Nature Search

Holistic evaluation of large language models for medical tasks with MedHELM

MedHELM, an extensible evaluation framework including a new taxonomy for classifying medical tasks and a benchmark of many datasets across these categories, enables the evaluation of large language models on real-world clinical tasks.

Suhana Bedi
Hejie Cui
Nigam H. Shah
Research20 Jan 2026
Nature Medicine

P: 1-9
Author Correction: Preferential inhibition of adaptive immune system dynamics by glucocorticoids in patients after acute surgical trauma

Edward A. Ganio
Natalie Stanley
Brice Gaudilliere
Amendments and CorrectionsOpen Access03 Sept 2020
Nature Communications

Volume: 11, P: 1
Erratum: Critical assessment of automated flow cytometry data analysis techniques

Nima Aghaeepour
Greg Finak
Richard H Scheuermann
Amendments and Corrections29 Apr 2013
Nature Methods

Volume: 10, P: 445
Correction: Corrigendum: Critical assessment of automated flow cytometry data analysis techniques

Nima Aghaeepour
Greg Finak
Richard H Scheuermann
Amendments and Corrections29 Apr 2013
Nature Methods

Volume: 10, P: 445
Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature

The authors present a deep learning method that deconvolutes ATAC-seq samples into cell type-specific chromatin accessibility profiles. Applied on 191 samples, the method unveils cell type-specific pathways and nominates potential epigenetic mediators underlying resilience to Alzheimer’s disease.

Eloise Berson
Anjali Sreenivas
Thomas J. Montine
ResearchOpen Access16 Aug 2023
Nature Communications

Volume: 14, P: 1-11
VoPo leverages cellular heterogeneity for predictive modeling of single-cell data

Single-cell technologies are increasingly prominent in clinical applications, but predictive modelling with such data in large cohorts has remained computationally challenging. We developed a new algorithm, ‘VoPo’, for predictive modelling and visualization of single cell data for translational applications.

Natalie Stanley
Ina A. Stelzer
Nima Aghaeepour
ResearchOpen Access27 Jul 2020
Nature Communications

Volume: 11, P: 1-9
Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions

Recent advances have increased the dimensionality and complexity of immunological data. The authors developed a machine learning approach to incorporate prior immunological knowledge and applied it on clinical examples and a simulation study. The approach may be useful for high-dimensional datasets in clinical settings where the cohort size is limited.

Anthony Culos
Amy S. Tsai
Nima Aghaeepour
Research12 Oct 2020
Nature Machine Intelligence

Volume: 2, P: 619-628
Preferential inhibition of adaptive immune system dynamics by glucocorticoids in patients after acute surgical trauma

Glucocorticoids (GC) are commonly used to suppress undesirable inflammatory responses. Here the authors show, using hi-dimensional flow cytometry data, that GC treatment following major surgeries alters adaptive immunity without significant modulation of innate immune responses or pain/functional impairment.

Edward A. Ganio
Natalie Stanley
Brice Gaudilliere
ResearchOpen Access27 Jul 2020
Nature Communications

Volume: 11, P: 1-12
Omics approaches: interactions at the maternal–fetal interface and origins of child health and disease

Maide Ozen
Nima Aghaeepour
Lauren L. Jantzie
Reviews10 Oct 2022
Pediatric Research

Volume: 93, P: 366-375
Unlocking human immune system complexity through AI

Advancements in artificial intelligence (AI) have led to unprecedented success in modeling technically challenging domains including language, audio, image and video understanding. Here we discuss the opportunities represented by recent AI methods to advance immunology research.

Eloise Berson
Philip Chung
Nima Aghaeepour
Comments & Opinion09 Aug 2024
Nature Methods

Volume: 21, P: 1400-1402
Author Correction: AI-guided precision parenteral nutrition for neonatal intensive care units

Thanaphong Phongpreecha
Marc Ghanem
Nima Aghaeepour
Amendments and CorrectionsOpen Access09 Apr 2025
Nature Medicine

Volume: 31, P: 2070
A machine learning approach to leveraging electronic health records for enhanced omics analysis

COMET, an artificial intelligence method that improves the analysis of small medical studies using large clinical databases, has been created. COMET can help develop better artificial intelligence tools and identify key biomarkers across many diseases, potentially changing medical research.

Samson J. Mataraso
Camilo A. Espinosa
Nima Aghaeepour
ResearchOpen Access16 Jan 2025
Nature Machine Intelligence

Volume: 7, P: 293-306
Author Correction: A machine learning approach to leveraging electronic health records for enhanced omics analysis

Samson J. Mataraso
Camilo A. Espinosa
Nima Aghaeepour
Amendments and CorrectionsOpen Access18 Mar 2025
Nature Machine Intelligence

Volume: 7, P: 673
AI-guided precision parenteral nutrition for neonatal intensive care units

An artificial intelligence model defines a data-driven set of total parenteral nutrition compositions to assist clinicians in personalized treatment of neonates in intensive care and is able to adapt recommendations to patient status, with validation from large external cohorts and a blinded reader study.

Thanaphong Phongpreecha
Marc Ghanem
Nima Aghaeepour
ResearchOpen Access25 Mar 2025
Nature Medicine

Volume: 31, P: 1882-1894
AI learning for pediatric right ventricular assessment: development and validation across multiple centers

Charitha Reddy
Yi Yan
Xuefeng B. Ling
ResearchOpen Access09 Dec 2025
npj Digital Medicine

Volume: 8, P: 1-8
Changes in preterm birth and stillbirth during COVID-19 lockdowns in 26 countries

An analysis of 52 million births in 26 countries shows small reductions in preterm birth during the first to third months of lockdown. Further research is needed to examine causal pathways.

Clara Calvert
Meredith (Merilee) Brockway
Meghan B. Azad
ResearchOpen Access27 Feb 2023
Nature Human Behaviour

Volume: 7, P: 529-544
Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

Greg Finak
Marc Langweiler
J Philip McCoy
ResearchOpen Access10 Feb 2016
Scientific Reports

Volume: 6, P: 1-11
Discovery of sparse, reliable omic biomarkers with Stabl

Stabl selects sparse and reliable biomarker candidates from predictive models.

Julien Hédou
Ivana Marić
Brice Gaudillière
ResearchOpen Access02 Jan 2024
Nature Biotechnology

Volume: 42, P: 1581-1593
Author Correction: Early response evaluation by single cell signaling profiling in acute myeloid leukemia

Benedicte Sjo Tislevoll
Monica Hellesøy
Bjørn Tore Gjertsen
Amendments and CorrectionsOpen Access30 Mar 2023
Nature Communications

Volume: 14, P: 1
Early response evaluation by single cell signaling profiling in acute myeloid leukemia

The molecular mechanisms underlying response to chemotherapy in Acute myeloid leukemia (AML) remain to be explored. Here, the authors perform 36-dimensional mass cytometry in 32 AML patients during intensive chemotherapy and suggest functional signalling analysis for prognosis prediction early after treatment in AML.

Benedicte Sjo Tislevoll
Monica Hellesøy
Bjørn Tore Gjertsen
ResearchOpen Access07 Jan 2023
Nature Communications

Volume: 14, P: 1-17
Early prediction of mortality and morbidities in VLBW preterm neonates using machine learning

Chi-Hung Shu
Rema Zebda
Mohan Pammi
Research08 Oct 2024
Pediatric Research

Volume: 97, P: 2056-2064
Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse

Mass cytometry of diagnostic biopsies from children with B cell precursor acute lymphoblastic leukemia identifies a signaling state that predicts relapse.

Zinaida Good
Jolanda Sarno
Kara L Davis
Research05 Mar 2018
Nature Medicine

Volume: 24, P: 474-483
Leveraging electronic health records from two hospital systems identifies male infertility-associated comorbidities across time

Woldemariam et al. identify male infertility associated comorbidities using electronic health records (EHR) from the University of California. Findings, which are validated in Stanford University’s EHR, include hypothyroidism and anemia.

Sarah R. Woldemariam
Feng Xie
Marina Sirota
ResearchOpen Access01 Sept 2025
Communications Medicine

Volume: 5, P: 1-19
Leveraging electronic health records and knowledge networks for Alzheimer’s disease prediction and sex-specific biological insights

Identifying individuals at risk of developing Alzheimer’s disease is an important task. Here Tang et al. leverage electronic health records to predict Alzheimer’s disease onset, and utilize knowledge networks to prioritize shared genes behind the clinical data as well as facilitate contextualization based on sex.

Alice S. Tang
Katherine P. Rankin
Marina Sirota
ResearchOpen Access21 Feb 2024
Nature Aging

Volume: 4, P: 379-395
Large-scale correlation network construction for unraveling the coordination of complex biological systems

An approach, CorALS, is proposed to enable the construction and analysis of large-scale correlation networks for high-dimensional biological data as an open-source framework in Python.

Martin Becker
Huda Nassar
Nima Aghaeepour
ResearchOpen Access13 Apr 2023
Nature Computational Science

Volume: 3, P: 346-359
Correction: Digital health application integrating wearable data and behavioral patterns improves metabolic health

Ashkan Dehghani Zahedani
Tracey McLaughlin
Michael Snyder
Amendments and CorrectionsOpen Access12 Jan 2024
npj Digital Medicine

Volume: 7, P: 1
Reassessing acquired neonatal intestinal diseases using unsupervised machine learning

Daniel R. Gipson
Alan L. Chang
Josef Neu
Research27 Feb 2024
Pediatric Research

Volume: 96, P: 165-171
Parkinson’s disease is characterized by vitamin B6-dependent inflammatory kynurenine pathway dysfunction

Edward N. Wilson
Jacob Umans
Katrin I. Andreasson
ResearchOpen Access26 Apr 2025
npj Parkinson's Disease

Volume: 11, P: 1-13
Single-cell analysis identifies a CD33⁺ subset of human cord blood cells with high regenerative potential

Knapp et al. analyse the heterogeneous molecular profiles and functions of CD49f human cord blood haematopoietic stem cells and report that a subset with CD33 expression has improved regenerative activity.

David J. H. F. Knapp
Colin A. Hammond
Connie J. Eaves
Research25 May 2018
Nature Cell Biology

Volume: 20, P: 710-720
Towards a new taxonomy of preterm birth

David K. Stevenson
Alan L. Chang
Ivana Marić
ReviewsOpen Access20 Nov 2024
Journal of Perinatology

Volume: 45, P: 1158-1162
Impact of digital health interventions on glycemic control and weight management

Arvind Veluvali
Ashkan Dehghani Zahedani
Michael P. Snyder
ResearchOpen Access09 Jan 2025
npj Digital Medicine

Volume: 8, P: 1-11
Transgenerational associations between newborn metabolic profiles and bronchopulmonary dysplasia in neonates born to mothers with an obese phenotype

Jonathan D. Reiss
Wei Yang
Gary M. Shaw
ResearchOpen Access07 Jan 2025
Scientific Reports

Volume: 15, P: 1-10
Prediction of late-onset preeclampsia using plasma proteomics: a longitudinal multi-cohort study

Ina J. Andresen
Manuela Zucknick
Trond M. Michelsen
ResearchOpen Access28 Dec 2024
Scientific Reports

Volume: 14, P: 1-19
Critical assessment of automated flow cytometry data analysis techniques

In this analysis, the authors directly compared the performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information of practical utility about the performance of the algorithms as applied to different data sets and challenges.

Nima Aghaeepour
Greg Finak
Richard H Scheuermann
ResearchOpen Access10 Feb 2013
Nature Methods

Volume: 10, P: 228-238
Discovery and validation of biomarkers to aid the development of safe and effective pain therapeutics: challenges and opportunities

In 2018, the Discovery and Validation of Biomarkers to Develop Non-Addictive Therapeutics for Pain workshop convened to discuss strategies to facilitate the development of biomarkers and end points for pain. The outcomes of this workshop are outlined in this Consensus Statement.

Karen D. Davis
Nima Aghaeepour
Mary Ann Pelleymounter
Reviews15 Jun 2020
Nature Reviews Neurology

Volume: 16, P: 381-400
Multimodal machine learning for modeling infant head circumference, mothers’ milk composition, and their shared environment

Martin Becker
Kelsey Fehr
Meghan B. Azad
ResearchOpen Access05 Feb 2024
Scientific Reports

Volume: 14, P: 1-18
Newborn screen metabolic panels reflect the impact of common disorders of pregnancy

Jonathan D. Reiss
Alan L. Chang
Karl G. Sylvester
Research20 Oct 2021
Pediatric Research

Volume: 92, P: 490-497
Digital health application integrating wearable data and behavioral patterns improves metabolic health

Ashkan Dehghani Zahedani
Tracey McLaughlin
Michael Snyder
ResearchOpen Access25 Nov 2023
npj Digital Medicine

Volume: 6, P: 1-15
Deep representation learning identifies associations between physical activity and sleep patterns during pregnancy and prematurity

Neal G. Ravindra
Camilo Espinosa
Nima Aghaeepour
ResearchOpen Access28 Sept 2023
npj Digital Medicine

Volume: 6, P: 1-16
Cross-species comparative analysis of single presynapses

Eloïse Berson
Chandresh R. Gajera
Thomas J. Montine
ResearchOpen Access24 Aug 2023
Scientific Reports

Volume: 13, P: 1-12
Advancing neonatal health: the promise and challenges of universal genome sequencing in newborn screening

David K. Stevenson
Ronald J. Wong
Ivana Marić
Comments & Opinion20 Jan 2025
Pediatric Research

Volume: 97, P: 1258-1260
Prediction of gestational age using urinary metabolites in term and preterm pregnancies

Kévin Contrepois
Songjie Chen
Michael P. Snyder
ResearchOpen Access16 May 2022
Scientific Reports

Volume: 12, P: 1-11
Risk assessment analysis for maternal autoantibody-related autism (MAR-ASD): a subtype of autism

Alexandra Ramirez-Celis
Martin Becker
Judy Van de Water
ResearchOpen Access22 Jan 2021
Molecular Psychiatry

Volume: 26, P: 1551-1560
Multivariate prediction of dementia in Parkinson’s disease

Thanaphong Phongpreecha
Brenna Cholerton
Thomas J. Montine
ResearchOpen Access25 Aug 2020
npj Parkinson's Disease

Volume: 6, P: 1-10
Author Correction: Prediction of gestational age using urinary metabolites in term and preterm pregnancies

Kévin Contrepois
Songjie Chen
Michael P. Snyder
Amendments and CorrectionsOpen Access17 Nov 2022
Scientific Reports

Volume: 12, P: 1
Black swans and ambitious overgeneralization in newborn intensive care

David K. Stevenson
Ronald J. Wong
Michael Katz
Comments & Opinion02 Oct 2021
Pediatric Research

Volume: 92, P: 357-359
Understanding health disparities

David K. Stevenson
Ronald J. Wong
Paul H. Wise
Comments & Opinion18 Dec 2018
Journal of Perinatology

Volume: 39, P: 354-358
Multiomics, artificial intelligence, and precision medicine in perinatology

Mohan Pammi
Nima Aghaeepour
Josef Neu
Reviews08 Jul 2022
Pediatric Research

Volume: 93, P: 308-315
Towards personalized medicine in maternal and child health: integrating biologic and social determinants

David K. Stevenson
Ronald J. Wong
Michael Katz
Comments & Opinion26 May 2020
Pediatric Research

Volume: 89, P: 252-258

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