Search Results - "Fernández, Domingo"

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology by Domingo-Fernández, Daniel, Baksi, Shounak, Schultz, Bruce, Gadiya, Yojana, Karki, Reagon, Raschka, Tamara, Ebeling, Christian, Hofmann-Apitius, Martin, Kodamullil, Alpha Tom

“…Abstract Summary The COVID-19 crisis has elicited a global response by the scientific community that has led to a burst of publications on the pathophysiology…”
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Root water transport of Helianthus annuus L. under iron oxide nanoparticle exposure by Martínez-Fernández, Domingo, Barroso, Didac, Komárek, Michael

“…The application of nanomaterials in commercially available products is increasing rapidly for agriculture, phytoremediation and biotechnology. Since plants…”
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BioKEEN: a library for learning and evaluating biological knowledge graph embeddings by Ali, Mehdi, Hoyt, Charles Tapley, Domingo-Fernández, Daniel, Lehmann, Jens, Jabeen, Hajira

“…Abstract Summary Knowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense…”
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The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling by Mubeen, Sarah, Hoyt, Charles Tapley, Gemünd, André, Hofmann-Apitius, Martin, Fröhlich, Holger, Domingo-Fernández, Daniel

“…Pathway-centric approaches are widely used to interpret and contextualize - data. However, databases contain different representations of the same biological…”
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On the correspondence between the transcriptomic response of a compound and its effects on its targets by Engler Hart, Chloe, Ence, Daniel, Healey, David, Domingo-Fernández, Daniel

“…Better understanding the transcriptomic response produced by a compound perturbing its targets can shed light on the underlying biological processes regulated…”
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Weighting Low-Intensity MS/MS Ions and m/z Frequency for Spectral Library Annotation by Engler Hart, Chloe, Kind, Tobias, Dorrestein, Pieter C., Healey, David, Domingo-Fernández, Daniel

“…Calculating spectral similarity is a fundamental step in MS/MS data analysis in untargeted metabolomics experiments, as it facilitates the identification of…”
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PathMe: merging and exploring mechanistic pathway knowledge by Domingo-Fernández, Daniel, Mubeen, Sarah, Marín-Llaó, Josep, Hoyt, Charles Tapley, Hofmann-Apitius, Martin

“…The complexity of representing biological systems is compounded by an ever-expanding body of knowledge emerging from multi-omics experiments. A number of…”
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Natural Products Have Increased Rates of Clinical Trial Success throughout the Drug Development Process by Domingo-Fernández, Daniel, Gadiya, Yojana, Preto, António José, Krettler, Christoph A., Mubeen, Sarah, Allen, August, Healey, David, Colluru, Viswa

“…Natural products (NPs) or their derivatives represent a large proportion of drugs that successfully progress through clinical trials to approval. This study…”
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Exposure of engineered nanomaterials to plants: Insights into the physiological and biochemical responses-A review by Zuverza-Mena, Nubia, Martínez-Fernández, Domingo, Du, Wenchao, Hernandez-Viezcas, Jose A., Bonilla-Bird, Nestor, López-Moreno, Martha L., Komárek, Michael, Peralta-Videa, Jose R., Gardea-Torresdey, Jorge L.

“…Recent investigations show that carbon-based and metal-based engineered nanomaterials (ENMs), components of consumer goods and agricultural products, have the…”
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Comparative effects of nanoscale zero-valent iron (nZVI) and Fe2O3 nanoparticles on root hydraulic conductivity of Solanum lycopersicum L by Martínez-Fernández, Domingo, Komárek, Michael

“…[Display omitted] •NZVI and nFe2O3 affected differently the nutritional status of tomato plants.•Root water conductivity was lowered by nFe2O3 (100mgL−1), but…”
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Interactions of two novel stabilizing amendments with sunflower plants grown in a contaminated soil by Michálková, Zuzana, Martínez-Fernández, Domingo, Komárek, Michael

“…Several efficient stabilizing amendments have been recently proposed for the remediation of metal(loid)-contaminated soils. However, information on their…”
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Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer’s Disease and Reconstruction of Relevant Biological Mechanisms by Khanna, Shashank, Domingo-Fernández, Daniel, Iyappan, Anandhi, Emon, Mohammad Asif, Hofmann-Apitius, Martin, Fröhlich, Holger

“…Alzheimer’s Disease (AD) is among the most frequent neuro-degenerative diseases. Early diagnosis is essential for successful disease management and chance to…”
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Drug2ways: Reasoning over causal paths in biological networks for drug discovery by Rivas-Barragan, Daniel, Mubeen, Sarah, Guim Bernat, Francesc, Hofmann-Apitius, Martin, Domingo-Fernández, Daniel

“…Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and, accordingly, guide…”
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Ensembles of knowledge graph embedding models improve predictions for drug discovery by Rivas-Barragan, Daniel, Domingo-Fernández, Daniel, Gadiya, Yojana, Healey, David

“…Recent advances in Knowledge Graphs (KGs) and Knowledge Graph Embedding Models (KGEMs) have led to their adoption in a broad range of fields and applications…”
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On the influence of several factors on pathway enrichment analysis by Mubeen, Sarah, Tom Kodamullil, Alpha, Hofmann-Apitius, Martin, Domingo-Fernández, Daniel

“…Abstract Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an…”
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Inhibition of neuroblastoma tumor growth by targeted delivery of microRNA-34a using anti-disialoganglioside GD2 coated nanoparticles by Tivnan, Amanda, Orr, Wayne Shannon, Gubala, Vladimir, Nooney, Robert, Williams, David E, McDonagh, Colette, Prenter, Suzanne, Harvey, Harry, Domingo-Fernández, Raquel, Bray, Isabella M, Piskareva, Olga, Ng, Catherine Y, Lode, Holger N, Davidoff, Andrew M, Stallings, Raymond L

“…Neuroblastoma is one of the most challenging malignancies of childhood, being associated with the highest death rate in paediatric oncology, underlining the…”
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PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures by Emon, Mohammad Asif, Domingo-Fernández, Daniel, Hoyt, Charles Tapley, Hofmann-Apitius, Martin

“…During the last decade, there has been a surge towards computational drug repositioning owing to constantly increasing -omics data in the biomedical research…”
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Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms by Figueiredo, Rebeca Queiroz, Raschka, Tamara, Kodamullil, Alpha Tom, Hofmann-Apitius, Martin, Mubeen, Sarah, Domingo-Fernández, Daniel

“…Abstract We attempt to address a key question in the joint analysis of transcriptomic data: can we correlate the patterns we observe in transcriptomic datasets…”
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Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery by Domingo-Fernández, Daniel, Gadiya, Yojana, Patel, Abhishek, Mubeen, Sarah, Rivas-Barragan, Daniel, Diana, Chris W, Misra, Biswapriya B, Healey, David, Rokicki, Joe, Colluru, Viswa

“…Network-based approaches are becoming increasingly popular for drug discovery as they provide a systems-level overview of the mechanisms underlying disease…”
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CLEP: a hybrid data- and knowledge-driven framework for generating patient representations by Bharadhwaj, Vinay Srinivas, Ali, Mehdi, Birkenbihl, Colin, Mubeen, Sarah, Lehmann, Jens, Hofmann-Apitius, Martin, Hoyt, Charles Tapley, Domingo-Fernández, Daniel

“…Abstract Summary As machine learning and artificial intelligence increasingly attain a larger number of applications in the biomedical domain, at their core,…”
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