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Journal Articles
- 2023
[j32]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)- [j31]Marco Alvarado Cano, Ginger Tsueng, Xinghua Zhou, Jiwen Xin, Laura D. Hughes, Julia Mullen, Andrew I. Su, Chunlei Wu:
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data. BMC Bioinform. 24(1): 159 (2023) - 2022
- [j30]Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian, Marco Alvarado Cano, Ginger Tsueng, Jiwen Xin, Julia Mullen, Yao Yao, Ricardo Avila, Greg Taylor, Andrew I. Su, Chunlei Wu:
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. Bioinform. 38(7): 2077-2079 (2022) - [j29]Michael Mayers, Roger Tu, Dylan Steinecke, Tong Shu Li, Núria Queralt-Rosinach, Andrew I. Su:
Design and application of a knowledge network for automatic prioritization of drug mechanisms. Bioinform. 38(10): 2880-2891 (2022) - 2020
- [j28]Núria Queralt-Rosinach, Gregory S. Stupp, Tong Shu Li, Michael Mayers, Maureen E. Hoatlin, Matthew Might, Benjamin M. Good, Andrew I. Su:
Structured reviews for data and knowledge-driven research. Database J. Biol. Databases Curation 2020 (2020) - [j27]Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su:
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts. Bioinform. 36(4): 1226-1233 (2020) - 2019
- [j26]Tim E. Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Chunlei Wu, Andrew I. Su:
ChlamBase: a curated model organism database for the Chlamydia research community. Database J. Biol. Databases Curation 2019: baz041 (2019) - [j25]Tim E. Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Gregory S. Stupp, Andra Waagmeester, Benjamin M. Good, Chunlei Wu, Andrew I. Su:
ChlamBase: a curated model organism database for the Chlamydia research community. Database J. Biol. Databases Curation 2019: baz091 (2019) - [j24]Michael Mayers, Tong Shu Li, Núria Queralt-Rosinach, Andrew I. Su:
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network. BMC Bioinform. 20(1): 653 (2019) - [j23]Ginger Tsueng, Arun Kumar, Max Nanis, Andrew I. Su:
Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements. Hum. Comput. 6: 56-82 (2019) - 2018
- [j22]Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su, Chunlei Wu:
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. BMC Bioinform. 19(1): 30:1-30:7 (2018) - [j21]Jennifer M. Radin, Steven R. Steinhubl, Andrew I. Su, Hansa Bhargava, Benjamin Greenberg, Brian M. Bot, Megan Doerr, Eric J. Topol:
The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app. npj Digit. Medicine 1 (2018) - 2017
- [j20]Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin M. Diesh, Nathan A. Dunn, Monica C. Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good:
WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. Database J. Biol. Databases Curation 2017: bax025 (2017) - 2016
- [j19]Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu:
Crowdsourcing in biomedicine: challenges and opportunities. Briefings Bioinform. 17(1): 23-32 (2016) - [j18]Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong:
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. Database J. Biol. Databases Curation 2016 (2016) - [j17]Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim E. Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn M. Schriml, Benjamin M. Good, Andrew I. Su:
Wikidata as a semantic framework for the Gene Wiki initiative. Database J. Biol. Databases Curation 2016 (2016) - [j16]Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su:
A crowdsourcing workflow for extracting chemical-induced disease relations from free text. Database J. Biol. Databases Curation 2016 (2016) - [j15]Tim E. Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su, Benjamin M. Good:
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. Database J. Biol. Databases Curation 2016 (2016) - [j14]Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good:
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. Bioinform. 32(13): 2072-2074 (2016) - [j13]Chunlei Wu, Xuefeng Jin, Ginger Tsueng, Cyrus Afrasiabi, Andrew I. Su:
BioGPS: building your own mash-up of gene annotations and expression profiles. Nucleic Acids Res. 44(Database-Issue): 313-316 (2016) - 2015
- [j12]Kathleen M. Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan M. Carland, Salvatore Loguercio, Andrew I. Su:
Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinform. 31(11): 1724-1728 (2015) - 2013
- [j11]Benjamin M. Good, Andrew I. Su:
Crowdsourcing for bioinformatics. Bioinform. 29(16): 1925-1933 (2013) - [j10]Erik L. Clarke, Salvatore Loguercio, Benjamin M. Good, Andrew I. Su:
A task-based approach for Gene Ontology evaluation. J. Biomed. Semant. 4(S-1): S4 (2013) - [j9]Chunlei Wu, Ian MacLeod, Andrew I. Su:
BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res. 41(Database-Issue): 561-565 (2013) - [j8]Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne:
Ten Simple Rules for Cultivating Open Science and Collaborative R&D. PLoS Comput. Biol. 9(9) (2013) - 2012
- [j7]Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio, Andrew I. Su:
Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database J. Biol. Databases Curation 2012 (2012) - [j6]Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio, Andrew I. Su:
Linking genes to diseases with a SNPedia-Gene Wiki mashup. J. Biomed. Semant. 3(S-1): S6 (2012) - [j5]Benjamin M. Good, Erik L. Clarke, Luca de Alfaro, Andrew I. Su:
The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res. 40(Database-Issue): 1255-1261 (2012) - 2011
- [j4]Banu Dost, Chunlei Wu, Andrew I. Su, Vineet Bafna:
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 8(3): 808-818 (2011) - 2010
- [j3]Jong-Min Lee, Jie Zhang, Andrew I. Su, John R. Walker, Tim Wiltshire, Kihwa Kang, Ella Dragileva, Tammy Gillis, Edith T. Lopez, Marie-Josee Boily, Michel Cyr, Isaac S. Kohane, James F. Gusella, Marcy E. MacDonald, Vanessa C. Wheeler:
A novel approach to investigate tissue-specific trinucleotide repeat instability. BMC Syst. Biol. 4: 29 (2010) - [j2]Jon W. Huss III, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel D. Pizarro, Faramarz Valafar, John B. Hogenesch, Andrew I. Su:
The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res. 38(Database-Issue): 633-639 (2010) - 2006
- [j1]Phillip McClurg, Mathew T. Pletcher, Tim Wiltshire, Andrew I. Su:
Comparative analysis of haplotype association mapping algorithms. BMC Bioinform. 7: 61 (2006)
Conference and Workshop Papers
- 2019
- [c10]Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su:
Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts. AKBC 2019 - 2018
- [c9]Annika Jacobsen, Andra Waagmeester, Rajaram Kaliyaperumal, Gregory S. Stupp, Lynn M. Schriml, Mark Thompson, Andrew I. Su, Marco Roos:
Wikidata as an intuitive resource towards semantic data modeling in data FAIRification. SWAT4LS 2018 - 2016
- [c8]Benjamin M. Good, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka, Timothy Putman, Andrew I. Su, Andra Waagmeester:
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration. ICBO/BioCreative 2016 - [c7]Benjamin M. Good, Timothy Putman, Andrew I. Su, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka:
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration. ICBO/BioCreative 2016 - [c6]Andra Waagmeester, Egon L. Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E. Putman, Julia Turner, Lynn M. Schriml, Paul Pavlidis, Andrew I. Su, Benjamin M. Good:
Linking Wikidata to the Rest of the Semantic Web. SWAT4LS 2016 - 2015
- [c5]Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu:
Session Introduction. Pacific Symposium on Biocomputing 2015: 267-269 - [c4]Benjamin M. Good, Max Nanis, Chunlei Wu, Andrew I. Su:
Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts. Pacific Symposium on Biocomputing 2015: 282-293 - [c3]Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Lynn M. Schriml, Andrew I. Su, Benjamin M. Good:
Wikidata: A Platform for Data Integration and Dissemination for the Life Sciences and Beyond. SWAT4LS 2015: 69-73 - 2012
- [c2]Salvatore Loguercio, Erik L. Clarke, Benjamin M. Good, Andrew I. Su:
A Task-Based Approach for Large-Scale Evaluation of the Gene Ontology. HISB 2012: 144 - [c1]Benjamin M. Good, Salvatore Loguercio, Max Nanis, Andrew I. Su:
genegames.org: High-Throughput Access to Biological Knowledge and Reasoning through Online Games. HISB 2012: 145
Informal and Other Publications
- 2023
- [i5]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) - 2015
- [i4]Tong Shu Li, Benjamin M. Good, Andrew I. Su:
Exposing ambiguities in a relation-extraction gold standard with crowdsourcing. CoRR abs/1505.06256 (2015) - [i3]Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good:
Branch: An interactive, web-based tool for testing hypotheses and developing predictive models. CoRR abs/1509.06808 (2015) - 2014
- [i2]Benjamin M. Good, Max Nanis, Andrew I. Su:
Microtask crowdsourcing for disease mention annotation in PubMed abstracts. CoRR abs/1408.1928 (2014) - 2013
- [i1]Benjamin M. Good, Andrew I. Su:
Crowdsourcing for Bioinformatics. CoRR abs/1302.6667 (2013)
Coauthor Index
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