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2024
Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature
Anne Costanzo, Don Clarke, Marie Holt, Siddhartha Sharma, Kenna Nagy, …, M G Finn, Paul B Savage, Michael Gottschalk, Jeremy Pettus, Luc Teyton
The Journal of Immunology
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01 Mar 2024
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doi:10.4049/jimmunol.2300769
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PMID: 38426888
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PMCID: PMC10944819
Perspectives on tracking data reuse across biodata resources
Karen E Ross, Frederic B Bastian, Matt Buys, Charles E Cook, Peter D’Eustachio, …, Darren A Natale, Karen Ross, C R Vinayaka, Yuqi Wang, Jian Zhang
Bioinformatics Advances
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01 Jan 2024
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doi:10.1093/bioadv/vbae057
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PMID: 38721398
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PMCID: PMC11076920
2023
DrugMechDB: A Curated Database of Drug Mechanisms
Adriana Carolina Gonzalez-Cavazos, Anna Tanska, Michael Mayers, Denise Carvalho-Silva, Brindha Sridharan, Patrick A. Rewers, Umasri Sankarlal, Lakshmanan Jagannathan, Andrew I. Su
Scientific Data
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16 Sep 2023
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doi:10.1038/s41597-023-02534-z
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PMID: 37717042
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PMCID: PMC10505144
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, …, Kristina Hanspers, Ayushi Agrawal, Alexander R Pico, Chunlei Wu, Andrew I Su
Bioinformatics
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01 Sep 2023
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doi:10.1093/bioinformatics/btad570
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PMID: 37707514
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PMCID: PMC11015316
Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database
Eric Hu, Tong Shu Li, Nathan E. Wineinger, Andrew I. Su
Alzheimer's Research & Therapy
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24 Jun 2023
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doi:10.1186/s13195-023-01255-0
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PMID: 37355615
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PMCID: PMC10290352
Drug Repurposing using consilience of Knowledge Graph Completion methods
Roger Tu, Meghamala Sinha, Carolina González, Eric Hu, Shehzaad Dhuliawala, Andrew McCallum, Andrew I. Su
Cold Spring Harbor Laboratory
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14 May 2023
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doi:10.1101/2023.05.12.540594
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PMID: 39149283
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PMCID: PMC11326126
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
Marco A. Cano, Ginger Tsueng, Xinghua Zhou, Jiwen Xin, Laura D. Hughes, Julia L. Mullen, Andrew I. Su, Chunlei Wu
BMC Bioinformatics
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20 Apr 2023
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doi:10.1186/s12859-023-05258-4
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PMID: 37081398
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PMCID: PMC10116472
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, …, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen, Laura D. Hughes
Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources
Ginger Tsueng, Julia L. Mullen, Manar Alkuzweny, Marco Cano, Benjamin Rush, …, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes
Developing a standardized but extendable framework to increase the findability of infectious disease datasets
Ginger Tsueng, Marco A. Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, …, Chunlei Wu, Liliana Brown, Reed S. Shabman, Laura D. Hughes, Serdar Turkarslan
Addressing barriers in FAIR data practices for biomedical data
Laura D. Hughes, Ginger Tsueng, Jack DiGiovanna, Thomas D. Horvath, Luke V. Rasmussen, …, Serdar Turkarslan, Qinglong Wu, Chunlei Wu, Andrew I. Su, Lars Pache
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, …, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu
Journal of Clinical and Translational Science
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01 Jan 2023
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doi:10.1017/cts.2023.619
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PMID: 37900350
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PMCID: PMC10603356
2022
A retrospective evaluation of a decade of Gene Wiki Reviews and their impact
Andre J. van Wijnen, Erica Golemis, Israel Hanukoglu, Stephen Kwok-Wing Tsui, Eric Hu, Sabah Ul-Hasan, Janet Joy, Andrew I. Su, Ginger Tsueng
Progress toward a universal biomedical data translator
Karamarie Fecho, Anne E. Thessen, Sergio E. Baranzini, Chris Bizon, Jennifer J. Hadlock, …, Greg Hyde, Adam Johs, Andrew I. Su, Guangrong Qin, Qian Zhu
Clinical and Translational Science
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06 Jun 2022
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doi:10.1111/cts.13301
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PMID: 35611543
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PMCID: PMC9372428
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, …, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall
Clinical and Translational Science
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06 Jun 2022
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doi:10.1111/cts.13302
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PMID: 36125173
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PMCID: PMC9372416
Design and application of a knowledge network for automatic prioritization of drug mechanisms
Michael Mayers, Roger Tu, Dylan Steinecke, Tong Shu Li, Núria Queralt-Rosinach, Andrew I Su
Bioinformatics
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06 Apr 2022
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doi:10.1093/bioinformatics/btac205
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PMID: 35561182
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PMCID: PMC9113361
Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis
Peter S. Thuy-Boun, Ana Y. Wang, Ana Crissien-Martinez, Janice H. Xu, Sandip Chatterjee, Gregory S. Stupp, Andrew I. Su, Walter J. Coyle, Dennis W. Wolan
Molecular & Cellular Proteomics
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01 Mar 2022
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doi:10.1016/j.mcpro.2022.100197
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PMID: 35033677
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PMCID: PMC8941213
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research
Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian, Marco Alvarado Cano, …, Yao Yao, Ricardo Avila, Greg Taylor, Andrew I Su, Chunlei Wu
Bioinformatics
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10 Jan 2022
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doi:10.1093/bioinformatics/btac017
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PMID: 35020801
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PMCID: PMC8963279
2021
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses
Andra Waagmeester, Egon L. Willighagen, Andrew I. Su, Martina Kutmon, Jose Emilio Labra Gayo, Daniel Fernández-Álvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. Koehorst
2020
Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer
Justin Wang, Ingrid Vallee, Aditi Dutta, Yu Wang, Zhongying Mo, Ze Liu, Haissi Cui, Andrew I. Su, Xiang-Lei Yang
Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity
Kwang Il Lee, Ramya Gamini, Merissa Olmer, Yasunari Ikuta, Joe Hasei, …, Shawn P. Grogan, Darryl D. D’Lima, Hiroshi Asahara, Andrew I. Su, Martin K. Lotz
Science Translational Medicine
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28 Oct 2020
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doi:10.1126/scitranslmed.aan7967
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PMID: 33115953
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PMCID: PMC7955769
Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing
Laura Riva, Shuofeng Yuan, Xin Yin, Laura Martin-Sancho, Naoko Matsunaga, …, Andrew I. Su, Adolfo García-Sastre, Arnab K. Chatterjee, Kwok-Yung Yuen, Sumit K. Chanda
Wikidata as a knowledge graph for the life sciences
Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M Good, Malachi Griffith, …, Roger Tu, Sabah Ul-Hasan, Egon Willighagen, Chunlei Wu, Andrew I Su
Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas
Kim M. Summers, Stephen J. Bush, Chunlei Wu, Andrew I. Su, Charity Muriuki, …, Lel Eory, Lindsey A. Waddell, Richard Talbot, Alan L. Archibald, David A. Hume
Frontiers in Genetics
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14 Feb 2020
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doi:10.3389/fgene.2019.01355
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PMID: 32117413
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PMCID: PMC7034361
Structured reviews for data and knowledge-driven research
Núria Queralt-Rosinach, Gregory S Stupp, Tong Shu Li, Michael Mayers, Maureen E Hoatlin, Matthew Might, Benjamin M Good, Andrew I Su
2019
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network
Michael Mayers, Tong Shu Li, Núria Queralt-Rosinach, Andrew I. Su
BMC Bioinformatics
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01 Dec 2019
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doi:10.1186/s12859-019-3297-0
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PMID: 31829175
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PMCID: PMC6907279
Advancing computational biology and bioinformatics research through open innovation competitions
Andrea Blasco, Michael G. Endres, Rinat A. Sergeev, Anup Jonchhe, N. J. Maximilian Macaluso, …, Bryan Briney, Chunlei Wu, Andrew I. Su, Aravind Subramanian, Karim R. Lakhani
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts
Ginger Tsueng, Max Nanis, Jennifer T Fouquier, Michael Mayers, Benjamin M Good, Andrew I Su
Bioinformatics
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03 Sep 2019
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doi:10.1093/bioinformatics/btz678
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PMID: 31504205
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PMCID: PMC8104067
Position β57 of I-A
g7
controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset
Louis Gioia, Marie Holt, Anne Costanzo, Siddhartha Sharma, Brian Abe, …, Andrew Su, Clayton Mathews, Yi-Guang Chen, Emil Unanue, Luc Teyton
Science Immunology
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02 Aug 2019
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doi:10.1126/sciimmunol.aaw6329
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PMID: 31471352
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PMCID: PMC6816460
Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements.
Ginger Tsueng, Arun Kumar, Steven Max Nanis, Andrew I Su
Human Computation
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02 Jun 2019
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doi:10.15346/hc.v6i1.4
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids
Oscar D. Murillo, William Thistlethwaite, Joel Rozowsky, Sai Lakshmi Subramanian, Rocco Lucero, …, Robert L. Raffai, Louise C. Laurent, Matthew E. Roth, Mark B. Gerstein, Aleksandar Milosavljevic
ChlamBase: a curated model organism database for the Chlamydia research community
Tim Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, …, Gregory S Stupp, Andra Waagmeester, Benjamin M Good, Chunlei Wu, Andrew I Su
2018
Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges
Siddhartha Sharma, Louis Gioia, Brian Abe, Marie Holt, Anne Costanzo, Lisa Kain, Andrew Su, Luc Teyton
Molecular Immunology
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01 Nov 2018
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doi:10.1016/j.molimm.2018.09.020
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PMID: 30300798
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PMCID: PMC6258053
Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis
K.M. Fisch, R. Gamini, O. Alvarez-Garcia, R. Akagi, M. Saito, Y. Muramatsu, T. Sasho, J.A. Koziol, A.I. Su, M.K. Lotz
Osteoarthritis and Cartilage
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01 Nov 2018
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doi:10.1016/j.joca.2018.07.012
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PMID: 30081074
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PMCID: PMC6245598
Association study of long-term kidney transplant rejection using whole-exome sequencing
Louis Gioia, Sunil Kurian, Tony S. Mondala, Laia Bassaganyas, Pui-Yan Kwok, Daniel R. Salomon, Andrew I. Su
Cold Spring Harbor Laboratory
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16 Oct 2018
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doi:10.1101/444497
The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis
Jeff Janes, Megan E. Young, Emily Chen, Nicole H. Rogers, Sebastian Burgstaller-Muehlbacher, …, Case W. McNamara, Matthew S. Tremblay, Andrew I. Su, Peter G. Schultz, Arnab K. Chatterjee
Proceedings of the National Academy of Sciences
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03 Oct 2018
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doi:10.1073/pnas.1810137115
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PMID: 30282735
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PMCID: PMC6196526
The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app
Jennifer M. Radin, Steven R. Steinhubl, Andrew I. Su, Hansa Bhargava, Benjamin Greenberg, Brian M. Bot, Megan Doerr, Eric J. Topol
npj Digital Medicine
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05 Sep 2018
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doi:10.1038/s41746-018-0052-2
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PMID: 31304325
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PMCID: PMC6550256
Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3–mediated translation initiation
Darren M. Hutt, Salvatore Loguercio, Daniela Martino Roth, Andrew I. Su, William E. Balch
Journal of Biological Chemistry
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01 Aug 2018
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doi:10.1074/jbc.RA118.003192
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PMID: 30006345
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PMCID: PMC6120211
Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass
Ana Y. Wang, Peter S. Thuy-Boun, Gregory S. Stupp, Andrew I. Su, Dennis W. Wolan
Cold Spring Harbor Laboratory
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11 Jul 2018
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doi:10.1101/367599
Exploring applications of crowdsourcing to cryo-EM
Jacob Bruggemann, Gabriel C. Lander, Andrew I. Su
Journal of Structural Biology
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01 Jul 2018
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doi:10.1016/j.jsb.2018.02.006
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PMID: 29486249
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PMCID: PMC6086358
A genome-wide survey of mutations in the Jurkat cell line
Louis Gioia, Azeem Siddique, Steven R. Head, Daniel R. Salomon, Andrew I. Su
Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection
Shang Ma, Stuart Cahalan, Gregory LaMonte, Nathan D. Grubaugh, Weizheng Zeng, …, Andrew I. Su, Eric Honore, Elizabeth A. Winzeler, Kristian G. Andersen, Ardem Patapoutian
FoxO transcription factors modulate autophagy and proteoglycan 4 in cartilage homeostasis and osteoarthritis
Tokio Matsuzaki, Oscar Alvarez-Garcia, Sho Mokuda, Keita Nagira, Merissa Olmer, …, Kohei Miyata, Yukio Akasaki, Andrew I. Su, Hiroshi Asahara, Martin K. Lotz
Science Translational Medicine
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14 Feb 2018
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doi:10.1126/scitranslmed.aan0746
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PMID: 29444976
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PMCID: PMC6204214
Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups
Clara Moon, Gregory S. Stupp, Andrew I. Su, Dennis W. Wolan
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su, Chunlei Wu
BMC Bioinformatics
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01 Feb 2018
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doi:10.1186/s12859-018-2041-5
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PMID: 29390967
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PMCID: PMC5796402
2017
Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells
Marie Holt, Anne Costanzo, Louis Gioia, Brian Abe, Andrew I. Su, Luc Teyton
Academics can help shape Wikipedia
Thomas Shafee, Daniel Mietchen, Andrew I. Su
Science Game Lab: tool for the unification of biomedical games with a purpose
Benjamin M. Good, Sarah Santini, Margaret Wallace, Nicholas Fortugno, John Szeder, Patrick Mooney, Jerome Waldispuhl, Ginger Tsueng, Andrew I Su
Cold Spring Harbor Laboratory
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10 Jul 2017
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doi:10.1101/156141
Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes
R. Akagi, Y. Akatsu, K.M. Fisch, O. Alvarez-Garcia, T. Teramura, Y. Muramatsu, M. Saito, T. Sasho, A.I. Su, M.K. Lotz
Osteoarthritis and Cartilage
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01 Jun 2017
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doi:10.1016/j.joca.2016.11.007
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PMID: 27884645
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PMCID: PMC5438901
EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices
Nikhil Gopal, Andrew Su, Chunlei Wu, Sean D. Mooney
Cold Spring Harbor Laboratory
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29 Mar 2017
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doi:10.1101/121178
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman, …, David H Spencer, Lukas D Wartman, Richard K Wilson, Elaine R Mardis, Obi L Griffith
Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease
Michael D. Mayers, Clara Moon, Gregory S. Stupp, Andrew I. Su, Dennis W. Wolan
Journal of Proteome Research
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23 Jan 2017
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doi:10.1021/acs.jproteome.6b00938
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PMID: 28052195
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PMCID: PMC5441882
WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata
Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin Diesh, …, Monica Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good
2016
Citizen Science for Mining the Biomedical Literature
Ginger Tsueng, Steven M. Nanis, Jennifer Fouquier, Benjamin M. Good, Andrew I. Su
Citizen Science: Theory and Practice
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31 Dec 2016
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doi:10.5334/cstp.56
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PMID: 30416754
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PMCID: PMC6226017
Gene Wiki Reviews—Raising the quality and accessibility of information about the human genome
Ginger Tsueng, Benjamin M. Good, Peipei Ping, Erica Golemis, Israel Hanukoglu, Andre J. van Wijnen, Andrew I. Su
Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy
O. Alvarez-Garcia, M. Olmer, R. Akagi, Y. Akasaki, K.M. Fisch, T. Shen, A.I. Su, M.K. Lotz
Osteoarthritis and Cartilage
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01 Sep 2016
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doi:10.1016/j.joca.2016.04.015
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PMID: 27118398
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PMCID: PMC4992644
A comprehensive and scalable database search system for metaproteomics
Sandip Chatterjee, Gregory S. Stupp, Sung Kyu Robin Park, Jean-Christophe Ducom, John R. Yates, Andrew I. Su, Dennis W. Wolan
Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage
Oscar Alvarez‐Garcia, Kathleen M. Fisch, Nathan E. Wineinger, Ryuichiro Akagi, Masahiko Saito, Takahisa Sasho, Andrew I. Su, Martin K. Lotz
Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems
Maggie P. Y. Lam, Vidya Venkatraman, Yi Xing, Edward Lau, Quan Cao, Dominic C. M. Ng, Andrew I. Su, Junbo Ge, Jennifer E. Van Eyk, Peipei Ping
Journal of Proteome Research
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19 Jul 2016
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doi:10.1021/acs.jproteome.6b00095
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PMID: 27356587
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PMCID: PMC5120959
Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long‐Term Outcomes
B.D. Modena, S.M. Kurian, L.W. Gaber, J. Waalen, A.I. Su, …, R.S. Sung, H. Shidban, L. Chan, M.M. Abecassis, D.R. Salomon
American Journal of Transplantation
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01 Jul 2016
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doi:10.1111/ajt.13728
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PMID: 26990570
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PMCID: PMC5501990
YY1 plays an essential role at all stages of B-cell differentiation
Eden Kleiman, Haiqun Jia, Salvatore Loguercio, Andrew I. Su, Ann J. Feeney
Proceedings of the National Academy of Sciences
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22 Jun 2016
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doi:10.1073/pnas.1606297113
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PMID: 27335461
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PMCID: PMC4941496
High-performance web services for querying gene and variant annotation
Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, …, Patricia L. Whetzel, Christopher J. Mungall, Sean D. Mooney, Andrew I. Su, Chunlei Wu
Extending gene ontology in the context of extracellular RNA and vesicle communication
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, …, Kasey Vickers, Marca H.M. Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C. Laurent
Journal of Biomedical Semantics
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12 Apr 2016
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doi:10.1186/s13326-016-0061-5
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PMID: 27076901
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PMCID: PMC4830068
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models
Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good
Bioinformatics
·
07 Mar 2016
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doi:10.1093/bioinformatics/btw117
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PMID: 27153723
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PMCID: PMC4920125
The Implicitome: A Resource for Rationalizing Gene-Disease Associations
Kristina M. Hettne, Mark Thompson, Herman H. H. B. M. van Haagen, Eelke van der Horst, Rajaram Kaliyaperumal, …, Gert-Jan B. van Ommen, Marco Roos, Peter A.C. ‘t Hoen, Barend Mons, Erik A. Schultes
Wikidata as a semantic framework for the Gene Wiki initiative
Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim Putman, …, Chinmay Naik, Paul Pavlidis, Lynn Schriml, Benjamin M Good, Andrew I Su
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text
Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes
Tim E. Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su, Benjamin M. Good
A crowdsourcing workflow for extracting chemical-induced disease relations from free text
Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
2015
BioGPS: building your own mash-up of gene annotations and expression profiles
Chunlei Wu, Xuefeng Jin, Ginger Tsueng, Cyrus Afrasiabi, Andrew I. Su
Prioritizing Proteomics Assay Development for Clinical Translation
Maggie P.Y. Lam, Vidya Venkatraman, Quan Cao, Ding Wang, T. Umut Dincer, …, Andrew I. Su, Yi Xing, Junbo Ge, Peipei Ping, Jennifer E. Van Eyk
Journal of the American College of Cardiology
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01 Jul 2015
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doi:10.1016/j.jacc.2015.04.072
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PMID: 26160638
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Tobias Meißner, Kathleen M Fisch, Louis Gioia, Andrew I Su
BMC Medical Genomics
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21 May 2015
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doi:10.1186/s12920-015-0095-z
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PMID: 25989980
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PMCID: PMC4494802
The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors
Jeffrey S. Wieskopf, Jayanti Mathur, Walrati Limapichat, Michael R. Post, Mona Al-Qazzaz, …, Sarah C. R. Lummis, M. Imad Damaj, Henry A. Lester, Ardem Patapoutian, Jeffrey S. Mogil
Science Translational Medicine
·
13 May 2015
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doi:10.1126/scitranslmed.3009986
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PMID: 25972004
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PMCID: PMC5018401
Crowdsourcing in biomedicine: challenges and opportunities
Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu
Briefings in Bioinformatics
·
17 Apr 2015
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doi:10.1093/bib/bbv021
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PMID: 25888696
·
PMCID: PMC4719068
Harnessing the Heart of Big Data
Sarah B. Scruggs, Karol Watson, Andrew I. Su, Henning Hermjakob, John R. Yates, Merry L. Lindsey, Peipei Ping
Circulation Research
·
27 Mar 2015
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doi:10.1161/CIRCRESAHA.115.306013
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PMID: 25814682
·
PMCID: PMC4721634
Omics Pipe: a community-based framework for reproducible multi-omics data analysis
Kathleen M. Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan M. Carland, Salvatore Loguercio, Andrew I. Su
Bioinformatics
·
30 Jan 2015
·
doi:10.1093/bioinformatics/btv061
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PMID: 25637560
·
PMCID: PMC4443682
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies
Sai Lakshmi Subramanian, Robert R. Kitchen, Roger Alexander, Bob S. Carter, Kei‐Hoi Cheung, …, Matthew E. Roth, Joel S. Rozowsky, Andrew I. Su, Mark B. Gerstein, Aleksandar Milosavljevic
Journal of Extracellular Vesicles
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01 Jan 2015
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doi:10.3402/jev.v4.27497
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PMID: 26320941
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PMCID: PMC4553261
2014
MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS
BENJAMIN M GOOD, MAX NANIS, CHUNLEI WU, ANDREW I SU
Biocomputing 2015
·
01 Nov 2014
·
doi:10.1142/9789814644730_0028
CROWDSOURCING AND MINING CROWD DATA
ROBERT LEAMAN, BENJAMIN M. GOOD, ANDREW I. su, ZHIYONG LU
Biocomputing 2015
·
01 Nov 2014
·
doi:10.1142/9789814644730_0026
Oxidative Stress Diverts tRNA Synthetase to Nucleus for Protection against DNA Damage
Na Wei, Yi Shi, Lan N. Truong, Kathleen M. Fisch, Tao Xu, …, Yun-Shiuan Olivia Hsu, Shuji Kishi, Andrew I. Su, Xiaohua Wu, Xiang-Lei Yang
Molecular Cell
·
01 Oct 2014
·
doi:10.1016/j.molcel.2014.09.006
·
PMID: 25284223
·
PMCID: PMC4224670
MyGene.info: gene annotation query as a service
Chunlei Wu, Adam Mark, Andrew I. Su
Cold Spring Harbor Laboratory
·
18 Sep 2014
·
doi:10.1101/009332
Organizing knowledge to enable personalization of medicine in cancer
Benjamin M Good, Benjamin J Ainscough, Josh F McMichael, Andrew I Su, Obi L Griffith
Functional expression of dental plaque microbiota
Scott N. Peterson, Tobias Meissner, Andrew I. Su, Erik Snesrud, Ana C. Ong, Nicholas J. Schork, Walter A. Bretz
Frontiers in Cellular and Infection Microbiology
·
14 Aug 2014
·
doi:10.3389/fcimb.2014.00108
·
PMID: 25177549
·
PMCID: PMC4132376
The Cure: Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast Cancer Survival Prediction
Benjamin M Good, Salvatore Loguercio, Obi L Griffith, Max Nanis, Chunlei Wu, Andrew I Su
2013
Gene Wiki Reviews: Marrying crowdsourcing with traditional peer review
Andrew I. Su, Benjamin M. Good, Andre J. van Wijnen
Ten Simple Rules for Cultivating Open Science and Collaborative R&D
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
PLoS Computational Biology
·
26 Sep 2013
·
doi:10.1371/journal.pcbi.1003244
·
PMID: 24086123
·
PMCID: PMC3784487
Deep Sequencing of the Murine Igh Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies
Nancy M. Choi, Salvatore Loguercio, Jiyoti Verma-Gaur, Stephanie C. Degner, Ali Torkamani, Andrew I. Su, Eugene M. Oltz, Maxim Artyomov, Ann J. Feeney
The Journal of Immunology
·
01 Sep 2013
·
doi:10.4049/jimmunol.1301279
·
PMID: 23898036
·
PMCID: PMC3778908
Identification of Regulatory Elements That Control PPARγ Expression in Adipocyte Progenitors
Wen-Ling Chou, Andrea Galmozzi, David Partida, Kevin Kwan, Hui Yeung, Andrew I. Su, Enrique Saez
Dizeez: An Online Game for Human Gene-Disease Annotation
Salvatore Loguercio, Benjamin M. Good, Andrew I. Su
Unifying model for molecular determinants of the preselection Vβ repertoire
Suhasni Gopalakrishnan, Kinjal Majumder, Alexander Predeus, Yue Huang, Olivia I. Koues, …, Salvatore Loguercio, Andrew I. Su, Ann J. Feeney, Maxim N. Artyomov, Eugene M. Oltz
Proceedings of the National Academy of Sciences
·
05 Aug 2013
·
doi:10.1073/pnas.1304048110
·
PMID: 23918392
·
PMCID: PMC3752219
Crowdsourcing for bioinformatics
Benjamin M. Good, Andrew I. Su
Bioinformatics
·
19 Jun 2013
·
doi:10.1093/bioinformatics/btt333
·
PMID: 23782614
·
PMCID: PMC3722523
Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Diverse ER Proteostasis Environments
Matthew D. Shoulders, Lisa M. Ryno, Joseph C. Genereux, James J. Moresco, Patricia G. Tu, Chunlei Wu, John R. Yates, Andrew I. Su, Jeffery W. Kelly, R. Luke Wiseman
A task-based approach for Gene Ontology evaluation
Erik L Clarke, Salvatore Loguercio, Benjamin M Good, Andrew I Su
Journal of Biomedical Semantics
·
01 Apr 2013
·
doi:10.1186/2041-1480-4-S1-S4
·
PMID: 23734599
·
PMCID: PMC3633003
Zone‐specific gene expression patterns in articular cartilage
Shawn P. Grogan, Stuart F. Duffy, Chantal Pauli, James A. Koziol, Andrew I. Su, Darryl D. D’Lima, Martin K. Lotz
2012
BioGPS and MyGene.info: organizing online, gene-centric information
Chunlei Wu, Ian MacLeod, Andrew I. Su
A gene expression atlas of the domestic pig
Tom C Freeman, Alasdair Ivens, J Kenneth Baillie, Dario Beraldi, Mark W Barnett, …, Andrew I Su, Kim M Summers, Christopher K Tuggle, Alan L Archibald, David A Hume
genegames.org: High-Throughput Access to Biological Knowledge and Reasoning through Online Games
Benjamin M. Good, Salvatore Loguercio, Max Nanis, Andrew I. Su
2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology
·
01 Sep 2012
·
doi:10.1109/HISB.2012.70
Identification of Serum-Derived Sphingosine-1-Phosphate as a Small Molecule Regulator of YAP
Eric Miller, Jiayi Yang, Michael DeRan, Chunlei Wu, Andrew I. Su, Ghislain M.C. Bonamy, Jun Liu, Eric C. Peters, Xu Wu
BioGPS and GXD: mouse gene expression data—the benefits and challenges of data integration
Martin Ringwald, Chunlei Wu, Andrew I. Su
The evolution of dynamin to regulate clathrin‐mediated endocytosis
Ya‐Wen Liu, Andrew I. Su, Sandra L. Schmid
Linking genes to diseases with a SNPedia-Gene Wiki mashup
Benjamin M Good, Erik L Clarke, Salvatore Loguercio, Andrew I Su
Journal of Biomedical Semantics
·
24 Apr 2012
·
doi:10.1186/2041-1480-3-S1-S6
·
PMID: 22541597
·
PMCID: PMC3337266
Building a biomedical semantic network in Wikipedia with Semantic Wiki Links
B. M. Good, E. L. Clarke, S. Loguercio, A. I. Su
2011
Mining the Gene Wiki for functional genomic knowledge
Benjamin M Good, Douglas G Howe, Simon M Lin, Warren A Kibbe, Andrew I Su
The Gene Wiki in 2011: community intelligence applied to human gene annotation
Benjamin M. Good, Erik L. Clarke, Luca de Alfaro, Andrew I. Su
CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma
Yue Hu, Anna V. Galkin, Chunlei Wu, Venkateshwar Reddy, Andrew I. Su
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data
Banu Dost, Chunlei Wu, Andrew Su, Vineet Bafna
IEEE/ACM Transactions on Computational Biology and Bioinformatics
·
01 May 2011
·
doi:10.1109/TCBB.2010.34
·
PMID: 20479508
Games with a scientific purpose
Benjamin M Good, Andrew I Su
2010
Phenotypic Characterization of a Genetically Diverse Panel of Mice for Behavioral Despair and Anxiety
Brooke H. Miller, Laura E. Schultz, Anisha Gulati, Andrew I. Su, Mathew T. Pletcher
Integrative Analysis of Low- and High-Resolution eQTL
Salvatore Loguercio, Rupert W. Overall, Jacob J. Michaelson, Tim Wiltshire, Mathew T. Pletcher, Brooke H. Miller, John R. Walker, Gerd Kempermann, Andrew I. Su, Andreas Beyer
A novel approach to investigate tissue-specific trinucleotide repeat instability
Jong-Min Lee, Jie Zhang, Andrew I Su, John R Walker, Tim Wiltshire, …, Michel Cyr, Isaac Kohane, James F Gusella, Marcy E MacDonald, Vanessa C Wheeler
Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency
Rodolfo Gonzalez, Lori L. Jennings, Mark Knuth, Anthony P. Orth, Heath E. Klock, …, Deborah G. Nguyen, Evan Y. Snyder, Peter G. Schultz, Jennifer L. Harris, Scott A. Lesley
Proceedings of the National Academy of Sciences
·
23 Feb 2010
·
doi:10.1073/pnas.0914019107
·
PMID: 20133595
·
PMCID: PMC2840467
2009
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, …, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su
A Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells
Eric E. Zhang, Andrew C. Liu, Tsuyoshi Hirota, Loren J. Miraglia, Genevieve Welch, …, Jon W. Huss, Jeff Janes, Andrew I. Su, John B. Hogenesch, Steve A. Kay
The Gene Wiki: community intelligence applied to human gene annotation
Jon W. Huss, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B. Hogenesch, Andrew I. Su
Genome-Wide Haplotype Association Mapping in Mice Identifies a Genetic Variant in CER1 Associated With BMD and Fracture in Southern Chinese Women
Paul LF Tang, Ching-Lung Cheung, Pak C Sham, Philip McClurg, Bob Lee, …, Julian A Tanner, Andrew I Su, Kathryn SE Cheah, Annie WC Kung, You-Qiang Song
A Common and Unstable Copy Number Variant Is Associated with Differences in Glo1 Expression and Anxiety-Like Behavior
Richard Williams, Jackie E. Lim, Bettina Harr, Claudia Wing, Ryan Walters, …, Andrew I. Su, Greta Sokoloff, Lisa M. Tarantino, Justin O. Borevitz, Abraham A. Palmer
Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus
John Paul Pezacki, Selena M Sagan, Angela M Tonary, Yanouchka Rouleau, Sylvie Bélanger, Lubica Supekova, Andrew I Su
2008
Genetical Genomics: Spotlight on QTL Hotspots
Rainer Breitling, Yang Li, Bruno M. Tesson, Jingyuan Fu, Chunlei Wu, …, Alice Gerrits, Leonid V. Bystrykh, Gerald de Haan, Andrew I. Su, Ritsert C. Jansen
A Gene Wiki for Community Annotation of Gene Function
Jon W Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J Vickers, Faramarz Valafar, Andrew I Su
Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators
Chunlei Wu, David L. Delano, Nico Mitro, Stephen V. Su, Jeff Janes, …, Akira Kohsaka, Joseph Bass, Enrique Saez, Tim Wiltshire, Andrew I. Su
Expression analysis of G Protein-Coupled Receptors in mouse macrophages
Jane E Lattin, Kate Schroder, Andrew I Su, John R Walker, Jie Zhang, …, Kaoru Saijo, Christopher K Glass, David A Hume, Stuart Kellie, Matthew J Sweet
2007
Genomewide Association Analysis in Diverse Inbred Mice: Power and Population Structure
Phillip McClurg, Jeff Janes, Chunlei Wu, David L Delano, John R Walker, …, Kazuhiro Shimomura, Akira Kohsaka, Joseph Bass, Tim Wiltshire, Andrew I Su
Power-law-like distributions in biomedical publications and research funding
Andrew I Su, John B Hogenesch
2006
Reply to “Normalization procedures and detection of linkage signal in genetical-genomics experiments”
Elissa J Chesler, Leonid Bystrykh, Gerald de Haan, Michael P Cooke, Andrew Su, Kenneth F Manly, Robert W Williams
Nature Genetics
·
01 Aug 2006
·
doi:10.1038/ng0806-856
Visual Artificial Tongue for Quantitative Metal‐Cation Analysis by an Off‐the‐Shelf Dye Array
Jae Wook Lee, Jun‐Seok Lee, Mira Kang, Andrew I. Su, Young‐Tae Chang
An efficient rapid system for profiling the cellular activities of molecular libraries
Jonathan S. Melnick, Jeff Janes, Sungjoon Kim, Jim Y. Chang, Daniel G. Sipes, …, Robert Downs, Nathanael S. Gray, Peter G. Schultz, Markus Warmuth, Jeremy S. Caldwell
Proceedings of the National Academy of Sciences
·
21 Feb 2006
·
doi:10.1073/pnas.0511292103
·
PMID: 16492761
·
PMCID: PMC1413928
Comparative analysis of haplotype association mapping algorithms
Phillip McClurg, Mathew T Pletcher, Tim Wiltshire, Andrew I Su
The influence of cholesterol and lipid metabolism on host cell structure and hepatitis C virus replication
Selena M Sagan, Yanouchka Rouleau, Cynthia Leggiadro, Lubica Supekova, Peter G Schultz, Andrew I Su, John Paul Pezacki
2005
Large-Scale Profiling of Rab GTPase Trafficking Networks: The Membrome
Cemal Gurkan, Hilmar Lapp, Christelle Alory, Andrew I. Su, John B. Hogenesch, William E. Balch
Molecular Biology of the Cell
·
01 Aug 2005
·
doi:10.1091/mbc.E05-01-0062
·
PMID: 15944222
·
PMCID: PMC1182321
Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes
Jing Yang, Andrew I. Su, Wen-Hsiung Li
HierS: Hierarchical Scaffold Clustering Using Topological Chemical Graphs
Steven J. Wilkens, Jeff Janes, Andrew I. Su
Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'
Leonid Bystrykh, Ellen Weersing, Bert Dontje, Sue Sutton, Mathew T Pletcher, …, Rudi Alberts, Ritsert C Jansen, Robert W Williams, Michael P Cooke, Gerald de Haan
Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells
Jiang F. Zhong, Yi Zhao, Susan Sutton, Andrew Su, Yuxia Zhan, …, Chunli Yan, Tim Gallaher, Patrick B. Johnston, W. French Anderson, Michael P. Cooke
2004
Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse
Mathew T Pletcher, Philip McClurg, Serge Batalov, Andrew I Su, S. Whitney Barnes, …, Deborah Nusskern, Molly A Bogue, Richard J Mural, Beverly Paigen, Tim Wiltshire
A gene atlas of the mouse and human protein-encoding transcriptomes
Andrew I. Su, Tim Wiltshire, Serge Batalov, Hilmar Lapp, Keith A. Ching, …, Mimi Hayakawa, Gabriel Kreiman, Michael P. Cooke, John R. Walker, John B. Hogenesch
Applications of a Rat Multiple Tissue Gene Expression Data Set
John R. Walker, Andrew I. Su, David W. Self, John B. Hogenesch, Hilmar Lapp, Rainer Maier, Daniel Hoyer, Graeme Bilbe
2003
Genome-Wide Analysis of CREB Target Genes Reveals A Core Promoter Requirement for cAMP Responsiveness
Michael D Conkright, Ernesto Guzmán, Lawrence Flechner, Andrew I Su, John B Hogenesch, Marc Montminy
Molecular Cell
·
01 May 2003
·
doi:10.1016/S1097-2765(03)00199-0
Genome-Wide Analysis of CREB Target Genes Reveals A Core Promoter Requirement for cAMP Responsiveness
Michael D. Conkright, Ernesto Guzmán, Lawrence Flechner, Andrew I. Su, John B. Hogenesch, Marc Montminy
2002
Genomic analysis of the host response to hepatitis C virus infection
Andrew I. Su, John P. Pezacki, Lisa Wodicka, Amy D. Brideau, Lubica Supekova, …, Stefan Wieland, Jens Bukh, Robert H. Purcell, Peter G. Schultz, Francis V. Chisari
Large Scale Molecular Analysis Identifies Genes with Altered Expression in Salivary Adenoid Cystic Carcinoma
Henry F. Frierson, Adel K. El-Naggar, John B. Welsh, Lisa M. Sapinoso, Andrew I. Su, Jun Cheng, Takashi Saku, Christopher A. Moskaluk, Garret M. Hampton
The American Journal of Pathology
·
01 Oct 2002
·
doi:10.1016/S0002-9440(10)64408-2
·
PMID: 12368205
·
PMCID: PMC1867312
Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice
Andrew I. Su, Luca G. Guidotti, John Paul Pezacki, Francis V. Chisari, Peter G. Schultz
Genomic Effects of Polyamide/DNA Interactions on mRNA Expression
Lubica Supekova, John Paul Pezacki, Andrew I. Su, Colin J. Loweth, Rainer Riedl, Bernhard Geierstanger, Peter G. Schultz, David E. Wemmer
Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock
Satchidananda Panda, Marina P. Antoch, Brooke H. Miller, Andrew I. Su, Andrew B. Schook, Marty Straume, Peter G. Schultz, Steve A. Kay, Joseph S. Takahashi, John B. Hogenesch
Large-scale analysis of the human and mouse transcriptomes
Andrew I. Su, Michael P. Cooke, Keith A. Ching, Yaron Hakak, John R. Walker, …, Aziz Moqrich, Ardem Patapoutian, Garret M. Hampton, Peter G. Schultz, John B. Hogenesch
2001
Synthesis and Biological Evaluation of Myoseverin Derivatives: Microtubule Assembly Inhibitors
Young-Tae Chang, Sarah M. Wignall, Gustavo R. Rosania, Nathanael S. Gray, Sarah R. Hanson, …, Ho-Sang Moon, Sameep B. Sangankar, Omar Perez, Rebecca Heald, Peter G. Schultz
Molecular classification of human carcinomas by use of gene expression signatures.
A I Su, J B Welsh, L M Sapinoso, S G Kern, P Dimitrov, …, P G Schultz, S M Powell, C A Moskaluk, H F Frierson, G M Hampton
Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer.
J B Welsh, L M Sapinoso, A I Su, S G Kern, J Wang-Rodriguez, C A Moskaluk, H F Frierson, G M Hampton
A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes
John B. Hogenesch, Keith A. Ching, Serge Batalov, Andrew I. Su, John R. Walker, Yingyao Zhou, Steve A. Kay, Peter G. Schultz, Michael P. Cooke
Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type
Gayathri Ratnaswamy, Mary E. Huff, Andrew I. Su, Severine Rion, Jeffery W. Kelly
2000
Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation
Andrew I. Su, David M. Lorber, G. Scott Weston, Walter A. Baase, Brian W. Matthews, Brian K. Shoichet
Proteins: Structure, Function, and Genetics
·
01 Jan 2000
·
doi:10.1002/1097-0134(20010201)42:2<279::AID-PROT150>3.0.CO;2-U
·
PMID: 11119652