PubMed Mentions
The links below are to publications on PubMed referring to BRAIN Initiative - Cell Census Network (BICCN). This list is gathered weekly from PubMed automatically and was last updated on December 17, 2025.
| Publication/References | |
| Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. Description: Puchades, Maja A, et al. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. ''PLoS One''. 2019; '''14''' (5):e0216796 | |
| Turning the Tide of Data Sharing. Description: Ascoli, Giorgio A. Turning the Tide of Data Sharing. ''Neuroinformatics''. 2019 Oct; '''17''' (4):473-474 | |
| The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Description: Wang, Quanxin, et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. ''Cell''. 2020 May 14; '''181''' (4):936-953.e20 | |
| An atlas of cortical arealization identifies dynamic molecular signatures. Description: Bhaduri, Aparna, et al. An atlas of cortical arealization identifies dynamic molecular signatures. ''Nature''. 2021 Oct; '''598''' (7879):200-204 | |
| Graded heterogeneity of metabotropic signaling underlies a continuum of cell-intrinsic temporal responses in unipolar brush cells. Description: Guo, Chong, et al. Graded heterogeneity of metabotropic signaling underlies a continuum of cell-intrinsic temporal responses in unipolar brush cells. ''Nat Commun''. 2021 Oct 7; '''12''' (1):5491 | |
| HypoMap-a unified single-cell gene expression atlas of the murine hypothalamus. Description: Steuernagel, Lukas, et al. HypoMap-a unified single-cell gene expression atlas of the murine hypothalamus. ''Nat Metab''. 2022 Oct; '''4''' (10):1402-1419 | |
| Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. Description: Shen, Rongbo, et al. Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. ''Nat Commun''. 2022 Dec 10; '''13''' (1):7640 | |
| The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. Description: Ament, Seth A, et al. The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. ''Nucleic Acids Res''. 2023 Jan 6; '''51''' (D1):D1075-D1085 | |
| Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. Description: Kawaguchi, Risa Karakida, et al. Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. ''Brief Bioinform''. 2023 Jan 19; '''24''' (1): | |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. Description: Moore, Josh, et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. ''bioRxiv''. 2023 Feb 25; | |
| A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Description: Yao, Zizhen, et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. ''bioRxiv''. 2023 Mar 6; | |
| A molecularly defined and spatially resolved cell atlas of the whole mouse brain. Description: Zhang, Meng, et al. A molecularly defined and spatially resolved cell atlas of the whole mouse brain. ''bioRxiv''. 2023 Mar 7; | |
| A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. Description: Zeighami, Yashar, et al. A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. ''PLoS Biol''. 2023 Apr; '''21''' (4):e3002058 | |
| A guide to the BRAIN Initiative Cell Census Network data ecosystem. Description: Hawrylycz, Michael, et al. A guide to the BRAIN Initiative Cell Census Network data ecosystem. ''PLoS Biol''. 2023 Jun; '''21''' (6):e3002133 | |
| BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets. Description: Manubens-Gil, Linus, et al. BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets. ''Nat Methods''. 2023 Jun; '''20''' (6):824-835 | |
| AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. Description: Kleven, Heidi, et al. AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. ''Sci Data''. 2023 Jul 26; '''10''' (1):486 | |
| Model-based compound hypothesis testing for snATAC-seq data with PACS. Description: Miao, Zhen, et al. Model-based compound hypothesis testing for snATAC-seq data with PACS. ''bioRxiv''. 2023 Jul 31; | |
| Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. Description: Kalhor, Kian, et al. Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. ''bioRxiv''. 2023 Aug 19; | |
| Spatiotemporal molecular dynamics of the developing human thalamus. Description: Kim, Chang N, et al. Spatiotemporal molecular dynamics of the developing human thalamus. ''bioRxiv''. 2023 Aug 22; | |
| Harnessing computational spatial omics to explore the spatial biology intricacies. Description: Yuan, Zhiyuan, et al. Harnessing computational spatial omics to explore the spatial biology intricacies. ''Semin Cancer Biol''. 2023 Oct; '''95''': 25-41 | |
| A cellular resolution atlas of Broca's area. Description: Costantini, Irene, et al. A cellular resolution atlas of Broca's area. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eadg3844 | |
| A comparative atlas of single-cell chromatin accessibility in the human brain. Description: Li, Yang Eric, et al. A comparative atlas of single-cell chromatin accessibility in the human brain. ''Science''. 2023 Oct 13; '''382''' (6667):eadf7044 | |
| A family portrait of human brain cells. Description: Weninger, Alyssa, et al. A family portrait of human brain cells. ''Science''. 2023 Oct 13; '''382''' (6667):168-169 | |
| A marmoset brain cell census reveals regional specialization of cellular identities. Description: Krienen, Fenna M, et al. A marmoset brain cell census reveals regional specialization of cellular identities. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eadk3986 | |
| A quest into the human brain. Description: Maroso, Mattia. A quest into the human brain. ''Science''. 2023 Oct 13; '''382''' (6667):166-167 | |
| A single-cell multi-omic atlas spanning the adult rhesus macaque brain. Description: Chiou, Kenneth L, et al. A single-cell multi-omic atlas spanning the adult rhesus macaque brain. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eadh1914 | |
| Comparative transcriptomics reveals human-specific cortical features. Description: Jorstad, Nikolas L, et al. Comparative transcriptomics reveals human-specific cortical features. ''Science''. 2023 Oct 13; '''382''' (6667):eade9516 | |
| Comprehensive cell atlas of the first-trimester developing human brain. Description: Braun, Emelie, et al. Comprehensive cell atlas of the first-trimester developing human brain. ''Science''. 2023 Oct 13; '''382''' (6667):eadf1226 | |
| Diversity of primate brain cells unraveled. Description: Komiyama, Takaki. Diversity of primate brain cells unraveled. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eadl0650 | |
| Human voltage-gated Na(+) and K(+) channel properties underlie sustained fast AP signaling. Description: Wilbers, Rene, et al. Human voltage-gated Na(+) and K(+) channel properties underlie sustained fast AP signaling. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eade3300 | |
| Interindividual variation in human cortical cell type abundance and expression. Description: Johansen, Nelson, et al. Interindividual variation in human cortical cell type abundance and expression. ''Science''. 2023 Oct 13; '''382''' (6667):eadf2359 | |
| Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. Description: Micali, Nicola, et al. Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. ''Science''. 2023 Oct 13; '''382''' (6667):eadf3786 | |
| Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex. Description: Chartrand, Thomas, et al. Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex. ''Science''. 2023 Oct 13; '''382''' (6667):eadf0805 | |
| Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Description: Zhu, Kaiyi, et al. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eadg3754 | |
| Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex. Description: Lee, Brian R, et al. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex. ''Science''. 2023 Oct 13; '''382''' (6667):eadf6484 | |
| Single-cell analysis of prenatal and postnatal human cortical development. Description: Velmeshev, Dmitry, et al. Single-cell analysis of prenatal and postnatal human cortical development. ''Science''. 2023 Oct 13; '''382''' (6667):eadf0834 | |
| Single-cell DNA methylation and 3D genome architecture in the human brain. Description: Tian, Wei, et al. Single-cell DNA methylation and 3D genome architecture in the human brain. ''Science''. 2023 Oct 13; '''382''' (6667):eadf5357 | |
| Structural and functional specializations of human fast-spiking neurons support fast cortical signaling. Description: Wilbers, Rene, et al. Structural and functional specializations of human fast-spiking neurons support fast cortical signaling. ''Sci Adv''. 2023 Oct 13; '''9''' (41):eadf0708 | |
| Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Description: Jorstad, Nikolas L, et al. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. ''Science''. 2023 Oct 13; '''382''' (6667):eadf6812 | |
| Transcriptomic diversity of cell types across the adult human brain. Description: Siletti, Kimberly, et al. Transcriptomic diversity of cell types across the adult human brain. ''Science''. 2023 Oct 13; '''382''' (6667):eadd7046 | |
| A single-cell genomic atlas for maturation of the human cerebellum during early childhood. Description: Ament, Seth A, et al. A single-cell genomic atlas for maturation of the human cerebellum during early childhood. ''Sci Transl Med''. 2023 Nov 8; '''15''' (721):eade1283 | |
| Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus. Description: Herb, Brian R, et al. Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus. ''Sci Adv''. 2023 Nov 10; '''9''' (45):eadf6251 | |
| Molecularly defined and spatially resolved cell atlas of the whole mouse brain. Description: Zhang, Meng, et al. Molecularly defined and spatially resolved cell atlas of the whole mouse brain. ''Nature''. 2023 Dec; '''624''' (7991):343-354 | |
| Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs. Description: Carraro, Caterina, et al. Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs. ''Front Mol Neurosci''. 2024; '''17''': 1414886 | |
| The Brain Image Library: A Community-Contributed Microscopy Resource for Neuroscientists. Description: Kenney, Mariah, et al. The Brain Image Library: A Community-Contributed Microscopy Resource for Neuroscientists. ''bioRxiv''. 2024 Jan 10; | |
| Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections. Description: Stouffer, Kaitlin M, et al. Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections. ''Nat Commun''. 2024 Apr 25; '''15''' (1):3530 | |
| CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations. Description: Hu, Zhirui, et al. CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations. ''bioRxiv''. 2024 May 17; | |
| Improving replicability in single-cell RNA-Seq cell type discovery with Dune. Description: Roux de Bezieux, Hector, et al. Improving replicability in single-cell RNA-Seq cell type discovery with Dune. ''BMC Bioinformatics''. 2024 May 24; '''25''' (1):198 | |
| Single-cell and spatial alterations of neural cells and circuits in clinical and translational medicine. Description: Wang, William, et al. Single-cell and spatial alterations of neural cells and circuits in clinical and translational medicine. ''Clin Transl Med''. 2024 Jun; '''14''' (6):e1696 | |
| Integrated platform for multiscale molecular imaging and phenotyping of the human brain. Description: Park, Juhyuk, et al. Integrated platform for multiscale molecular imaging and phenotyping of the human brain. ''Science''. 2024 Jun 14; '''384''' (6701):eadh9979 | |
| A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping. Description: Dong, Pengfei, et al. A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping. ''Nat Commun''. 2024 Nov 22; '''15''' (1):10113 | |
| Neuronal diversity and stereotypy at multiple scales through whole brain morphometry. Description: Liu, Yufeng, et al. Neuronal diversity and stereotypy at multiple scales through whole brain morphometry. ''Nat Commun''. 2024 Nov 26; '''15''' (1):10269 | |
| The BRAIN Initiative data-sharing ecosystem: Characteristics, challenges, benefits, and opportunities. Description: Iyer, Sudhanvan, et al. The BRAIN Initiative data-sharing ecosystem: Characteristics, challenges, benefits, and opportunities. ''Elife''. 2024 Nov 27; '''13''': | |
| PCA-based spatial domain identification with state-of-the-art performance. Description: Schaub, Darius P, et al. PCA-based spatial domain identification with state-of-the-art performance. ''Bioinformatics''. 2024 Dec 26; '''41''' (1): | |
| xIV-LDDMM Toolkit: A Suite of Image-Varifold Based Technologies for Representing and Mapping 3D Imaging and Spatial-omics Data Simultaneously Across Scales. Description: Stouffer, Kaitlin M, et al. xIV-LDDMM Toolkit: A Suite of Image-Varifold Based Technologies for Representing and Mapping 3D Imaging and Spatial-omics Data Simultaneously Across Scales. ''bioRxiv''. 2025 Jun 14; | |
| CellWalker2: Multi-omic discovery using hierarchical cell type relationships. Description: Hu, Zhirui, et al. CellWalker2: Multi-omic discovery using hierarchical cell type relationships. ''Cell Genom''. 2025 Jul 9; '''5''' (7):100886 | |
| Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus. Description: Traunmuller, Lisa, et al. Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus. ''Nat Commun''. 2025 Aug 21; '''16''' (1):7787 | |
| The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales. Description: Stouffer, Kaitlin M, et al. The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales. ''Commun Biol''. 2025 Sep 30; '''8''' (1):1401 | |
| Making genomic data FAIR through effective Data Portals. Description: Speir, Matthew L, et al. Making genomic data FAIR through effective Data Portals. ''Sci Data''. 2025 Nov 28; '''12''' (1):1872 |