Verification and reproducible curation of the BioModels repository.

Authors: Smith LP; Department of Bioengineering, University of Washington, Seattle, Washington, United States of America., Malik-Sheriff RS; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom., Nguyen TVN; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom., Hermjakob H; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom., Karr J; Icahn School of Medicine at Mount Sinai, New York, New York, United States of America., Shaikh B; Icahn School of Medicine at Mount Sinai, New York, New York, United States of America., Drescher L; University of Connecticut School of Medicine, Farmington, Connecticut, United States of America., Moraru II; University of Connecticut School of Medicine, Farmington, Connecticut, United States of America., Schaff JC; University of Connecticut School of Medicine, Farmington, Connecticut, United States of America., Agmon E; University of Connecticut School of Medicine, Farmington, Connecticut, United States of America., Patrie AA; University of Connecticut School of Medicine, Farmington, Connecticut, United States of America., Blinov ML; University of Connecticut School of Medicine, Farmington, Connecticut, United States of America., Hellerstein JL; eScience Institute, University of Washington, Seattle, Washington, United States of America., May EE; Department of Medical Microbiology and Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America., Nickerson DP; Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand., Gennari JH; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America., Sauro HM; Department of Bioengineering, University of Washington, Seattle, Washington, United States of America.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Dec 04; Vol. 21 (12), pp. e1013239. Date of Electronic Publication: 2025 Dec 04 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Programming Languages* , Systems Biology*/methods , Data Curation*/methods , Databases, Factual* , Models, Biological*, Reproducibility of Results ; Computer Simulation ; Computational Biology/methods ; Humans

Automating HotSpot health physics code for enhanced radiological risk assessment using python.

Authors: Maglas NNM; College of Nuclear Science and Technology, Harbin Engineering University, Harbin, 150001, China; Thamar University, Republic of Yemen, Faculty of Science, Department of Physics, Yemen; National Atomic Energy Commission-Yemen (NATEC), Sana'a, Yemen. Electronic address: najeep2252a@gmail.com., Najar M; College of Nuclear Science and Technology, Harbin Engineering University, Harbin, 150001, China. Electronic address: najar18najar@gmail.com., Qiang Z; College of Nuclear Science and Technology, Harbin Engineering University, Harbin, 150001, China. Electronic address: zhaoqiang@hrbeu.edu.cn.

Source: Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine [Appl Radiat Isot] 2025 Dec; Vol. 226, pp. 112150. Date of Electronic Publication: 2025 Sep 02.

Publication Type: Journal Article

Journal Info: Publisher: Pergamon Press Country of Publication: England NLM ID: 9306253 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1872-9800 (Electronic) Linking ISSN: 09698043 NLM ISO Abbreviation: Appl Radiat Isot Subsets: MEDLINE

MeSH Terms: Health Physics*/methods , Radioactive Hazard Release* , Software* , Programming Languages* , Radiation Monitoring*/methods, Risk Assessment/methods ; Humans ; Automation ; Radiation Dosage

Leveraging open-source large language models (LLMs) in scoping reviews: a case study on disability and AI applications.

Authors: Bayani A; Centre de recherche en santé publique, Université de Montréal et CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Canada; Laboratoire Transformation Numérique en Santé (LabTNS), Québec, Canada., Epoh Ewane LP; Centre de recherche en santé publique, Université de Montréal et CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Canada; Department of Social and Preventive Medicine, School of Public Health & Centre de Recherche en Santé Publique, Université de Montréal, Montreal, QC, Canada; Laboratoire Solidarités and Global Health, Québec, Canada., Oliveira Dos Anjos DS; Centre de recherche en santé publique, Université de Montréal et CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Canada; Laboratoire Transformation Numérique en Santé (LabTNS), Québec, Canada., Mac-Seing M; Centre de recherche en santé publique, Université de Montréal et CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Canada; Department of Social and Preventive Medicine, School of Public Health & Centre de Recherche en Santé Publique, Université de Montréal, Montreal, QC, Canada; Laboratoire Solidarités and Global Health, Québec, Canada., Nikiema JN; Centre de recherche en santé publique, Université de Montréal et CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Canada; Laboratoire Transformation Numérique en Santé (LabTNS), Québec, Canada; Department of Management, Evaluation and Health Policy, School of Public Health, Université de Montréal, Québec, Canada. Electronic address: jean.nikiema@umontreal.ca.

Source: International journal of medical informatics [Int J Med Inform] 2025 Dec; Vol. 204, pp. 106048. Date of Electronic Publication: 2025 Jul 23.

Publication Type: Journal Article; Scoping Review

Journal Info: Publisher: Elsevier Science Ireland Ltd Country of Publication: Ireland NLM ID: 9711057 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1872-8243 (Electronic) Linking ISSN: 13865056 NLM ISO Abbreviation: Int J Med Inform Subsets: MEDLINE

MeSH Terms: Artificial Intelligence* , Natural Language Processing* , Persons with Disabilities* , Data Mining*/methods , Programming Languages*, Humans ; Scoping Review as Topic ; Large Language Models

Evaluating Locally Run Large Language Models (Gemma 2, Mistral Nemo, and Llama 3) for Outpatient Otorhinolaryngology Care: Retrospective Study.

Authors: Buhr CR; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362.; School of Medicine, University of St Andrews, St Andrews, United Kingdom., Seifen C; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362., Bahr-Hamm K; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362., Huppertz T; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362., Pordzik J; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362., Smith H; School of Computer Science, University of St Andrews, St Andrews, United Kingdom., Kelsey T; School of Computer Science, University of St Andrews, St Andrews, United Kingdom., Blaikie A; School of Medicine, University of St Andrews, St Andrews, United Kingdom., Matthias C; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362., Kuhn S; Institute for Digital Medicine, Philipps University Marburg, University Hospital Giessen and Marburg, Marburg, Germany., Eckrich J; Department of Otorhinolaryngology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz, 55131, Germany, +49 6131 17 7362.

Source: JMIR formative research [JMIR Form Res] 2025 Nov 25; Vol. 9, pp. e76896. Date of Electronic Publication: 2025 Nov 25.

Publication Type: Journal Article

Journal Info: Publisher: JMIR Publications Country of Publication: Canada NLM ID: 101726394 Publication Model: Electronic Cited Medium: Internet ISSN: 2561-326X (Electronic) Linking ISSN: 2561326X NLM ISO Abbreviation: JMIR Form Res Subsets: MEDLINE

MeSH Terms: Otolaryngology*/methods , Ambulatory Care*/methods , Programming Languages*, Retrospective Studies ; Humans ; Female ; Male ; Outpatients/statistics & numerical data ; Adult ; Middle Aged ; Large Language Models

Visual language model-assisted spectral CT reconstruction by diffusion and low-rank priors from limited-angle measurements.

Authors: Wang Y; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Liang N; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Ren J; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Zhang X; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Shen Y; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Cai A; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Zheng Z; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Li L; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China., Yan B; Department of Henan Key Laboratory of Imaging and Intelligent Processing, Information Engineering University, Zhengzhou, People's Republic of China.

Source: Physics in medicine and biology [Phys Med Biol] 2025 Nov 17; Vol. 70 (23). Date of Electronic Publication: 2025 Nov 17.

Publication Type: Journal Article

Journal Info: Publisher: IOP Publishing Country of Publication: England NLM ID: 0401220 Publication Model: Electronic Cited Medium: Internet ISSN: 1361-6560 (Electronic) Linking ISSN: 00319155 NLM ISO Abbreviation: Phys Med Biol Subsets: MEDLINE

MeSH Terms: Tomography, X-Ray Computed*/methods , Image Processing, Computer-Assisted*/methods , Programming Languages*, Diffusion ; Artifacts ; Humans ; Phantoms, Imaging

Accelerating systematic reviews: a novel 1-wk screening protocol using rule-based automation with AI-assisted Python coding.

Authors: Robleto E; Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States.; Division of Cardiology, Department of Medicine, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States.; Miami Veterans' Affairs Medical Center, Research & Development Services, Miami, Florida, United States., Shehadeh LA; Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States.; Division of Cardiology, Department of Medicine, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, United States.; Miami Veterans' Affairs Medical Center, Research & Development Services, Miami, Florida, United States.

Source: American journal of physiology. Heart and circulatory physiology [Am J Physiol Heart Circ Physiol] 2025 Nov 01; Vol. 329 (5), pp. H1391-H1413. Date of Electronic Publication: 2025 Sep 12.

Publication Type: Journal Article

Journal Info: Publisher: American Physiological Society Country of Publication: United States NLM ID: 100901228 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1522-1539 (Electronic) Linking ISSN: 03636135 NLM ISO Abbreviation: Am J Physiol Heart Circ Physiol Subsets: MEDLINE

MeSH Terms: Systematic Reviews as Topic* , Artificial Intelligence* , Programming Languages*, Humans ; Automation

Using large language models to automate summarization of CT simulation orders in radiation oncology.

Authors: Cao M; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Hu S; Corcoran College of Arts and Sciences, George Washington University-Washington DC, Washington DC, USA., Sharp J; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Clouser EL; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Holmes JM; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Lam LL; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Ding X; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Toesca DS; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Raulston BC; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Lindholm WS; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Patel SH; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Vora SA; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Wang P; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA., Liu W; Department of Radiation Oncology, Mayo Clinic Hospital, Phoenix, Arizona, USA.

Source: Journal of applied clinical medical physics [J Appl Clin Med Phys] 2025 Nov; Vol. 26 (11), pp. e70310.

Publication Type: Journal Article

Journal Info: Publisher: Wiley on behalf of American Association of Physicists in Medicine Country of Publication: United States NLM ID: 101089176 Publication Model: Print Cited Medium: Internet ISSN: 1526-9914 (Electronic) Linking ISSN: 15269914 NLM ISO Abbreviation: J Appl Clin Med Phys Subsets: MEDLINE

MeSH Terms: Tomography, X-Ray Computed*/methods , Radiation Oncology*/methods , Neoplasms*/radiotherapy , Neoplasms*/diagnostic imaging , Radiotherapy Planning, Computer-Assisted*/methods , Programming Languages*, Humans ; Workflow ; Computer Simulation ; Large Language Models

Benchmarking cell type and gene set annotation by large language models with AnnDictionary.

Authors: Crowley G; Department of Bioengineering, Stanford University, Stanford, California, USA., Quake SR; Department of Bioengineering, Stanford University, Stanford, California, USA. steve@quake-lab.org.; Department of Applied Physics, Stanford University, Stanford, CA, USA. steve@quake-lab.org.; Chan Zuckerberg Initiative, Redwood City, CA, USA. steve@quake-lab.org.

Corporate Authors: Tabula Sapiens Consortium

Source: Nature communications [Nat Commun] 2025 Oct 28; Vol. 16 (1), pp. 9511. Date of Electronic Publication: 2025 Oct 28.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Benchmarking* , Molecular Sequence Annotation*/methods , Software* , Programming Languages* , Computational Biology*/methods, Humans ; Large Language Models

multiSMD - A Python Toolset for Multidirectional Steered Molecular Dynamics.

Authors: Walczewska-Szewc K; Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziądzka 5, 87-100 Toruń, Poland., Niklas B; Department of Animal Physiology and Neurobiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland., Szewc K; ESS Engineering Software Steyr GmbH, Berggasse 35, 4400 Steyr, Austria., Nowak W; Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziądzka 5, 87-100 Toruń, Poland.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2025 Oct 27; Vol. 65 (20), pp. 10803-10807. Date of Electronic Publication: 2025 Oct 02.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

MeSH Terms: Molecular Dynamics Simulation* , Software* , Programming Languages*, Ligands ; Proteins/chemistry ; Proteins/metabolism ; Protein Binding

A Decade of SBOL Visual: Growing Adoption of a Diagram Standard for Engineering Biology.

Authors: Buecherl L; Biological Engineering Department, Utah State University, Logan, Utah 84322, United States., Buson FX; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, U.K., Sørensen GH; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, U.K., Vitalis C; Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States., Kubaczka E; Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64283, Germany., Vidal G; Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States., Bartley B; Intelligent Software & Systems, RTX BBN Technologies, Cambridge, Massachusetts 02138, United States., Ho YK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, U.K., Mısırlı G; School of Computer Science and Mathematics, Keele University, Staffordshire ST5 5BG, U.K., Gorochowski TE; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, U.K., Beal J; Intelligent Software & Systems, RTX BBN Technologies, Cambridge, Massachusetts 02138, United States., Myers CJ; Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States., Vaidyanathan P; Data Science and Software Development, Oxford Biomedica, Oxford OX4 6LT, U.K.

Source: ACS synthetic biology [ACS Synth Biol] 2025 Oct 17; Vol. 14 (10), pp. 3822-3830. Date of Electronic Publication: 2025 Sep 28.

Publication Type: Journal Article; Review

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101575075 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2161-5063 (Electronic) Linking ISSN: 21615063 NLM ISO Abbreviation: ACS Synth Biol Subsets: MEDLINE

MeSH Terms: Synthetic Biology*/methods , Synthetic Biology*/standards , Programming Languages* , Genetic Engineering*/methods, Humans

From Guidelines to Code: Formalizing STOPP/START Criteria Using LLMs and RAG for Clinical Decision Support.

Authors: Adrouji S; Sorbonne Université, INSERM, Université Sorbonne Paris Nord, LIMICS, Paris France., Mouazer A; Sorbonne Université, INSERM, Université Sorbonne Paris Nord, LIMICS, Paris France.; Hôpital Pitié-Salpêtrière, AP-HP, Paris, France., Lamy JB; Sorbonne Université, INSERM, Université Sorbonne Paris Nord, LIMICS, Paris France.

Source: Studies in health technology and informatics [Stud Health Technol Inform] 2025 Oct 02; Vol. 332, pp. 42-46.

Publication Type: Journal Article

Journal Info: Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9214582 Publication Model: Print Cited Medium: Internet ISSN: 1879-8365 (Electronic) Linking ISSN: 09269630 NLM ISO Abbreviation: Stud Health Technol Inform Subsets: MEDLINE

MeSH Terms: Decision Support Systems, Clinical*/organization & administration , Practice Guidelines as Topic* , Natural Language Processing* , Programming Languages*, Humans

Towards GraphQL-Based Interoperability Between Business Meta-Models and FHIR Resources.

Authors: Saarelaid E; eMedLab at Tallinn University of Technology, Tallinn, Estonia., Randmaa R; eMedLab at Tallinn University of Technology, Tallinn, Estonia., Piho G; eMedLab at Tallinn University of Technology, Tallinn, Estonia., Ross P; eMedLab at Tallinn University of Technology, Tallinn, Estonia.; Research Department, East Tallinn Central Hospital, Tallinn, Estonia.

Source: Studies in health technology and informatics [Stud Health Technol Inform] 2025 Oct 02; Vol. 332, pp. 200-204.

Publication Type: Journal Article

Journal Info: Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9214582 Publication Model: Print Cited Medium: Internet ISSN: 1879-8365 (Electronic) Linking ISSN: 09269630 NLM ISO Abbreviation: Stud Health Technol Inform Subsets: MEDLINE

MeSH Terms: Electronic Health Records*/organization & administration , Health Information Interoperability* , Information Storage and Retrieval*/methods , Programming Languages*

Pre-Meta: priors-augmented retrieval for LLM-based metadata generation.

Authors: Tinn P; SINTEF AS, Oslo 0373, Norway., Sørbø S; SINTEF AS, Oslo 0373, Norway., Jiang S; SINTEF AS, Oslo 0373, Norway., Voutetakis K; Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece., Giounis SM; Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece., Pilalis E; Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.; e-NIOS Applications PC, Kallithea 17671, Greece., Papadodima O; Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece., Roman D; SINTEF AS, Oslo 0373, Norway.; Bucharest University of Economic Studies, Bucharest 010374, Romania.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Oct 02; Vol. 41 (10).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Metadata* , Software* , Programming Languages* , Genomics*/methods , Information Storage and Retrieval*/methods , Computational Biology*/methods, Databases, Genetic ; High-Throughput Nucleotide Sequencing

A FHIR-Powered Python Implementation of the SENECA Algorithm for Sepsis Subtyping.

Authors: King AJ; University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States., Horvat CM; University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States., Schlessinger D; Kaiser Permanente LLC, Research and Evaluation, Oakland, California, United States., Hochheiser H; University of Pittsburgh School of Medicine, Biomedical Informatics, Pittsburgh, Pennsylvania, United States., Bui KV; University of Pittsburgh School of Medicine, Biomedical Informatics, Pittsburgh, Pennsylvania, United States., Kennedy JN; University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States., Brant EB; University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States., Shalaby J; Elimu Informatics, El Cerrito, California, United States., Angus DC; University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States., Liu VX; Kaiser Permanente LLC, Research and Evaluation, Oakland, California, United States., Seymour CW; University of Pittsburgh School of Medicine, Critical Care Medicine, Pittsburgh, Pennsylvania, United States.

Source: Applied clinical informatics [Appl Clin Inform] 2025 Oct; Vol. 16 (5), pp. 1588-1594. Date of Electronic Publication: 2025 Nov 07.

Publication Type: Journal Article

Journal Info: Publisher: Thieme Country of Publication: Germany NLM ID: 101537732 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1869-0327 (Electronic) Linking ISSN: 18690327 NLM ISO Abbreviation: Appl Clin Inform Subsets: MEDLINE

MeSH Terms: Sepsis*/classification , Sepsis*/diagnosis , Algorithms* , Health Information Interoperability* , Programming Languages*, Humans ; Electronic Health Records ; Data Warehousing

Evaluating Medium Scale, Open-Source Large Language Models: Towards Decision Support in a Precision Oncology Care Delivery Context.

Authors: Kaufmes K; MOLIT Institute, Heilbronn, Germany., Mathes G; MOLIT Institute, Heilbronn, Germany., Vladimirova D; SLK Clinics, Heilbronn, Germany., Berger S; SLK Clinics, Heilbronn, Germany., Fegeler C; MOLIT Institute, Heilbronn, Germany.; University of Heilbronn, Heilbronn, Germany., Sigle S; MOLIT Institute, Heilbronn, Germany.

Source: Studies in health technology and informatics [Stud Health Technol Inform] 2025 Sep 03; Vol. 331, pp. 81-90.

Publication Type: Journal Article

Journal Info: Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9214582 Publication Model: Print Cited Medium: Internet ISSN: 1879-8365 (Electronic) Linking ISSN: 09269630 NLM ISO Abbreviation: Stud Health Technol Inform Subsets: MEDLINE

MeSH Terms: Precision Medicine*/methods , Medical Oncology*/methods , Decision Support Systems, Clinical*/organization & administration , Programming Languages* , Neoplasms*/therapy , Neoplasms*/diagnosis, Humans ; Large Language Models

Biomedical Information Integration via Adaptive Large Language Model Construction.

Authors: Xue X, Wu ME, Khan F

Source: IEEE journal of biomedical and health informatics [IEEE J Biomed Health Inform] 2025 Sep; Vol. 29 (9), pp. 6381-6394.

Publication Type: Journal Article

Journal Info: Publisher: Institute of Electrical and Electronics Engineers Country of Publication: United States NLM ID: 101604520 Publication Model: Print Cited Medium: Internet ISSN: 2168-2208 (Electronic) Linking ISSN: 21682194 NLM ISO Abbreviation: IEEE J Biomed Health Inform Subsets: MEDLINE

MeSH Terms: Medical Informatics*/methods , Programming Languages*, Humans ; Algorithms ; Databases, Factual ; Large Language Models

Discovering subnetworks in SBML models.

Authors: Hellerstein JL; eScience Institute, University of Washington, Seattle, WA, 98195, United States.; Paul G. Allen School of Computer Science, University of Washington, Seattle, WA, 98195, United States.; Department of Bioengineering, University of Washington, Seattle, WA, 98195, United States., Smith LP; Paul G. Allen School of Computer Science, University of Washington, Seattle, WA, 98195, United States., Tatka LT; Talus Bioscience, Seattle, WA, 98122, United States., Andrews SS; Department of Bioengineering, University of Washington, Seattle, WA, 98195, United States., Kochen MA; Software Applications and Technology, Rocky Mountain Division, Applied Research Associates, Inc, Bentonville, AR, 72212, United States., Sauro HM; eScience Institute, University of Washington, Seattle, WA, 98195, United States.; Department of Bioengineering, University of Washington, Seattle, WA, 98195, United States.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Sep 01; Vol. 41 (9).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Systems Biology*/methods , Software* , Programming Languages* , Models, Biological*, Algorithms

A LLM-Based Hybrid-Transformer Diagnosis System in Healthcare.

Authors: Wu D, Nie L, Mumtaz RA, Agarwal K

Source: IEEE journal of biomedical and health informatics [IEEE J Biomed Health Inform] 2025 Sep; Vol. 29 (9), pp. 6428-6439.

Publication Type: Journal Article

Journal Info: Publisher: Institute of Electrical and Electronics Engineers Country of Publication: United States NLM ID: 101604520 Publication Model: Print Cited Medium: Internet ISSN: 2168-2208 (Electronic) Linking ISSN: 21682194 NLM ISO Abbreviation: IEEE J Biomed Health Inform Subsets: MEDLINE

MeSH Terms: Image Interpretation, Computer-Assisted*/methods , Neural Networks, Computer* , Programming Languages*, Humans ; Algorithms

Benchmarking large language models for genomic knowledge with GeneTuring.

Authors: Shang X; Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States., Liao X; Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States., Ji Z; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, 2424 Erwin Road, Durham, NC 27705, United States., Hou W; Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States.; Data Science Institute, Columbia University, 550 West 120th Street, New York, NY 10027, United States.

Source: Briefings in bioinformatics [Brief Bioinform] 2025 Aug 31; Vol. 26 (5).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Genomics*/methods , Benchmarking* , Software* , Programming Languages* , Computational Biology*/methods, Humans ; Large Language Models

Evaluation of Arden Syntax v3.0 to Represent Population-Level Clinical Decision Support Knowledge in Electronic Clinical Quality Measures.

Authors: Jenders RA; Charles Drew University & University of California, Los Angeles, California USA.

Source: Studies in health technology and informatics [Stud Health Technol Inform] 2025 Aug 07; Vol. 329, pp. 1564-1565.

Publication Type: Journal Article

Journal Info: Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9214582 Publication Model: Print Cited Medium: Internet ISSN: 1879-8365 (Electronic) Linking ISSN: 09269630 NLM ISO Abbreviation: Stud Health Technol Inform Subsets: MEDLINE

MeSH Terms: Decision Support Systems, Clinical*/standards , Electronic Health Records*/standards , Quality Assurance, Health Care*/standards , Natural Language Processing* , Programming Languages* , Vocabulary, Controlled*, Humans