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1

STHELAR, a multi-tissue dataset linking spatial transcriptomics and histology for cell type annotation
Giraud-Sauveur, Félicie ; Blampey, Quentin ; Benkirane, Hakim ; et al.

Cell type annotation Tumor micro environment Computer vision Cancer Spatial Transcriptomics Whole slide images …
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2

Cell-free genome-wide transcriptomics through machine learning optimization
Wagner, Léa ; Hoang, An ; Rue, Olivier ; et al.
SEED 2025, Jun 2025, Houston, United States

Houston, United States Cell-free Escherichia coli Phage T7 Active learning Machine learning …
Konferenz
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3

jsPCA: fast, scalable, and interpretable identification of spatial domains and variable genes across multi-slice and multi-sample spatial transcriptomics data
Assali, Ines ; Escande, Paul ; Villoutreix, Paul ; et al.

Spatial transcriptomics... Spatial transcriptomics Spatial statistics Machine learning Spatial Domains Spatially Variable Genes …
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4

adverSCarial: a toolkit for exposing classifier vulnerabilities in single-cell transcriptomics
Fievet, Ghislain ; Broséus, Julien ; Meyre, David ; et al.
ISMB/ECCB2025, Jul 2025, Liverpool, United Kingdom

Liverpool, United Kingdo... Single-cell transcriptom... XAI Explainable AI scRNA-seq single-cell RN... ML Machine Learning R Bioconductor …
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5

RNA2seg: a generalist model for cell segmentation in image-based spatial transcriptomics
Defard, Thomas ; Blondel, Alice ; Bellow, Sebastien ; et al.

Spatial Transcriptomics... Spatial Transcriptomics Cell Segmentation Deep Learning [INFO.INFO-CV]Computer S... Computer Vision and Patt... …
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6

A strategy for multimodal integration of transcriptomics, proteomics, and radiomics data for the prediction of recurrence in patients with IDH-mutant gliomas
Chouleur, Tiffanie ; Etchegaray, Christèle ; Villain, Laura ; et al.
International Journal of Cancer. 157(3):573-587

IDH‐Mutant Glioma Multimodal Integration Proteomic Radiomic Transcriptomic [SDV.CAN]Life Sciences [... …
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7

Metabolomics and Transcriptomics Analyses Reveal the Mechanisms of Sulforaphane Conversion and Adaptive Strategies in the Absence of Glucose by Lactiplantibacillus plantarum
Wang, Yunping ; Wang, Lintai ; Luo, Liping ; et al.
Journal of Agricultural and Food Chemistry. 73(50):31906-31917

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8

Prospective, international, multisite comparison of platelet isolation techniques for genome-wide transcriptomics: communication from the SSC of the ISTH
Banerjee, Meenakshi ; Rowley, Jesse ; Stubben, Chris ; et al.
Journal of Thrombosis and Haemostasis. 22(10):2922-2934

leukocytes next-generation RNA-seq platelets platelet transcriptomics [SDV]Life Sciences [q-bi...
Zeitschrift
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9

Integrating AI and Transcriptomics to Identify Biomarkers of Pesticide Exposure
Rojas-Velazquez, David ; Lopez-Rincon, Alejandro ; Div. Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University ; et al.
FIGON Dutch Medicine Days DMD, Oct 2025, Leiden, Netherlands

Leiden, Netherlands [INFO]Computer Science [...
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10

Integrated spatial and multimodal single‐cell transcriptomics reveal patient‐dependent cell heterogeneity in splenic marginal zone lymphoma
Cerapio, Juan, Pablo ; Gravelle, Pauline ; Quillet‐mary, Anne ; et al.
Journal of Pathology. 263(4-5):442-453

multimodal omics single-cell RNA-sequenci... spatial transcriptomics lymphoma microenvironment [SDV]Life Sciences [q-bi...
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11

Identification of the Cytokines, Growth Factors and Their Receptors Expressed by Human Blood Eosinophils: A Transcriptomics Approach
Esnault, Stéphane ; Delaunay, Emeline ; Dendooven, Arnaud ; et al.
Clinical and Experimental Allergy, 2025, Clinical and Experimental Allergy, ⟨10.1111/cea.70115⟩

transcriptomics surface receptors segmental bronchoprovoca... growth factors eosinophils cytokines …
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12

Liver Lipidomics, Histology, Transcriptomics, and Clinical Chemistry of Rats Intraperitoneally Treated with Fumonisin B1 for 5 days
Szabó, András ; Péter, Mária ; Balogh, Gábor ; et al.
Journal of Agricultural and Food Chemistry. 73(39):24975-24996

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13

Transcriptomics and Neuropeptidomics of the Cockroach Rhyparobia maderae to Characterize the Neuropeptide Landscape of the Cockroach’s Circadian Clock
Neupert, Susanne ; Shoaib, Sohail H. ; Schendzielorz, Julia ; et al.
Journal of Proteome Research. 24(11):5370-5389

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14

Spatial transcriptomics iterative hierarchical clustering (stIHC): A novel method for identifying spatial gene co‐expression modules
Higgins, Catherine ; Li, Jingyi Jessica ; Carey, Michelle
Quantitative Biology. 13(4)

31 Biological Sciences (... 3102 Bioinformatics and... 3105 Genetics (for-2020) Genetics (rcdc) Biotechnology (rcdc) Human Genome (rcdc) …
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15

Transcriptomics-Driven Engineering of Yarrowia lipolytica for Enhanced Fatty Acid Biosynthesis
Qiao, He ; Dong, Zaihang ; Yu, Bofan ; et al.
ACS Synthetic Biology. 14(9):3520-3529

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16

Single cell transcriptomics and development of gametocyte-specific molecular markers for avian malaria parasites
Berthomieu, A ; Gandon, Sylvain ; Talman, Am ; et al.

[SDV.MP.PAR]Life Science... Microbiology and Parasit... Parasitology [SDV.BA.MVSA]Life Scienc... Animal biology Veterinary medicine and... …
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17

Advances in the application of spatial transcriptomics in understanding development and disease
Li, Yao ; Zheng, Qian-Wen ; Li, Mingpeng ; et al.
Molecular and Cellular Biochemistry: An International Journal for Chemical Biology in Health and Disease. :1-16

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18

Integrative transcriptomics defines CD36 as a key regulator of immunometabolic signaling in acute myeloid leukemia
Ashaq, Muhammad Sameer ; Zhou, Qian ; Li, Yanxia ; et al.
Genes & Genomics. :1-21

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19

Harnessing transcriptomics for discovery of natural products to overcome acquired cancer resistance
Yeo, Heerim ; Kim, Sang-Yun ; Park, Sang-Min
Archives of Pharmacal Research. :1-29

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20

Optimization of an Escherichia coli lysate-based cell-free system for genome-wide transcriptomics
Optimisation d'un système cell-free à base de lysat d'Escherichia coli pour des approches de transcriptomique à l'échelle du génome
Wagner, Léa ; MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) ; et al.
Génomique, Transcriptomique et Protéomique [q-bio.GN]. Université Paris-Saclay, 2025. Français. ⟨NNT : 2025UPASL129⟩

Direct RNA sequencing Transcriptomics Machine learning T7 Phage Escherichia coli Cell-Free …
Dissertation
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