Alexander R. Pico

According to our database, Alexander R. Pico authored at least 30 papers between 1999 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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, Eric Zhou, Rohan Juneja, Yao Yao, Madhumita Narayan, Kristina Hanspers, Ayushi Agrawal, Alexander R. Pico, Chunlei Wu, Andrew I. Su

Bioinform., September, 2023

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, Trey Ideker, Klas Karis, Sophie N. Liu, Keiichiro Ono, Alexander R. Pico, Dexter Pratt

Bioinform., March, 2023

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, Elaine C. Meng, Conrad C. Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren M. Sanders, Sylvain V. Costes, Krish Bharat, Arjun Chakraborty, Alexander R. Pico, Taline Mardirossian, Michael J. Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark A. Musen, Sharat Israni, Sui Huang, Peter W. Rose, Charlotte A. Nelson, Sergio E. Baranzini

Bioinform., February, 2023

2021

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, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter, Andra Waagmeester, Egon L. Willighagen, Laurent A. Winckers, Chris T. A. Evelo, Alexander R. Pico

PLoS Comput. Biol., 2021

WikiPathways: connecting communities.

Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N. Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N. Lopes, Friederike Ehrhart, Lauren J. Dupuis, Laurent A. Winckers, Susan L. Coort, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico, Martina Kutmon

Nucleic Acids Res., 2021

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

Krishna Choudhary, Alexander R. Pico

F1000Research, 2021

2019

RCy3: Network biology using Cytoscape from within R.

Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico

F1000Research, 2019

2018

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

Denise N. Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L. Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz, Marianthi Kalafati, Marvin Martens, Ryan A. Miller, Kozo Nishida, Linda Rieswijk, Andra Waagmeester, Lars M. T. Eijssen, Chris T. A. Evelo, Alexander R. Pico, Egon L. Willighagen

Nucleic Acids Res., 2018

Identifier Mapping in Cytoscape: <i>idmapper</i>.

Adam Treister, Alexander R. Pico

F1000Research, 2018

The Cytoscape Automation app article collection.

Barry Demchak, David Otasek, Alexander R. Pico, Gary D. Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H. Morris, William J. R. Longabaugh, Christian Tannus Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, Trey Ideker

F1000Research, 2018

2016

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

Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan A. Miller, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico

PLoS Comput. Biol., 2016

Reactome from a WikiPathways Perspective.

Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. A. Evelo

PLoS Comput. Biol., 2016

WikiPathways: capturing the full diversity of pathway knowledge.

Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon L. Willighagen, Anwesha Bohler, Jonathan Mélius, Andra Waagmeester, Sravanthi R. Sinha, Ryan A. Miller, Susan L. Coort, Elisa Cirillo, Bart Smeets, Chris T. A. Evelo, Alexander R. Pico

Nucleic Acids Res., 2016

2015

PathVisio 3: An Extendable Pathway Analysis Toolbox.

Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo

PLoS Comput. Biol., 2015

PSFC: a Pathway Signal Flow Calculator App for Cytoscape.

Lilit Nersisyan, Graham Johnson, Megan Riel-Mehan, Alexander R. Pico, Arsen Arakelyan

F1000Research, 2015

CyAnimator: Simple Animations of Cytoscape Networks.

John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin

F1000Research, 2015

2014

The Cytoscape app article collection.

Alexander R. Pico, Gary D. Bader, Barry Demchak, Oriol Guitart Pla, Timothy Hull, William J. R. Longabaugh, Christian Tannus Lopes, Samad Lotia, Piet Molenaar, Jason Montojo, John H. Morris, Keiichiro Ono, Benno Schwikowski, David Welker, Trey Ideker

F1000Research, 2014

enhancedGraphics: a Cytoscape app for enhanced node graphics.

John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico

F1000Research, 2014

BridgeDb app: unifying identifier mapping services for Cytoscape.

Jianjiong Gao, Chao Zhang, Martijn P. van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico

F1000Research, 2014

2013

NOA: a cytoscape plugin for network ontology analysis.

Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico

Bioinform., 2013

Cytoscape App Store.

Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico

Bioinform., 2013

2012

WikiPathways: building research communities on biological pathways.

Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. A. Evelo, Alexander R. Pico

Nucleic Acids Res., 2012

Mosaic: making biological sense of complex networks.

Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, Alexander R. Pico

Bioinform., 2012

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

Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. A. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis

Bioinform., 2012

2010

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

Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo

BMC Bioinform., 2010

2009

Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors.

Nathan Salomonis, Brandon Nelson, Karen Vranizan, Alexander R. Pico, Kristina Hanspers, Allan Kuchinsky, Linda Ta, Mark Mercola, Bruce R. Conklin

PLoS Comput. Biol., 2009

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

Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, Ru-Fang Yeh, Joseph Wiemels, John K. Wiencke, Tarik Tihan, Bruce R. Conklin, Margaret R. Wrensch

Nucleic Acids Res., 2009

2008

Presenting and exploring biological pathways with PathVisio.

Martijn P. van Iersel, Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Susan L. Coort, Bruce R. Conklin, Chris T. A. Evelo

BMC Bioinform., 2008

2007

GenMAPP 2: new features and resources for pathway analysis.

Nathan Salomonis, Kristina Hanspers, Alexander C. Zambon, Karen Vranizan, Steven C. Lawlor, Kam D. Dahlquist, Scott Doniger, Joshua M. Stuart, Bruce R. Conklin, Alexander R. Pico

BMC Bioinform., 2007

1999

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

Brent A. Field, Alexander R. Pico, Richard T. Marrocco

Neurocomputing, 1999