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Andrew Su Principal Investigator he/him

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Andrew Su, Ph.D., is the Elden and Verna Strahm Professor at the Scripps Research Institute in the Department of Integrative Structural and Computational Biology (ISCB). Dr. Su earned his PhD in chemistry at Scripps Research in 2002, and was the Associate Director of Bioinformatics at The Genomics Institute of the Novartis Research Foundation (GNF) before returning to Scripps Research as a faculty member in 2011.

The Su lab focuses on building and applying bioinformatics infrastructure for biomedical discovery. Dr. Su has had a long-standing interest in leveraging crowdsourcing to organize and integrate knowledge though projects like the Gene Wiki and Wikidata. In partnership with Chunlei Wu’s lab, he has also worked extensively on creating biomedical APIs and enabling API interoperability through the BioThings project. Most recently, his lab has a particular emphasis on constructing and mining knowledge graphs for drug repurposing. In all this work, the Su lab has embraced the principles of open science, open data, and open source software.

Andrew received his Ph.D. in Chemistry from The Scripps Research Institute, and BA degrees in Chemistry, Computing and Information Systems, and Integrated Science from Northwestern University.

Publications

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  ·  01 Mar 2024  ·  doi:10.4049/jimmunol.2300769  ·  PMID: 38426888  ·  PMCID: PMC10944819

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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  ·  01 Jan 2024  ·  doi:10.1093/bioadv/vbae057  ·  PMID: 38721398  ·  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  ·  16 Sep 2023  ·  doi:10.1038/s41597-023-02534-z  ·  PMID: 37717042  ·  PMCID: PMC10505144

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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  ·  01 Sep 2023  ·  doi:10.1093/bioinformatics/btad570  ·  PMID: 37707514  ·  PMCID: PMC11015316

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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  ·  24 Jun 2023  ·  doi:10.1186/s13195-023-01255-0  ·  PMID: 37355615  ·  PMCID: PMC10290352

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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  ·  14 May 2023  ·  doi:10.1101/2023.05.12.540594  ·  PMID: 39149283  ·  PMCID: PMC11326126

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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  ·  20 Apr 2023  ·  doi:10.1186/s12859-023-05258-4  ·  PMID: 37081398  ·  PMCID: PMC10116472

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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

Nature Methods  ·  23 Feb 2023  ·  doi:10.1038/s41592-023-01769-3  ·  PMID: 36823332  ·  PMCID: PMC10399614

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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

Nature Methods  ·  23 Feb 2023  ·  doi:10.1038/s41592-023-01770-w  ·  PMID: 36823331  ·  PMCID: PMC10393269

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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

Scientific Data  ·  23 Feb 2023  ·  doi:10.1038/s41597-023-01968-9  ·  PMID: 36823157  ·  PMCID: PMC9950378

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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

Scientific Data  ·  23 Feb 2023  ·  doi:10.1038/s41597-023-01969-8  ·  PMID: 36823198  ·  PMCID: PMC9950056

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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  ·  01 Jan 2023  ·  doi:10.1017/cts.2023.619  ·  PMID: 37900350  ·  PMCID: PMC10603356

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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

Gene  ·  01 Jul 2022  ·  doi:10.1016/j.gene.2022.146534  ·  PMID: 35525475

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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  ·  06 Jun 2022  ·  doi:10.1111/cts.13301  ·  PMID: 35611543  ·  PMCID: PMC9372428

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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  ·  06 Jun 2022  ·  doi:10.1111/cts.13302  ·  PMID: 36125173  ·  PMCID: PMC9372416

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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  ·  06 Apr 2022  ·  doi:10.1093/bioinformatics/btac205  ·  PMID: 35561182  ·  PMCID: PMC9113361

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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  ·  01 Mar 2022  ·  doi:10.1016/j.mcpro.2022.100197  ·  PMID: 35033677  ·  PMCID: PMC8941213

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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  ·  10 Jan 2022  ·  doi:10.1093/bioinformatics/btac017  ·  PMID: 35020801  ·  PMCID: PMC8963279

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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

BMC Biology  ·  22 Jan 2021  ·  doi:10.1186/s12915-020-00940-y  ·  PMID: 33482803  ·  PMCID: PMC7820539

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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

Genes  ·  22 Nov 2020  ·  doi:10.3390/genes11111384  ·  PMID: 33266490  ·  PMCID: PMC7700366

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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  ·  28 Oct 2020  ·  doi:10.1126/scitranslmed.aan7967  ·  PMID: 33115953  ·  PMCID: PMC7955769

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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

Nature  ·  24 Jul 2020  ·  doi:10.1038/s41586-020-2577-1  ·  PMID: 32707573  ·  PMCID: PMC7603405

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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

eLife  ·  17 Mar 2020  ·  doi:10.7554/elife.52614  ·  PMID: 32180547  ·  PMCID: PMC7077981

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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  ·  14 Feb 2020  ·  doi:10.3389/fgene.2019.01355  ·  PMID: 32117413  ·  PMCID: PMC7034361

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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

Database  ·  01 Jan 2020  ·  doi:10.1093/database/baaa015  ·  PMID: 32283553  ·  PMCID: PMC7153956

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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  ·  01 Dec 2019  ·  doi:10.1186/s12859-019-3297-0  ·  PMID: 31829175  ·  PMCID: PMC6907279

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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

PLOS ONE  ·  27 Sep 2019  ·  doi:10.1371/journal.pone.0222165  ·  PMID: 31560691  ·  PMCID: PMC6764653

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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  ·  03 Sep 2019  ·  doi:10.1093/bioinformatics/btz678  ·  PMID: 31504205  ·  PMCID: PMC8104067

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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  ·  02 Aug 2019  ·  doi:10.1126/sciimmunol.aaw6329  ·  PMID: 31471352  ·  PMCID: PMC6816460

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Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements.

Ginger Tsueng, Arun Kumar, Steven Max Nanis, Andrew I Su

Human Computation  ·  02 Jun 2019  ·  doi:10.15346/hc.v6i1.4

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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

Cell  ·  01 Apr 2019  ·  doi:10.1016/j.cell.2019.02.018  ·  PMID: 30951672  ·  PMCID: PMC6616370

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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

Database  ·  01 Jan 2019  ·  doi:10.1093/database/baz041  ·  PMID: 30985891  ·  PMCID: PMC6463448

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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  ·  01 Nov 2018  ·  doi:10.1016/j.molimm.2018.09.020  ·  PMID: 30300798  ·  PMCID: PMC6258053

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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  ·  01 Nov 2018  ·  doi:10.1016/j.joca.2018.07.012  ·  PMID: 30081074  ·  PMCID: PMC6245598

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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  ·  16 Oct 2018  ·  doi:10.1101/444497

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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  ·  03 Oct 2018  ·  doi:10.1073/pnas.1810137115  ·  PMID: 30282735  ·  PMCID: PMC6196526

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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  ·  05 Sep 2018  ·  doi:10.1038/s41746-018-0052-2  ·  PMID: 31304325  ·  PMCID: PMC6550256

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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  ·  01 Aug 2018  ·  doi:10.1074/jbc.RA118.003192  ·  PMID: 30006345  ·  PMCID: PMC6120211

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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  ·  11 Jul 2018  ·  doi:10.1101/367599

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Exploring applications of crowdsourcing to cryo-EM

Jacob Bruggemann, Gabriel C. Lander, Andrew I. Su

Journal of Structural Biology  ·  01 Jul 2018  ·  doi:10.1016/j.jsb.2018.02.006  ·  PMID: 29486249  ·  PMCID: PMC6086358

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A genome-wide survey of mutations in the Jurkat cell line

Louis Gioia, Azeem Siddique, Steven R. Head, Daniel R. Salomon, Andrew I. Su

BMC Genomics  ·  08 May 2018  ·  doi:10.1186/s12864-018-4718-6  ·  PMID: 29739316  ·  PMCID: PMC5941560

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Biocuration: Distilling data into knowledge

PLOS Biology  ·  16 Apr 2018  ·  doi:10.1371/journal.pbio.2002846  ·  PMID: 29659566  ·  PMCID: PMC5919672

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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

Cell  ·  01 Apr 2018  ·  doi:10.1016/j.cell.2018.02.047  ·  PMID: 29576450  ·  PMCID: PMC5889333

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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  ·  14 Feb 2018  ·  doi:10.1126/scitranslmed.aan0746  ·  PMID: 29444976  ·  PMCID: PMC6204214

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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

PROTEOMICS  ·  01 Feb 2018  ·  doi:10.1002/pmic.201700391  ·  PMID: 29319931  ·  PMCID: PMC5921860

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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  ·  01 Feb 2018  ·  doi:10.1186/s12859-018-2041-5  ·  PMID: 29390967  ·  PMCID: PMC5796402

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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

Methods in Molecular Biology  ·  10 Dec 2017  ·  doi:10.1007/978-1-4939-7514-3_14  ·  PMID: 29224077

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Academics can help shape Wikipedia

Thomas Shafee, Daniel Mietchen, Andrew I. Su

Science  ·  11 Aug 2017  ·  doi:10.1126/science.aao0462  ·  PMID: 28798122

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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  ·  10 Jul 2017  ·  doi:10.1101/156141

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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  ·  01 Jun 2017  ·  doi:10.1016/j.joca.2016.11.007  ·  PMID: 27884645  ·  PMCID: PMC5438901

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EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

Nikhil Gopal, Andrew Su, Chunlei Wu, Sean D. Mooney

Cold Spring Harbor Laboratory  ·  29 Mar 2017  ·  doi:10.1101/121178

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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

Nature Genetics  ·  31 Jan 2017  ·  doi:10.1038/ng.3774  ·  PMID: 28138153  ·  PMCID: PMC5367263

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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  ·  23 Jan 2017  ·  doi:10.1021/acs.jproteome.6b00938  ·  PMID: 28052195  ·  PMCID: PMC5441882

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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

Database  ·  01 Jan 2017  ·  doi:10.1093/database/bax025  ·  PMID: 28365742  ·  PMCID: PMC5467579

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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  ·  31 Dec 2016  ·  doi:10.5334/cstp.56  ·  PMID: 30416754  ·  PMCID: PMC6226017

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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

Gene  ·  01 Nov 2016  ·  doi:10.1016/j.gene.2016.04.053  ·  PMID: 27150585  ·  PMCID: PMC5944608

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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  ·  01 Sep 2016  ·  doi:10.1016/j.joca.2016.04.015  ·  PMID: 27118398  ·  PMCID: PMC4992644

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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

BMC Genomics  ·  16 Aug 2016  ·  doi:10.1186/s12864-016-2855-3  ·  PMID: 27528457  ·  PMCID: PMC4986259

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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

Arthritis & Rheumatology  ·  27 Jul 2016  ·  doi:10.1002/art.39643  ·  PMID: 26881698  ·  PMCID: PMC4963260

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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  ·  19 Jul 2016  ·  doi:10.1021/acs.jproteome.6b00095  ·  PMID: 27356587  ·  PMCID: PMC5120959

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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  ·  01 Jul 2016  ·  doi:10.1111/ajt.13728  ·  PMID: 26990570  ·  PMCID: PMC5501990

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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  ·  22 Jun 2016  ·  doi:10.1073/pnas.1606297113  ·  PMID: 27335461  ·  PMCID: PMC4941496

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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

Genome Biology  ·  06 May 2016  ·  doi:10.1186/s13059-016-0953-9  ·  PMID: 27154141  ·  PMCID: PMC4858870

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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  ·  12 Apr 2016  ·  doi:10.1186/s13326-016-0061-5  ·  PMID: 27076901  ·  PMCID: PMC4830068

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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  ·  doi:10.1093/bioinformatics/btw117  ·  PMID: 27153723  ·  PMCID: PMC4920125

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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

PLOS ONE  ·  26 Feb 2016  ·  doi:10.1371/journal.pone.0149621  ·  PMID: 26919047  ·  PMCID: PMC4769089

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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

Database  ·  01 Jan 2016  ·  doi:10.1093/database/baw015  ·  PMID: 26989148  ·  PMCID: PMC4795929

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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

Database  ·  01 Jan 2016  ·  doi:10.1093/database/baw094  ·  PMID: 27307137  ·  PMCID: PMC4908671

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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

Database  ·  01 Jan 2016  ·  doi:10.1093/database/baw028  ·  PMID: 27022157  ·  PMCID: PMC4822648

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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

Database  ·  01 Jan 2016  ·  doi:10.1093/database/baw051  ·  PMID: 27087308  ·  PMCID: PMC4834205

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2015

BioGPS: building your own mash-up of gene annotations and expression profiles

Chunlei Wu, Xuefeng Jin, Ginger Tsueng, Cyrus Afrasiabi, Andrew I. Su

Nucleic Acids Research  ·  17 Nov 2015  ·  doi:10.1093/nar/gkv1104  ·  PMID: 26578587  ·  PMCID: PMC4702805

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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  ·  01 Jul 2015  ·  doi:10.1016/j.jacc.2015.04.072  ·  PMID: 26160638

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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  ·  21 May 2015  ·  doi:10.1186/s12920-015-0095-z  ·  PMID: 25989980  ·  PMCID: PMC4494802

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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  ·  doi:10.1126/scitranslmed.3009986  ·  PMID: 25972004  ·  PMCID: PMC5018401

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Crowdsourcing in biomedicine: challenges and opportunities

Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu

Briefings in Bioinformatics  ·  17 Apr 2015  ·  doi:10.1093/bib/bbv021  ·  PMID: 25888696  ·  PMCID: PMC4719068

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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  ·  doi:10.1161/CIRCRESAHA.115.306013  ·  PMID: 25814682  ·  PMCID: PMC4721634

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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  ·  PMID: 25637560  ·  PMCID: PMC4443682

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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  ·  01 Jan 2015  ·  doi:10.3402/jev.v4.27497  ·  PMID: 26320941  ·  PMCID: PMC4553261

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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

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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

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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

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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

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Organizing knowledge to enable personalization of medicine in cancer

Benjamin M Good, Benjamin J Ainscough, Josh F McMichael, Andrew I Su, Obi L Griffith

Genome Biology  ·  27 Aug 2014  ·  doi:10.1186/s13059-014-0438-7  ·  PMID: 25222080  ·  PMCID: PMC4281950

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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

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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

JMIR Serious Games  ·  29 Jul 2014  ·  doi:10.2196/games.3350  ·  PMID: 25654473  ·  PMCID: PMC4307816

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2013

Gene Wiki Reviews: Marrying crowdsourcing with traditional peer review

Andrew I. Su, Benjamin M. Good, Andre J. van Wijnen

Gene  ·  01 Dec 2013  ·  doi:10.1016/j.gene.2013.08.093  ·  PMID: 24012870

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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

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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

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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

PLoS ONE  ·  29 Aug 2013  ·  doi:10.1371/journal.pone.0072511  ·  PMID: 24009687  ·  PMCID: PMC3757023

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Dizeez: An Online Game for Human Gene-Disease Annotation

Salvatore Loguercio, Benjamin M. Good, Andrew I. Su

PLoS ONE  ·  07 Aug 2013  ·  doi:10.1371/journal.pone.0071171  ·  PMID: 23951102  ·  PMCID: PMC3737187

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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

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Crowdsourcing for bioinformatics

Benjamin M. Good, Andrew I. Su

Bioinformatics  ·  19 Jun 2013  ·  doi:10.1093/bioinformatics/btt333  ·  PMID: 23782614  ·  PMCID: PMC3722523

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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

Cell Reports  ·  01 Apr 2013  ·  doi:10.1016/j.celrep.2013.03.024  ·  PMID: 23583182  ·  PMCID: PMC3754422

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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

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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

Arthritis & Rheumatism  ·  28 Jan 2013  ·  doi:10.1002/art.37760  ·  PMID: 23124445  ·  PMCID: PMC3558601

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2012

BioGPS and MyGene.info: organizing online, gene-centric information

Chunlei Wu, Ian MacLeod, Andrew I. Su

Nucleic Acids Research  ·  21 Nov 2012  ·  doi:10.1093/nar/gks1114  ·  PMID: 23175613  ·  PMCID: PMC3531157

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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

BMC Biology  ·  15 Nov 2012  ·  doi:10.1186/1741-7007-10-90  ·  PMID: 23153189  ·  PMCID: PMC3814290

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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

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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

Chemistry & Biology  ·  01 Aug 2012  ·  doi:10.1016/j.chembiol.2012.07.005  ·  PMID: 22884261

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BioGPS and GXD: mouse gene expression data—the benefits and challenges of data integration

Martin Ringwald, Chunlei Wu, Andrew I. Su

Mammalian Genome  ·  31 Jul 2012  ·  doi:10.1007/s00335-012-9408-0  ·  PMID: 22847375  ·  PMCID: PMC3469763

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The evolution of dynamin to regulate clathrin‐mediated endocytosis

Ya‐Wen Liu, Andrew I. Su, Sandra L. Schmid

BioEssays  ·  16 May 2012  ·  doi:10.1002/bies.201200033  ·  PMID: 22592980  ·  PMCID: PMC5715466

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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

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Building a biomedical semantic network in Wikipedia with Semantic Wiki Links

B. M. Good, E. L. Clarke, S. Loguercio, A. I. Su

Database  ·  20 Mar 2012  ·  doi:10.1093/database/bar060  ·  PMID: 22434829  ·  PMCID: PMC3308151

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2011

Mining the Gene Wiki for functional genomic knowledge

Benjamin M Good, Douglas G Howe, Simon M Lin, Warren A Kibbe, Andrew I Su

BMC Genomics  ·  01 Dec 2011  ·  doi:10.1186/1471-2164-12-603  ·  PMID: 22165947  ·  PMCID: PMC3271090

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The Gene Wiki in 2011: community intelligence applied to human gene annotation

Benjamin M. Good, Erik L. Clarke, Luca de Alfaro, Andrew I. Su

Nucleic Acids Research  ·  09 Nov 2011  ·  doi:10.1093/nar/gkr925  ·  PMID: 22075991  ·  PMCID: PMC3245148

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CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma

Yue Hu, Anna V. Galkin, Chunlei Wu, Venkateshwar Reddy, Andrew I. Su

PLoS ONE  ·  10 Oct 2011  ·  doi:10.1371/journal.pone.0025807  ·  PMID: 22016777  ·  PMCID: PMC3189939

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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

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Games with a scientific purpose

Benjamin M Good, Andrew I Su

Genome Biology  ·  01 Jan 2011  ·  doi:10.1186/gb-2011-12-12-135  ·  PMID: 22204700  ·  PMCID: PMC3334605

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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

PLoS ONE  ·  29 Dec 2010  ·  doi:10.1371/journal.pone.0014458  ·  PMID: 21206921  ·  PMCID: PMC3012073

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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

PLoS ONE  ·  10 Nov 2010  ·  doi:10.1371/journal.pone.0013920  ·  PMID: 21085707  ·  PMCID: PMC2978079

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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

BMC Systems Biology  ·  19 Mar 2010  ·  doi:10.1186/1752-0509-4-29  ·  PMID: 20302627  ·  PMCID: PMC2856555

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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

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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

Genome Biology  ·  17 Nov 2009  ·  doi:10.1186/gb-2009-10-11-r130  ·  PMID: 19919682  ·  PMCID: PMC3091323

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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

Cell  ·  01 Oct 2009  ·  doi:10.1016/j.cell.2009.08.031  ·  PMID: 19765810  ·  PMCID: PMC2777987

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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

Nucleic Acids Research  ·  15 Sep 2009  ·  doi:10.1093/nar/gkp760  ·  PMID: 19755503  ·  PMCID: PMC2808918

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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

Journal of Bone and Mineral Research  ·  01 Jun 2009  ·  doi:10.1359/jbmr.081258  ·  PMID: 19113921

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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

PLoS ONE  ·  06 Mar 2009  ·  doi:10.1371/journal.pone.0004649  ·  PMID: 19266052  ·  PMCID: PMC2650792

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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

BMC Chemical Biology  ·  16 Jan 2009  ·  doi:10.1186/1472-6769-9-2  ·  PMID: 19149867  ·  PMCID: PMC2651120

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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

PLoS Genetics  ·  24 Oct 2008  ·  doi:10.1371/journal.pgen.1000232  ·  PMID: 18949031  ·  PMCID: PMC2563687

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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

PLoS Biology  ·  08 Jul 2008  ·  doi:10.1371/journal.pbio.0060175  ·  PMID: 18613750  ·  PMCID: PMC2443188

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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

PLoS Genetics  ·  09 May 2008  ·  doi:10.1371/journal.pgen.1000070  ·  PMID: 18464898  ·  PMCID: PMC2346558

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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

Immunome Research  ·  01 Jan 2008  ·  doi:10.1186/1745-7580-4-5  ·  PMID: 18442421  ·  PMCID: PMC2394514

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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

Genetics  ·  01 May 2007  ·  doi:10.1534/genetics.106.066241  ·  PMID: 17409088  ·  PMCID: PMC1893038

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Power-law-like distributions in biomedical publications and research funding

Andrew I Su, John B Hogenesch

Genome Biology  ·  01 Jan 2007  ·  doi:10.1186/gb-2007-8-4-404  ·  PMID: 17472739  ·  PMCID: PMC1895997

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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

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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

Chemistry – A European Journal  ·  17 Jul 2006  ·  doi:10.1002/chem.200600307  ·  PMID: 16715541

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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

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Comparative analysis of haplotype association mapping algorithms

Phillip McClurg, Mathew T Pletcher, Tim Wiltshire, Andrew I Su

BMC Bioinformatics  ·  09 Feb 2006  ·  doi:10.1186/1471-2105-7-61  ·  PMID: 16466585  ·  PMCID: PMC1409800

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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

Biochemistry and Cell Biology  ·  01 Feb 2006  ·  doi:10.1139/o05-149  ·  PMID: 16462891

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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

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Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes

Jing Yang, Andrew I. Su, Wen-Hsiung Li

Molecular Biology and Evolution  ·  29 Jun 2005  ·  doi:10.1093/molbev/msi206  ·  PMID: 15987875

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HierS:  Hierarchical Scaffold Clustering Using Topological Chemical Graphs

Steven J. Wilkens, Jeff Janes, Andrew I. Su

Journal of Medicinal Chemistry  ·  08 Apr 2005  ·  doi:10.1021/jm049032d  ·  PMID: 15857124

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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

Nature Genetics  ·  13 Feb 2005  ·  doi:10.1038/ng1497  ·  PMID: 15711547

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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

Proceedings of the National Academy of Sciences  ·  04 Feb 2005  ·  doi:10.1073/pnas.0409459102  ·  PMID: 15695585  ·  PMCID: PMC548308

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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

PLoS Biology  ·  09 Nov 2004  ·  doi:10.1371/journal.pbio.0020393  ·  PMID: 15534693  ·  PMCID: PMC526179

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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

Proceedings of the National Academy of Sciences  ·  09 Apr 2004  ·  doi:10.1073/pnas.0400782101  ·  PMID: 15075390  ·  PMCID: PMC395923

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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

Genome Research  ·  01 Apr 2004  ·  doi:10.1101/gr.2161804  ·  PMID: 15060018  ·  PMCID: PMC383321

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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

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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 Apr 2003  ·  doi:10.1016/S1097-2765(03)00134-5  ·  PMID: 12718894

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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

Proceedings of the National Academy of Sciences  ·  19 Nov 2002  ·  doi:10.1073/pnas.202608199  ·  PMID: 12441396  ·  PMCID: PMC137774

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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

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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

Proceedings of the National Academy of Sciences  ·  12 Aug 2002  ·  doi:10.1073/pnas.122359899  ·  PMID: 12177410  ·  PMCID: PMC123230

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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

Chemistry & Biology  ·  01 Jul 2002  ·  doi:10.1016/S1074-5521(02)00174-6  ·  PMID: 12144926

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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

Cell  ·  01 May 2002  ·  doi:10.1016/S0092-8674(02)00722-5  ·  PMID: 12015981

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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

Proceedings of the National Academy of Sciences  ·  19 Mar 2002  ·  doi:10.1073/pnas.012025199  ·  PMID: 11904358  ·  PMCID: PMC123671

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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

Journal of Medicinal Chemistry  ·  21 Nov 2001  ·  doi:10.1021/jm010451+  ·  PMID: 11741468

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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

Cancer research  ·  15 Oct 2001  ·  pmid:11606367  ·  PMID: 11606367

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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

Cancer research  ·  15 Aug 2001  ·  pmid:11507037  ·  PMID: 11507037

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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

Cell  ·  01 Aug 2001  ·  doi:10.1016/S0092-8674(01)00467-6  ·  PMID: 11534548

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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

Proceedings of the National Academy of Sciences  ·  20 Feb 2001  ·  doi:10.1073/pnas.041452598  ·  PMID: 11226240  ·  PMCID: PMC30139

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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

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