Publications


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2014
71. 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).

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 A, 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)

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)