A. Vandenbon

发表

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

Alexis Vandenbon, Daron M Standley, Shizuo Akira, 2012, BMC Genomics.

Modeling tissue-specific structural patterns in human and mouse promoters

Kenta Nakai, Alexis Vandenbon, K. Nakai, 2009, Nucleic acids research.

Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster

K. Nakai, A. Nose, A. Vandenbon, 2017, PeerJ.

A Set of Structural Features Defines the Cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster

K. Nakai, A. Vandenbon, Y. López, 2014, PloS one.

A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data

A. Vandenbon, Diego Diez, 2019, Nature Communications.

singleCellHaystack: Finding surprising genes in single-cell transcriptome data

A. Vandenbon, Diego Diez, 2019 .

Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs

S. Akira, Yutaka Suzuki, A. Vandenbon, 2016, BMC Genomics.

singleCellHaystack: Finding surprising genes in 2-dimensional representations of single cell transcriptome data

A. Vandenbon, Diego Diez, 2019 .

Codon bias confers stability to human mRNAs

M. Landthaler, O. Takeuchi, A. Vandenbon, 2019, EMBO reports.

Coadministered Antigen Follicular Helper Cell Responses to the Inflammation That Induces Th 2 Cell and T-Cyclodextrin Spikes Local β Hydroxypropyl

H. Yamada, C. Coban, K. Ishii, 2015 .

Hydroxypropyl-β-Cyclodextrin Spikes Local Inflammation That Induces Th2 Cell and T Follicular Helper Cell Responses to the Coadministered Antigen

H. Yamada, C. Coban, K. Ishii, 2015, The Journal of Immunology.

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Piero Carninci, Y. Hayashizaki, T. Lassmann, 2014, Proceedings of the National Academy of Sciences.

Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs.

Yutaka Suzuki, O. Takeuchi, A. Vandenbon, 2017, Cell reports.

Systems biology approaches to toll-like receptor signaling

S. Akira, D. Standley, K. Takeda, 2012, Wiley interdisciplinary reviews. Systems biology and medicine.

Markov Chain-based Promoter Structure Modeling for Tissue-specific Expression Pattern Prediction

K. Nakai, A. Vandenbon, T. Kusakabe, 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.

The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation.

S. Akira, D. Standley, O. Takeuchi, 2012, Immunity.

A qualitative host‐pathogen interaction in the Theobroma cacao‐Moniliophthora perniciosa pathosystem

M. Shaw, A. Vandenbon, 2007 .

Regnase-1 Prevents Pulmonary Arterial Hypertension Through mRNA Degradation of Interleukin-6 and Platelet-Derived Growth Factor in Alveolar Macrophages

O. Takeuchi, A. Vandenbon, H. Ishibashi-Ueda, 2022, Circulation.

Enhancement of Regnase-1 expression with stem loop–targeting antisense oligonucleotides alleviates inflammatory diseases

O. Takeuchi, A. Vandenbon, M. Kinoshita, 2022, Science Translational Medicine.

Microarray analysis of macrophage response to infection with Streptococcus oralis reveals the immunosuppressive effect of hydrogen peroxide.

H. Kuwata, A. Vandenbon, Y. Kumagai, 2017, Biochemical and biophysical research communications.

The N6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity

O. Takeuchi, D. Morgens, Kyuho Han, 2022, Nature Communications.

Microarray and gene co-expression analysis reveals that melatonin attenuates immune responses and modulates actin rearrangement in macrophages.

H. Kuwata, A. Vandenbon, Y. Kumagai, 2017, Biochemical and biophysical research communications.

A universal differential expression prediction tool for single-cell and spatial genomics data

A. Vandenbon, Diego Diez, 2022, bioRxiv.

Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment

A. Vandenbon, D. Motooka, T. Kohwi-Shigematsu, 2017, Nature Immunology.

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

K. Nakai, S. Akira, Yoshiaki Tanaka, 2010, Nature Immunology.

Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex

S. Akira, D. Standley, O. Takeuchi, 2014, The EMBO journal.

Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation

S. Akira, Yutaka Suzuki, D. Standley, 2013, Cell.

Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue-specific expression prediction.

K. Nakai, A. Vandenbon, 2008, Genome informatics. International Conference on Genome Informatics.

Cyclin J–CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism

D. Standley, Y. Ishihama, O. Takeuchi, 2022, Science Signaling.

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

K. Nakai, Yutaka Suzuki, A. Vandenbon, 2016, bioRxiv.

Codon Bias Confers Stability to mRNAs via ILF2 in Humans

M. Landthaler, O. Takeuchi, A. Vandenbon, 2019, bioRxiv.

Codon Optimality Confers GC-Rich-Induced Stability to mRNAs in Humans

M. Landthaler, O. Takeuchi, A. Vandenbon, 2019 .

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

S. Akira, D. Standley, A. Vandenbon, 2012, BMC Genomics.

Zinc Finger Protein St18 Protects against Septic Death by Inhibiting VEGF-A from Macrophages.

Mikaël M. Martino, S. Akira, O. Takeuchi, 2020, Cell reports.

Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by regnase-1

Yutaka Suzuki, O. Takeuchi, T. Hirai, 2020, European Respiratory Journal.

Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data

A. Vandenbon, 2021, bioRxiv.

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

Shimon Sakaguchi, Alexis Vandenbon, Naganari Ohkura, 2016, Proceedings of the National Academy of Sciences.

IκBζ is essential for natural killer cell activation in response to IL-12 and IL-18

S. Akira, O. Takeuchi, T. Satoh, 2010, Proceedings of the National Academy of Sciences.

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

Osamu Takeuchi, Uwe Ohler, Daron M. Standley, 2015, Cell.

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites

Shunsuke Teraguchi, Yutaro Kumagai, Daron M. Standley, 2013, BMC Bioinformatics.

Murine breast cancers disorganize the liver transcriptome in a zonated manner

A. Suzuki, A. Vandenbon, S. Kawaoka, 2022, bioRxiv.

Guidance for RNA-seq co-expression estimates: the importance of data normalization, batch effects, and correlation measures

A. Vandenbon, 2021 .

Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment

A. Vandenbon, D. Motooka, T. Kohwi-Shigematsu, 2016, Nature Immunology.

Advances and Applications in Bioinformatics and Chemistry Dovepress Mapping Circulating Serum Mirnas to Their Immune-related Target Mrnas

K. Ishii, D. Standley, A. Vandenbon, 2022 .

A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response

A. Vandenbon, T. Honda, M. Tomura, 2016, Scientific Reports.

Pulmonary Regnase-1 orchestrates the interplay of epithelium and adaptive immune systems to protect against pneumonia

Yutaka Suzuki, O. Takeuchi, T. Hirai, 2018, Mucosal Immunology.

Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs

S. Akira, Yutaka Suzuki, A. Vandenbon, 2016, BMC Genomics.

A universal tool for predicting differentially active features in single-cell and spatial genomics data

A. Vandenbon, Diego Diez, 2023, Scientific reports.

A universal differential expression prediction tool for single-cell and spatial genomics data

A. Vandenbon, Diego Diez, 2023, bioRxiv.

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation

Yutaka Suzuki, D. Standley, O. Takeuchi, 2014, BMC Genomics.

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression

K. Nakai, A. Vandenbon, Martin Loza, 2023, bioRxiv.

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

K. Nakai, Yutaka Suzuki, A. Vandenbon, 2016, Genome Biology.

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression

K. Nakai, A. Vandenbon, Martin Loza, 2023, bioRxiv.

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations.

Alexis Vandenbon, Daron M Standley, Shizuo Akira, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Selective elimination of CD169+ macrophages in lymph nodes invaded by breast cancers

A. Vandenbon, S. Kawaoka, M. Toi, 2023, bioRxiv.

Pulmonary Regnase-1 orchestrates the interplay of epithelium and adaptive immune systems to protect against pneumonia

Yutaka Suzuki, O. Takeuchi, T. Hirai, 2018, Mucosal Immunology.

Advances and Applications in Bioinformatics and Chemistry Dovepress Mapping Circulating Serum Mirnas to Their Immune-related Target Mrnas

K. Ishii, D. Standley, A. Vandenbon, 2022 .

Hematopoietic cell-derived IL-15 supports NK cell development in scattered and clustered localization within the bone marrow.

T. Hara, Shinya Abe, A. Vandenbon, 2023, Cell reports.

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

I. Amit, Amir Giladi, M. Landthaler, 2023, Blood.

A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data

Alexis Vandenbon, Diego Diez, A. Vandenbon, 2020, Nature Communications.