Andrew I. Su, Ph.D. - Publications

Scripps Research Institute, La Jolla, La Jolla, CA, United States 
bioinformatics, genetics, genomics

141 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Hughes L, Gangavarapu K, Latif AA, Mullen J, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves C, Zaiets K, Cano M, Zhou J, Qian Z, Sattler R, ... ... Su A, et al. genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Research Square. PMID 35794893 DOI: 10.21203/  0.499
2022 Cano M, Tsueng G, Zhou X, Hughes LD, Mullen JL, Xin J, Su AI, Wu C. Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data. Biorxiv : the Preprint Server For Biology. PMID 35677074 DOI: 10.1101/2021.09.02.458726  0.638
2022 Mayers M, Tu R, Steinecke D, Li TS, Queralt-Rosinach N, Su AI. Design and application of a knowledge network for automatic prioritization of drug mechanisms. Bioinformatics (Oxford, England). 38: 2880-2891. PMID 35561182 DOI: 10.1093/bioinformatics/btac205  0.769
2022 Mayers M, Tu R, Steinecke D, Li TS, Queralt-Rosinach N, Su AI. Design and application of a knowledge network for automatic prioritization of drug mechanisms. Bioinformatics (Oxford, England). PMID 35385070 DOI: 10.1093/bioinformatics/btac205  0.769
2022 Tsueng G, Mullen J, Alkuzweny M, Cano M, Rush B, Haag E, Curators O, Alaa Abdel L, Zhou X, Qian Z, Andersen KG, Wu C, Su AI, Gangavarapu K, Hughes LD. Research Library: A standardized, searchable platform to discover and explore COVID-19 resources and data. Biorxiv : the Preprint Server For Biology. PMID 35132411 DOI: 10.1101/2022.01.20.477133  0.507
2022 Thuy-Boun PS, Wang AY, Crissien-Martinez A, Xu JH, Chatterjee S, Stupp GS, Su AI, Coyle WJ, Wolan DW. Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiome identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis. Molecular & Cellular Proteomics : McP. 100197. PMID 35033677 DOI: 10.1016/j.mcpro.2022.100197  0.752
2022 Lelong S, Zhou X, Afrasiabi C, Qian Z, Cano MA, Tsueng G, Xin J, Mullen J, Yao Y, Avila R, Taylor G, Su AI, Wu C. BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. Bioinformatics (Oxford, England). PMID 35020801 DOI: 10.1093/bioinformatics/btac017  0.67
2020 Lee KI, Gamini R, Olmer M, Ikuta Y, Hasei J, Baek J, Alvarez-Garcia O, Grogan SP, D'Lima DD, Asahara H, Su AI, Lotz MK. Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity. Science Translational Medicine. 12. PMID 33115953 DOI: 10.1126/scitranslmed.aan7967  0.768
2020 Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV, Chang MW, Chan JF, Cao J, Poon VK, Herbert KM, ... ... Su AI, et al. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature. PMID 32707573 DOI: 10.1038/S41586-020-2577-1  0.783
2020 Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Burgstaller-Muehlbacher S, Pache L, De Jesus PP, Hull MV, Chang M, Chan JF, Cao J, Poon VK, Herbert K, Nguyen TT, ... ... Su A, et al. A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals. Biorxiv : the Preprint Server For Biology. PMID 32511357 DOI: 10.1101/2020.04.16.044016  0.783
2020 Queralt-Rosinach N, Stupp GS, Li TS, Mayers M, Hoatlin ME, Might M, Good BM, Su AI. Structured reviews for data and knowledge-driven research. Database : the Journal of Biological Databases and Curation. 2020. PMID 32283553 DOI: 10.1093/Database/Baaa015  0.788
2020 Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, ... ... Su AI, et al. Wikidata as a knowledge graph for the life sciences. Elife. 9. PMID 32180547 DOI: 10.7554/Elife.52614  0.776
2020 Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, ... ... Su AI, et al. Author response: Wikidata as a knowledge graph for the life sciences Elife. DOI: 10.7554/Elife.52614.Sa2  0.737
2019 Summers KM, Bush SJ, Wu C, Su AI, Muriuki C, Clark EL, Finlayson HA, Eory L, Waddell LA, Talbot R, Archibald AL, Hume DA. Functional Annotation of the Transcriptome of the Pig, , Based Upon Network Analysis of an RNAseq Transcriptional Atlas. Frontiers in Genetics. 10: 1355. PMID 32117413 DOI: 10.3389/Fgene.2019.01355  0.599
2019 Mayers M, Li TS, Queralt-Rosinach N, Su AI. Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network. Bmc Bioinformatics. 20: 653. PMID 31829175 DOI: 10.1186/S12859-019-3297-0  0.782
2019 Blasco A, Endres MG, Sergeev RA, Jonchhe A, Macaluso NJM, Narayan R, Natoli T, Paik JH, Briney B, Wu C, Su AI, Subramanian A, Lakhani KR. Advancing computational biology and bioinformatics research through open innovation competitions. Plos One. 14: e0222165. PMID 31560691 DOI: 10.1371/Journal.Pone.0222165  0.547
2019 Tsueng G, Nanis M, Fouquier JT, Mayers M, Good BM, Su AI. Applying Citizen Science to Gene, Drug, and Disease Relationship Extraction from Biomedical Abstracts. Bioinformatics (Oxford, England). PMID 31504205 DOI: 10.1093/Bioinformatics/Btz678  0.787
2019 Gioia L, Holt M, Costanzo A, Sharma S, Abe B, Kain L, Nakayama M, Wan X, Su A, Mathews C, Chen YG, Unanue E, Teyton L. Position β57 of I-A controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset. Science Immunology. 4. PMID 31471352 DOI: 10.1126/Sciimmunol.Aaw6329  0.642
2019 Putman T, Hybiske K, Jow D, Afrasiabi C, Lelong S, Cano MA, Stupp GS, Waagmeester A, Good BM, Wu C, Su AI. ChlamBase: a curated model organism database for the Chlamydia research community. Database : the Journal of Biological Databases and Curation. 2019. PMID 31211397 DOI: 10.1093/database/baz091  0.766
2019 Putman T, Hybiske K, Jow D, Afrasiabi C, Lelong S, Cano MA, Wu C, Su AI. ChlamBase: a curated model organism database for the Chlamydia research community. Database : the Journal of Biological Databases and Curation. 2019. PMID 30985891 DOI: 10.1093/Database/Baz041  0.782
2019 Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, ... ... Su AI, et al. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 177: 463-477.e15. PMID 30951672 DOI: 10.1016/J.Cell.2019.02.018  0.784
2019 Sharma S, Gioia L, Abe B, Holt M, Costanzo A, Kain L, Su A, Teyton L. Corrigendum to "Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges" [Mol. Immunol. 103 (2018) 191-199]. Molecular Immunology. PMID 30732931 DOI: 10.1016/J.Molimm.2019.01.011  0.645
2018 Sharma S, Gioia L, Abe B, Holt M, Costanzo A, Kain L, Su A, Teyton L. Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges. Molecular Immunology. 103: 191-199. PMID 30300798 DOI: 10.1016/J.Molimm.2018.09.020  0.671
2018 Janes J, Young ME, Chen E, Rogers NH, Burgstaller-Muehlbacher S, Hughes LD, Love MS, Hull MV, Kuhen KL, Woods AK, Joseph SB, Petrassi HM, McNamara CW, Tremblay MS, Su AI, et al. The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis. Proceedings of the National Academy of Sciences of the United States of America. 115: 10750-10755. PMID 30282735 DOI: 10.1073/Pnas.1810137115  0.778
2018 Fisch KM, Gamini R, Alvarez-Garcia O, Akagi R, Saito M, Muramatsu Y, Sasho T, Koziol JA, Su AI, Lotz MK. Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis. Osteoarthritis and Cartilage. PMID 30081074 DOI: 10.1016/J.Joca.2018.07.012  0.796
2018 Wang AY, Thuy-Boun PS, Stupp GS, Su AI, Wolan DW. Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass. Journal of Proteome Research. 17: 2978-2986. PMID 30019906 DOI: 10.1021/Acs.Jproteome.8B00166  0.728
2018 Hutt DM, Loguercio S, Roth DM, Su AI, Balch WE. Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation. The Journal of Biological Chemistry. 293: 13477-13495. PMID 30006345 DOI: 10.1074/Jbc.Ra118.003192  0.725
2018 Gioia L, Siddique A, Head SR, Salomon DR, Su AI. A genome-wide survey of mutations in the Jurkat cell line. Bmc Genomics. 19: 334. PMID 29739316 DOI: 10.1186/S12864-018-4718-6  0.649
2018 Ma S, Cahalan S, LaMonte G, Grubaugh ND, Zeng W, Murthy SE, Paytas E, Gamini R, Lukacs V, Whitwam T, Loud M, Lohia R, Berry L, Khan SM, Janse CJ, ... ... Su AI, et al. Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection. Cell. 173: 443-455.e12. PMID 29576450 DOI: 10.1016/J.Cell.2018.02.047  0.757
2018 Bruggemann J, Lander GC, Su AI. Exploring applications of crowdsourcing to cryo-EM. Journal of Structural Biology. 203: 37-45. PMID 29486249 DOI: 10.1016/J.Jsb.2018.02.006  0.664
2018 Matsuzaki T, Alvarez-Garcia O, Mokuda S, Nagira K, Olmer M, Gamini R, Miyata K, Akasaki Y, Su AI, Asahara H, Lotz MK. FoxO transcription factors modulate autophagy and proteoglycan 4 in cartilage homeostasis and osteoarthritis. Science Translational Medicine. 10. PMID 29444976 DOI: 10.1126/Scitranslmed.Aan0746  0.758
2018 Xin J, Afrasiabi C, Lelong S, Adesara J, Tsueng G, Su AI, Wu C. Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. Bmc Bioinformatics. 19: 30. PMID 29390967 DOI: 10.1186/S12859-018-2041-5  0.679
2018 Moon C, Stupp GS, Su AI, Wolan DW. Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups. Proteomics. 18. PMID 29319931 DOI: 10.1002/Pmic.201700391  0.754
2018 Holt M, Costanzo A, Gioia L, Abe B, Su AI, Teyton L. Gene Profiling and T Cell Receptor Sequencing from Antigen-Specific CD4 T Cells. Methods in Molecular Biology (Clifton, N.J.). 1712: 217-238. PMID 29224077 DOI: 10.1007/978-1-4939-7514-3_14  0.648
2018 Lelong S, Afrasiabi C, Xin J, Cano M, Tsueng G, Su AI, Wu C. BioThings Studio: an API gateway for biomedical knowledge F1000research. 7. DOI: 10.7490/F1000Research.1115797.1  0.654
2017 Shafee T, Mietchen D, Su AI. Academics can help shape Wikipedia. Science (New York, N.Y.). 357: 557-558. PMID 28798122 DOI: 10.1126/SCIENCE.AAO0462;  0.333
2017 Putman TE, Lelong S, Burgstaller-Muehlbacher S, Waagmeester A, Diesh C, Dunn N, Munoz-Torres M, Stupp GS, Wu C, Su AI, Good BM. WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. Database : the Journal of Biological Databases and Curation. 2017. PMID 28365742 DOI: 10.1093/database/bax025  0.795
2017 Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, ... ... Su AI, et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics. 49: 170-174. PMID 28138153 DOI: 10.1038/Ng.3774  0.708
2017 Mayers MD, Moon C, Stupp GS, Su AI, Wolan DW. Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease. Journal of Proteome Research. 16: 1014-1026. PMID 28052195 DOI: 10.1021/Acs.Jproteome.6B00938  0.78
2017 Afrasiabi C, Lelong S, Xin J, Tsueng G, Su AI, Wu C. BioThings SDK: a toolkit for building high-performance data APIs in biology F1000research. 6. DOI: 10.7490/F1000Research.1114587.1  0.653
2017 Xin J, Afrasiabi C, Lelong S, Su AI, Wu C. BioThings Explorer: utilizing JSON-LD for linking biological APIs to facilitate knowledge discovery F1000research. 6. DOI: 10.7490/F1000Research.1114451.1  0.682
2017 Mitraka E, Waagmeester A, Queralt-Rosinach N, Burgstaller-Muehlbacher S, Stupp G, Schriml L, McMichael JF, Ainscough B, Griffith M, Griffith OL, Su AI, Good BM. 10 steps to integrate CIViCdb with other public data in Wikidata F1000research. 6. DOI: 10.7490/F1000Research.1113836.1  0.763
2017 Stupp GS, Queralt-Rosinach N, Putman T, Burgstaller-Muehlbacher S, Waagmeester A, Su AI, Good BM. Best practices for data provenance in Wikidata F1000research. 6. DOI: 10.7490/F1000Research.1113800.1  0.76
2017 Gamini R, Alvarez-Garcia O, Su A, Lotz M. Articular Cartilage Specific Gene Expression Pattern: Identification of Novel Transcription Factors That are Enriched In Cartilage Osteoarthritis and Cartilage. 25: S214. DOI: 10.1016/J.Joca.2017.02.370  0.782
2016 Tsueng G, Nanis SM, Fouquier J, Good BM, Su AI. Citizen Science for Mining the Biomedical Literature. Citizen Science : Theory and Practice. 1. PMID 30416754 DOI: 10.5334/cstp.56  0.628
2016 Akagi R, Akatsu Y, Fisch KM, Alvarez-Garcia O, Teramura T, Muramatsu Y, Saito M, Sasho T, Su AI, Lotz MK. Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes. Osteoarthritis and Cartilage. PMID 27884645 DOI: 10.1016/J.Joca.2016.11.007  0.603
2016 Chatterjee S, Stupp GS, Park SK, Ducom JC, Yates JR, Su AI, Wolan DW. A comprehensive and scalable database search system for metaproteomics. Bmc Genomics. 17: 642. PMID 27528457 DOI: 10.1186/S12864-016-2855-3  0.752
2016 Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P. Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. Journal of Proteome Research. 15: 4126-4134. PMID 27356587 DOI: 10.1021/Acs.Jproteome.6B00095  0.313
2016 Kleiman E, Jia H, Loguercio S, Su AI, Feeney AJ. YY1 plays an essential role at all stages of B-cell differentiation. Proceedings of the National Academy of Sciences of the United States of America. 113: E3911-20. PMID 27335461 DOI: 10.1073/Pnas.1606297113  0.722
2016 Bravo À, Li TS, Su AI, Good BM, Furlong LI. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. Database : the Journal of Biological Databases and Curation. 2016. PMID 27307137 DOI: 10.1093/Database/Baw094  0.703
2016 Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, et al. High-performance web services for querying gene and variant annotation. Genome Biology. 17: 91. PMID 27154141 DOI: 10.1186/S13059-016-0953-9  0.79
2016 Gangavarapu K, Babji V, Meißner T, Su AI, Good BM. Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. Bioinformatics (Oxford, England). 32: 2072-2074. PMID 27153723 DOI: 10.1093/Bioinformatics/Btw117  0.724
2016 Tsueng G, Good BM, Ping P, Golemis E, Hanukoglu I, van Wijnen AJ, Su AI. Gene Wiki Reviews-Raising the quality and accessibility of information about the human genome. Gene. 592: 235-8. PMID 27150585 DOI: 10.1016/J.Gene.2016.04.053  0.674
2016 Alvarez-Garcia O, Olmer M, Akagi R, Akasaki Y, Fisch KM, Shen T, Su AI, Lotz MK. Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy. Osteoarthritis and Cartilage / Oars, Osteoarthritis Research Society. PMID 27118398 DOI: 10.1016/J.Joca.2016.04.015  0.586
2016 Li TS, Bravo À, Furlong LI, Good BM, Su AI. A crowdsourcing workflow for extracting chemical-induced disease relations from free text. Database : the Journal of Biological Databases and Curation. 2016. PMID 27087308 DOI: 10.1093/Database/Baw051  0.675
2016 Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, ... ... Su AI, et al. Extending gene ontology in the context of extracellular RNA and vesicle communication. Journal of Biomedical Semantics. 7: 19. PMID 27076901 DOI: 10.1186/S13326-016-0061-5  0.359
2016 Putman TE, Burgstaller-Muehlbacher S, Waagmeester A, Wu C, Su AI, Good BM. Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. Database : the Journal of Biological Databases and Curation. 2016. PMID 27022157 DOI: 10.1093/Database/Baw028  0.813
2016 Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, Naik C, Pavlidis P, Schriml L, Good BM, Su AI. Wikidata as a semantic framework for the Gene Wiki initiative. Database : the Journal of Biological Databases and Curation. 2016. PMID 26989148 DOI: 10.1093/Database/Baw015  0.811
2016 Hettne KM, Thompson M, van Haagen HH, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JF, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, et al. The Implicitome: A Resource for Rationalizing Gene-Disease Associations. Plos One. 11: e0149621. PMID 26919047 DOI: 10.1371/Journal.Pone.0149621  0.724
2016 Alvarez-Garcia O, Fisch KM, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK. Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage. Arthritis & Rheumatology (Hoboken, N.J.). 68: 1876-86. PMID 26881698 DOI: 10.1002/Art.39643  0.6
2016 Wu C, Jin X, Tsueng G, Afrasiabi C, Su AI. BioGPS: building your own mash-up of gene annotations and expression profiles. Nucleic Acids Research. 44: D313-6. PMID 26578587 DOI: 10.1093/Nar/Gkv1104  0.565
2016 Khare R, Good BM, Leaman R, Su AI, Lu Z. Crowdsourcing in biomedicine: challenges and opportunities. Briefings in Bioinformatics. 17: 23-32. PMID 25888696 DOI: 10.1093/Bib/Bbv021  0.666
2016 Xin J, Afrasiabi C, Lelong S, Tsueng G, Mayers MD, Mooney SD, Su AI, Wu C. Biothings APIs: linked high-performance APIs for biological entities F1000research. 5. DOI: 10.7490/F1000Research.1113452.1  0.643
2016 Xin J, Wu C, Afrasiabi C, Lelong S, Tsueng G, Su AI. and providing gene and genetic variant annotations as a service F1000research. 5. DOI: 10.7490/F1000Research.1112806.1  0.665
2015 Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. Journal of Extracellular Vesicles. 4: 27497. PMID 26320941 DOI: 10.3402/Jev.V4.27497  0.345
2015 Lam MP, Venkatraman V, Cao Q, Wang D, Dincer TU, Lau E, Su AI, Xing Y, Ge J, Ping P, Van Eyk JE. Prioritizing Proteomics Assay Development for Clinical Translation. Journal of the American College of Cardiology. 66: 202-4. PMID 26160638 DOI: 10.1016/J.Jacc.2015.04.072  0.312
2015 Meißner T, Fisch KM, Gioia L, Su AI. OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing. Bmc Medical Genomics. 8: 24. PMID 25989980 DOI: 10.1186/S12920-015-0095-Z  0.781
2015 Wieskopf JS, Mathur J, Limapichat W, Post MR, Al-Qazzaz M, Sorge RE, Martin LJ, Zaykin DV, Smith SB, Freitas K, Austin JS, Dai F, Zhang J, Marcovitz J, Tuttle AH, ... ... Su AI, et al. The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors. Science Translational Medicine. 7: 287ra72. PMID 25972004 DOI: 10.1126/Scitranslmed.3009986  0.75
2015 Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR, Lindsey ML, Ping P. Harnessing the heart of big data. Circulation Research. 116: 1115-9. PMID 25814682 DOI: 10.1161/Circresaha.115.306013  0.346
2015 Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI. Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinformatics (Oxford, England). 31: 1724-8. PMID 25637560 DOI: 10.1093/Bioinformatics/Btv061  0.792
2015 Good BM, Nanis M, Wu C, Su AI. Microtask crowdsourcing for disease mention annotation in PubMed abstracts. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 282-93. PMID 25592589  0.71
2015 Leaman R, Good BM, Su AI, Lu Z. Crowdsourcing and mining crowd data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 267-9. PMID 25592587  0.599
2015 Meißner T, Fisch KM, Gioia L, Su AI. From Fastq to Drug Recommendation – Automated Cancer Report Generation using OncoRep & Omics Pipe F1000research. 4. DOI: 10.7490/F1000Research.1110018.1  0.767
2015 Alvarez-Garcia O, Fisch K, Akagi R, Su A, Lotz M. Differential DNA methylation and reduced expression of critical transcription factors in human oa cartilage Osteoarthritis and Cartilage. 23: A72-A73. DOI: 10.1016/J.Joca.2015.02.148  0.587
2015 Alvarez-Garcia O, Akagi R, Akasaki Y, Fisch K, Su A, Lotz M. Suppression of REDD1 in OA cartilage, a novel mechanism for dysregulated mTOR activation Osteoarthritis and Cartilage. 23: A31. DOI: 10.1016/J.Joca.2015.02.074  0.576
2014 Good BM, Loguercio S, Griffith OL, Nanis M, Wu C, Su AI. The cure: design and evaluation of a crowdsourcing game for gene selection for breast cancer survival prediction. Jmir Serious Games. 2: e7. PMID 25654473 DOI: 10.2196/games.3350  0.79
2014 Wei N, Shi Y, Truong LN, Fisch KM, Xu T, Gardiner E, Fu G, Hsu YO, Kishi S, Su AI, Wu X, Yang XL. Oxidative stress diverts tRNA synthetase to nucleus for protection against DNA damage. Molecular Cell. 56: 323-332. PMID 25284223 DOI: 10.1016/J.Molcel.2014.09.006  0.575
2014 Good BM, Ainscough BJ, McMichael JF, Su AI, Griffith OL. Organizing knowledge to enable personalization of medicine in cancer. Genome Biology. 15: 438. PMID 25222080 DOI: 10.1186/S13059-014-0438-7  0.646
2014 Peterson SN, Meissner T, Su AI, Snesrud E, Ong AC, Schork NJ, Bretz WA. Functional expression of dental plaque microbiota. Frontiers in Cellular and Infection Microbiology. 4: 108. PMID 25177549 DOI: 10.3389/Fcimb.2014.00108  0.597
2014 Fisch K, Saito M, Akagi R, Duffy S, Alvarez-Garcia O, Grogan S, D’Lima D, Su A, Lotz M. Integrative Omics profiling of osteoarthritis Osteoarthritis and Cartilage. 22: S231-S232. DOI: 10.1016/J.Joca.2014.02.446  0.587
2013 Masum H, Rao A, Good BM, Todd MH, Edwards AM, Chan L, Bunin BA, Su AI, Thomas Z, Bourne PE. Ten simple rules for cultivating open science and collaborative R&D. Plos Computational Biology. 9: e1003244. PMID 24086123 DOI: 10.1371/Journal.Pcbi.1003244  0.657
2013 Su AI, Good BM, van Wijnen AJ. Gene Wiki Reviews: marrying crowdsourcing with traditional peer review. Gene. 531: 125. PMID 24012870 DOI: 10.1016/J.Gene.2013.08.093  0.636
2013 Loguercio S, Good BM, Su AI. Dizeez: an online game for human gene-disease annotation. Plos One. 8: e71171. PMID 23951102 DOI: 10.1371/Journal.Pone.0071171  0.814
2013 Gopalakrishnan S, Majumder K, Predeus A, Huang Y, Koues OI, Verma-Gaur J, Loguercio S, Su AI, Feeney AJ, Artyomov MN, Oltz EM. Unifying model for molecular determinants of the preselection Vβ repertoire. Proceedings of the National Academy of Sciences of the United States of America. 110: E3206-15. PMID 23918392 DOI: 10.1073/Pnas.1304048110  0.731
2013 Choi NM, Loguercio S, Verma-Gaur J, Degner SC, Torkamani A, Su AI, Oltz EM, Artyomov M, Feeney AJ. Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies. Journal of Immunology (Baltimore, Md. : 1950). 191: 2393-402. PMID 23898036 DOI: 10.4049/Jimmunol.1301279  0.731
2013 Good BM, Su AI. Crowdsourcing for bioinformatics. Bioinformatics (Oxford, England). 29: 1925-33. PMID 23782614 DOI: 10.1093/Bioinformatics/Btt333  0.664
2013 Clarke EL, Loguercio S, Good BM, Su AI. A task-based approach for Gene Ontology evaluation. Journal of Biomedical Semantics. 4: S4. PMID 23734599 DOI: 10.1186/2041-1480-4-S1-S4  0.804
2013 Shoulders MD, Ryno LM, Genereux JC, Moresco JJ, Tu PG, Wu C, Yates JR, Su AI, Kelly JW, Wiseman RL. Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments. Cell Reports. 3: 1279-92. PMID 23583182 DOI: 10.1016/J.Celrep.2013.03.024  0.504
2013 Wu C, Macleod I, Su AI. BioGPS and organizing online, gene-centric information. Nucleic Acids Research. 41: D561-5. PMID 23175613 DOI: 10.1093/Nar/Gks1114  0.591
2013 Grogan SP, Duffy SF, Pauli C, Koziol JA, Su AI, D'Lima DD, Lotz MK. Zone-specific gene expression patterns in articular cartilage. Arthritis and Rheumatism. 65: 418-28. PMID 23124445 DOI: 10.1002/Art.37760  0.319
2013 Loguercio S, Good BM, Su AI. Correction: Dizeez: An Online Game for Human Gene-Disease Annotation Plos One. 8. DOI: 10.1371/Annotation/Efa93B55-C8F0-4943-B922-A585D68F0Bd0  0.779
2012 Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, et al. A gene expression atlas of the domestic pig. Bmc Biology. 10: 90. PMID 23153189 DOI: 10.1186/1741-7007-10-90  0.557
2012 Miller E, Yang J, DeRan M, Wu C, Su AI, Bonamy GM, Liu J, Peters EC, Wu X. Identification of serum-derived sphingosine-1-phosphate as a small molecule regulator of YAP. Chemistry & Biology. 19: 955-62. PMID 22884261 DOI: 10.1016/J.Chembiol.2012.07.005  0.611
2012 Ringwald M, Wu C, Su AI. BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 23: 550-8. PMID 22847375 DOI: 10.1007/S00335-012-9408-0  0.596
2012 Good BM, Clarke EL, Loguercio S, Su AI. Linking genes to diseases with a SNPedia-Gene Wiki mashup. Journal of Biomedical Semantics. 3: S6. PMID 22541597 DOI: 10.1186/2041-1480-3-S1-S6  0.806
2012 Good BM, Clarke EL, Loguercio S, Su AI. Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database : the Journal of Biological Databases and Curation. 2012: bar060. PMID 22434829 DOI: 10.1093/Database/Bar060  0.808
2012 Good BM, Clarke EL, de Alfaro L, Su AI. The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Research. 40: D1255-61. PMID 22075991 DOI: 10.1093/Nar/Gkr925  0.693
2012 Good BM, Loguercio S, Nanis M, Su AI. High-throughput access to biological knowledge and reasoning through online games Proceedings - 2012 Ieee 2nd Conference On Healthcare Informatics, Imaging and Systems Biology, Hisb 2012. 145. DOI: 10.1109/HISB.2012.70  0.78
2011 Good BM, Su AI. Games with a scientific purpose. Genome Biology. 12: 135. PMID 22204700 DOI: 10.1186/Gb-2011-12-12-135  0.615
2011 Good BM, Howe DG, Lin SM, Kibbe WA, Su AI. Mining the Gene Wiki for functional genomic knowledge. Bmc Genomics. 12: 603. PMID 22165947 DOI: 10.1186/1471-2164-12-603  0.71
2011 Hu Y, Galkin AV, Wu C, Reddy V, Su AI. CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma. Plos One. 6: e25807. PMID 22016777 DOI: 10.1371/Journal.Pone.0025807  0.584
2011 Dost B, Wu C, Su A, Bafna V. TCLUST: a fast method for clustering genome-scale expression data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 808-18. PMID 20479508 DOI: 10.1109/Tcbb.2010.34  0.549
2011 Barretina J, Stransky N, Caponigro G, Kim S, Margolin A, Venkhatesan K, Kryukov G, Berger M, Monahan J, Morais P, Meltzer J, Mahan S, Sonkin D, Raman P, Jones M, ... ... Su A, et al. Abstract 5455: Integrative analysis of the Cancer Cell Line Encyclopedia reveals genetic and transcriptional predictors of compound sensitivity Cancer Research. 71: 5455-5455. DOI: 10.1158/1538-7445.Am2011-5455  0.339
2010 Loguercio S, Overall RW, Michaelson JJ, Wiltshire T, Pletcher MT, Miller BH, Walker JR, Kempermann G, Su AI, Beyer A. Integrative analysis of low- and high-resolution eQTL. Plos One. 5: e13920. PMID 21085707 DOI: 10.1371/Journal.Pone.0013920  0.738
2010 Gonzalez R, Jennings LL, Knuth M, Orth AP, Klock HE, Ou W, Feuerhelm J, Hull MV, Koesema E, Wang Y, Zhang J, Wu C, Cho CY, Su AI, Batalov S, et al. Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency. Proceedings of the National Academy of Sciences of the United States of America. 107: 3552-7. PMID 20133595 DOI: 10.1073/Pnas.0914019107  0.789
2010 Huss JW, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI. The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Research. 38: D633-9. PMID 19755503 DOI: 10.1093/Nar/Gkp760  0.78
2010 Barretina J, Caponigro G, Kim S, Stransky N, Venkhatesan K, Reddy V, Berger M, Morrissey M, Morais P, Meltzer J, Thibault J, Mahan S, Sonkin D, Che J, Raman P, ... ... Su A, et al. Abstract 2620: The Cancer Cell Line Encyclopedia project: From integrative cancer genomics to personalized cancer therapy Cancer Research. 70: 2620-2620. DOI: 10.1158/1538-7445.Am10-2620  0.34
2010 Stransky N, Venkhatesan K, Morrissey M, Barretina J, Raman P, Getz G, Berger M, Johannessen C, Callahan A, Morais P, Mahan S, Gupta S, Onofrio R, Sougnez C, Winckler W, ... ... Su A, et al. Abstract 105: Integrative analysis of genomic and pharmacologic data from the Cancer Cell Line Encyclopedia Cancer Research. 70: 105-105. DOI: 10.1158/1538-7445.Am10-105  0.376
2010 Stransky N, Venkatesan K, Barretina J, Caponigro G, Margolin A, Morrissey M, Raman P, Getz G, Berger M, Johannessen C, Callahan A, Morais P, Mahan S, Gupta S, Onofrio R, ... ... Su A, et al. Abstract PR4: Integrative analysis of genomic and pharmacologic data from the Cancer Cell Line Encyclopedia Clinical Cancer Research. 16. DOI: 10.1158/1078-0432.Tcmusa10-Pr4  0.354
2009 Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biology. 10: R130. PMID 19919682 DOI: 10.1186/Gb-2009-10-11-R130  0.809
2009 Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, Janes J, Su AI, Hogenesch JB, Kay SA. A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell. 139: 199-210. PMID 19765810 DOI: 10.1016/J.Cell.2009.08.031  0.796
2009 Williams R, Lim JE, Harr B, Wing C, Walters R, Distler MG, Teschke M, Wu C, Wiltshire T, Su AI, Sokoloff G, Tarantino LM, Borevitz JO, Palmer AA. A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior. Plos One. 4: e4649. PMID 19266052 DOI: 10.1371/Journal.Pone.0004649  0.514
2009 Tang PL, Cheung CL, Sham PC, McClurg P, Lee B, Chan SY, Smith DK, Tanner JA, Su AI, Cheah KS, Kung AW, Song YQ. Genome-wide haplotype association mapping in mice identifies a genetic variant in CER1 associated with BMD and fracture in southern Chinese women. Journal of Bone and Mineral Research : the Official Journal of the American Society For Bone and Mineral Research. 24: 1013-21. PMID 19113921 DOI: 10.1359/Jbmr.081258  0.359
2008 Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, Jansen RC. Genetical genomics: spotlight on QTL hotspots. Plos Genetics. 4: e1000232. PMID 18949031 DOI: 10.1371/Journal.Pgen.1000232  0.551
2008 Hogenesch JB, Su AI. Clock gene wikis available: join the "long tail". Journal of Biological Rhythms. 23: 456-7. PMID 18838611 DOI: 10.1177/0748730408322866  0.758
2008 Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI. A gene wiki for community annotation of gene function. Plos Biology. 6: e175. PMID 18613750 DOI: 10.1371/Journal.Pbio.0060175  0.573
2008 Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, Walker JR, Glynne RJ, Cooke MP, Takahashi JS, Shimomura K, ... ... Su AI, et al. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. Plos Genetics. 4: e1000070. PMID 18464898 DOI: 10.1371/Journal.Pgen.1000070  0.796
2007 Su AI, Hogenesch JB. Power-law-like distributions in biomedical publications and research funding. Genome Biology. 8: 404. PMID 17472739 DOI: 10.1186/Gb-2007-8-4-404  0.768
2007 McClurg P, Janes J, Wu C, Delano DL, Walker JR, Batalov S, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Wiltshire T, Su AI. Genomewide association analysis in diverse inbred mice: power and population structure. Genetics. 176: 675-83. PMID 17409088 DOI: 10.1534/Genetics.106.066241  0.775
2006 Lee JW, Lee JS, Kang M, Su AI, Chang YT. Visual artificial tongue for quantitative metal-cation analysis by an off-the-shelf dye array. Chemistry (Weinheim An Der Bergstrasse, Germany). 12: 5691-6. PMID 16715541 DOI: 10.1002/Chem.200600307  0.521
2006 Melnick JS, Janes J, Kim S, Chang JY, Sipes DG, Gunderson D, Jarnes L, Matzen JT, Garcia ME, Hood TL, Beigi R, Xia G, Harig RA, Asatryan H, Yan SF, ... ... Su AI, et al. An efficient rapid system for profiling the cellular activities of molecular libraries. Proceedings of the National Academy of Sciences of the United States of America. 103: 3153-8. PMID 16492761 DOI: 10.1073/Pnas.0511292103  0.774
2006 Sagan SM, Rouleau Y, Leggiadro C, Supekova L, Schultz PG, Su AI, Pezacki JP. The influence of cholesterol and lipid metabolism on host cell structure and hepatitis C virus replication. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 84: 67-79. PMID 16462891 DOI: 10.1139/O05-149  0.512
2005 Yang J, Su AI, Li WH. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Molecular Biology and Evolution. 22: 2113-8. PMID 15987875 DOI: 10.1093/Molbev/Msi206  0.332
2005 Gurkan C, Lapp H, Alory C, Su AI, Hogenesch JB, Balch WE. Large-scale profiling of Rab GTPase trafficking networks: the membrome. Molecular Biology of the Cell. 16: 3847-64. PMID 15944222 DOI: 10.1091/Mbc.E05-01-0062  0.749
2005 Wilkens SJ, Janes J, Su AI. HierS: hierarchical scaffold clustering using topological chemical graphs. Journal of Medicinal Chemistry. 48: 3182-93. PMID 15857124 DOI: 10.1021/Jm049032D  0.767
2005 Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nature Genetics. 37: 225-32. PMID 15711547 DOI: 10.1038/Ng1497  0.36
2005 Zhong JF, Zhao Y, Sutton S, Su A, Zhan Y, Zhu L, Yan C, Gallaher T, Johnston PB, Anderson WF, Cooke MP. Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells. Proceedings of the National Academy of Sciences of the United States of America. 102: 2448-53. PMID 15695585 DOI: 10.1073/Pnas.0409459102  0.331
2004 Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, Mural RJ, Paigen B, Wiltshire T. Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. Plos Biology. 2: e393. PMID 15534693 DOI: 10.1371/Journal.Pbio.0020393  0.308
2004 Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America. 101: 6062-7. PMID 15075390 DOI: 10.1073/Pnas.0400782101  0.774
2004 Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D, Bilbe G. Applications of a rat multiple tissue gene expression data set. Genome Research. 14: 742-9. PMID 15060018 DOI: 10.1101/Gr.2161804  0.778
2003 Conkright MD, Guzmán E, Flechner L, Su AI, Hogenesch JB, Montminy M. Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Molecular Cell. 11: 1101-8. PMID 12718894 DOI: 10.1016/S1097-2765(03)00134-5  0.764
2002 Su AI, Pezacki JP, Wodicka L, Brideau AD, Supekova L, Thimme R, Wieland S, Bukh J, Purcell RH, Schultz PG, Chisari FV. Genomic analysis of the host response to hepatitis C virus infection. Proceedings of the National Academy of Sciences of the United States of America. 99: 15669-74. PMID 12441396 DOI: 10.1073/Pnas.202608199  0.498
2002 Frierson HF, El-Naggar AK, Welsh JB, Sapinoso LM, Su AI, Cheng J, Saku T, Moskaluk CA, Hampton GM. Large scale molecular analysis identifies genes with altered expression in salivary adenoid cystic carcinoma. The American Journal of Pathology. 161: 1315-23. PMID 12368205 DOI: 10.1016/S0002-9440(10)64408-2  0.346
2002 Su AI, Guidotti LG, Pezacki JP, Chisari FV, Schultz PG. Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice. Proceedings of the National Academy of Sciences of the United States of America. 99: 11181-6. PMID 12177410 DOI: 10.1073/Pnas.122359899  0.57
2002 Supekova L, Pezacki JP, Su AI, Loweth CJ, Riedl R, Geierstanger B, Schultz PG, Wemmer DE. Genomic effects of polyamide/DNA interactions on mRNA expression. Chemistry & Biology. 9: 821-7. PMID 12144926 DOI: 10.1016/S1074-5521(02)00174-6  0.793
2002 Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 109: 307-20. PMID 12015981 DOI: 10.1016/S0092-8674(02)00722-5  0.783
2002 Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB. Large-scale analysis of the human and mouse transcriptomes. Proceedings of the National Academy of Sciences of the United States of America. 99: 4465-70. PMID 11904358 DOI: 10.1073/Pnas.012025199  0.815
2001 Chang YT, Wignall SM, Rosania GR, Gray NS, Hanson SR, Su AI, Merlie J, Moon HS, Sangankar SB, Perez O, Heald R, Schultz PG. Synthesis and biological evaluation of myoseverin derivatives: microtubule assembly inhibitors. Journal of Medicinal Chemistry. 44: 4497-500. PMID 11741468 DOI: 10.1021/Jm010451+  0.764
2001 Su AI, Welsh JB, Sapinoso LM, Kern SG, Dimitrov P, Lapp H, Schultz PG, Powell SM, Moskaluk CA, Frierson HF, Hampton GM. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Research. 61: 7388-93. PMID 11606367  0.523
2001 Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell. 106: 413-5. PMID 11534548 DOI: 10.1016/S0092-8674(01)00467-6  0.792
2001 Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins. 42: 279-93. PMID 11119652 DOI: 10.1002/1097-0134(20010201)42:2<279::Aid-Prot150>3.0.Co;2-U  0.503
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