Alexander R. Pico

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 17

Top Topics

Graphical Representations

Valuable Knowledge

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

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
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinform. 39 (2) (2023)
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
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. Bioinform. 39 (9) (2023)
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
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinform. 39 (3) (2023)
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
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. CoRR (2023)
Krishna Choudhary, Alexander R. Pico
Introducing R as a smart version of calculators enables beginners to explore it on their own. F1000Research 10 (2021)
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
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLoS Comput. Biol. 17 (8) (2021)
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
WikiPathways: connecting communities. Nucleic Acids Res. 49 (Database-Issue) (2021)
Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
RCy3: Network biology using Cytoscape from within R. F1000Research 8 (2019)
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
The Cytoscape Automation app article collection. F1000Research 7 (2018)
Adam Treister, Alexander R. Pico
. F1000Research 7 (2018)
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
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 46 (Database-Issue) (2018)
Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan A. Miller, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput. Biol. 12 (6) (2016)
Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. A. Evelo
Reactome from a WikiPathways Perspective. PLoS Comput. Biol. 12 (5) (2016)
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
WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 44 (Database-Issue) (2016)
Lilit Nersisyan, Graham Johnson, Megan Riel-Mehan, Alexander R. Pico, Arsen Arakelyan
PSFC: a Pathway Signal Flow Calculator App for Cytoscape. F1000Research 4 (2015)
Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo
PathVisio 3: An Extendable Pathway Analysis Toolbox. PLoS Comput. Biol. 11 (2) (2015)
John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
CyAnimator: Simple Animations of Cytoscape Networks. F1000Research 4 (2015)
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
The Cytoscape app article collection. F1000Research 3 (2014)
Jianjiong Gao, Chao Zhang, Martijn P. van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico
BridgeDb app: unifying identifier mapping services for Cytoscape. F1000Research 3 (2014)
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Research 3 (2014)
Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico
NOA: a cytoscape plugin for network ontology analysis. Bioinform. 29 (16) (2013)
Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico
Cytoscape App Store. Bioinform. 29 (10) (2013)
Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. A. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis
GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinform. 28 (16) (2012)
Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, Alexander R. Pico
Mosaic: making biological sense of complex networks. Bioinform. 28 (14) (2012)
Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. A. Evelo, Alexander R. Pico
WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 40 (Database-Issue) (2012)
Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinform. 11 (2010)
Nathan Salomonis, Brandon Nelson, Karen Vranizan, Alexander R. Pico, Kristina Hanspers, Allan Kuchinsky, Linda Ta, Mark Mercola, Bruce R. Conklin
Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors. PLoS Comput. Biol. 5 (11) (2009)
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
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res. 37 (Database-Issue) (2009)
Martijn P. van Iersel, Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Susan L. Coort, Bruce R. Conklin, Chris T. A. Evelo
Presenting and exploring biological pathways with PathVisio. BMC Bioinform. 9 (2008)
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
GenMAPP 2: new features and resources for pathway analysis. BMC Bioinform. 8 (2007)
Brent A. Field, Alexander R. Pico, Richard T. Marrocco
Local cortical injections of glutamate and noradrenaline alter high-frequency (245 Hz) neuronal activity in rat cortex. Neurocomputing (1999)