Publications

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2022

130. Mayers M, Tu R, Steinecke D, Queralt-Rosinach N, Su AI Design and Application of a Knowledge Network for Automatic Prioritization of Drug Mechanisms. Bioinformatics. 2022 Apr 06;btac205. doi: 10.1093/bioinformatics/btac205. PMID: 35385070 PMCID: XXXX (PubMed) (PDF)

2021

129. Waagmeester A, Willighagen EL, Su AI, Kutmon M, Gayo JEL, Fernández-Álvarez D, Groom Q, Schaap PJ, Verhagen LM, Koehorst JJ A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. BMC Biol. 2021 Jan 22;19(1):12. doi: 10.1186/s12915-020-00940-y. PMID: 33482803 PMCID: PMC7820539 (PubMed) (PDF)

2020

128. Wang J, Vallee I, Dutta A, Wang Y, Mo Z, Liu Z, Cui H, Su AI, Yang, XL Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer. XL.Genes (Basel). 2020 Nov 22;11(11):1384. doi: 10.3390/genes11111384. PMID: 33266490 PMCID: PMC7700366 (PubMed) (PDF)

127. 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. Sci Transl Med. 2020 Oct 28;12(567):eaan7967. doi: 10.1126/scitranslmed.aan7967. PMID: 33115953 PMCID: PMC7955769 (PubMed) (PDF)

126. 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, Cheng K, Nguyen TH, Rubanov A, Pu Y, Nguyen C, Choi A, Rathnasinghe R, Schotsaert M, Miorin L, Dejosez M, Zwaka TP, Sit KY, Martinez-Sobrido L, Liu WC, White KM, Chapman ME, Lendy EK, Glynne RJ, Albrecht R, Ruppin E, Mesecar AD, Johnson JR, Benner C, Sun R, Schultz PG, Su AI, García-Sastre A, Chatterjee AK, Yuen KY, Chanda SK. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature. 2020 Oct;586(7827):113-119. doi: 10.1038/s41586-020-2577-1. PMID: 32707573 PMCID: PMC7603405 (PubMed) (PDF)

125. 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, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Wikidata as a knowledge graph for the life sciences. Elife. 2020 Mar 17;9:e52614. doi: 10.7554/eLife.52614. PMID: 32180547 PMCID: PMC7077981 (PubMed) (PDF)

124. 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. 2020 Feb 15;36(4):1226-1233. doi: 10.1093/bioinformatics/btz678. PMID: 31504205 PMCID: PMC8104067 (PubMed) (PDF)

123. 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, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas. Front Genet. 2020 Feb 14;10:1355. doi: 10.3389/fgene.2019.01355. PMID: 32117413 PMCID: PMC7034361 (PubMed) (PDF)

122. 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 (Oxford). 2020 Jan 1;2020:baaa015. doi: 10.1093/database/baaa015. PMID: 32283553 PMCID: PMC7153956 (PubMed) (PDF)

2019

121. Mayers M, Li TS, Queralt-Rosinach N, Su AI. Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network. BMC Bioinformatics. 2019 Dec 11;20(1):653. doi: 10.1186/s12859-019-3297-0. PMID: 31829175 PMCID: PMC6907279 (PubMed) (PDF)

120. 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. 2019 Sep 27;14(9):e0222165. doi: 10.1371/journal.pone.0222165. PMID: 31560691 PMCID: PMC6764653 (PubMed)  (PDF)

119. Tsueng G, Kumar A, Nanis SM, Su AI. Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements. Hum Comput (Fairfax). 2019;6(1):56-82. PubMed PMID: 31363486; PubMed Central PMCID: PMC6667230. (PubMed) (PDF)

118. 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 (Oxford). 2019 Jan 1;2019. pii: baz041. doi: 10.1093/database/baz041. (PubMed) (PDF)

117. 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, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T,Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018. (PubMed) (PDF)

2018

116. 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 Cartilage. 2018 Nov;26(11):1531-1538. doi: 10.1016/j.joca.2018.07.012. (PubMed) (PDF)

115. 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, Schultz PG, Chatterjee AK. The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis. Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):10750-10755. doi: 10.1073/pnas.1810137115. (PubMed) (PDF)

114. Wang AY, Thuy-Boun PS, Stupp GS, Su AI, Wolan DW. Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass. J Proteome Res. 2018 Sep 7;17(9):2978-2986. doi: 10.1021/acs.jproteome.8b00166. (PubMed) (PDF)

113. Radin JM, Steinhubl SR, Su AI, Bhargava H, Greenberg B, Bot BM, Doerr M, Topol EJ. The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app NPJ Digit Med. 2018 Sep 5;1:45. doi: 10.1038/s41746-018-0052-2. PMID: 31304325 PMCID: PMC6550256 (PubMed)(PDF)

112. 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. J Biol Chem. 2018 Aug 31;293(35):13477-13495. doi: 10.1074/jbc.RA118.003192. (PubMed) (PDF)

111. Bruggemann J, Lander GC, Su AI. Exploring applications of crowdsourcing to cryo-EM. J Struct Biol. 2018 Jul;203(1):37-45. doi: 10.1016/j.jsb.2018.02.006. (PubMed) (PDF)

110. Gioia L, Siddique A, Head SR, Salomon DR, Su AI. A genome-wide survey of mutations in the Jurkat cell line. BMC Genomics. 2018 May 8;19(1):334. doi: 10.1186/s12864-018-4718-6. (PubMed) (PDF)

109. 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, Bandell M, Schmedt C, Wengelnik K, Su AI, Honore E, Winzeler EA, Andersen KG, Patapoutian A. Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection. Cell. 2018 Apr 5;173(2):443-455.e12. doi: 10.1016/j.cell.2018.02.047. (PubMed) (PDF)

108. 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. Sci Transl Med. 2018 Feb 14;10(428). doi: 10.1126/scitranslmed.aan0746. (PubMed) (PDF)

107. Moon C, Stupp GS, Su AI, Wolan DW. Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups. Proteomics. 2018 Feb;18(3-4). doi: 10.1002/pmic.201700391. (PubMed) (PDF) 

106. 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. 2018 Feb 1;19(1):30. doi: 10.1186/s12859-018-2041-5. (PubMed) (PDF)

105. 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 Mol Biol. 2018;1712:217-238. doi: 10.1007/978-1-4939-7514-3_14. (PubMed) (PDF)

2017

104. Shafee T, Mietchen D, Su AI. Academics can help shape Wikipedia. Science. 2017 Aug 11;357(6351):557-558. doi: 10.1126/science.aao0462. (PubMed) (PDF)

103. 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 Cartilage. 2017 Jun;25(6):943-951. doi: 10.1016/j.joca.2016.11.007. (PubMed) (PDF)

102. 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. J Proteome Res. 2017 Feb 3;16(2):1014-1026. doi: 10.1021/acs.jproteome.6b00938. (PubMed) (PDF)

101. 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, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. (PubMed) (PDF)

100. 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 (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax025. (PubMed) (PDF)

2016

99. Tsueng G, Nanis SM, Fouquier J, Good BM, Su AI. Citizen Science for Mining the Biomedical Literature. Citiz Sci. 2016;1(2). doi: 10.5334/cstp.56. (PubMed) (PDF)

98. 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. 2016 Nov 5;592(2):235-8. doi: 10.1016/j.gene.2016.04.053. (PubMed) (PDF)

97. 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. J Proteome Res. 2016 Nov 4;15(11):4126-4134. doi: 10.1021/acs.jproteome.6b00095. (PubMed) (PDF)

96. 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 Cartilage. 2016 Sep;24(9):1639-47. doi: 10.1016/j.joca.2016.04.015. (PubMed) (PDF)

95. Chatterjee S, Stupp GS, Park SK, Ducom JC, Yates JR 3rd, Su AI, Wolan DW. A comprehensive and scalable database search system for metaproteomics. BMC Genomics. 2016 Aug 16;17(1):642. doi: 10.1186/s12864-016-2855-3. (PubMed) (PDF)

94. 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 Rheumatol. 2016 Aug;68(8):1876-86. doi: 10.1002/art.39643. (PubMed) (PDF)

93. Kleiman E, Jia H, Loguercio S, Su AI, Feeney AJ. YY1 plays an essential role at all stages of B-cell differentiation. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):E3911-20. doi: 10.1073/pnas.1606297113. (PubMed) (PDF)

92. Modena BD, Kurian SM, Gaber LW, Waalen J, Su AI, Gelbart T, Mondala TS, Head SR, Papp S, Heilman R, Friedewald JJ, Flechner SM, Marsh CL, Sung RS, Shidban H, Chan L, Abecassis MM, Salomon DR. Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes. Am J Transplant. 2016 Jul;16(7):1982-98. doi: 10.1111/ajt.13728. (PubMed) (PDF)

91. Gangavarapu K, Babji V, Meißner T, Su AI, Good BM. Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. Bioinformatics. 2016 Jul 1;32(13):2072-2074. doi: 10.1093/bioinformatics/btw117. (PubMed) (PDF)

90. 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 (Oxford). 2016;2016. doi: 10.1093/database/baw094. (PubMed) (PDF)

89. 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, Wu C. High-performance web services for querying gene and variant annotation. Genome Biol. 2016 May 6;17(1):91. doi: 10.1186/s13059-016-0953-9. (PubMed) (PDF)

88. Li TS, Bravo À, Furlong LI, Good BM, Su AI. A crowdsourcing workflow for extracting chemical-induced disease relations from free text. Database (Oxford). 2016;2016. doi: 10.1093/database/baw051. (PubMed) (PDF)

87. 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, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC. Extending gene ontology in the context of extracellular RNA and vesicle communication. J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5. (PubMed) (PDF)

86. 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 (Oxford). 2016 Mar 28;2016. pii: baw028. doi: 10.1093/database/baw028. (PubMed) (PDF)

85. Modena BD, Kurian SM, Gaber LW, Waalen J, Su AI, Gelbart T, Mondala TS, Head SR, Papp S, Heilman R, Friedewald JJ, Flechner SM, Marsh CL, Sung RS, Shidban H, Chan L, Abecassis MM, Salomon DR. Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes. Am J Transplant. 2016 Jul;16(7):1982-98. doi: 10.1111/ajt.13728. (PubMed) (PDF)

84. 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 (Oxford). 2016 Mar 17;2016. pii: baw015. doi: 10.1093/database/baw015. (PubMed) (PDF)

83. 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, Kors JA, den Dunnen J, van Ommen GJ, Roos M, ‘t Hoen PA, Mons B, Schultes EA. The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PLoS One. 2016 Feb 26;11(2):e0149621. doi: 10.1371/journal.pone.0149621. (PubMed) (PDF)

82. 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 Rheumatol. 2016 Aug;68(8):1876-86. doi: 10.1002/art.39643. (PubMed) (PDF)

81. Tsueng G, Nanis SM, Fouquier J, Good BM, Su AI. Citizen Science for Mining the Biomedical Literature. Citiz Sci. 2016;1(2). pii: 14. doi: 10.5334/cstp.56. (PubMed) (PDF)

80. Wu C, Jin X, Tsueng G, Afrasiabi C, Su AI. BioGPS: building your own mash-up of gene annotations and expression profiles. Nucleic Acids Res. 2016 Jan 4;44(D1):D313-6. doi: 10.1093/nar/gkv1104. (PubMed) (PDF)

79. Khare R, Good BM, Leaman R, Su AI, Lu Z. Crowdsourcing in biomedicine: challenges and opportunities. Brief Bioinform. 2016 Jan;17(1):23-32. doi: 10.1093/bib/bbv021. (PubMed) (PDF)

2015

78. 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. J Extracell Vesicles. 2015 Aug 28;4:27497. doi: 10.3402/jev.v4.27497. (PubMed) (PDF)

77. 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. J Am Coll Cardiol. 2015 Jul 14;66(2):202-4. doi: 10.1016/j.jacc.2015.04.072. (PubMed) (PDF)

76. 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 Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z. (PubMed) (PDF)

75.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, Slepian PM, Clarke S, Drenan RM, Janes J, Al Sharari S, Segall SK, Aasvang EK, Lai W, Bittner R, Richards CI, Slade GD, Kehlet H, Walker J, Maskos U, Changeux JP, Devor M, Maixner W, Diatchenko L, Belfer I, Dougherty DA, Su AI, Lummis SC, Imad Damaj M, Lester HA, Patapoutian A, Mogil JS. The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors. Sci Transl Med. 2015 May 13;7(287):287ra72. doi: 10.1126/scitranslmed.3009986. (PubMed) (PDF)

74. Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR 3rd, Lindsey ML, Ping P. Harnessing the heart of big data. Circ Res. 2015 Mar 27;116(7):1115-9. doi: 10.1161/CIRCRESAHA.115.306013. (PubMed) (PDF)

73. Good BM, Nanis M, Wu C, Su AI. Microtask crowdsourcing for disease mention annotation in PubMed abstracts. Pac Symp Biocomput. 2015:282-93. (PubMed) (PDF)

2014

72. Fisch KM, Meißner T, Gioia L, Ducom JC, Carland T, Loguercio S, Su AI. Omics Pipe: A Computational Framework for Reproducible Multi-Omics Data Analysis. 2014. (PDF) (bioRxiv).

71. 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. Mol Cell. 2014 Oct 23;56(2):323-332. doi: 10.1016/j.molcel.2014.09.006. (PubMed) (PDF)

70. Good BM, Ainscough BJ, McMichael JF, Su AI, Griffith OL. Organizing knowledge to enable personalization of medicine in cancer. Genome Biology. 2014, 15:438. (PDF)

69. Peterson SN, Meissner T, Su AI, Snesrud E, Ong AC, Schork NJ, Bretz WA. Functional Expression of Dental Plaque Microbiota. Front. Cell. Infect. Microbiol. 4(108). doi: 10.3389/fcimb.2014.00108 (PDF).

68. 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 2014;2(2):e7 (PDF).

2013

67. 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 Comput Biol. 2013;9(9):e1003244. doi: 10.1371/journal.pcbi.1003244 (PubMed) (PDF)

66. Su AI, Good BM, van Wijnen AJ. Gene Wiki Reviews: Marrying crowdsourcing with traditional peer review. (2013) Gene. 531(2):125. doi: 10.1016/j.gene.2013.08.093. (PubMed) (PDF)

65. Chou WL, Galmozzi A, Partida D, Kwan K, Yeung H, Su AI, Saez E. (2013) Identification of Regulatory Elements That Control PPARγ Expression in Adipocyte Progenitors. PLOS ONE. 8(8):e72511. doi: 10.1371/journal.pone.0072511. (PubMed) (PDF)

64. Loguercio S, Good BM, Su AI. (2013) Dizeez: an Online Game for Human Gene-Disease Annotation. PLOS ONE. 8(8):e71171. doi: 10.1371/journal.pone.0071171. (PubMed) (PDF)

63. Gopalakrishnan S, Majumder K, Predeus A, Huang Y, Koues OI, Verma-Gaur J, Loguercio S, Su AI, Feeney AJ, Artyomov MN, Oltz EM. (2013) Unifying model for molecular determinants of the preselection Vβ repertoire. Proc Natl Acad Sci U S A. 110(34):E3206-15. doi: 10.1073/pnas.1304048110. (PubMed)

62. Choi NM, Loguercio S, Verma-Gaur J, Degner SC, Torkamani A, Su AI, Oltz EM, Artyomov M, Feeney AJ. (2013) Deep sequencing of the murine igh repertoire reveals complex regulation of nonrandom v gene rearrangement frequencies. J Immunol. 191(5):2393-402. doi: 10.4049/jimmunol.1301279. (PubMed)

61. Good BM, Su AI. (2013) Crowdsourcing for Bioinformatics. Bioinformatics. 15;29(16):1925-33. doi: 10.1093/bioinformatics/btt333 (PubMed)

60. Clarke EL, Loguercio S, Good BM, Su AI. (2013) A task-based approach for Gene Ontology evaluation. J Biomed Semantics. 4 Suppl 1:S4. doi: 10.1186/2041-1480-4-S1-S4. (PubMed) (PDF)

59. Shoulders MD, Ryno LM, Genereux JC, Moresco JJ, Tu PG, Wu C, Yates JR 3rd, Su AI, Kelly JW, Wiseman RL. (2013) Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments. Cell Rep. 3(4):1279-92. doi: 10.1016/j.celrep.2013.03.024. (PubMed)

58. Wu C, Macleod I, Su AI. (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res. 41(D1):D561-5. doi: 10.1093/nar/gks1114. (PubMed) (PDF)

2012

57. 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, Tuggle CK, Archibald AL, Hume DA. (2012) A gene expression atlas of the domestic pig. BMC Biol. 10:90. doi: 10.1186/1741-7007-10-90. (PubMed) (PDF)

56. Grogan SP, Duffy SF, Pauli C, Koziol JA, Su AI, D’Lima DD, Lotz MK (2012) Zone-specific gene expression patterns in articular cartilage. Arthritis Rheum. doi: 10.1002/art.37760. (PubMed)

55. Ringwald M, Wu C, Su AI (2012) BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. Mamm Genome. 23(9-10):550-8. (Pubmed) (PDF)

54. Miller E, Yang J, Deran M, Wu C, Su AI, Bonamy GM, Liu J, Peters EC, Wu X (2012) Identification of serum-derived sphingosine-1-phosphate as a small molecule regulator of yap. Chem Biol., 19(8):955-62. (PubMed) (PDF)

53. Good BM, Clarke EL, Loguercio S, Su AI (2012) Linking genes to diseases with a SNPedia-Gene Wiki mashup. J Biomed Semantics. 3 Suppl 1:S6. (PubMed) (PDF)

52. Liu YW, Su AI, Schmid SL (2012) The evolution of dynamin to regulate clathrin-mediated endocytosis: Speculations on the evolutionarily late appearance of dynamin relative to clathrin-mediated endocytosis. Bioessays, May 16. doi: 10.1002/bies.201200033. [Epub ahead of print] (PubMed)

51. Good BM, Clarke EL, Loguercio S, Su AI (2012) Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database (Oxford). 2012 Mar 20; 2012:bar060. (PubMed) (PDF)

50. Good BM, Clarke EL, de Alfaro L, Su AI (2012) The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res., 40(1):D1255-61. (PubMed) (PDF)

2011

49. Good BM, Howe DG, Lin SM, Kibbe WA, Su AI (2011) Mining the Gene Wiki for functional genomic knowledge. BMC Genomics, 12(1):603. (PubMed) (PDF)

48. Good BM, and Su AI (2011) Games with a scientific purpose. Genome Biol., 12(12):135. (PubMed) (PDF)

47. Hu Y, Galkin AV, Wu C, Reddy V, Su AI (2011) CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma. PLoS ONE 6(10): e25807. doi:10.1371/journal.pone.0025807 (PubMed) (PDF)

46. Good BM and Su AI (2011) Mining Gene Ontology Annotations From Hyperlinks in the Gene Wiki. Proceedings of the Translational Bioinformatics Conference. http://proceedings.amia.org/T2011 (PDF)

2010

45. Miller BH, Schultz LE, Gulati A, Su AI, Pletcher MT (2010) Phenotypic characterization of a genetically diverse panel of mice for behavioral despair and anxiety. PLoS One., 29;5(12):e14458. (PubMed) (PDF)

44. Loguercio S, Overall RW, Michaelson JJ, Wiltshire T, Pletcher MT, Miller BH, Walker JR, Kempermann G, Su AI, Beyer A. (2010) Integrative analysis of low- and high-resolution eQTL. PLoS One. 5(11):e13920. (PubMed) (PDF)

43. Dost B, Wu C, Su AI, Bafna V (2010) TCLUST: A Fast Method for Clustering Genome-Scale Expression Data.  IEEE/ACM Trans Comput Biol Bioinform, http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.34. (PubMed) (PDF)

42. Lee JM, Zhang J, Su AI, Walker JR, Wiltshire T, Kang K, Dragileva E, Gillis T, Lopez ET, Boily MJ, Cyr M, Kohane I, Gusella JF, MacDonald ME, Wheeler VC (2010) HA novel approach to investigate tissue-specific trinucleotide repeat instability.  BMC Syst Biol., 19(4):29. (PubMed) (PDF)

41. 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, Chen H, Johnson K, Laffitte B, Nguyen DG, Snyder EY, Schultz PG, Harris JL, Lesley SA (2010) Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency. Proc Natl Acad Sci U S A, 107(8):3552-7. (PubMed) (PDF)

40. Huss JW, 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB and Su AI (2010) The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res., 38:D633-D639. (PubMed) (PDF)

2009

** 39. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, 3rd and Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol, 10:R130. (PubMed) (PDF)

38. Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, 3rd, Janes J, Su AI, Hogenesch JB and Kay SA (2009) A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell, 139:199-210. (PubMed) (PDF)

37. Williams Rt, Lim JE, Harr B, Wing C, Walters R, Distler MG, Teschke M, Wu C, Wiltshire T, Su AI, Sokoloff G, Tarantino LM, Borevitz JO and Palmer AA (2009) A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior. PLoS One, 4:e4649. (PubMed) (PDF)

36. Pezacki JP, Sagan SM, Tonary AM, Rouleau Y, Belanger S, Supekova L and Su AI (2009) Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus. BMC Chem Biol, 9:2. (PubMed) (PDF)

35. Tang PL, Cheung CL, Sham PC, McClurg P, Lee B, Chan SY, Smith DK, Tanner JA, Su AI, Cheah KS, Kung AW and Song YQ (2009) Genome-wide haplotype association mapping in mice identifies a genetic variant in CER1 associated with BMD and fracture in southern Chinese women. J Bone Miner Res, 24:1013-21. (PubMed) (PDF)

2008

34. Hogenesch JB and Su AI (2008) Clock gene wikis available: join the “long tail”. J Biol Rhythms, 23:456-7. (PubMed) (PDF)

33. Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI and Jansen RC (2008) Genetical genomics: spotlight on QTL hotspots. PLoS Genet, 4:e1000232. (PubMed) (PDF)

32. Huss JW, 3rd, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F and Su AI (2008) A gene wiki for community annotation of gene function. PLoS Biol, 6:e175. (PubMed) (PDF)

      Media coverage:

31. 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, Kohsaka A, Bass J, Saez E, Wiltshire T and Su AI (2008) Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet, 4:e1000070. (PubMed) (PDF)

* 30. Lattin JE, Schroder K, Su AI, Walker JR, Zhang J, Wiltshire T, Saijo K, Glass CK, Hume DA, Kellie S and Sweet MJ (2008) Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res, 4:5. (PubMed) (PDF)

2007

29. Su AI and Hogenesch JB (2007) Power-law-like distributions in biomedical publications and research funding. Genome Biol, 8:404. (PubMed) (PDF)

28. McClurg P, Janes J, Wu C, Delano DL, Walker JR, Batalov S, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Wiltshire T and Su AI (2007) Genomewide association analysis in diverse inbred mice: power and population structure. Genetics, 176:675-83. (PubMed) (PDF)

2006

27. Lee JW, Lee JS, Kang M, Su AI and Chang YT (2006) Visual artificial tongue for quantitative metal-cation analysis by an off-the-shelf dye array. Chemistry, 12:5691-6. (PubMed) (PDF)

* 26. 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, Zhou Y, Gu XJ, Saadat A, Zhou V, King FJ, Shaw CM, Su AI, Downs R, Gray NS, Schultz PG, Warmuth M and Caldwell JS (2006) An efficient rapid system for profiling the cellular activities of molecular libraries. Proc Natl Acad Sci U S A, 103:3153-8. (PubMed) (PDF)

25. McClurg P, Pletcher MT, Wiltshire T and Su AI (2006) Comparative analysis of haplotype association mapping algorithms. BMC Bioinformatics, 7:61. (PubMed) (PDF)

24. Sagan SM, Rouleau Y, Leggiadro C, Supekova L, Schultz PG, Su AI and Pezacki JP (2006) The influence of cholesterol and lipid metabolism on host cell structure and hepatitis C virus replication. Biochem Cell Biol, 84:67-79. (PubMed) (PDF)

2005

23. Zhong JF, Zhao Y, Sutton S, Su A, Zhan Y, Zhu L, Yan C, Gallaher T, Johnston PB, Anderson WF and Cooke MP (2005) Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells. Proc Natl Acad Sci U S A, 102:2448-53. (PubMed) (PDF)

22. Yang J, Su AI and Li WH (2005) Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol, 22:2113-8. (PubMed) (PDF)

21. Gurkan C, Lapp H, Alory C, Su AI, Hogenesch JB and Balch WE (2005) Large-scale profiling of Rab GTPase trafficking networks: the membrome. Mol Biol Cell, 16:3847-64. (PubMed) (PDF)

20. Wilkens SJ, Janes J and Su AI (2005) HierS: Hierarchical Scaffold Clustering Using Topological Chemical Graphs. J Med Chem, 48:3182-93. (PubMed) (PDF)

** 19. 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, Cooke MP and de Haan G (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nat Genet, 37:225-32. (PubMed) (PDF)

2004

* 18. Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, Mural RJ, Paigen B and Wiltshire T (2004) Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS Biol, 2:e393. (PubMed) (PDF)

**** 17. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR and Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A, 101:6062-7. (PubMed) (PDF)

** 16. Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D and Bilbe G (2004) Applications of a rat multiple tissue gene expression data set. Genome Res, 14:742-9. (PubMed) (PDF)

2003

15. Batalov S, Su AI, Ching KA and Fletcher CF (2003) Functional annotation of RIKEN mouse cDNA clones using GNF expression atlas. Genome Res, 13:1556-1557. (PDF)

* 14. Conkright MD, Guzman E, Flechner L, Su AI, Hogenesch JB and Montminy M (2003) Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol Cell, 11:1101-8. (PubMed) (PDF)

2002

** 13. Su AI, Pezacki JP, Wodicka L, Brideau AD, Supekova L, Thimme R, Wieland S, Bukh J, Purcell RH, Schultz PG and Chisari FV (2002) Genomic analysis of the host response to hepatitis C virus infection. Proc Natl Acad Sci U S A, 99:15669-74. (PubMed) (PDF)

* 12. Frierson HF, Jr., El-Naggar AK, Welsh JB, Sapinoso LM, Su AI, Cheng J, Saku T, Moskaluk CA and Hampton GM (2002) Large scale molecular analysis identifies genes with altered expression in salivary adenoid cystic carcinoma. Am J Pathol, 161:1315-23. (PubMed) (PDF)

* 11. Su AI, Guidotti LG, Pezacki JP, Chisari FV and Schultz PG (2002) Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice. Proc Natl Acad Sci U S A, 99:11181-6. (PubMed) (PDF)

10. Supekova L, Pezacki JP, Su AI, Loweth CJ, Riedl R, Geierstanger B, Schultz PG and Wemmer DE (2002) Genomic effects of polyamide/DNA interactions on mRNA expression. Chem Biol, 9:821-7. (PubMed) (PDF)

*** 9. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS and Hogenesch JB (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell, 109:307-20. (PubMed) (PDF)

**** 8. 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 and Hogenesch JB (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A, 99:4465-70. (PubMed) (PDF)

2001

7. Chang YT, Wignall SM, Rosania GR, Gray NS, Hanson SR, Su AI, Merlie J, Jr., Moon HS, Sangankar SB, Perez O, Heald R and Schultz PG (2001) Synthesis and biological evaluation of myoseverin derivatives: microtubule assembly inhibitors. J Med Chem, 44:4497-500. (PubMed) (PDF)

** 6. Su AI, Welsh JB, Sapinoso LM, Kern SG, Dimitrov P, Lapp H, Schultz PG, Powell SM, Moskaluk CA, Frierson HF, Jr. and Hampton GM (2001) Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res, 61:7388-93. (PubMed) (PDF)

* 5. Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG and Cooke MP (2001) A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell, 106:413-5. (PubMed) (PDF)

*** 4. Welsh JB, Sapinoso LM, Su AI, Kern SG, Wang-Rodriguez J, Moskaluk CA, Frierson HF, Jr. and Hampton GM (2001) Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res, 61:5974-8. (PubMed) (PDF)

3. Wolkenberg SE and Su AI (2001) Combinatorial synthesis and discovery of an antibiotic compound: An experiment suitable for high school and undergraduate laboratories. J Med Chem, 78:784-5. (PDF)

2. Ratnaswamy G, Huff ME, Su AI, Rion S and Kelly JW (2001) Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type. Proc Natl Acad Sci U S A, 98:2334-9. (PubMed) (PDF)

1. Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW and Shoichet BK (2001) Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins, 42:279-93. (PubMed) (PDF)

(**** 1000, *** 500, ** 250, or * 100 citations)