Search Results - "Walhout, Albertha Jm"

Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans by Watson, Emma, Olin-Sandoval, Viridiana, Hoy, Michael J, Li, Chi-Hua, Louisse, Timo, Yao, Victoria, Mori, Akihiro, Holdorf, Amy D, Troyanskaya, Olga G, Ralser, Markus, Walhout, Albertha Jm

“…Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or…”
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Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy in co-cultured cancer cells by Sayin, Serkan, Rosener, Brittany, Li, Carmen G, Ho, Bao, Ponomarova, Olga, Ward, Doyle V, Walhout, Albertha J M, Mitchell, Amir

“…Drug metabolism by the microbiome can influence anticancer treatment success. We previously suggested that chemotherapies with antimicrobial activity can…”
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Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities by Narasimhan, Kamesh, Lambert, Samuel A, Yang, Ally W H, Riddell, Jeremy, Mnaimneh, Sanie, Zheng, Hong, Albu, Mihai, Najafabadi, Hamed S, Reece-Hoyes, John S, Fuxman Bass, Juan I, Walhout, Albertha J M, Weirauch, Matthew T, Hughes, Timothy R

“…Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of…”
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EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression by Barrasa, M Inmaculada, Vaglio, Philippe, Cavasino, Fabien, Jacotot, Laurent, Walhout, Albertha J M

“…Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome…”
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Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels by Yilmaz, Lutfu Safak, Li, Xuhang, Nanda, Shivani, Fox, Bennett, Schroeder, Frank, Walhout, Albertha JM

“…Metabolism is a highly compartmentalized process that provides building blocks for biomass generation during development, homeostasis, and wound healing, and…”
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Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns by Reece-Hoyes, John S, Shingles, Jane, Dupuy, Denis, Grove, Christian A, Walhout, Albertha J M, Vidal, Marc, Hope, Ian A

“…The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. Transcription…”
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Systems‐level transcriptional regulation of Caenorhabditis elegans metabolism by Nanda, Shivani, Jacques, Marc‐Antoine, Wang, Wen, Myers, Chad L, Yilmaz, L Safak, Walhout, Albertha JM

“…Metabolism is controlled to ensure organismal development and homeostasis. Several mechanisms regulate metabolism, including allosteric control and…”
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Caenorhabditis elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor by Giese, Gabrielle E, Walker, Melissa D, Ponomarova, Olga, Zhang, Hefei, Li, Xuhang, Minevich, Gregory, Walhout, Albertha Jm

“…Vitamin B12 is an essential micronutrient that functions in two metabolic pathways: the canonical propionate breakdown pathway and the…”
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A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions by Fuxman Bass, Juan I, Pons, Carles, Kozlowski, Lucie, Reece‐Hoyes, John S, Shrestha, Shaleen, Holdorf, Amy D, Mori, Akihiro, Myers, Chad L, Walhout, Albertha JM

“…Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive…”
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Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host by Rosener, Brittany, Sayin, Serkan, Oluoch, Peter O, García González, Aurian P, Mori, Hirotada, Walhout, Albertha Jm, Mitchell, Amir

“…Metabolism of host-targeted drugs by the microbiome can substantially impact host treatment success. However, since many host-targeted drugs inadvertently…”
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Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression by Macneil, Lesley T, Walhout, Albertha J M

“…In any given cell, thousands of genes are expressed and work in concert to ensure the cell's function, fitness, and survival. Each gene, in turn, must be…”
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C. elegans and its bacterial diet as a model for systems-level understanding of host–microbiota interactions by Zhang, Jingyan, Holdorf, Amy D, Walhout, Albertha JM

“…Highlights • C. elegans and its bacterial diet is an excellent model system for mammalian host–microbiota interactions. • C. elegans carries a distinct and…”
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Metabolic network modeling with model organisms by Yilmaz, L Safak, Walhout, Albertha JM

“…•A genome-scale metabolic network model (GSMNM) represents all metabolism.•GSMNMs in model organisms help basic understanding and method development.•Recently,…”
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Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits by Watson, Emma, MacNeil, Lesley T., Ritter, Ashlyn D., Yilmaz, L. Safak, Rosebrock, Adam P., Caudy, Amy A., Walhout, Albertha J.M.

“…Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the…”
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Many transcription factors contribute to C.ￂ elegans growth and fat storage by Mori, Akihiro, Holdorf, Amy D, Walhout, Albertha JM

“…Reverse genetic screens by RNA interference (RNAi) in model organisms such as the nematode Caenorhabditis elegans have provided numerous insights into gene…”
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The interplay between transcription factors and microRNAs in genome-scale regulatory networks by Martinez, Natalia J., Walhout, Albertha J. M.

“…Metazoan genomes contain thousands of protein‐coding and non‐coding RNA genes, most of which are differentially expressed, i.e., at different locations, at…”
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What does biologically meaningful mean? A perspective on gene regulatory network validation by Walhout, Albertha J M

“…Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological…”
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Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping by Walhout, Albertha J M

“…Metazoan genomes contain thousands of protein-coding and noncoding RNA genes, most of which are differentially expressed, i.e., at different locations or at…”
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A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity by Martinez, Natalia J, Ow, Maria C, Barrasa, M Inmaculada, Hammell, Molly, Sequerra, Reynaldo, Doucette-Stamm, Lynn, Roth, Frederick P, Ambros, Victor R, Walhout, Albertha J M

“…MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both…”
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Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms by Watson, Emma, Yilmaz, L. Safak, Walhout, Albertha J.M

“…Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes…”
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