Systems Biology

Optimized Detection and Inference of Names in scRNA-seq data
Janyerkye Tulyeu, David Priest, James B. Wing, Jonas Nørskov Søndergaard

bioRxiv 2025.01.27.634698; doi: https://doi.org/10.1101/2025.01.27.634698 New Results

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GRNFomer: Accurate Gene Regulatory Network Inference Using Graph Transformer
Akshata Hegde, Jianlin Cheng

bioRxiv 2025.01.26.634966; doi: https://doi.org/10.1101/2025.01.26.634966 New Results

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Decoy-seq unlocks scalable genetic screening for regulatory small noncoding RNAs
Benedict Choi, Sushil Sobti, Larisa M. Soto, Trey Charbonneau, Aiden Sababi, Albertas Navickas, Hamed S. Najafabadi, Hani Goodarzi

bioRxiv 2025.01.25.634869; doi: https://doi.org/10.1101/2025.01.25.634869 New Results

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Growth rate controls the sensitivity of gene regulatory circuits
Thomas Julou, Théo Gervais, Daan de Groot, Erik van Nimwegen

bioRxiv 2022.04.03.486858; doi: https://doi.org/10.1101/2022.04.03.486858 New Results

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Mathematical Programming and Graph Neural Networks illuminate functional heterogeneity of pathways in disease
Charalampos P. Triantafyllidis

bioRxiv 2024.12.28.630070; doi: https://doi.org/10.1101/2024.12.28.630070 New Results

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MINERVA FAIR assessment fosters open science & scientific crowd-sourcing in systems biomedicine
Irina Balaur, Danielle Welter, Adrien Rougny, Esther Thea Inau, Alexander Mazein, Soumyabrata Ghosh, Reinhard Schneider, Dagmar Waltemath, Marek Ostaszewski, Venkata Satagopam

bioRxiv 2024.08.28.610042; doi: https://doi.org/10.1101/2024.08.28.610042 New Results

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The effect of surface properties on the interactions of particles and marine mucous filters
Yuval Jacobi, José A. Epstein, Ariella Paz, Uri Shavit, Gitai Yahel, Guy Z. Ramon

bioRxiv 2025.01.21.634085; doi: https://doi.org/10.1101/2025.01.21.634085 New Results

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A Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis
Omid Ardalani, Patrick V. Phaneuf, Jayanth Krishnan, Gaoyuan Li, Joshua Burrows, Lars K. Nielsen, Bernhard O. Palsson

bioRxiv 2025.01.23.634541; doi: https://doi.org/10.1101/2025.01.23.634541 New Results

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Global loss of responsiveness in key regulator metabolites and elevated enzyme proteins as metabolic dysregulation in skeletal muscle and liver of obese mice during starvation
Dongzi Li, Keigo Morita, Toshiya Kokaji, Atsushi Hatano, Akiyoshi Hirayama, Tomoyoshi Soga, Yutaka Suzuki, Masaki Matsumoto, Takaho Tsuchiya, Haruka Ozaki, Satoshi Ohno, Hiroshi Inoue, Yuka Inaba, Hikaru Sugimoto, Yifei Pan, Shinya Kuroda

bioRxiv 2025.01.22.634184; doi: https://doi.org/10.1101/2025.01.22.634184 New Results

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Mapping cell-cell fusion at single-cell resolution
Andrea L. Gardner, Lan Zheng, Kennedy Howland, Andrew Saunders, Andrea Ramirez, Patrik Parker, Chisom Iloegbunam, Daylin Morgan, Tyler A. Jost, Amy Brock

bioRxiv 2024.12.11.627873; doi: https://doi.org/10.1101/2024.12.11.627873 New Results

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Systems Biology

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