NITRC: BRAIN Initiative - Cell Census Network (BICCN): PubMed Mentions: Display Document

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.

Publication/References
The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Description: Ecker, Joseph R, et al. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. ''Neuron''. 2017 Nov 1; '''96''' (3):542-557
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Description: Preissl, Sebastian, et al. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. ''Nat Neurosci''. 2018 Mar; '''21''' (3):432-439
Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons. Description: Chatterjee, Soumya, et al. Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons. ''Nat Neurosci''. 2018 Apr; '''21''' (4):638-646
Genetic Dissection of Neural Circuits: A Decade of Progress. Description: Luo, Liqun, et al. Genetic Dissection of Neural Circuits: A Decade of Progress. ''Neuron''. 2018 May 16; '''98''' (4):865
Genetic approaches to access cell types in mammalian nervous systems. Description: He, Miao, et al. Genetic approaches to access cell types in mammalian nervous systems. ''Curr Opin Neurobiol''. 2018 Jun; '''50''': 109-118
Mesoscale connectomics. Description: Zeng, Hongkui. Mesoscale connectomics. ''Curr Opin Neurobiol''. 2018 Jun; '''50''': 154-162
cAMP-inducible coactivator CRTC3 attenuates brown adipose tissue thermogenesis. Description: Yoon, Young-Sil, et al. cAMP-inducible coactivator CRTC3 attenuates brown adipose tissue thermogenesis. ''Proc Natl Acad Sci U S A''. 2018 Jun 5; '''115''' (23):E5289-E5297
clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. Description: Risso, Davide, et al. clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. ''PLoS Comput Biol''. 2018 Sep; '''14''' (9):e1006378
Robust single-cell DNA methylome profiling with snmC-seq2. Description: Luo, Chongyuan, et al. Robust single-cell DNA methylome profiling with snmC-seq2. ''Nat Commun''. 2018 Sep 20; '''9''' (1):3824
Dynamic DNA methylation: In the right place at the right time. Description: Luo, Chongyuan, et al. Dynamic DNA methylation: In the right place at the right time. ''Science''. 2018 Sep 28; '''361''' (6409):1336-1340
Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq). Description: Paul, Anirban, et al. Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq). ''J Vis Exp''. 2018 Oct 26;
Integration of gene expression and brain-wide connectivity reveals the multiscale organization of mouse hippocampal networks. Description: Bienkowski, Michael S, et al. Integration of gene expression and brain-wide connectivity reveals the multiscale organization of mouse hippocampal networks. ''Nat Neurosci''. 2018 Nov; '''21''' (11):1628-1643
Shared and distinct transcriptomic cell types across neocortical areas. Description: Tasic, Bosiljka, et al. Shared and distinct transcriptomic cell types across neocortical areas. ''Nature''. 2018 Nov; '''563''' (7729):72-78
On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model. Description: Lee, Brian C, et al. On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model. ''PLoS Comput Biol''. 2018 Dec; '''14''' (12):e1006610
Deterministic column subset selection for single-cell RNA-Seq. Description: McCurdy, Shannon R, et al. Deterministic column subset selection for single-cell RNA-Seq. ''PLoS One''. 2019; '''14''' (1):e0210571
ESTIMATING DIFFEOMORPHIC MAPPINGS BETWEEN TEMPLATES AND NOISY DATA: VARIANCE BOUNDS ON THE ESTIMATED CANONICAL VOLUME FORM. Description: Tward, Daniel J, et al. ESTIMATING DIFFEOMORPHIC MAPPINGS BETWEEN TEMPLATES AND NOISY DATA: VARIANCE BOUNDS ON THE ESTIMATED CANONICAL VOLUME FORM. ''Q Appl Math''. 2019; '''77''': 467-488
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
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Description: Schiebinger, Geoffrey, et al. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. ''Cell''. 2019 Mar 7; '''176''' (6):1517
Complementary networks of cortical somatostatin interneurons enforce layer specific control. Description: Naka, Alexander, et al. Complementary networks of cortical somatostatin interneurons enforce layer specific control. ''Elife''. 2019 Mar 18; '''8''':
An active texture-based digital atlas enables automated mapping of structures and markers across brains. Description: Chen, Yuncong, et al. An active texture-based digital atlas enables automated mapping of structures and markers across brains. ''Nat Methods''. 2019 Apr; '''16''' (4):341-350
Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Description: Cole, Michael B, et al. Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. ''Cell Syst''. 2019 Apr 24; '''8''' (4):315-328.e8
Extrastriate connectivity of the mouse dorsal lateral geniculate thalamic nucleus. Description: Bienkowski, Michael S, et al. Extrastriate connectivity of the mouse dorsal lateral geniculate thalamic nucleus. ''J Comp Neurol''. 2019 May 15; '''527''' (9):1419-1442
Perspectives on defining cell types in the brain. Description: Mukamel, Eran A, et al. Perspectives on defining cell types in the brain. ''Curr Opin Neurobiol''. 2019 Jun; '''56''': 61-68
Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity. Description: Welch, Joshua D, et al. Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity. ''Cell''. 2019 Jun 13; '''177''' (7):1873-1887.e17
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Description: Gaublomme, Jellert T, et al. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. ''Nat Commun''. 2019 Jul 2; '''10''' (1):2907
Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging. Description: Li, Anan, et al. Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging. ''Genomics Proteomics Bioinformatics''. 2019 Aug; '''17''' (4):337-343
TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain. Description: Wang, Yimin, et al. TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain. ''Nat Commun''. 2019 Aug 2; '''10''' (1):3474
The diversity of GABAergic neurons and neural communication elements. Description: Huang, Z Josh, et al. The diversity of GABAergic neurons and neural communication elements. ''Nat Rev Neurosci''. 2019 Sep; '''20''' (9):563-572
The Visual Cortex in Context. Description: Froudarakis, Emmanouil, et al. The Visual Cortex in Context. ''Annu Rev Vis Sci''. 2019 Sep 15; '''5''': 317-339
High-definition spatial transcriptomics for in situ tissue profiling. Description: Vickovic, Sanja, et al. High-definition spatial transcriptomics for in situ tissue profiling. ''Nat Methods''. 2019 Oct; '''16''' (10):987-990
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Description: Lee, Dong-Sung, et al. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. ''Nat Methods''. 2019 Oct; '''16''' (10):999-1006
Turning the Tide of Data Sharing. Description: Ascoli, Giorgio A. Turning the Tide of Data Sharing. ''Neuroinformatics''. 2019 Oct; '''17''' (4):473-474
Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior. Description: Kim, Dong-Wook, et al. Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior. ''Cell''. 2019 Oct 17; '''179''' (3):713-728.e17
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Description: Zhu, Chenxu, et al. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. ''Nat Struct Mol Biol''. 2019 Nov; '''26''' (11):1063-1070
Hierarchical organization of cortical and thalamic connectivity. Description: Harris, Julie A, et al. Hierarchical organization of cortical and thalamic connectivity. ''Nature''. 2019 Nov; '''575''' (7781):195-202
Enhanced and unified anatomical labeling for a common mouse brain atlas. Description: Chon, Uree, et al. Enhanced and unified anatomical labeling for a common mouse brain atlas. ''Nat Commun''. 2019 Nov 7; '''10''' (1):5067
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks. Description: Smith, Stephen J, et al. Single-cell transcriptomic evidence for dense intracortical neuropeptide networks. ''Elife''. 2019 Nov 11; '''8''':
Monosynaptic tracing: a step-by-step protocol. Description: Lavin, Thomas K, et al. Monosynaptic tracing: a step-by-step protocol. ''J Chem Neuroanat''. 2019 Dec; '''102''': 101661
Fast analysis of scATAC-seq data using a predefined set of genomic regions. Description: Giansanti, Valentina, et al. Fast analysis of scATAC-seq data using a predefined set of genomic regions. ''F1000Res''. 2020; '''9''': 199
Heavy-tailed kernels reveal a finer cluster structure in t-SNE visualisations. Description: Kobak, Dmitry, et al. Heavy-tailed kernels reveal a finer cluster structure in t-SNE visualisations. ''Mach Learn Knowl Discov Databases''. 2020; '''11906''': 124-139
Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics. Description: Gorin, Gennady, et al. Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics. ''PLoS One''. 2020; '''15''' (3):e0230736
The Spatial and Cell-Type Distribution of SARS-CoV-2 Receptor ACE2 in the Human and Mouse Brains. Description: Chen, Rongrong, et al. The Spatial and Cell-Type Distribution of SARS-CoV-2 Receptor ACE2 in the Human and Mouse Brains. ''Front Neurol''. 2020; '''11''': 573095
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. Description: Schafflick, David, et al. Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. ''Nat Commun''. 2020 Jan 14; '''11''' (1):247
Droplet scRNA-seq is not zero-inflated. Description: Svensson, Valentine. Droplet scRNA-seq is not zero-inflated. ''Nat Biotechnol''. 2020 Feb; '''38''' (2):147-150
Protein velocity and acceleration from single-cell multiomics experiments. Description: Gorin, Gennady, et al. Protein velocity and acceleration from single-cell multiomics experiments. ''Genome Biol''. 2020 Feb 18; '''21''' (1):39
Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex. Description: Cadwell, Cathryn R, et al. Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex. ''Elife''. 2020 Mar 5; '''9''':
Trajectory-based differential expression analysis for single-cell sequencing data. Description: Van den Berge, Koen, et al. Trajectory-based differential expression analysis for single-cell sequencing data. ''Nat Commun''. 2020 Mar 5; '''11''' (1):1201
Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients. Description: Rydbirk, Rasmus, et al. Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients. ''Acta Neuropathol Commun''. 2020 Mar 9; '''8''' (1):29
Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. Description: Bucur, Octavian, et al. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. ''Nat Protoc''. 2020 May; '''15''' (5):1649-1672
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
Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis. Description: Ding, Song-Lin, et al. Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis. ''Cell Rep''. 2020 May 19; '''31''' (7):107648
Disease-associated astrocytes in Alzheimer's disease and aging. Description: Habib, Naomi, et al. Disease-associated astrocytes in Alzheimer's disease and aging. ''Nat Neurosci''. 2020 Jun; '''23''' (6):701-706
Expansion Microscopy for Beginners: Visualizing Microtubules in Expanded Cultured HeLa Cells. Description: Zhang, Chi, et al. Expansion Microscopy for Beginners: Visualizing Microtubules in Expanded Cultured HeLa Cells. ''Curr Protoc Neurosci''. 2020 Jun; '''92''' (1):e96
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Description: Ding, Jiarui, et al. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. ''Nat Biotechnol''. 2020 Jun; '''38''' (6):737-746
BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. Description: Huang, Longwen, et al. BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. ''Cell''. 2020 Jul 9; '''182''' (1):177-188.e27
A Systematic Evaluation of Interneuron Morphology Representations for Cell Type Discrimination. Description: Laturnus, Sophie, et al. A Systematic Evaluation of Interneuron Morphology Representations for Cell Type Discrimination. ''Neuroinformatics''. 2020 Oct; '''18''' (4):591-609
Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice. Description: Veldman, Matthew B, et al. Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice. ''Neuron''. 2020 Oct 14; '''108''' (1):111-127.e6
Jointly defining cell types from multiple single-cell datasets using LIGER. Description: Liu, Jialin, et al. Jointly defining cell types from multiple single-cell datasets using LIGER. ''Nat Protoc''. 2020 Nov; '''15''' (11):3632-3662
A curated database reveals trends in single-cell transcriptomics. Description: Svensson, Valentine, et al. A curated database reveals trends in single-cell transcriptomics. ''Database (Oxford)''. 2020 Nov 28; '''2020''':
A community-based transcriptomics classification and nomenclature of neocortical cell types. Description: Yuste, Rafael, et al. A community-based transcriptomics classification and nomenclature of neocortical cell types. ''Nat Neurosci''. 2020 Dec; '''23''' (12):1456-1468
The cellular basis of distinct thirst modalities. Description: Pool, Allan-Hermann, et al. The cellular basis of distinct thirst modalities. ''Nature''. 2020 Dec; '''588''' (7836):112-117
Neuron class-specific responses govern adaptive myelin remodeling in the neocortex. Description: Yang, Sung Min, et al. Neuron class-specific responses govern adaptive myelin remodeling in the neocortex. ''Science''. 2020 Dec 18; '''370''' (6523):
Common cell type nomenclature for the mammalian brain. Description: Miller, Jeremy A, et al. Common cell type nomenclature for the mammalian brain. ''Elife''. 2020 Dec 29; '''9''':
mbkmeans: Fast clustering for single cell data using mini-batch k-means. Description: Hicks, Stephanie C, et al. mbkmeans: Fast clustering for single cell data using mini-batch k-means. ''PLoS Comput Biol''. 2021 Jan; '''17''' (1):e1008625
Neuronal classification from network connectivity via adjacency spectral embedding. Description: Mehta, Ketan, et al. Neuronal classification from network connectivity via adjacency spectral embedding. ''Netw Neurosci''. 2021; '''5''' (3):689-710
Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. Description: Rapti, Georgia. Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. ''Front Neurosci''. 2021; '''15''': 787753
Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. Description: Xu, Chenling, et al. Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. ''Mol Syst Biol''. 2021 Jan; '''17''' (1):e9620
Spatially resolved transcriptomics in neuroscience. Description: Close, Jennie L, et al. Spatially resolved transcriptomics in neuroscience. ''Nat Methods''. 2021 Jan; '''18''' (1):23-25
PACAP is a pathogen-inducible resident antimicrobial neuropeptide affording rapid and contextual molecular host defense of the brain. Description: Lee, Ernest Y, et al. PACAP is a pathogen-inducible resident antimicrobial neuropeptide affording rapid and contextual molecular host defense of the brain. ''Proc Natl Acad Sci U S A''. 2021 Jan 5; '''118''' (1):
Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Description: Alon, Shahar, et al. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. ''Science''. 2021 Jan 29; '''371''' (6528):
Initialization is critical for preserving global data structure in both t-SNE and UMAP. Description: Kobak, Dmitry, et al. Initialization is critical for preserving global data structure in both t-SNE and UMAP. ''Nat Biotechnol''. 2021 Feb; '''39''' (2):156-157
Multimodal cross-registration and quantification of metric distortions in marmoset whole brain histology using diffeomorphic mappings. Description: Lee, Brian C, et al. Multimodal cross-registration and quantification of metric distortions in marmoset whole brain histology using diffeomorphic mappings. ''J Comp Neurol''. 2021 Feb; '''529''' (2):281-295
Reply to: UMI or not UMI, that is the question for scRNA-seq zero-inflation. Description: Svensson, Valentine. Reply to: UMI or not UMI, that is the question for scRNA-seq zero-inflation. ''Nat Biotechnol''. 2021 Feb; '''39''' (2):160
Patch-seq: Past, Present, and Future. Description: Lipovsek, Marcela, et al. Patch-seq: Past, Present, and Future. ''J Neurosci''. 2021 Feb 3; '''41''' (5):937-946
Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Description: Fang, Rongxin, et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. ''Nat Commun''. 2021 Feb 26; '''12''' (1):1337
In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Description: Payne, Andrew C, et al. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. ''Science''. 2021 Feb 26; '''371''' (6532):
BARcode DEmixing through Non-negative Spatial Regression (BarDensr). Description: Chen, Shuonan, et al. BARcode DEmixing through Non-negative Spatial Regression (BarDensr). ''PLoS Comput Biol''. 2021 Mar; '''17''' (3):e1008256
Joint probabilistic modeling of single-cell multi-omic data with totalVI. Description: Gayoso, Adam, et al. Joint probabilistic modeling of single-cell multi-omic data with totalVI. ''Nat Methods''. 2021 Mar; '''18''' (3):272-282
Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Description: Zhu, Chenxu, et al. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. ''Nat Methods''. 2021 Mar; '''18''' (3):283-292
*Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x).** Description: Booeshaghi, A Sina, et al. Normalization of single-cell RNA-seq counts by log(x + 1)* or log(1 + x). ''Bioinformatics''. 2021 Mar 2;
Alternating sources of perisomatic inhibition during behavior. Description: Dudok, Barna, et al. Alternating sources of perisomatic inhibition during behavior. ''Neuron''. 2021 Mar 17; '''109''' (6):997-1012.e9
Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Description: Eze, Ugomma C, et al. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. ''Nat Neurosci''. 2021 Apr; '''24''' (4):584-594
Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces. Description: Ding, Jiarui, et al. Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces. ''Nat Commun''. 2021 May 5; '''12''' (1):2554
Connectivity characterization of the mouse basolateral amygdalar complex. Description: Hintiryan, Houri, et al. Connectivity characterization of the mouse basolateral amygdalar complex. ''Nat Commun''. 2021 May 17; '''12''' (1):2859
Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Description: Sun, Yu-Chi, et al. Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. ''Nat Neurosci''. 2021 Jun; '''24''' (6):873-885
Control of impulsivity by Gi-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex. Description: van der Veen, Bastiaan, et al. Control of impulsivity by Gi-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex. ''Commun Biol''. 2021 Jun 2; '''4''' (1):662
The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic. Description: Karlinsky, Ariel, et al. The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic. ''medRxiv''. 2021 Jun 4;
BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq. Description: Gustafsson, Johan, et al. BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq. ''Genome Biol''. 2021 Jun 8; '''22''' (1):174
Neural basis of opioid-induced respiratory depression and its rescue. Description: Liu, Shijia, et al. Neural basis of opioid-induced respiratory depression and its rescue. ''Proc Natl Acad Sci U S A''. 2021 Jun 8; '''118''' (23):
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Description: Yao, Zizhen, et al. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. ''Cell''. 2021 Jun 10; '''184''' (12):3222-3241.e26
Organization of the inputs and outputs of the mouse superior colliculus. Description: Benavidez, Nora L, et al. Organization of the inputs and outputs of the mouse superior colliculus. ''Nat Commun''. 2021 Jun 28; '''12''' (1):4004
Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset. Description: Karlinsky, Ariel, et al. Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset. ''Elife''. 2021 Jun 30; '''10''':
Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. Description: Lu, Shaina, et al. Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. ''PLoS Biol''. 2021 Jul; '''19''' (7):e3001341
Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Description: Melsted, Pall, et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. ''Nat Biotechnol''. 2021 Jul; '''39''' (7):813-818
Molecular logic of cellular diversification in the mouse cerebral cortex. Description: Di Bella, Daniela J, et al. Molecular logic of cellular diversification in the mouse cerebral cortex. ''Nature''. 2021 Jul; '''595''' (7868):554-559
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Description: Harris, Benjamin D, et al. Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. ''Cell Syst''. 2021 Jul 21; '''12''' (7):748-756.e3
CloudReg: automatic terabyte-scale cross-modal brain volume registration. Description: Chandrashekhar, Vikram, et al. CloudReg: automatic terabyte-scale cross-modal brain volume registration. ''Nat Methods''. 2021 Aug; '''18''' (8):845-846
Compressed sensing for highly efficient imaging transcriptomics. Description: Cleary, Brian, et al. Compressed sensing for highly efficient imaging transcriptomics. ''Nat Biotechnol''. 2021 Aug; '''39''' (8):936-942
Iterative single-cell multi-omic integration using online learning. Description: Gao, Chao, et al. Iterative single-cell multi-omic integration using online learning. ''Nat Biotechnol''. 2021 Aug; '''39''' (8):1000-1007
Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Description: Fischer, Stephan, et al. Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. ''Nat Protoc''. 2021 Aug; '''16''' (8):4031-4067
Metabolic modeling of single Th17 cells reveals regulators of autoimmunity. Description: Wagner, Allon, et al. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity. ''Cell''. 2021 Aug 5; '''184''' (16):4168-4185.e21
Evaluating single-cell cluster stability using the Jaccard similarity index. Description: Tang, Ming, et al. Evaluating single-cell cluster stability using the Jaccard similarity index. ''Bioinformatics''. 2021 Aug 9; '''37''' (15):2212-2214
Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data. Description: Lause, Jan, et al. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data. ''Genome Biol''. 2021 Sep 6; '''22''' (1):258
A multimodal cell census and atlas of the mammalian primary motor cortex. Description: A multimodal cell census and atlas of the mammalian primary motor cortex. ''Nature''. 2021 Oct; '''598''' (7879):86-102
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
An atlas of gene regulatory elements in adult mouse cerebrum. Description: Li, Yang Eric, et al. An atlas of gene regulatory elements in adult mouse cerebrum. ''Nature''. 2021 Oct; '''598''' (7879):129-136
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Description: Yao, Zizhen, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. ''Nature''. 2021 Oct; '''598''' (7879):103-110
A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types. Description: Kozareva, Velina, et al. A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types. ''Nature''. 2021 Oct; '''598''' (7879):214-219
Cellular anatomy of the mouse primary motor cortex. Description: Munoz-Castaneda, Rodrigo, et al. Cellular anatomy of the mouse primary motor cortex. ''Nature''. 2021 Oct; '''598''' (7879):159-166
Comparative cellular analysis of motor cortex in human, marmoset and mouse. Description: Bakken, Trygve E, et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. ''Nature''. 2021 Oct; '''598''' (7879):111-119
DNA methylation atlas of the mouse brain at single-cell resolution. Description: Liu, Hanqing, et al. DNA methylation atlas of the mouse brain at single-cell resolution. ''Nature''. 2021 Oct; '''598''' (7879):120-128
Epigenomic diversity of cortical projection neurons in the mouse brain. Description: Zhang, Zhuzhu, et al. Epigenomic diversity of cortical projection neurons in the mouse brain. ''Nature''. 2021 Oct; '''598''' (7879):167-173
Farewell, Neuroinformatics! Description: Ascoli, Giorgio A, et al. Farewell, Neuroinformatics! ''Neuroinformatics''. 2021 Oct; '''19''' (4):551-552
Genetic dissection of the glutamatergic neuron system in cerebral cortex. Description: Matho, Katherine S, et al. Genetic dissection of the glutamatergic neuron system in cerebral cortex. ''Nature''. 2021 Oct; '''598''' (7879):182-187
Isoform cell-type specificity in the mouse primary motor cortex. Description: Booeshaghi, A Sina, et al. Isoform cell-type specificity in the mouse primary motor cortex. ''Nature''. 2021 Oct; '''598''' (7879):195-199
Morphological diversity of single neurons in molecularly defined cell types. Description: Peng, Hanchuan, et al. Morphological diversity of single neurons in molecularly defined cell types. ''Nature''. 2021 Oct; '''598''' (7879):174-181
Phenotypic variation of transcriptomic cell types in mouse motor cortex. Description: Scala, Federico, et al. Phenotypic variation of transcriptomic cell types in mouse motor cortex. ''Nature''. 2021 Oct; '''598''' (7879):144-150
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH. Description: Zhang, Meng, et al. Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH. ''Nature''. 2021 Oct; '''598''' (7879):137-143
The mouse cortico-basal ganglia-thalamic network. Description: Foster, Nicholas N, et al. The mouse cortico-basal ganglia-thalamic network. ''Nature''. 2021 Oct; '''598''' (7879):188-194
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
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Description: Biancalani, Tommaso, et al. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. ''Nat Methods''. 2021 Nov; '''18''' (11):1352-1362
Visuomotor control in mice and primates. Description: Tehovnik, E J, et al. Visuomotor control in mice and primates. ''Neurosci Biobehav Rev''. 2021 Nov; '''130''': 185-200
How many markers are needed to robustly determine a cell's type? Description: Fischer, Stephan, et al. How many markers are needed to robustly determine a cell's type? ''iScience''. 2021 Nov 19; '''24''' (11):103292
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Decoding molecular and cellular heterogeneity of mouse nucleus accumbens. Description: Chen, Renchao, et al. Decoding molecular and cellular heterogeneity of mouse nucleus accumbens. ''Nat Neurosci''. 2021 Dec; '''24''' (12):1757-1771
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Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. Description: Jiang, Shengdian, et al. Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. ''Neuroinformatics''. 2022 Feb 19;
Systems-based approaches to study immunometabolism. Description: Purohit, Vinee, et al. Systems-based approaches to study immunometabolism. ''Cell Mol Immunol''. 2022 Mar; '''19''' (3):409-420
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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):
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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
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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
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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
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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):
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