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2020 – today
- 2023
[j21]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)- [j20]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) - [j19]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) - [i10]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 abs/2304.09344 (2023) - 2021
- [j18]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): D613-D621 (2021) - [j17]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) - [i9]Krishna Choudhary, Alexander R. Pico:
Introducing R as a smart version of calculators enables beginners to explore it on their own. F1000Research 10: 859 (2021)
2010 – 2019
- 2019
- [i8]Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico:
RCy3: Network biology using Cytoscape from within R. F1000Research 8: 1774 (2019) - 2018
- [j16]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): D661-D667 (2018) - [i7]Adam Treister, Alexander R. Pico:
Identifier Mapping in Cytoscape: idmapper. F1000Research 7: 725 (2018) - [i6]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: 800 (2018) - 2016
- [j15]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): 488-494 (2016) - [j14]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) - [j13]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) - 2015
- [j12]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) - [i5]Lilit Nersisyan, Graham Johnson, Megan Riel-Mehan, Alexander R. Pico, Arsen Arakelyan:
PSFC: a Pathway Signal Flow Calculator App for Cytoscape. F1000Research 4: 480 (2015) - [i4]John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin:
CyAnimator: Simple Animations of Cytoscape Networks. F1000Research 4: 482 (2015) - 2014
- [i3]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: 138 (2014) - [i2]John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico:
enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Research 3: 147 (2014) - [i1]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: 148 (2014) - 2013
- [j11]Samad Lotia, Jason Montojo, Yue Dong, Gary D. Bader, Alexander R. Pico:
Cytoscape App Store. Bioinform. 29(10): 1350-1351 (2013) - [j10]Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico:
NOA: a cytoscape plugin for network ontology analysis. Bioinform. 29(16): 2066-2067 (2013) - 2012
- [j9]Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, Alexander R. Pico:
Mosaic: making biological sense of complex networks. Bioinform. 28(14): 1943-1944 (2012) - [j8]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): 2209-2210 (2012) - [j7]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): 1301-1307 (2012) - 2010
- [j6]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: 5 (2010)
2000 – 2009
- 2009
- [j5]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): 803-809 (2009) - [j4]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) - 2008
- [j3]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) - 2007
- [j2]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)
1990 – 1999
- 1999
- [j1]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 26-27: 123-130 (1999)
Coauthor Index
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