ArXiv最新文献

{"title":"Diffusion MRI invariants: from the group of rotations to a complete neuroimaging fingerprint.","authors":"Santiago Coelho, Jenny Chen, Filip Szczepankiewicz, Els Fieremans, Dmitry S Novikov","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Water diffusion gives rise to micrometer-scale sensitivity of diffusion MRI (dMR) to cellular-level tissue structure. The advent of precision medicine and quantitative imaging hinges on revealing the information content of dMR, and providing its parsimonious basis- and hardware-independent ``fingerprint\". Here we focus on the geometry of a multi-dimensional dMR signal, derive a complete set of 21 diffusion and covariance tensor invariants in terms of irreducible representations of the group of rotations, and relate them to tissue properties. Conventional dMR metrics are shown to be redundant, while most of the invariants provide novel complementary information. Our complete set of invariants for the kurtosis tensor improves multiple sclerosis classification in a cohort of 1189 subjects. We design acquisitions based on icosahedral vertices guaranteeing minimal number of measurements to determine the most used invariants in only 1--2 minutes for the whole brain. Representing dMR signals via scalar invariant maps with definite symmetries will underpin machine learning classifiers of brain pathology, development, and aging, while fast protocols will enable translation of advanced dMR into clinical practice.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11398539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.","authors":"Rahi Navelkar, Andrea Cosolo, Bogdan Bintu, Yubao Cheng, Vincent Gardeux, Silvia Gutnik, Taihei Fujimori, Antonina Hafner, Atishay Jay, Bojing Blair Jia, Adam Paul Jussila, Gerard Llimos, Antonios Lioutas, Nuno M C Martins, William J Moore, Yodai Takei, Frances Wong, Kaifu Yang, Huaiying Zhang, Quan Zhu, Magda Bienko, Lacramioara Bintu, Long Cai, Bart Deplancke, Marcelo Nollmann, Susan E Mango, Bing Ren, Peter J Park, Ahilya N Sawh, Andrew Schroeder, Jason R Swedlow, Golnaz Vahedi, Chao-Ting Wu, Sarah Aufmkolk, Alistair N Boettiger, Irene Farabella, Caterina Strambio-De-Castillia, Siyuan Wang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A key output of the NIH-Common Fund 4D Nucleome (4DN) project ^1,2 is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease. Despite this progress, results from Chromatin Tracing FISH-omics experiments are difficult to share, reuse, and subject to third-party downstream analysis due to the lack of standard specifications for data exchange. Following up on the recent publication of Microscopy Metadata specifications ^3,4, we present the 4DN FISH Omics Format - Chromatin Tracing (FOF-CT), a community-developed data standard for processed results derived from a wide variety of imaging techniques for Chromatin Tracing, with the most recent studies falling roughly into two categories: ball-and-stick and volumetric based on whether they represent the targeted genomic segment as individual fluorescence spots or as clouds of single-molecule localizations. To demonstrate the value and potential use of FOF-CT to promote the FAIR sharing of the results obtained from Chromatin Tracing techniques, this manuscript will focus on ball-and-stick Chromatin Tracing techniques, including those described by the pioneering Chromatin Tracing study of Wang et al. ⁵ as well as Optical Reconstruction of Chromatin Architecture (ORCA) ⁶, microscopy-based chromosome conformation capture (Hi-M) ⁷, Multiplexed Imaging of Nucleome Architectures (MINA) ⁸, DNA Sequential Fluorescence In Situ Hybridization (DNA seqFISH/seqFISH+) ^9-11, Oligopaint Fluorescent In Situ Sequencing (OligoFISSEQ) ¹², DNA Multiplexed error-robust fluorescence in situ hybridization (DNA-MERFISH) ¹³, and In-situ Genomic Sequencing (IGS) ¹⁴. The manuscript will describe the structure of the format and present a collection of FOF-CT datasets that were recently deposited to the 4DN Data Portal ¹⁵ and the Open Microscopy Environment (OME) Image Data Resource (IDR) platform ¹⁶ and are ideally suited for promoting reuse, exchange, further processing, and integrative modeling. Furthermore, the manuscript will present examples of analysis pipelines that could be applied more widely due to the existence of the FOF-CT exchange data format and provide examples of biological conclusions that could be drawn thanks to the availability of such datasets.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A theory of ecological invasions and its implications for eco-evolutionary dynamics.","authors":"Zhijie Feng, Emmy Blumenthal, Pankaj Mehta, Akshit Goyal","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Predicting the outcomes of species invasions is a central goal of ecology, a task made especially challenging due to ecological feedbacks. To address this, we develop a general theory of ecological invasions applicable to a wide variety of ecological models: including Lotka-Volterra models, consumer resource models, and models with cross feeding. Importantly, our framework remains valid even when invading evolved (non-random) communities and accounts for invasion-driven species extinctions. We derive analytical expressions relating invasion fitness to invader abundance, shifts in the community, and extinction probabilities. These results can be understood through a new quantity we term ``dressed invasion fitness'', which augments the traditional notion of invasion fitness by incorporating ecological feedbacks. We apply our theory to analyze short-term evolutionary dynamics through a series of invasions by mutants whose traits are correlated with an existing parent. We demonstrate that, generically, mutants and parents can coexist, often by driving the extinction of low-abundance species. We validate theoretical predictions against experimental datasets spanning ecosystems from plants to microbial protists. Our work highlights the central role of ecological feedbacks in shaping community responses to invasions and mutations, suggesting that parent-mutant coexistence is widespread in eco-evolutionary dynamics.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Yeast growth is controlled by the proportional scaling of mRNA and ribosome concentrations.","authors":"Xin Gao, Michael Lanz, Rosslyn Grosely, Jonas Cremer, Joseph Puglisi, Jan M Skotheim","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Despite growth being fundamental to all aspects of cell biology, we do not yet know its organizing principles in eukaryotic cells. Classic models derived from the bacteria E. coli posit that protein-synthesis rates are set by mass-action collisions between charged tRNAs produced by metabolic enzymes and mRNA-bound ribosomes. These models show that faster growth is achieved by simultaneously raising both ribosome content and peptide elongation speed. Here, we test if these models are valid for eukaryotes by combining single-molecule tracking, spike-in RNA sequencing, and proteomics in 15 carbon- and nitrogen-limited conditions using the budding yeast S. cerevisiae. Ribosome concentration increases linearly with growth rate, as in bacteria, but the peptide elongation speed remains constant (~9 amino acids/s) and charged tRNAs are not limiting. Total mRNA concentration rises in direct proportion to ribosomes, driven by enhanced RNA polymerase II occupancy of the genome. We show that a simple kinetic model of mRNA-ribosome binding predicts both the fraction of active ribosomes, the growth rate, and responses to transcriptional perturbations. Yeast accelerate growth by coordinately and proportionally co-up-regulating total mRNA and ribosome concentrations, not by speeding elongation. Taken together, our work establishes a new framework for eukaryotic growth control and resource allocation.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multimodal concentric surface coils for enhanced sensitivity in MR imaging.","authors":"Yunkun Zhao, Aditya A Bhosale, Xiaoliang Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This study presents the design, simulation, and experimental validation of a novel multimodal concentric surface coil for MR imaging, developed to achieve higher B1 field efficiency while maintaining low SAR for enhanced imaging performance. The coil comprises multiple electromagnetically coupled concentric resonators of varying sizes. The resonant frequency of a desired mode is tuned to 127 MHz, as an example, to demonstrate the performance of the proposed technique at 3 Tesla. Fullwave electromagnetic simulations of the proposed design and bench tests of fabricated prototypes were conducted to evaluate the coil's B1 field efficiency and distribution, multimodal resonance behavior, scattering parameters, and SAR performance. Inductive Current Elimination or magnetic wall decoupling was implemented to enhance channel isolation in a multi channel configuration to demonstrate the feasibility of applying this multimodal technique to RF array design and parallel imaging. Experimental results show that the proposed concentric coil achieves higher B1 field efficiency and reduced SAR compared to a conventional surface coil of the same size operating at 3 Tesla. Bench measurements on the prototypes confirmed successful tuning and impedance matching, with measured S11 and S21 parameters validating the effectiveness of the decoupling strategy. B1 mapping experiments further demonstrated efficient RF power delivery across multiple planes. These findings suggest that the proposed multimodal concentric coil has the potential to serve as a promising alternative to conventional surface coils for high performance MR imaging, offering enhanced RF efficiency, reduced SAR, and the ability to construct multichannel RF arrays.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Goals and the Structure of Experience.","authors":"Nadav Amir, Stas Tiomkin, Angela Langdon","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Purposeful behavior is a hallmark of natural and artificial intelligence. Its acquisition is often believed to rely on world models, comprising both descriptive (what <i>is</i>) and prescriptive (what is <i>desirable</i>) aspects that identify and evaluate state of affairs in the world, respectively. Canonical computational accounts of purposeful behavior, such as reinforcement learning, posit distinct components of a world model comprising a <i>state representation</i> (descriptive aspect) and a <i>reward function</i> (prescriptive aspect). However, an alternative possibility, which has not yet been computationally formulated, is that these two aspects instead co-emerge interdependently from an agent's <i>goal</i>. Here, we describe a computational framework of goal-directed state representation in cognitive agents, in which the descriptive and prescriptive aspects of a world model co-emerge from agent-environment interaction sequences, or <i>experiences</i>. Drawing on Buddhist epistemology, we introduce a construct of goal-directed, or <i>telic</i>, states, defined as classes of goal-equivalent experience distributions. Telic states provide a parsimonious account of goal-directed learning in terms of the statistical divergence between behavioral policies and desirable experience features. We review empirical and theoretical literature supporting this novel perspective and discuss its potential to provide a unified account of behavioral, phenomenological and neural dimensions of purposeful behaviors across diverse substrates.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visualizing Poloidal Orientation in DNA Minicircles.","authors":"Tony Lemos, Harold D Kim","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A short (<150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as the poloidal orientation. Despite theoretical and computational predictions, experimental evidence for this phenomenon has been lacking. In this study, we introduce a single-molecule approach to visualize the poloidal orientation of DNA minicircles. We constructed a set of DNA minicircles, each containing a single biotin located at a different position along one helical turn of the dsDNA, and imaged the location of biotin-bound NeutrAvidin relative to the DNA minicircle using atomic force microscopy (AFM). We applied this approach to two DNA sequences previously predicted to exhibit strongly preferred poloidal orientations. The observed relative positions of NeutrAvidin shifted between the inside and outside of the minicircle with different phases, indicating distinct poloidal orientations for the two sequences. Coarse-grained simulations revealed narrowly distributed poloidal orientations with different mean orientations for each sequence, consistent with the AFM results. Together, our findings provide experimental confirmation of preferred poloidal orientations in DNA minicircles, offering insights into the intrinsic dynamics of circular DNA.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cherenkov Imaged Bio-Morphological Features Verify Patient Positioning With Deformable Tissue Translocation in Breast Radiation Therapy.","authors":"Yao Chen, Savannah M Decker, Petr Bruza, David J Gladstone, Lesley A Jarvis, Brian W Pogue, Kimberley S Samkoe, Rongxiao Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Purpose: </strong>Accurate patient positioning is crucial for precise radiation therapy dose delivery, as errors in positioning can profoundly influence treatment outcomes. This study introduces a novel application for loco-regional tissue deformation tracking via Cherenkov image analysis during fractionated breast cancer radiation therapy. The primary objective of this research was to develop and test an algorithmic method for Cherenkov-based position accuracy quantification, particularly for loco-regional deformations, which do not have an ideal method for quantification during radiation therapy.</p><p><strong>Methods and materials: </strong>Bio-morphological features in the Cherenkov images, such as vessels, were segmented. A rigid/nonrigid combined registration technique was employed to pinpoint both inter- and intrafractional positioning variations. The methodology was tested on an anthropomorphic chest phantom experiment via shifting a treatment couch with known distances and inducing respiratory motion to simulate interfraction setup uncertainties and intrafraction motions, respectively. It was then applied to a data set of fractionated whole breast radiation therapy human imaging (n = 10 patients).</p><p><strong>Results: </strong>The methodology provided quantified positioning variations comprising 2 components: a global shift determined through rigid registration and a 2-dimensional variation map illustrating loco-regional tissue deformation quantified via nonrigid registration. Controlled phantom testing yielded an average accuracy of 0.83 mm for couch translations up to 20 mm in various directions. Analysis of clinical Cherenkov imaging data from 10 breast cancer patients compared with their first imaged fraction revealed an interfraction setup variation of 3.7 ± 2.4 mm in the global shift and loco-regional deformation up to 3.3 ± 1.9 mm (95th percentile of all regional deformation).</p><p><strong>Conclusions: </strong>This study introduces the use of Cherenkov visualized bio-morphological features to quantify the global and local variations in patient positioning based on rigid and nonrigid registrations. This new approach demonstrates the feasibility of providing quantitative guidance for inter/intrafraction positioning, particularly for the loco-regional deformations that have been unappreciated in current practice with conventional imaging techniques.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New Insights into Automatic Treatment Planning for Cancer Radiotherapy Using Explainable Artificial Intelligence.","authors":"Md Mainul Abrar, Xun Jia, Yujie Chi","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objective: </strong>This study aims to uncover the opaque decision-making process of an artificial intelligence (AI) agent for automatic treatment planning.</p><p><strong>Approach: </strong>We examined a previously developed AI agent based on the Actor-Critic with Experience Replay (ACER) network, which automatically tunes treatment planning parameters (TPPs) for inverse planning in prostate cancer intensity modulated radiotherapy. We selected multiple checkpoint ACER agents from different stages of training and applied an explainable AI (EXAI) method to analyze the attribution from dose-volume histogram (DVH) inputs to TPP-tuning decisions. We then assessed each agent's planning efficacy and efficiency, and evaluated their policy space and final TPP tuning space. Combining findings from these approaches, we systematically examined how ACER agents generated high-quality treatment plans in response to different DVH inputs.</p><p><strong>Main results: </strong>Attribution analysis revealed that ACER agents progressively learned to identify dose-violation regions from DVH inputs and promote appropriate TPP-tuning actions to mitigate them. Organ-wise similarities between DVH attributions and dose-violation reductions ranged from 0.25 to 0.5 across tested agents. While all agents achieved comparably high final planning scores, their planning efficiency and stability differed. Agents with stronger attribution-violation similarity required fewer tuning steps ( 12-13 vs. 22), exhibited a more concentrated TPP-tuning space with lower entropy ( 0.3 vs. 0.6), converged on adjusting only a few key TPPs, and showed smaller discrepancies between practical tuning steps and the theoretical steps needed to move from initial values to the final TPP space. Putting together, these findings indicate that high-performing ACER agents can effectively identify dose violations from DVH inputs and employ a global tuning strategy to achieve high-quality treatment planning.</p><p><strong>Significance: </strong>This study demonstrates that the AI agent learns effective TPP-tuning strategies, exhibiting behaviors similar to those of experienced human planners. Improved interpretability of the agent's decision-making process may enhance clinician trust and inspire new strategies for automatic treatment planning.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the FAIRness and Sustainability of the NHGRI Resources Ecosystem.","authors":"Larry Babb, Carol Bult, Vincent J Carey, Robert J Carroll, Benjamin C Hitz, Chris J Mungall, Heidi L Rehm, Michael C Schatz, Alex Wagner","doi":"","DOIUrl":"","url":null,"abstract":"&lt;p&gt;&lt;p&gt;In 2024, individuals funded by NHGRI to support genomic community resources completed a Self-Assessment Tool (SAT) to evaluate their application of the FAIR (Findable, Accessible, Interoperable, and Reusable) principles and assess their sustainability. By collecting insights from the self-administered questionnaires and conducting personal interviews, a valuable perspective was gained on the FAIRness and sustainability of the NHGRI resources. The results highlighted several challenges and key areas the NHGRI resource community could improve by working together to form recommendations to address these challenges. The next step was the formation of an Organizing Committee to identify which challenges could lead to best practices or guidelines for the community. The workshop's Organizing Committee comprised four members from the NHGRI resource community: Carol Bult, PhD, Chris Mungall, PhD, Heidi Rehm, PhD, and Michael Schatz, PhD. In December 2024, the Organizing Committee engaged with the NHGRI resource community to refine these challenges further, inviting feedback on potential focus areas for a future workshop. This collaborative approach led to two informative webinars in December 2024, highlighting specific challenges in data curation, data processing, metadata tools, and variant identifiers within the NHGRI resources. Throughout the workshop planning process, the four Organizing Committee members worked together to create and develop themes, design breakout sessions, and create a detailed agenda. The workshop's agenda was intentionally structured to ensure participants could generate implementable recommendations for the NHGRI resource community. The two-day workshop was held in Bethesda, MD, on March 3-4, 2025. The challenges received from NHGRI resources were classified into four key categories, forming the basis of the workshop. The four key categories are variant identifiers, data processing, data curation, and metadata tools. They are briefly described below, with greater details on their challenges and recommendations in subsequent sections. Metadata Tools:While metadata is vital for capturing context in genomic datasets, its usage and relevance can vary by domain, making it difficult to standardize usage. While various methods exist for annotating and extracting metadata, incomplete or inconsistent annotations often result in ineffective data sharing and interoperability, further reducing data usability and reproducibility.Data Curation:Curation of annotations for genomics data is critical for FAIR-ness. Scalable curation solutions are challenging because of the multiple components for curation, including harmonizing data sets, data cleaning, and annotation. The workshop focused on identifying which aspects of data curation could be streamlined using computational methods while considering the barriers to increased automation.Variant Identifiers:Variant identifiers are standardized representations of genetic variants, crucial for","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144982155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}