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Initial sequencing and analysis of the human genome

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The sequence of the human genome

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Initial sequencing and comparative analysis of the mouse genome

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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

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RefSeq and LocusLink: NCBI gene-centered resources

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Single-Cell Transcriptional Analysis of Neuronal Progenitors

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MGD: the Mouse Genome Database

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An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature

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A transcriptome atlas of the mouse brain at cellular resolution

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Generation of a Nr2f2- driven inducible Cre mouse to target interstitial cells in the reproductive system

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The AERO System: A 3D-Like Approach for Recording Gene Expression Patterns in the Whole Mouse Embryo

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Analyses of binding partners and functional domains for the developmentally essential protein Hmx3a/HMX3

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Epigenetic signature of very low birth weight in young adult life

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Biologically Relevant Laminin-511 Moderates the Derivation and Proliferation of Human Lens Epithelial Stem/Progenitor-Like Cells

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Identification and Characterization of a Novel Gene, dapr, Involved in Skeletal Muscle Differentiation and Protein Kinase B Signaling

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Smad4 controls proliferation of interstitial cells in the neonatal kidney

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Generation of a biotinylatable Sox2 mouse model to identify Sox2 complexes in vivo

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Characterization of the Regulatory Region of the Dopa Decarboxylase Gene in Medaka: An in vivo Green Fluorescent Protein Reporter Assay Combined with a Simple TA-Cloning Method

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Guest Editors’ Introduction

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Coronary vessel assembly involves patterned endocardial sprouting and tip-cell-to artery specificationPreprint

Cano, E., Paech, J., Kanda, M., Lindberg, E. L., Hollfinger, I., Braeuning, C., Fischer, C., Hübner, N., & Gerhardt, H. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.20.517740 · Cited by 5

Neurodevelopmental effects of exposure to environmentally relevant concentrations of perfluorooctane sulfonic acid (PFOS), perfluorobutanesulfonic acid (PFBS) and 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA) on larval zebrafish: Multi-omics and neuropathology perspective

Cao, X., Li, Y., Liu, X., Li, K., Hong, S., Chen, H., Rao, Q., Li, H., Deng, Z., & Song, W. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.138744 · Cited by 4

Shared Lineage, Distinct Outcomes: Yap and Taz Loss Differentially Impact Schwann and Olfactory Ensheathing Cell Development Without Disrupting GnRH ‐1 Migration

Taroc, E. Z. M., Amato, E., Semon, A. M., Dolphin, N. M., Beck, B., Belin, S., Poitelon, Y., & Forni, P. E. (2025) · Glia · doi:10.1002/glia.70057 · Cited by 4

The mouse Gene Expression Database (GXD): 2026 update

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Ribosomal S6 kinase signaling regulates neuronal viability during development and confers resistance to excitotoxic cell death in mature neurons

Hoyt, K. R., Horning, P., Ang, P. G., Karelina, K., & Obrietan, K. H. (2024) · Neuroscience · doi:10.1016/j.neuroscience.2024.08.012 · Cited by 4

VSTM2A reverses immunosuppression in colorectal cancer by antagonizing the PD-L1/PD-1 interaction

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The trabecular and compact myocardium of adult vertebrate ventricles are transcriptionally similar despite morphological differences

Mulleners, O. J., van der Maarel, L. E., Christoffels, V. M., & Jensen, B. (2025) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15296 · Cited by 4

Molecular profiling of the vestibular lamina highlights a key role for Hedgehog signalling

Qiu, T., Hutečková, B., Seppala, M., Cobourne, M. T., Chen, Z., Hovořáková, M., Buchtová, M., & Tucker, A. S. (2023) · Development · doi:10.1242/dev.201464 · Cited by 4

Transcriptome Profile of the Rat Adrenal Gland: Parenchymal and Interstitial Cells

Tyczewska, M., Sujka‐Kordowska, P., Szyszka, M., Jopek, K., Blatkiewicz, M., Malendowicz, L. K., & Ruciński, M. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24119159 · Cited by 4

A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 ocular retardation J mice

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The methylmalonic aciduria related genes, Mmaa, Mmab, and Mut, are broadly expressed in placental and embryonic tissues during mouse organogenesis

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aGEM: an integrative system for analyzing spatial-temporal gene-expression information

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Large-Scale Whole Mount In Situ Hybridization of Mouse Embryos

Shimizu, H., Uchibe, K., & Asahara, H. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-232-2_13 · Cited by 4

Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case

McClelland, K. S., & Yao, H. H. (2017) · Sexual Development · doi:10.1159/000455113 · Cited by 4

Analysis of low‐correlated spatial gene expression patterns: a clustering approach in the mouse brain data hosted in the Allen Brain Atlas

Rosati, P., Lupaşcu, C. A., & Tegolo, D. (2018) · IET Computer Vision · doi:10.1049/iet-cvi.2018.5217 · Cited by 4

Gene‐targeted deletion in mice of the Ets−1 transcription factor, a candidate gene in the Jacobsen syndrome kidney “critical region,” causes abnormal kidney development

Ye, M., Xu, L., Fu, M., Chen, D., Mattina, T., Zuffardi, O., Rossi, E. G., Bush, K. T., Nigám, S. K., & Grossfeld, P. (2018) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.40481 · Cited by 4

Accumulation of α-2,6-sialyoglycoproteins in the muscle sarcoplasm due to Trichinella sp. invasion

Milcheva, R. S., Janega, P., Celec, P., Petkova, S. L., Hurníková, Z., Izrael-Vlková, B., Todorova, K. S., & Babál, P. (2019) · Open Life Sciences · doi:10.1515/biol-2019-0053 · Cited by 4

Lumican regulates cervical corticospinal axon collateralization via non-autonomous crosstalk between distinct corticospinal neuron subpopulationsPreprint

Itoh, Y., Sahni, V., Shnider, S. J., & Macklis, J. D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.26.437104 · Cited by 4

Six3 and Six6 jointly control diverse target genes in multiple cell populations over developmental trajectories of mouse embryonic retinal progenitor cells

Ferrena, A., Zhang, X., Shrestha, R., Zheng, D., & Liu, W. (2024) · PLoS ONE · doi:10.1371/journal.pone.0308839 · Cited by 3

The MuSK Receptor Family

Burden, S. J., Hubbard, S. R., Zhang, W., & Yumoto, N. (2015) · Springer eBooks · doi:10.1007/978-3-319-11888-8_9 · Cited by 4

Runx2-interacting genes identified by yeast two-hybrid screening of libraries generated from hypertrophic chondrocytes.

Li, F., Mi, R., Fan, C., Zhang, P., Zhu, T., Wang, Q., Lu, Y., Gu, J., & Zheng, Q. (2016) · PubMed Central · Cited by 3

Of Molecules and Mechanisms

Benson, D. L. (2019) · Journal of Neuroscience · doi:10.1523/jneurosci.0743-19.2019 · Cited by 3

Primer on FGF3

Hutchings, C., & Sela‐Donenfeld, D. (2023) · Differentiation · doi:10.1016/j.diff.2023.09.003 · Cited by 3

Altered GABAA receptor expression as biomarker of mercury toxicity in embryonic neurogenesis

Ayensu, W. K., Isokpehi, R. D., Cohly, H., Murray, J. M., Webb, D. J., & Tchounwou, P. B. (2009) · ORNL Biomedical Science & Engineering Conference (BSEC) · doi:10.1109/bsec.2009.5090491 · Cited by 3

Exome sequencing revealed USP9X and COL2A1 mutations in a large family with multiple epiphyseal dysplasia

Luo, Z.-J., Li, H., Yang, L., Kang, B., & Cai, T. (2022) · Bone · doi:10.1016/j.bone.2022.116508 · Cited by 3

Characterization of interstitial heterogeneity in the developing kidneyPreprint

England, A. R., Chaney, C. P., Das, A., Patel, M., Malewsak, A., Armendariz, D. A., Hon, G. C., Strand, D. W., Drake, K. A., & Carroll, T. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.02.973966 · Cited by 3

Illuminating the Terminal Nerve: Uncovering the Link between GnRH-1 and Olfactory DevelopmentPreprint

Amato, E., Taroc, E. Z. M., & Forni, P. E. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.31.555770 · Cited by 3

Orthologs of Drosophila pointed and Arginine kinase 1 impact sleep in mice

Harbison, S. T., Peiravi, M., Zhang, F., Yimam, S., Noguchi, A. C., & Springer, D. (2024) · SLEEP Advances · doi:10.1093/sleepadvances/zpae092 · Cited by 2

IFITM2 Modulates Endocytosis Maintaining Neural Stem Cells in Developing Neocortex

Lv, Y., Zou, W., Li, L., Zhang, S., Liang, J., Pu, J., & Jiao, J. (2025) · Advanced Science · doi:10.1002/advs.202501593 · Cited by 2

Suppression of miR‐148a‐3p Can Promote Bone Healing by Enhancing Angiogenesis‐Osteogenesis Coupling Through the PI3K/Akt Pathway

Li, X., Rong, K., Huang, Y., Zhao, Z., Xu, C., Li, L., Zhang, Y., Yan, Y., Huang, W., Zhang, Y., et al. (2025) · The FASEB Journal · doi:10.1096/fj.202500432r · Cited by 2

Pathogenic XPO1 variants cause a dominant neurodevelopmental disorder

van Oirsouw, A. S. E., Nedbalová, P., Hančárová, M., Prchal, J., Prchalová, D., Vlčková, M., Bendová, Š., Monaghan, K. G., Dyer, L. M., Chen, Y., et al. (2025) · Genetics in Medicine · doi:10.1016/j.gim.2025.101555 · Cited by 2

Bcl11a deficiency in cerebellar Purkinje cells causes ataxia and autistic-like behavior by altering Vav3

Zhang, J., Li, Y.-X., Huang, Q., Yuan, Y., Chen, J.-Y., Yang, F.-W., Yang, L., Liu, L., & Yu, Y. (2025) · Molecular Psychiatry · doi:10.1038/s41380-025-03175-x · Cited by 3

A compendium of expression patterns of cholesterol biosynthetic enzymes in the mouse embryo

Şişecioğlu, M., Budak, H., Geffers, L., Çankaya, M., Çiftçi, M., Christina Thaller, B., Gregor Eichele, C., Küfrevioğlu, Ö. İ., & Özdemіr, H. (2015) · Journal of Lipid Research · doi:10.1194/jlr.m059634 · Cited by 2

Out of Line or Altered States? Neural Progenitors as a Target in a Polygenic Neurodevelopmental Disorder

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Gastric hypoplasia in mice lacking fibroblast growth factor 9

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Developmental expression patterns of protein kinase A catalytic subunits in zebrafish

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Optimization of In Situ Hybridization and Co-expression Analysis in the Central Nervous System

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Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain

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Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain

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Was the tail bud the ancestral centre where the fin developmental program evolved in chordates?

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Manual and Automated Whole-Mount In Situ Hybridization for Systematic Gene Expression Analysis in Embryonic Zebrafish Forebrain

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Regulatory Functions of Pax1 and Pax9 in Mammalian Cells

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A Genome-Wide Association Study (GWAS) for Bronchopulmonary Dysplasia

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Development of an in-vitro high-throughput screening system to identify modulators of genitalia development

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Current Needs for New Therapeutic Agents and Discovery Strategies—A Systems Pharmacology Approach

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Correction: Rare Copy Number Variants Contribute to Congenital Left-Sided Heart Disease

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Reduced Dietary Protein Induces Changes in the Dental Proteome

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Generating Diversity and Specificity through Developmental Cell Signaling

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The Genetics of Cryptorchidism

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Deimination in Ocular Tissues: Present and Future

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Gabor Features for the Classification and Evaluation of Chromogenic In-Situ Hybridization Images

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High-Throughput In Situ Hybridization: Systematical Production of Gene Expression Data and Beyond

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Utilizing Autoencoders for Analysis and Classification of Microscopic in Situ Hybridization Images

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Current State of In Situ Gene Expression Studies in Animal Tissues

Bytov, M. V., Zubareva, V. D., Volskaya, S. V., Khatsko, S. L., Shkuratova, I. A., & Sokolova, O. V. (2024) · Russian Journal of Genetics · doi:10.1134/s1022795424010046 · Cited by 1

Human Adapted Prosomeric Model: A Future for Brainstem Tumor Classification

Gualán, A. P. M., Güngör, A., Cezayirli, P. C., Rahmanov, S., Gurses, M. E., Puelles, L., & Türe, U. (2024) · Brain Research · doi:10.1016/j.brainres.2024.148961 · Cited by 1

Clustering of low-correlated spatial gene expression patterns in the mouse brain in the Allen Brain Atlas

Rosati, P., Lupaşcu, C. A., & Tegolo, D. (2018) · International Conference on Computing and Network Communications · doi:10.1109/coconet.2018.8476886 · Cited by 1

Gene Regulatory Programs in the Development of Hypothalamic Arcuate Nucleus Neurons

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Visualization of image data from cells to

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Csmd2 interacts with Dab1 and is Required in Reelin-Mediated Neuronal MaturationPreprint

Gutierrez, M. A., Dwyer, B. E., & Franco, S. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.30.925537 · Cited by 1

“Integration of multimodal data in the developing tooth reveals candidate dental disease genes”Preprint

Winchester, E. W., Hardy, A., & Cotney, J. L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.15.483501 · Cited by 1

Targeted H3K9 acetylation at lncSox1 promoter by cell type-specific epigenome editing promotes intermediate progenitor proliferation in developing mouse cortexPreprint

Sokpor, G., Ulmke, P. A., Nguyen, H. D., Pham, L., Kakani, P., Chu, V. T., Arnold, S. J., Brand‐Saberi, B., Nguyen, H. P., & Tuoc, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.05.621758 · Cited by 1

Transcript Profiling Tools

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Functional analysis of transcription factor mScrt2 in cortical neurogenesis

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Growing Up POMC: Pro-opiomelanocortin in the Developing Brain

Padilla, S. L. (2011) · doi:10.7916/d80g3s3v

SURVEY AND SUMMARY More than a decade of developmental gene expression atlases: where are we now?

de Boer, B. A., Ruijter, J. M., Voorbraak, F. P. J. M., & Moorman, A. F. M. (2009)

Advances in genomic study of cortical projection neurons

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Integrated Annotation and Analysis of In Situ Hybridization Images Using the ImAnno System: Application to the Ear and Sensory Organs of the Fetal Mouse

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Visually Relating Gene Expression and in vivo DNA Binding Data

Huang, M.-Y., Mackey, L. W., Keränen, S. V. E., Weber, G. H., Jordan, M. I., Knowles, D. W., Biggin, M. D., & Bernd Hamann, A. (2011) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2011.85

Nucleic Acid Extraction and Detection Across Two-Dimensional Tissue Samples

Armani, M. D. (2010) · University Libraries (University of Maryland)

BoneMorphogeneticProteins,EyePatterning,and RetinocollicularMapFormationintheMouse

Plas, D. T., & Dhande, O. S. (2008)

Regulation and expression of genes associated with neurodegeneration with brain iron accumulation

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Transcriptional regulation of FEV, a human serotonin neuron developmental control gene

Krueger, K. C. (2009) · OhioLink ETD Center (Ohio Library and Information Network)

In Vivo Analysis of Human LHX3 Gene Regulation

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Effects of Dicer Inactivation in the Developing Mouse Adrenal Cortex and Micro-RNAs in Adrenocortical Carcinoma.

Krill, K. T. (2014) · Deep Blue (University of Michigan)

A Genome-Wide Association Study for Identifying the Susceptibility Genes to Interstitial Lung Disorder in Rheumatoid Arthritis Patients

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Gene expression profile data of the developing small intestine of Id2-deficient mice

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From inside-out to outside-in: cortical lamination development in the Reelin-deficient neocortex

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Early Concepts and Terminology

Collins, P. (2020) · Elsevier eBooks · doi:10.1016/b978-0-7020-6956-7.00001-4

Novel Algorithms for Cross-Ontology Multi-Level Data Mining

Manda, P. (2020)

Identification of enamel knot gene signature within the developing mouse molarPreprint

Winchester, E. W., & Cotney, J. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.14.448115

Faculty Opinions recommendation of Neural stem cells direct axon guidance via their radial fiber scaffold.

Pasterkamp, R. J., & van Battum, E. Y. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738379358.793584781

Molecular mechanisms underlying cortical (mal)formation: case studies of ESCO2 and EXOSC10

Ulmke, P. A. (2021) · doi:10.53846/goediss-8819

Faculty Opinions recommendation of Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain.

Kiebler, M. A., Moya, S. M. F., & Ehses, J. (2017) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727072594.793538406

Correction: Correlating Global Gene Regulation to Angiogenesis in the Developing Chick Extra-Embryonic Vascular System

Javerzat, S., Franco, M., Herbert, J. J., Platonova, N., Peille, A.-L., Pantesco, V., Vos, J. D., Assou, S., Bicknell, R., Bikfalvi, A., et al. (2010) · PLoS ONE · doi:10.1371/annotation/110bdc8c-b16e-4043-816c-a3f8105ca061

miR-148a-3p inhibits osteogenesis by targeting Itga11 via PI3K/Akt/GSK3/β-catenin pathwayPreprint

Chen, X., Rong, K., Li, X., Han, W., Pang, Y., & Chai, G. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.23.513322

Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axonsPreprint

Liu, W., Shrestha, R., Lowe, A., Zhang, X., & Spaeth, L. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.22.533827

Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axonsPreprint

Liu, W., Shrestha, R., Lowe, A., Zhang, X., & Spaeth, L. (2023) · eLife · doi:10.7554/elife.87306.1

Reviewer #2 (Public Review): Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axons

(2023) · eLife · doi:10.7554/elife.87306.1.sa0

Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axonsPreprint

Liu, W., Shrestha, R., Lowe, A., Zhang, X., & Spaeth, L. (2023) · eLife · doi:10.7554/elife.87306.2

Genome-wide association study for age-related hearing loss in CFW micePreprint

Polesskaya, O., Boussaty, E. C., Cheng, R., Lamonte, O. A., Zhou, T. Y., Du, E. Y., Sanches, T. M., Nguyen, K., Okamoto, M., Palmer, A. A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.10.598304

GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 32(Database issue

Visel, A., Christina Thaller, B., & Gregor Eichele, C. (2004)

GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res 2004;32(Database issue):D552–6

Visel, A., Christina Thaller, B., & Gregor Eichele, C. (2016)

EMAGE: a spatial database of gene expression patterns during mouse embryo development

Christiansen, J. H. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj006 · Cited by 97

WEBLOGS: Weighty Matters

(2006) · Science · doi:10.1126/science.311.5758.153e

A Gene Expression Map of the Mouse Brain

Visel, A., Ahdidan, J., & Eichele, G. (2003) · Springer eBooks · doi:10.1007/978-1-4615-1079-6_2 · Cited by 7