF":42.7,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148305766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Transitioning from speech to language brain–computer interfaces","authors":"Jinlong Li, Aditya Singh, Nitin Tandon","doi":"10.1038/s44222-026-00460-4","DOIUrl":"10.1038/s44222-026-00460-4","url":null,"abstract":"Speech brain–computer interfaces have promoted communication restoration in individuals with anarthria by decoding intended speech from sensorimotor cortical activity. The next generation of communication neuroprostheses could enable the decoding of conceptual representations and thereby support more individuals with expressive aphasia with compromised word retrieval.","PeriodicalId":74248,"journal":{"name":"Nature reviews bioengineering","volume":"4 8","pages":"702-704"},"PeriodicalIF":42.7,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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