Publications from 2004
  1. "5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation" Chia Lin WEI, Patrick Wei Pern NG, Kuo Ping CHIU, Chee Hong Wong, Chin Chin Ang, Leonard LIPOVICH, Edison Tak-Bun LIU, Yijun RUAN (2004) Proc Natl Acad Sci USA. 101 (32) . 11701-6


  2. "A human in vitro model system for investigating genome-wide host responses to SARS coronavirus infection." Ng Lisa F P, Hibberd Martin L, Ooi Eng-Eong, Tang Kin -Fai, Neo Soek-Ying, Tan Jenny, Murthy Karuturi R Krishna, Vega Vinsensius B, Chia Jer-Ming, Liu Edison T, Ren Ee-Chee (2004) BMC Infect. Dis. 2004 Sep 9 ; 4 : 34


  3. "A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments." Broët Philippe, Lewin Alex, Richardson Sylvia, Dalmasso Cyril, Magdelenat Henri (2004) Bioinformatics 2004 Nov 1 ; 20(16) : 2562-71


  4. "Automatic prediction of protein domains from sequence information using a hybrid learning system." Nagarajan Niranjan, Yona Golan (2004) Bioinformatics 2004 Jun 12 ; 20(9) : 1335-60 Epub 1970 Jan 1


  5. "BEARR: Batch Extraction and Analysis of cis-Regulatory Regions" Vinsensius Berlian VEGA, Bangarusamy DK, Lance D MILLER, Edison Tak-Bun LIU, Lin CY (2004) Nucleic Acids Res. 32: . W257-60


  6. "BRCA1 interacts with and is required for paclitaxel-induced activation of mitogen-activated protein kinase kinase kinase 3" Gilmore PM, McCabe N, Quinn JE, Kennedy RD, Gorski JJ, Andrews HN, McWilliams S, Carty M, Mullan PB, Duprex WP, Edison Tak-Bun LIU, Johnston PG, Harkin DP (2004) Cancer Res. 64(12) . 4148-54


  7. "BRCA1-mediated repression of select X chromosome genes" Jazaeri AA, Chandramouli GV, Aprelikova O, Nuber UA, Sotiriou C, Edison Tak-Bun LIU, Ropers HH, Yee CJ, Boyd J, Barrett JC (2004) J Transl Med. 21;2(1) . 32


  8. "Capillary Isoelectric Focusing in Pseudo-closed Channel Coupled to Matrix Assisted Laser Desorption/Ionization Mass Spectrometry for Protein Analysis" Mok MLS, Hua Lin, Phua JBC, Wee MKT, Newman Siu-Kwan SZE (2004) 129 . 109-110


  9. "Coupled induction of iNOS and p53 upregulation in renal resident cells may be linked with apoptotic activity in the pathogenesis of progressive IgA nephropathy" Qiu LQ, Sinniah R, Hsu, Stephen I-Hong (2004) J Am Soc Nephrol. 15 (8) . 2066-2078


  10. "Detection of SARS CoV in blood of infected patients" Lisa Fong-Poh NG, Wong MS, Koh S, Ooi E.E., Tang K.F., Leong H.N., Ling A.E., Agathe L.L.C., Tan J., Edison Tak-Bun LIU, Ee Chee REN, Ng L.C., Martin Lloyd HIBBERD (2004) J. Clin. Micro.. 42 . 347-350


  11. "Detection of severe acute respiratory syndrome coronavirus in blood of infected patients." Ng Lisa F P, Wong Michelle, Koh Susie, Ooi Eng-Eong, Tang King-Fai, Leong Hoe-Nam, Ling Ai-Ee, Agathe Lora V, Tan Jenny, Liu Edison T, Ren Ee-Chee, Ng Lee-Ching, Hibberd Martin L (2004) J. Clin. Microbiol. 2004 Jan ; 42(1) : 347-50


  12. "Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells" Chin-Yo Lin, Anders Strom, Vinsensius Berlian VEGA, Say Li Kong, Ai Li Yeo, Jane THOMSEN, Wan Ching Chan, Balraj Doray, Dhinoth K Bangarusamy, Adaikalavan Ramasamy, Liza A Vergara, Suisheng Tang, Allen Chong, Vladimir B Bajic, Lance D MILLER, Jan-Ake Gustafsson, Edison Tak-Bun LIU (2004) Genome Biol. Aug 12 5(9) . R66


  13. "Distributed Evolutionary Strategy for Searching Oligo sets of Yeast Genome" Tay, A, Tan, KC, Cai, J, Huck Hui NG (2004) In Recent Advances in Simulated Evolution and Learning, World Scientific, 2004


  14. "Efficient isolation of cDNA clones encoding rheumatoid arthritis autoantigens by lambda phage surface display" Niwa, M, Fukuoka, K. J, Fujimoto, T, Ichiro MARUYAMA (2004) J. Biotechnol. 114 . 55-58


  15. "Embryonic Cell Lines with Endothelial Potential: An In Vitro System for Studying Endothelial Differentiation" Yin, Y, Que, J, Teh, M, Cao, W. P, El Oakley, R. M, Sai Kiang LIM (2004) Arteriosclerosis, Thrombosis and Vascular Biology. 24 . 691- 696


  16. "Expression genomics and cancer biology" Edison Tak-Bun LIU (2004) Pharmacogenomics. 5(8) . 1117-28


  17. "Expression Profiling and Breast Cancer Biology" Lance D MILLER, Edison Tak-Bun LIU (2004) Breast Disease. 19 . 29-34


  18. "Fine mapping of the 11q22-23 tumor suppressive region and involvement of TSLC1 in nasopharyngeal carcinoma" Lung HL, Cheng Y, Kumaran MK, Edison Tak-Bun LIU, Murakami Y, Chan CY, Yau WL, Ko JM, Stanbridge EJ, Lung ML (2004) Int J Cancer. 20;112(4) . 628


  19. "Gene expression correlating with response to paclitaxel in ovarian carcinoma xenografts" Bani MR, Nicoletti MI, Alkharouf NW, Ghilardi C, Petersen D, Erba E, Sausville EA, Edison Tak-Bun LIU, Giavazzi R (2004) Mol Cancer Ther. Feb;3(2) . 111-21


  20. "Gene expression profiles of epithelial cells microscopically isolated from a breast-invasive ductal carcinoma and a nodal metastasis" I. Zucchi, E. Mento, Vladimir A KUZNETSOV, M. Scotti, V. Valsecchi, B. Simionati, E. Vicinanza, G. Valle, S. Pilotti, R. Reinbold, P. Vezzoni, A. Albertini, R. Dulbecco (2004) PNAS. 101(52) . 18147-18152


  21. "Genome-Wide cDNA Oligo Probe Design and Its Applications in Schizosaccharomyces Pombe" Lin K, Liu J, Lance D MILLER, Wong, L (2004) Chapter 15, The Practical Bioinformatician


  22. "Genome-wide expression profiling; a panel of mouse tissues discloses novel biological functions of liver X receptors in adrenals" Steffensen KR, Soek Ying NEO, Stulnig TM, Vinsensius Berlian VEGA, Rahman SS, Schuster GU, Gustafsson JA, Edison Tak-Bun LIU (2004) J Mol Endocrinol. 33(3) . 609-22


  23. "Genome-wide screen identified RhoH as a regulator of lymphpocyte LFA-1" Lisa K. Cherry, Xiaoyu Li, Bing LIM, Lloyd B. Klickstein (2004) Nature Immunology. 5 . 961-96


  24. "Global expression profiling identifies signatures of tumor virulence in MMTV-PyMT transgenic mice: correlation to human disease" Qiu TH, Chandramouli GV, Hunter KW, Alkharouf NW, Green JE, Edison Tak-Bun LIU (2004) Cancer Res. 64(17) . 5973-81


  25. "Heparin/heparan sulfate interacting protein plays a role in apoptosis induced by anticancer drugs." Liu JJ, Zhang J, Ramanan S, Julian J, Carson DD, Hooi SC (2004) Carcinogenesis 2004 Jun ; 25(6) : 873-9 Epub 1970 Jan 1


  26. "Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila DHmx" Wang, W, J. F. Grimmer, T. R. Van De Water, Thomas LUFKIN (2004) Developmental Cell. 7 . 439-453


  27. "Human ES Cell Transcriptome Profiling Enters Adolescence" Paul ROBSON (2004) Trends in Biotechnology. 22 . 609-612


  28. "Identification of cell cycle-regulated genes in fission yeast" X. Peng, Radha Krishna Murthy KARUTURI, Lance D MILLER, K. Lin, Y. Jia, P. Kondu, L. Wang, L. Wong, Edison Tak-Bun LIU, M.K. Balasubramanian, Jianhua LIU (2004) Mol. Biol. Cell 16: 1026-1042


  29. "Identification of Discriminators of Hepatoma by Gene Expression Profiling Using a Minimal Dataset Approach" Soek Ying NEO, Leow CY, Vinsensius Berlian VEGA, Long PM, Amirul Islam, Lai PBS, Edison Tak-Bun LIU, Ee Chee REN (2004) Hepatology. 39(4) . 944-953


  30. "Identification of genes encoding putative nucleoporins and transport factors in the fission yeast S. pombe" X. Chen, X. Du, Jianhua LIU, M. Balasubramanian, D. Balasundaram (2004) Yeast. 21: 495-509


  31. "Implications for domain fusion protein-protein interactions based on structural information" Jer-ming Chia, Prasanna R KOLATKAR (2004) BMC Bioinformatics. 5 . 161


  32. "Improved Fourier Transform Method for Unsupervised Cell-cycle Regulated Gene Prediction." Radha Krishna Murthy KARUTURI, Jianhua LIU (2004) Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference, Stanford, CA


  33. "Inhibition of SARS coronavirus in vitro with clinically approved anti-viral drugs" Tan, E.L.C., Ooi, E.E, Lin Chin Yo, Tan H.C., Ling A.E., Bing LIM, Lawrence STANTON (2004) Emerg Infect Dis. 10 (4) . 581-86


  34. "Insulin decreases the secretion of apoB-100 from hepatic HepG2 cells but does not decrease the secretion of apoB-48 from intestinal CaCo-2 cells." Allister Emma M, Pal Sebely, Thomson Andrew M, Helmerhorst Erik, Mamo John C L (2004) J. Biomed. Sci. 2004 Nov-Dec ; 11(6) : 789-98


  35. "Interrogating the transcriptome" Yijun RUAN, Le Ber P, Huck Hui NG, Edison Tak-Bun LIU (2004) Trends in Biotechnology. 22(1) . 23-30


  36. "Laboratory-acquired severe acute respiratory syndrome" Lim PL, Kurup A, Gopalakrishna G, Chan KP, Christopher WONG, Ng LC, Se-Thoe SY, Oon L, Bai X, Lawrence STANTON, Yijun RUAN, Lance D MILLER, Vinsensius Berlian VEGA, James L, Ooi PL, Kai CS, Olsen SJ, Ang B, Leo YS (2004) N Engl J Med. Apr 22;350(17) . 1740-5


  37. "Microarrays and Clinical Investigations" Edison Tak-Bun LIU, Radha Krishna Murthy KARUTURI (2004) The New England Journal of Medicine. 350 . 1595-1597


  38. "Molecular classification of liver cirrhosis in rat model by proteomics and bioinformatics" Xu, X., Leow, C.K., Lu, X., Zhang, X., Liu, J.S., Wong, W., Asperger, A., Deininger, S., Eastwood Hon-Chiu LEUNG (2004) Proteomics. 4 . 3235-3245


  39. "Molecular diversity and phylogenetic analysis of mariner-like transposons in the genome of the silkworm Bombyx mori." Kumaresan G, Mathavan S (2004) Insect Mol. Biol. 2004 Jun ; 13(3) : 259-71


  40. "Multi-tissue gene expression analysis in a mouse model of thyroid hormone resistance" Lance D MILLER, McPhie P, Suzuki H, Kato Y, Edison Tak-Bun LIU, Cheng S-Y (2004) Genome Biol. 5(5) . R31


  41. "Mutational dynamics of the SARS corona virus in cell culture and human population" Vinsensius Berlian VEGA, Yijun RUAN, Jianjun LIU, Lee W.H., Chia Lin WEI, Su Yun S.T., Tang K.F., Zhang Tao, Prasanna R KOLATKAR, Eong O.E., Ling A.E., Lawrence STANTON, Long P.M., Edison Tak-Bun LIU (2004) BMC Infectious Diseases 4(1):32-40


  42. "Myocardial Infarction in the C57BL/6J mouse – a quantifiable and highly reproducible experimental model" Salto-Tellez, M, Lim, S.Y, El Oakley R.M, Tang, T.P.L, Almsheqi, ZAM, Sai Kiang LIM (2004) Cardiovascular Pathology. 13 . 91-97


  43. "p53-regulated transcriptional program associated with genotoxic stress-induced apoptosis" Kho PS, Wang Z, Zhuang L, Li Y, Chew JL, Huck Hui NG, Edison Tak-Bun LIU, Qiang YU (2004) J Biol Chem. 279 . 21183


  44. "Patterns of Large-Scale Genomic Variation in Virulent and Avirulent Burkholderia Species" Catherine Ong, Ooi Chia Huey, Dongling Wang, Hweeling Chong, Ng Kim Chong, Fiona Rodrigues, May Ann Lee, Patrick Boon Ooi TAN (2004) Genome Research (2004, publication held to coincide with publication of the official B. pseudomallei genome sequence). 14 . 2295


  45. "Purpureotin: a novel di-dimeric C-type lectin-like protein from Trimeresurus purpureomaculatus venom is stabilized by noncovalent interactions" Xiaolei Li, Lu Zheng, Chunguang kong, Prasanna R KOLATKAR, Maxey C.M. Chung (2004) Archives of Biochemistry and Biophysics. 424 . 53-62


  46. "Representational oligonucleotide microarray analysis (ROMA) in pharmacogenomics" Edison Tak-Bun LIU (2004) Pharmacogenomics J. 4(2) . 74-6


  47. "Role of differential and cell type-specific expression of cell cycle regulatory proteins in mediating progressive glomerular injury in human IgA nephropathy" Lian-Qun Qiu, Raja Sinniah, Hsu, Stephen I-Hong (2004) Lab Invest. 84 . 1112-25


  48. "Searching Oligo Sets of Human Chromosome 12 using Evolutionary Strategies" Joe, YY, Tay, A, Dong, ZY, Huck Hui NG, Xu H (2004) International Journal of Systems Science, Special issue of Evolutionary Computation Application in Systems and Control


  49. "Spontaneous fusion of adult BM cells with embryonic fibroblast feeder: Hybrid cell lines with endothelial potential" Que J, El Oakley R.M, Salto-Tellez M, Wong N, de Kleijn D.P, Teh M, Retnam L, Sai Kiang LIM (2004) In Vitro Cell Dev Biol Anim. 40(5) . 143-149


  50. "Strategies for Directing the Differentiation of Stem Cells Into the Osteogenic Lineage In Vitro" Boon Chin Heng, Tong Cao, Lawrence STANTON, Paul ROBSON, Bjorn Olsen (2004) Journal of Bone and Mineral Research. 19 . 1379-1394


  51. "Strategies for directing the differentiation of stem cells into the osteogenic lineage in vitro." Heng Boon Chin, Cao Tong, Stanton Lawrence Walter, Robson Paul, Olsen Bjorn (2004) Bone Miner. Res. 2004 Sep ; 19(9) : 1379-94


  52. "Subtree Transfer Distance for Degree-d Phylogenies" Hon WK, Kao, MY, Lam TW, Yiu SM, Sung WK (2004) International Journal of Foundations of Computer Science (IJFCS), 2004


  53. "Susceptibility to Cell Death Induced by Blockade of MAPK Pathway in Human Colorectal Cancer Cells Carrying Ras Mutations Is Dependent on p53 Status" Wang Z, Li YQ, Edison Tak-Bun LIU, Qiang YU (2004) Biochem Biophys Res Commun. Sep 17; 322(2) . 609-13


  54. "The CtBP2 co-repressor is regulated by NADH-dependent dimerization and possesses a novel N-terminal repression domain" Sharon S.C. Thio, Joseph V. Bonventre, Hsu, Stephen I-Hong (2004) Nucleic Acids Res. 32 . 1836-1847


  55. "The FRK/RAK tyrosine kinase participates in cytokine-induced islet cell toxicity" Welsh M, Welsh C, Ekman M, Dixelius J, Hagerkvist R, Anneren C, Akerblom B, Mahboobi S, Chandrasekharan S, Edison Tak-Bun LIU (2004) Biochem J. Jun 8 . Epub ahead of print


  56. "The maturing of the human embryonic stem cell transcriptome profile." Robson Paul (2004) Trends Biotechnol. 2004 Dec ; 22(12) : 609-12


  57. "The N-degron approach to create temperature-sensitive mutants in S. pombe" R. Srividya, L. Zheng, Jianhua LIU, M. Balasubramanian (2004) Methods. 33: 206-212


  58. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)" Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Yijun RUAN, Chia Lin WEI, Sinnakarupan MATHAVAN, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team (2004) Genome Research. 14 . 2121-2127


  59. "Tracking the Evolution of the SARS Coronavirus using Rapid, High-throughput, High-density Resequencing Arrays" Christopher WONG, Albert, T.J, Vinsensius Berlian VEGA, Norton, J.E., Cutler, D.J., Richmond, T.A, Lawrence STANTON, Edison Tak-Bun LIU, Lance D MILLER (2004) Genome Research. 14(3) . 398-405


  60. "Transcriptome characterization elucidates signaling networks that control human embryonic stem cell growth and differentiation" Brandenberger R, Wei H, Zhang S., Lei S., Murage J., Fisk G.J., Li Y., Xu C., Fang R., Guegler K., Rao M.S., Mandalam R., Lebkowski J., Lawrence STANTON (2004) Nature Biotechnology. 22 . 707-716


  61. "Twin births in Singapore: a population-based study using the national birth registry" Chia KS, Lee JJM, Cheung P, Cheung KH, Mark Thomas SEIELSTAD, Wilcox MM, Edison Tak-Bun LIU (2004) Annals Academy of Medicine Singapore. 33 . 195-199


  62. "Two-sample statistics for testing the equality of survival functions against improper semi-parametric accelerated failure time alternatives: an application to the analysis of a breast cancer clinical trial." Broët Philippe, Tsodikov Alexander, De Rycke Yann, Moreau Thierry (2004) 2004 Jun ; 10(2) : 103-20


  63. "Unbiased Mapping of Transcription Factor Binding Sites Along Human Chromosomes 21 and 22 Points to Widespread Regulation of Non-Coding RNAs" Cawley, S, Bekiranov, S, Huck Hui NG, Kapranov, P, Sekinger, E, Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, AJ, Wheeler, R, Wong, B, Drenkow, J, Yamanaka, M, Patel, S, Brubaker, S, Tammana, H, Helt, G, Struhl, K, Gingeras, TR (2004) Cell. 116 . 499-509


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