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Benchmarking of the robustness of mechanistic generative models in cellular trajectory and gene regulatory network joint inference

• Authors : Maugé, Yann; Ventre, Elias;

Subjects: scRNAseq; cellular trajectory; gene regulatory networkMontpellier; France

• Source: Journées de Biostatistique 2025 ; https://inria.hal.science/hal-05469365 ; Journées de Biostatistique 2025, Nov 2025, Montpellier, France. 2025

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Benchmarking of the robustness of mechanistic generative models in cellular trajectory and gene regulatory network joint inference

• Authors : Maugé, Yann; Ventre, Elias;

Subjects: scRNAseq; cellular trajectory; gene regulatory networkMontpellier; France

• Source: Journées de Biostatistique 2025 ; https://inria.hal.science/hal-05469365 ; Journées de Biostatistique 2025, Nov 2025, Montpellier, France. 2025

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Gene regulatory network structure help us understand how complex phenotypes adapt

• Authors : Stone, Katherine; Platig, John; Austerlitz, Frederic ...

Subjects: Polygenic selection; EQTL networks; Polygenic traitsMontréal (Québec)Montréal (Québec), Canada

• Source: Evolution 2024 ; https://hal.inrae.fr/hal-04646904 ; Evolution 2024, Jul 2024, Montréal (Québec), Canada

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Gene regulatory network structure help us understand how complex phenotypes adapt

• Authors : Stone, Katherine; Platig, John; Austerlitz, Frederic ...

Subjects: Polygenic traits; EQTL networks; Polygenic selectionMontréal (Québec)Montréal (Québec), Canada

• Source: Evolution 2024 ; https://hal.inrae.fr/hal-04646904 ; Evolution 2024, Jul 2024, Montréal (Québec), Canada

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Image_2_A gene regulatory network model that recovers the abaxial-adaxial polarity in Arabidopsis thaliana leaf primordium.jpeg

• Authors : Mariana Yuste; Alma Piñeyro-Nelson; Eugenio Azpeitia

Subjects: Evolutionary Biology; Ecology; Invasive Species Ecology

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Image_1_A gene regulatory network model that recovers the abaxial-adaxial polarity in Arabidopsis thaliana leaf primordium.jpeg

• Authors : Mariana Yuste; Alma Piñeyro-Nelson; Eugenio Azpeitia

Subjects: Evolutionary Biology; Ecology; Invasive Species Ecology

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Image1_MicroRNAs provide negative feedback and stability in gene regulatory network models of cell-state transitions.pdf

• Authors : Milad Razavi-Mohseni; Michael A. Beer

Subjects: Genetics; Molecular Biology; Epigenetics (incl. Genome Methylation and Epigenomics)

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Investigation of transcriptional dynamics in the Caenorhabditis elegans intestine gene regulatory network

• Authors : Williams, Robert Thomas Patton, author; Osborne Nishimura, Erin, advisor; Wilusz, Carol, committee member

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a, Predicted gene regulatory network of Streptomyces coelicolor based on 17 well-known regulators. Each node in the network represents a (regulatory) gene, and every edge represents a PWM predicted regulatory interaction between nodes. The edges colored in dark gray indicate strong PWM prediction scores, while the lighter gray shades represent weaker interactions. Matches within BGC regions are depicted as triangles. In six regions (black circled), the matches fall within a co-expressed region, highlighting their functional relation to these compounds. b, Representation of the four co-expressed regions, including the locations of their detected TFBSs as colored dots. All predicted TFBSs have been experimentally validated in pre-existing work. The data underlying this figure can be found at https://zenodo.org/records/15106944.

• Authors : Hannah E. Augustijn; Zachary L. Reitz; Le Zhang

Subjects: Biochemistry; Genetics; Hematology

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a, Predicted gene regulatory network of Streptomyces coelicolor based on 17 well-known regulators. Each node in the network represents a (regulatory) gene, and every edge represents a PWM predicted regulatory interaction between nodes. The edges colored in dark gray indicate strong PWM prediction scores, while the lighter gray shades represent weaker interactions. Matches within BGC regions are depicted as triangles. In six regions (black circled), the matches fall within a co-expressed region, highlighting their functional relation to these compounds. b, Representation of the four co-expressed regions, including the locations of their detected TFBSs as colored dots. All predicted TFBSs have been experimentally validated in pre-existing work. The data underlying this figure can be found at https://zenodo.org/records/15106944.

• Authors : Hannah E. Augustijn; Zachary L. Reitz; Le Zhang

Subjects: Biochemistry; Genetics; Hematology

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