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Mary Yang

TitleProfessor - STEM
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentInformation Science
Address2801 South University Avenue
Little Rock AR 72204
Phone+1 (501) 9165243
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions. Don't see publications published under other names? Login to add alternative names.
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    1. Zhang W, Huckaby B, Talburt J, Weissman S, Yang MQ. cnnImpute: missing value recovery for single cell RNA sequencing data. Sci Rep. 2024 02 16; 14(1):3946. PMID: 38365936.
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    2. Ma J, Pettit N, Talburt J, Wang S, Weissman SM, Yang MQ. Integrating Single-Cell Transcriptome and Network Analysis to Characterize the Therapeutic Response of Chronic Myeloid Leukemia. Int J Mol Sci. 2022 Nov 18; 23(22). PMID: 36430822.
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    3. Yang F, Darsey JA, Ghosh A, Li HY, Yang MQ, Wang S. Artificial Intelligence and Cancer Drug Development. Recent Pat Anticancer Drug Discov. 2022; 17(1):2-8. PMID: 34323201.
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    4. Li D, Xu J, Yang MQ. Gene Regulation Analysis Reveals Perturbations of Autism Spectrum Disorder during Neural System Development. Genes (Basel). 2021 11 27; 12(12). PMID: 34946850.
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    5. Li Q, Yang MQ. Comparison of machine learning approaches for enhancing Alzheimer's disease classification. PeerJ. 2021; 9:e10549. PMID: 33665002.
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    6. Yang MQ, Weissman SM, Yang W, Zhang J, Canaan A, Guan R. Correction to: MISC: missing imputation for single-cell RNA sequencing data. BMC Syst Biol. 2019 Jan 22; 13(1):13. PMID: 30670065.
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    7. Cao P, Yang Z, Sun L, Liang Y, Yang MQ, Guan R. Image Captioning with Bidirectional Semantic Attention-Based Guiding of Long Short-Term Memory. Neural Process Lett. 2019 Aug; 50(1):103-119. PMID: 35035261.
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    8. He G, Liang Y, Chen Y, Yang W, Liu JS, Yang MQ, Guan R. A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity. BMC Syst Biol. 2018 12 14; 12(Suppl 7):116. PMID: 30547805.
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    9. Li D, Yang W, Arthur C, Liu JS, Cruz-Niera C, Yang MQ. Systems biology analysis reveals new insights into invasive lung cancer. BMC Syst Biol. 2018 12 14; 12(Suppl 7):117. PMID: 30547817.
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    10. Yang MQ, Weissman SM, Yang W, Zhang J, Canaann A, Guan R. MISC: missing imputation for single-cell RNA sequencing data. BMC Syst Biol. 2018 12 14; 12(Suppl 7):114. PMID: 30547798.
      View in: PubMed
    11. Hu L, Zhang R, Yuan Q, Gao Y, Yang MQ, Zhang C, Huang J, Sun Y, Yang W, Yang JY, Min ZL, Cheng J, Deng Y, Hu X. The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by A?25-35 triggered in SH-SY5Y cell. BMC Syst Biol. 2018 12 14; 12(Suppl 7):119. PMID: 30547775.
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    12. Guo M, Lu S, Huang H, Wang Y, Yang MQ, Yang Y, Fan Z, Jiang B, Deng Y. Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer. BMC Syst Biol. 2018 12 14; 12(Suppl 7):118. PMID: 30547784.
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    13. Cogill SB, Srivastava AK, Yang MQ, Wang L. Co-expression of long non-coding RNAs and autism risk genes in the developing human brain. BMC Syst Biol. 2018 12 14; 12(Suppl 7):91. PMID: 30547845.
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    14. Li D, Yang W, Zhang Y, Yang JY, Guan R, Xu D, Yang MQ. Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature. BMC Med Genomics. 2018 Nov 20; 11(Suppl 5):106. PMID: 30453959.
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    15. Zhang Y, Yang W, Li D, Yang JY, Guan R, Yang MQ. Toward the precision breast cancer survival prediction utilizing combined whole genome-wide expression and somatic mutation analysis. BMC Med Genomics. 2018 Nov 20; 11(Suppl 5):104. PMID: 30454048.
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    16. Guan R, Wang X, Yang MQ, Zhang Y, Zhou F, Yang C, Liang Y. Author Correction: Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways. Sci Rep. 2018 Jun 07; 8(1):8995. PMID: 29875368.
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    17. Li D, Yang MQ. Correction to: Identification and characterization of conserved lncRNAs in human and rat brain. BMC Bioinformatics. 2018 05 24; 19(1):181. PMID: 29793423.
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    18. Li D, Yang W, Zhang J, Yang JY, Guan R, Yang MQ. Erratum: Dan Li et al.; Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma. Genes 2018, 9, 12. Genes (Basel). 2018 05 14; 9(5). PMID: 29757968.
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    19. Guan R, Wang X, Marchese M, Yang MQ, Liang Y, Yang C. Feature space learning model. J Ambient Intell Humaniz Comput. 2019 May; 10(5):2029-2040. PMID: 31068980.
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    20. Guan R, Wang X, Yang MQ, Zhang Y, Zhou F, Yang C, Liang Y. Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways. Sci Rep. 2018 01 10; 8(1):267. PMID: 29321535.
      View in: PubMed
    21. Li D, Yang W, Zhang J, Yang JY, Guan R, Yang MQ. Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma. Genes (Basel). 2018 Jan 05; 9(1). PMID: 29303984.
      View in: PubMed
    22. Li D, Yang MQ. Identification and characterization of conserved lncRNAs in human and rat brain. BMC Bioinformatics. 2017 12 28; 18(Suppl 14):489. PMID: 29297275.
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    23. Yang MQ, Li D, Yang W, Zhang Y, Liu J, Tong W. A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer. Comput Struct Biotechnol J. 2017; 15:463-470. PMID: 29158875.
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    24. Zhao W, Yang MQ. Dependability enhancing mechanisms for integrated clinical environments. J Supercomput. 2017 Oct; 73(10):4207-4220. PMID: 29081597.
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    25. Yang MQ, Elnitski L. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PLoS One. 2016; 11(10):e0163353. PMID: 27788148.
      View in: PubMed
    26. Zhou H, Manthey J, Lioutikova E, Yang W, Yoshigoe K, Yang MQ, Wang H. The up-regulation of Myb may help mediate EGCG inhibition effect on mouse lung adenocarcinoma. Hum Genomics. 2016 07 25; 10 Suppl 2:19. PMID: 27461468.
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    27. Chen X, Li J, Hu L, Yang W, Lu L, Jin H, Wei Z, Yang JY, Arabnia HR, Liu JS, Yang MQ, Deng Y. The clinical significance of snail protein expression in gastric cancer: a meta-analysis. Hum Genomics. 2016 07 25; 10 Suppl 2:22. PMID: 27461247.
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    28. Chen X, Chen X, Xu Y, Yang W, Wu N, Ye H, Yang JY, Hong Q, Xin Y, Yang MQ, Deng Y, Duan S. Association of six CpG-SNPs in the inflammation-related genes with coronary heart disease. Hum Genomics. 2016 07 25; 10 Suppl 2:21. PMID: 27461004.
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    29. Yang MQ, Yoshigoe K, Yang W, Tong W, Qin X, Dunker A, Chen Z, Arbania HR, Liu JS, Niemierko A, Yang JY. The emerging genomics and systems biology research lead to systems genomics studies. BMC Genomics. 2014; 15 Suppl 11:I1. PMID: 25558922.
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    30. Zhou H, Chen JX, Yang CS, Yang MQ, Deng Y, Wang H. Gene regulation mediated by microRNAs in response to green tea polyphenol EGCG in mouse lung cancer. BMC Genomics. 2014; 15 Suppl 11:S3. PMID: 25559244.
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    31. Deng Y, Ai J, Guan X, Wang Z, Yan B, Zhang D, Liu C, Wilbanks MS, Escalon BL, Meyers SA, Yang MQ, Perkins EJ. MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity. BMC Genomics. 2014; 15 Suppl 11:S1. PMID: 25559034.
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    32. Yang MQ, Laflamme K, Gotea V, Joiner CH, Seidel NE, Wong C, Petrykowska HM, Lichtenberg J, Lee S, Welch L, Gallagher PG, Bodine DM, Elnitski L. Genome-wide detection of a TFIID localization element from an initial human disease mutation. Nucleic Acids Res. 2011 Mar; 39(6):2175-87. PMID: 21071415.
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    33. Wang L, Huang C, Yang MQ, Yang JY. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol. 2010 May 28; 4 Suppl 1:S3. PMID: 20522253.
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    34. Zhang X, Wang T, Luo H, Yang JY, Deng Y, Tang J, Yang MQ. 3D protein structure prediction with genetic tabu search algorithm. BMC Syst Biol. 2010 May 28; 4 Suppl 1:S6. PMID: 20522256.
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    35. Laflamme K, Owen AN, Devlin EE, Yang MQ, Wong C, Steiner LA, Garrett LJ, Elnitski L, Gallagher PG, Bodine DM. Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. Mol Cell Biol. 2010 Jul; 30(14):3493-502. PMID: 20479128.
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    36. Yang MQ, Niemierko A, Yang JY, Jin Y. Promoting inter/multidisciplinary education and research in bioinformatics, systems biology and intelligent computing. Int J Comput Biol Drug Des. 2009; 2(3):207-20. PMID: 20090160.
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    37. Yang MQ, Yang JY. Lecture notes: 2010 and beyond, the decade of high-performance computing for the next-generation sequence analysis. Int J Comput Biol Drug Des. 2009; 2(2):204-6. PMID: 20090171.
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    38. Wang L, Yang MQ, Yang JY. Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S1. PMID: 19594868.
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    39. Lichtenberg J, Jacox E, Welch JD, Kurz K, Liang X, Yang MQ, Drews F, Ecker K, Lee SS, Elnitski L, Welch LR. Word-based characterization of promoters involved in human DNA repair pathways. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S18. PMID: 19594877.
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    40. Liu Q, Sung AH, Qiao M, Chen Z, Yang JY, Yang MQ, Huang X, Deng Y. Comparison of feature selection and classification for MALDI-MS data. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S3. PMID: 19594880.
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    41. Yang MQ, Athey BD, Arabnia HR, Sung AH, Liu Q, Yang JY, Mao J, Deng Y. High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics. BMC Genomics. 2009 Jul 07; 10 Suppl 1:I1. PMID: 19594867.
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    42. Piontkivska H, Yang MQ, Larkin DM, Lewin HA, Reecy J, Elnitski L. Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics. 2009 Apr 24; 10:189. PMID: 19393065.
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    43. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guig? R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, C?mara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Mor? DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24; 324(5926):522-8. PMID: 19390049.
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    44. Zeng XQ, Li GZ, Wu GF, Yang JY, Yang MQ. Irrelevant gene elimination for partial least squares based dimension reduction by using feature probes. Int J Data Min Bioinform. 2009; 3(1):85-103. PMID: 19432378.
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    45. Yang JY, Yang MQ. Predicting protein disorder by analyzing amino acid sequence. BMC Genomics. 2008 Sep 16; 9 Suppl 2:S8. PMID: 18831799.
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    46. Pirooznia M, Gong P, Yang JY, Yang MQ, Perkins EJ, Deng Y. ILOOP--a web application for two-channel microarray interwoven loop design. BMC Genomics. 2008 Sep 16; 9 Suppl 2:S11. PMID: 18831776.
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    47. Yang MQ, Elnitski LL. Diversity of core promoter elements comprising human bidirectional promoters. BMC Genomics. 2008 Sep 16; 9 Suppl 2:S3. PMID: 18831794.
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    48. Yang JY, Niemierko A, Yang MQ, Deng Y. Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes. BMC Genomics. 2008 Sep 16; 9 Suppl 2:S9. PMID: 18831800.
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    49. Yang JY, Yang MQ, Arabnia HR, Deng Y. Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research. BMC Genomics. 2008 Sep 16; 9 Suppl 2:I1. PMID: 18831773.
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    50. Li GZ, Bu HL, Yang MQ, Zeng XQ, Yang JY. Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis. BMC Genomics. 2008 Sep 16; 9 Suppl 2:S24. PMID: 18831790.
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    51. Yang MQ, Taylor J, Elnitski L. Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics. 2008 May 28; 9 Suppl 6:S9. PMID: 18541062.
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    52. Li GZ, Meng HH, Lu WC, Yang JY, Yang MQ. Asymmetric bagging and feature selection for activities prediction of drug molecules. BMC Bioinformatics. 2008 May 28; 9 Suppl 6:S7. PMID: 18541060.
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    53. Zeng XQ, Li GZ, Yang JY, Yang MQ, Wu GF. Dimension reduction with redundant gene elimination for tumor classification. BMC Bioinformatics. 2008 May 28; 9 Suppl 6:S8. PMID: 18541061.
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    54. Yang JY, Yang MQ. Identification of Intrinsically Unstructured Proteins using hierarchical classifier. Int J Data Min Bioinform. 2008; 2(2):121-33. PMID: 18767350.
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    55. Habib T, Zhang C, Yang JY, Yang MQ, Deng Y. Supervised learning method for the prediction of subcellular localization of proteins using amino acid and amino acid pair composition. BMC Genomics. 2008; 9 Suppl 1:S16. PMID: 18366605.
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    56. Yang JY, Yang MQ, Zhu MM, Arabnia HR, Deng Y. Promoting synergistic research and education in genomics and bioinformatics. BMC Genomics. 2008; 9 Suppl 1:I1. PMID: 18366597.
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    57. Oldfield CJ, Meng J, Yang JY, Yang MQ, Uversky VN, Dunker AK. Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics. 2008; 9 Suppl 1:S1. PMID: 18366598.
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    58. Yang JY, Yang MQ, Luo Z, Ma Y, Li J, Deng Y, Huang X. A hybrid machine learning-based method for classifying the Cushing's Syndrome with comorbid adrenocortical lesions. BMC Genomics. 2008; 9 Suppl 1:S23. PMID: 18366613.
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    59. Yang JY, Li GZ, Meng HH, Yang MQ, Deng Y. Improving prediction accuracy of tumor classification by reusing genes discarded during gene selection. BMC Genomics. 2008; 9 Suppl 1:S3. PMID: 18366616.
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    60. Pirooznia M, Yang JY, Yang MQ, Deng Y. A comparative study of different machine learning methods on microarray gene expression data. BMC Genomics. 2008; 9 Suppl 1:S13. PMID: 18366602.
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    61. Yang MQ, Elnitski LL. Prediction-based approaches to characterize bidirectional promoters in the mammalian genome. BMC Genomics. 2008; 9 Suppl 1:S2. PMID: 18366609.
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    62. Yang JY, Yang MQ, Dunker AK, Deng Y, Huang X. Investigation of transmembrane proteins using a computational approach. BMC Genomics. 2008; 9 Suppl 1:S7. PMID: 18366620.
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    63. Liu Q, Yang J, Chen Z, Yang MQ, Sung AH, Huang X. Supervised learning-based tagSNP selection for genome-wide disease classifications. BMC Genomics. 2008; 9 Suppl 1:S6. PMID: 18366619.
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    64. Du P, Lin SM, Yang MQ, Yang JY. 2009 and beyond: the decade of personalised medicine. Int J Comput Biol Drug Des. 2008; 1(4):329-33. PMID: 20063461.
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    65. Li GZ, Yang JY, Lu WC, Li D, Yang MQ. Improving prediction accuracy of drug activities by utilising unlabelled instances with feature selection. Int J Comput Biol Drug Des. 2008; 1(1):1-13. PMID: 20054997.
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    66. Liu TY, Li GZ, Yang JY, Yang MQ. Feature selection for the imbalanced QSAR problems by using easyensemble. Int J Comput Biol Drug Des. 2008; 1(4):334-46. PMID: 20063462.
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    67. Land WH, Heine JJ, Raway T, Mizaku A, Kovalchuk N, Yang JY, Yang MQ. New statistical learning theory paradigms adapted to breast cancer diagnosis/classification using image and non-image clinical data. Int J Funct Inform Personal Med. 2008 Jan; 1(2):111-139. PMID: 26430470.
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    68. Yang MQ, Koehly LM, Elnitski LL. Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol. 2007 Apr 20; 3(4):e72. PMID: 17447839.
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    69. Luo Z, Li J, Qin Y, Ma Y, Liang X, Xian J, Lu D, Wei M, Yang JY, Yang MQ, He Z. Differential expression of human telomerase catalytic subunit mRNA by in situ hybridization in pheochromocytomas. Endocr Pathol. 2006; 17(4):387-98. PMID: 17525487.
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