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List of works by Alexander R. Pico

A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation

scientific article published on 26 August 2012

A travel guide to Cytoscape plugins

scientific article

Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions

scientific article

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors

scientific article

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation

scientific article

An Introduction to Pathway Analysis with GenMAPP

Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies

scientific article published on 31 December 2012

Associations of Circulating Extracellular RNAs With Myocardial Remodeling and Heart Failure

scientific article published on 01 September 2018

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation

scientific article published on 13 July 2020

Author response: Wikidata as a knowledge graph for the life sciences

scholarly article, peer review and author response published on 24 January 2020

BioHackJP 2023 Report R3: Expand the pathway analysis environment to non-model organisms

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

scientific article

BridgeDb app: unifying identifier mapping services for Cytoscape

scientific article published on July 2014

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

Circulating miRNAs and Risk of Sudden Death in Patients With Coronary Heart Disease

scientific article published on 30 October 2019

Comprehensive Metabolic Phenotyping Refines Cardiovascular Risk in Young Adults

scientific article published on 19 October 2020

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor

scientific article

CyAnimator: Simple Animations of Cytoscape Networks

scientific article

Cytoscape Automation: empowering workflow-based network analysis

scientific article published on 02 September 2019

Cytoscape app store

scientific article published on 16 April 2013

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

scientific article published in 2024

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage

scientific article published on 12 September 2012

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data

scientific article published on 15 March 2019

Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes

scientific article published on 9 February 2017

Fibrin drives thromboinflammation and neuropathology in COVID-19

scientific article published on 28 August 2024

Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration

scientific article published on 15 October 2018

Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets

scientific article

From scientific discovery to cures: bright stars within a galaxy

scientific article

GO-Elite: a flexible solution for pathway and ontology over-representation

scientific article

GenMAPP 2: new features and resources for pathway analysis

scientific article

Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis

scientific article published on 03 June 2013

Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors

scientific article published on 10 June 2015

Identifier Mapping in Cytoscape

Identifying Genes in Published Pathway Figure Images

article

Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology

scientific article published on 29 January 2013

Integration of biological networks and gene expression data using Cytoscape

scientific article (publication date: 2007)

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

scientific article

Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue.

scientific article

Introducing R as a smart version of calculators enables beginners to explore it on their own

scientific article published in 2021

Introducing R as a smart version of calculators enables beginners to explore it on their own

scientific article published in 2022

Local cortical injections of glutamate and noradrenaline alter high-frequency (245Hz) neuronal activity in rat cortex

Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk

scientific article published on 4 December 2015

Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community

scientific article published on 15 September 2020

MicroRNAs Associated With Reverse Left Ventricular Remodeling in Humans Identify Pathways of Heart Failure Progression

scientific article published in February 2018

Mining biological pathways using WikiPathways web services

scientific article

Mir-30d Regulates Cardiac Remodeling by Intracellular And Paracrine Signaling

scientific article published on 22 October 2020

Molecular Signature of Multisystem Cardiometabolic Stress and Its Association With Prognosis

scientific article published on 22 July 2020

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

scientific article

Mosaic: making biological sense of complex networks

scientific article

NOA: a cytoscape plugin for network ontology analysis

scientific article

PSFC: a Pathway Signal Flow Calculator App for Cytoscape

scientific article published on 5 August 2015

PathVisio 3: an extendable pathway analysis toolbox

scientific article

Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests.

scientific article published in June 2008

Pathway information extracted from 25 years of pathway figures

scientific article published on 09 November 2020

PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data

scientific article published on 20 May 2020

Presenting and exploring biological pathways with PathVisio

scientific article

Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community

scholarly article by Ravi V. Shah et al published January 2019 in Arteriosclerosis, Thrombosis, and Vascular Biology

Proteogenomic Characterization of Endometrial Carcinoma

scientific article published on 13 February 2020

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

scientific article published on 05 January 2021

Proteomic analysis of heart failure hospitalization among patients with chronic kidney disease: The Heart and Soul Study

scientific article published in PLoS ONE

RCy3: Network biology using Cytoscape from within R

scientific article published on 18 October 2019

Reactome from a WikiPathways Perspective

scientific article (publication date: May 2016)

Research synergy and drug development: Bright stars in neighboring constellations

scientific article published on 15 November 2017

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

scientific article

Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells

scientific article published on 28 October 2020

Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel

scientific article

Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution

scientific article

TELOMERE LENGTH VARIANTS ARE ASSOCIATED WITH HIGH-GRADE GLIOMA RISK: IDENTIFICATION OF A NOVEL GLIOMA RISK LOCUS BY GENOME-WIDE ASSOCIATION STUDY.

scientific article published in July 2014

Ten simple rules for creating reusable pathway models for computational analysis and visualization

scientific article published on 19 August 2021

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

scientific article (publication date: 4 January 2010)

The Cytoscape Automation app article collection.

scientific article

The Cytoscape app article collection.

scientific article published on July 2014

The Dynamic Platelet Transcriptome in Obesity and Weight Loss

scientific article published on 10 December 2020

The emerging world of wikis

scientific article

The public road to high-quality curated biological pathways

scientific article published in October 2008

Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation

scientific article published on 13 April 2020

Translational Epidemiology: Entering a Brave New World of Team Science

scientific article

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

scientific article

Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility

scientific article

Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk

scientific article

WikiPathways 2024: next generation pathway database

scientific article published on 6 November 2023

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

scientific article (publication date: 11 September 2014)

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

scientific article published in 2014

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

scientific article published on 10 November 2017

WikiPathways: building research communities on biological pathways

scientific article (publication date: 2012)

WikiPathways: capturing the full diversity of pathway knowledge

Research paper from 2016 about the WikiPathways database.

WikiPathways: connecting communities ⬇️

scientific article published on 19 November 2020

WikiPathways: pathway editing for the people

Research paper from 2008 about the WikiPathways database.

Wikidata as a FAIR knowledge graph for the life sciences

scholarly article posted as a preprint in BioRxiv on 11 February 2020

Wikidata as a knowledge graph for the life sciences ⬇️

scientific article published on 17 March 2020

enhancedGraphics: a Cytoscape app for enhanced node graphics

scientific article published on July 2014

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

scientific article published on 01 April 2019

scNetViz: from single cells to networks using Cytoscape

scientific article published on 07 June 2021

setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges.

scientific article published on July 2014

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