Publications by authors named "Alexander Pico"

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Risk factors for mortality in patients with kidney failure on hemodialysis identified by proteomic analysis of CRIC and PACE studies.
Yue Ren, Mark R Segal, Tariq Shafi, Alexander R Pico, Min-Gyoung Shin

Nat Commun· November 2025

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Cytoscape Web: bringing network biology to the browser.
Keiichiro Ono, Dylan Fong, Chengzhan Gao, Christopher Churas, Rudolf Pillich, Alexander R Pico

Nucleic Acids Res· July 2025

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Machine learning reveals prominent spontaneous behavioral changes and treatment efficacy in humanized and transgenic Alzheimer's disease models.
Stephanie R Miller, Kevin Luxem, Kelli Lauderdale, Pranav Nambiar, Patrick S Honma, Alexander R Pico

Cell Rep· November 2024

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Fibrin drives thromboinflammation and neuropathology in COVID-19.
Jae Kyu Ryu, Zhaoqi Yan, Mauricio Montano, Elif G Sozmen, Karuna Dixit, Alexander R Pico

Nature· September 2024

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Incident heart failure in chronic kidney disease: proteomics informs biology and risk stratification.
Ruth F Dubin, Rajat Deo, Yue Ren, Jianqiao Wang, Alexander R Pico

Eur Heart J· August 2024

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Current and future directions in network biology.
Marinka Zitnik, Michelle M Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Alexander R Pico

Bioinform Adv· August 2024

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Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.
Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D Bader, Alexander R Pico

Nucleic Acids Res· July 2024

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WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics.
John M Elizarraras, Yuxing Liao, Zhiao Shi, Qian Zhu, Alexander R Pico

Nucleic Acids Res· July 2024

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WikiPathways 2024: next generation pathway database.
Ayushi Agrawal, Hasan Balcı, Kristina Hanspers, Susan L Coort, Marvin Martens, Alexander R Pico

Nucleic Acids Res· January 2024

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In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.
Xuewen Chen, Augustinus G Haribowo, Alan H Baik, Andrea Fossati, Erica Stevenson, Alexander R Pico

Sci Adv· December 2023

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Using published pathway figures in enrichment analysis and machine learning.
Min-Gyoung Shin, Alexander R Pico

BMC Genomics· November 2023

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BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.
Jackson Callaghan, Colleen H Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, Alexander R Pico

Bioinformatics· September 2023

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Defining blood-induced microglia functions in neurodegeneration through multiomic profiling.
Andrew S Mendiola, Zhaoqi Yan, Karuna Dixit, Jeffrey R Johnson, Mehdi Bouhaddou, Alexander R Pico

Nat Immunol· July 2023

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Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing.
Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D Bader, Alexander R Pico

ArXiv· July 2023

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Using Published Pathway Figures in Enrichment Analysis and Machine Learning.
Min-Gyoung Shin, Alexander Pico

bioRxiv· July 2023

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BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.
Jackson Callaghan, Colleen H Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, Alexander R Pico

ArXiv· April 2023

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NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.
Rudolf T Pillich, Jing Chen, Christopher Churas, Dylan Fong, Benjamin M Gyori, Alexander Pico

Bioinformatics· March 2023

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The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
John H Morris, Karthik Soman, Rabia E Akbas, Xiaoyuan Zhou, Brett Smith, Alexander R Pico

Bioinformatics· February 2023

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Introducing R as a smart version of calculators enables beginners to explore it on their own.
Krishna Choudhary, Alexander R Pico

F1000Res· July 2022

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scNetViz: from single cells to networks using Cytoscape.
Krishna Choudhary, Elaine C Meng, J Javier Diaz-Mejia, Gary D Bader, Alexander R Pico

F1000Res· January 2022

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COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Alexander R Pico

Mol Syst Biol· December 2021

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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Alexander R Pico

Mol Syst Biol· October 2021

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SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy.
Jae Kyu Ryu, Elif G Sozmen, Karuna Dixit, Mauricio Montano, Yusuke Matsui, Alexander R Pico

bioRxiv· October 2021

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Ten simple rules for creating reusable pathway models for computational analysis and visualization.
Kristina Hanspers, Martina Kutmon, Susan L Coort, Daniela Digles, Lauren J Dupuis, Alexander R Pico

PLoS Comput Biol· August 2021

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Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.
Chen Huang, Lijun Chen, Sara R Savage, Rodrigo Vargas Eguez, Yongchao Dou, Alexander R Pico

Cancer Cell· March 2021

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