Publications from 2005
  1. "A cell-based system for hepatitis b virus replication: significance of clinically enhanced viral replication in relation to deletions in viral core promoter" Pan H, Lisa Fong-Poh NG, Ee Chee REN, Chen WN (2005) Front Biosci. 10 . 2001-2004


  2. "A Nanosecond Laser Induced Photochemical Oxidation method for Protein Surface Mapping with Mass Spectrometry" Aye TT, Low TY, Newman Siu-Kwan SZE (2005) Analytical Chemistry


  3. "A Novel Linkage to Generalized Vitiligo On 4q13-q21 Identified in a Genome-wide Linkage Analysis of Chinese Families" Chen, W Huang, J Gui, S Yang, F Zhou, Q Xiong, H Wu, Y Cui, M Gao, W Li, J Li, K Yan, W Yuan, S Xu, Jianjun LIU, X Zhang (2005) Am J Hum Genet. 76(6) . 1057 65


  4. "A population-based LD map of the human chromosome 6p" Yu H.X, Chia J-M, Guillaume BOURQUE, Wong M.V, Chan S.H, Ee Chee REN (2005) Immunogenetics. DOI: 10.1007/s00251


  5. "A role for fission yeast phosphoinositide-dependent protein kinase homolog, Pdk1p, in the regulation of mitosis and cytokinesis" A. Bimbo, Jianhua LIU, M. K. Balasubramanian (2005) Mol. Biol. Cell. 16 . 3162-3175


  6. "A simple procedure for estimating the false discovery rate." Dalmasso Cyril, Broët Philippe, Moreau Thierry (2005) Bioinformatics 2005 Mar 1 ; 21(5) : 660-8


  7. "A Transforming Growth Factor β-induced Protein Stimulates Endocytosis and Is Up-regulated at the Immature State of Dendritic Cells" Weiping Cao, Patrick Tan, Chee How Lee, Haifeng Zhang, and Jinhua Lu (2005) BLOOD


  8. "Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22 frequently lack nonprimate sequence and genomic structure conservation" Leonard LIPOVICH, Mary-Claire King (2005) Genome Research


  9. "An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects and patient survival" Lance D MILLER, Smeds J, George J, Vinsensius Berlian VEGA, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Edison Tak-Bun LIU, Bergh J (2005) Proc Natl Acad Sci U S A. 102(38) . 13550-5


  10. "Analysis of 14 LRRK2 mutations in Parkinson's Plus Syndromes and Late Onset Parkinson's Disease" Tan EK, Skipper L, Chua E, Shen H, Wong MC, Pavanni R, Bonnard C, Kolatkar P, Jian-Jun Liu (2005) Mov Disord. 2005


  11. "Analysis of HUPO-PPP reference specimens using SELDI-TOF mass spectrometry: multi-institution correlation of spectra and identification of biomarkers" Rai, A, Semmes, O.J., Chan, D.W., Shipulina, N.V., Lim, L, Patel, M., Podusk, V, Caffrey, R.E, Morgan, W.T, Adam, B, Zhang, Z, Stemmer, P.M, Eastwood Hon-Chiu LEUNG (2005) Proteomics. 13 . 3467-74


  12. "Analysis of LRRK2 Functional Domains in Non-Dominant Parkinson’s Disease" Skipper L, Shen H,, Chua E, Bonnard C, Kolatkar P, Tan LCS, Jamora RD, Puvan K, KY Puong, Zhao Y, Pavanni R, Wong MC, Yuen Y, Farrer M, Liu JJ, Tan EK (2005) Neurology. 65:1319-1321


  13. "Anaylysis and comparison of complexity of proteoms based on counting the number of domain-to-protein links" Kuznetsov V.A., Pickalov V.V, Kanapin A.A (2005) Systems Biology (Eds: Kolchanov et al.) Nauka (2005)


  14. "Antisense transcription in the mammalian transcriptome" Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Leonard LIPOVICH, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C, RIKEN Genome Exploration Research Group, Genome Science Group (Genome Network Project Core Group), FANTOM Consortium (2005) Science. Sep 2;309(5740) . 1564-6


  15. "ARDS in SARS: cytokine mediators and treatment implications" Salto-Tellez M, Tan E, Bing LIM (2005) Cytokine. 29 . 92-94


  16. "Bias In the Estimation of False Discovery Rate and Sensitivity of Microarray Studies" Yudi Pawitan, Radha Krishna Murthy KARUTURI, Alexander Ploner (2005) Bioinformatics


  17. "Cell-cycle Regulated Promoter Motif Prediction using Time-course" Yingren Liu, Radha Krishna Murthy KARUTURI, Ken Wing Kin SUNG (2005) Microarray Data, to appear in the proc of IEEE Symposium on Bioinformatics & Bioengineering (BIBE05), Minneapolis, Minnesota, October, 2005


  18. "Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages" Guillaume BOURQUE, Zdobnov, E.M., Bork, P., Pevzner P.A., Tesler, G (2005) Genome Research. 15 . 98-110


  19. "Comparison of HER2 status by fluorescence in situ hybridization and immunohistochemistry to predict benefit from dose escalation of adjuvant doxorubicin-based therapy in node-positive breast cancer patients" Dressler LG, Berry DA, Broadwater G, Cowan D, Cox K, Griffin S, Miller A, Tse J, Novotny D, Persons DL, Barcos M, Henderson IC, Liu ET, Thor A, Budman D, Muss H, Norton L, Hayes DF (2005) J Clin Oncol. Jul 1;23(19):4287-97


  20. "Computing the Maximum Agreement of Phylogenetic Networks" Jansson J, Choy C, Sadakane K, Ken Wing Kin SUNG (2005) Theoretical Computer Science, 2005


  21. "Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression" Lam SH, Wu YL, Vega VB, Miller LD, Spitsbergen J, Tong Y, Zhan H, Govindarajan KR, Lee S, Mathavan S, Krishna Murthy KR, Buhler DR, Liu ET, Gong Z (2005) Nat Biotechnol. Dec 4; [Epub ahead of print]


  22. "Control of transcription through intragenic patterns of nucleosome composition" Jason D. Lieb and Neil D. Clarke (2005) Cell (Minireview)


  23. "Correlation of KIT and platelet-derived growth factor receptor alpha mutations with gene activation and expression profiles in gastrointestinal stromal tumors" Kang HJ, Nam SW, Kim H, Rhee H, Kim NG, Hyung WJ, Noh SH, Kim JH, Yun CO, Edison Tak-Bun LIU (2005) Oncogene. 24(6) . 1066-1074


  24. "Correlation test to assess low-level processing of high-density oligonucleotide microarray data" Ploner A, Lance D MILLER, Hall P, Bergh J, Pawitan Y (2005) BMC Bioinformatics. Mar 31 . 6(1):80


  25. "Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site." Jauch Ralf, Jäkel Stefan, Netter Catharina, Schreiter Kay, Aicher Babette, Jäckle Herbert, Wahl Markus C (2005) Structure 2005 Oct ; 13(10) : 1559-68


  26. "Determining the functionality of putative Tat-dependent signal peptides in Streptomyces coelicolor A3(2) by using two different reporter proteins." Li H, Jacques PE, Ghinet MG, Brzezinski R, Morosoli R (2005) Microbiology 2005 Jul ; 151(Pt 7) : 2189-98


  27. "Direct Genotyping Analysis and Viral Strain Determination of SARS-CoV in Clinical Samples" Jianjun LIU, Yijun RUAN, Lim Siew Lan, Edison Tak-Bun LIU, Lawrence STANTON, Martin Lloyd HIBBERD (2005) PLoS Medicine


  28. "Drug Discovery in the Lion City" Patrick Boon Ooi TAN (2005) Drug Discovery Today. 10 . 1143-1144


  29. "Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps" Murphy W.J., Larkin D.M., Everts-van der Wind A., Bourque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., Gatzke L., Hitte C., Meyers S.N., Ostrander E.A., Pape G., Parker H.G., Raudsepp T., Rogatcheva M.B., Schook L.B., Skow L.C., Welge M., Womack J.E., O’Brien S.J., Pevzner P.A., Lewin H.A (2005) Science. 309(5734): 613-617


  30. "Effective Algorithms for TagSNP Selection" Tie-Fei Liu, Yi Li, Jianjun LIU, Ankush Mittal, Pei-Lin Mao, Ken Wing Kin SUNG (2005) Journal of Bioinformatics and Computational Biology, 2005


  31. "Embryonic Stem Cells as a model for Systems Biology" Lim B, Thomson AM, Ng HH, Robson P (2005) Systems Biology 2, Oxford University Press; Eds, Rigoutsos I and Stephanoplous D


  32. "Explicit equilibrium modeling of transcription factor binding and gene regulation" Granek, JA, Neil CLARKE (2005) Genome Biology


  33. "Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts" Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, Liu ET, Miller L, Nordgren H, Ploner A, Sandelin K, Shaw PM, Smeds J, Skoog L, Wedren S, Bergh J (2005) Breast Cancer Res. Oct 3;7(6):R953-R964 [Epub ahead of print]


  34. "Gene expression profiling to identify oncogenic determinants of autocrine human growth hormone (hGH) in human mammary carcinoma" Xu XQ, Emerald BS, Goh EL, Kannan N, Lance D MILLER, Gluckman PD, Edison Tak-Bun LIU, Lobie PE (2005) J Biol Chem. Jun 24; 280(25):23987-4003


  35. "Gene identification signature (GIS) analysis for transcriptome analysis and genome annotation" Patrick Wei Pern NG, Chia Lin WEI, Ken Wing Kin SUNG, Kuo Ping CHIU, Leonard LIPOVICH, Ang Chin Chin, Sanjay GUPTA, Shahab Atif, Ridwan Azmi, Wong Chee Hong, Edison Tak-Bun LIU, Yijun RUAN (2005) Nature Method. 2(2) . 105-111


  36. "Gene profile and response to treatment" Smeds J, Lance D MILLER, Bjohle J, Hall P, Klaar S, Edison Tak-Bun LIU, Pawitan Y, Ploner A, Bergh J (2005) Ann Oncol. 16 Suppl 2:ii . 195-202


  37. "Genomic technologies and the interrogation of the transcriptome" Edison Tak-Bun LIU (2005) Mech Ageing Dev. 126(1) . 153-9


  38. "Hmx homeobox gene function in inner ear and nervous system cell-type specification and development" Wang, W., Thomas LUFKIN (2005) Experimental Cell Research. 306 . 373-379


  39. "Host heterogeneous ribonucleoprotein K (hnRNP K) as a potential target to suppress hepatitis B virus replication" Lisa Fong-Poh NG, Chan, Soh-ha, Cheng C.P.Paul, Eastwood Hon-Chiu LEUNG, Chen Wei-ning, Ee Chee REN (2005) PLoS Medicine. 2:673-683


  40. "Information theoretic approach for microarray based pathogen detection. Proceedings of the 6th WSEAS International Conference on Mathematics and Computers in Biology and Chemistry" George J, Ken Wing Kin SUNG, Lee W-H, Vinsensius Berlian VEGA, Lance D MILLER (2005)  


  41. "Inhibitors of histone deacetylases target Rb-E2F1 pathway for apoptosis induction through transcriptional activation of proapoptotic protein Bim" Zhao Yan, Tan Jing, Zhuang Li, Jiang Xia, Edison Liu, Qiang YU (2005) PNAS, 102(44): 16090-16095


  42. "Integrative Genomic, Transcriptional, and Proteomic Diversity in Natural Isolates of the Human Pathogen Burkholderia pseudomallei" Keli Ou, Catherine Ong, Shze Yung Koh, Fiona Rodrigues, Siew Hoon Sim, Daniel Wong, Chia Huey Ooi, Kim Chong Ng, Hiroyuki Jikuya, Chin Chin Yau, Sou Yen Soon, Djohan Kesuma, May Ann Lee, Patrick Boon Ooi TAN (2005) J. Bacteriology. 187 . 4276-4285


  43. "Microwave-assisted Specific Chemical Digestion for Rapid Protein Identification" Hua L, Low TY, Newman Siu-Kwan SZE (2005) Proteomics


  44. "Molecular Changes from Dysplastic Nodule to Hepatocellular Carcinoma through Gene Expression Profiling" Nam SW, Park JY, Ramasamy A, Shevade S, Islam A, Long PM, Park CK, Park SE, Kim SY, Lee SH, Park WS, Yoo NJ, Edison Tak-Bun LIU, Lance D MILLER, Lee JY (2005) Hepatology. Oct;42(4) . 809-18


  45. "Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A" Reid G, Metivier R, Lin CY, Denger S, Ibberson D, Ivacevic T, Brand H, Benes V, Liu ET, Gannon F (2005) Oncogene. Jul 21;24(31):4894-907


  46. "New technologies for high-throughput analysis" Liu ET (2005) Pharmacogenomics. Jul;6(5):469-71


  47. "Osteogenic differentiation within intact human embryoid bodies result in a marked increase in osteocalcin secretion after 12 days of in vitro culture, and formation of morphologically distinct nodule-like structures." Cao Tong, Heng Boon Chin, Ye Chao Peng, Liu Hua, Toh Wei Seong, Robson Paul, Li Pin, Hong Yun Han, Stanton Lawrence Walter (2005) 2005 Aug ; 37(4) : 325-34


  48. "Osteogenic diffn within intact human embryoid bodies result in a marked increase in osteocalcin secretion after 12 days of in vitro culture, and formn of morphologically distinct nodule-like structs" Cao T, Heng BC, Ye CP, Liu H, Toh WS, Paul ROBSON, Li P, Hong YH, Lawrence STANTON (2005) Tissue & Cell. Jun 22 [Epub ahead of print] 37:325-334


  49. "Pharmacological modulation of Glycogen synthase kinase-3β promotes p53-dependent apoptosis through a direct Bax-mediated mitochondrial pathway in colorectal cancer cells." Tan J, Zhuang L, Leong HS, Iyer NG, Edison Tak-Bun LIU, Qiang YU (2005) Cancer Research, 2005 Oct 1. 65(19) . 9012-20


  50. "Predictive neural networks for gene expression data analysis" Ah-Hwee Tan, Hong Pan (2005) Neural Networks. 18


  51. "Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells." Chew Joon-Lin, Loh Yuin-Han, Zhang Wensheng, Chen Xi, Tam Wai-Leong, Yeap Leng-Siew, Li Pin, Ang Yen-Sin, Lim Bing, Robson Paul, Ng Huck-Hui (2005) Mol. Cell. Biol. 2005 Jul ; 25(14) : 6031-46


  52. "RNA Viral Community in the Human Gut: Prevalence of plant pathogenic viruses" Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh, Martin L. Hibberd1, Edison T. Liu, Forest Rohwer and Yijun Ruan (2005) Plos Biology (2005)


  53. "Rooted Maximum Agreement Supertrees" Jansson J, Ng Joseph HK, Sadakane K, Ken Wing Kin SUNG (2005) Algorithmica, 2005


  54. "Rotation/twist model for the activation of the epidermal growth factor receptor" Ichiro MARUYAMA, Thankiah, S, Liu, P, Wohland, T (2005) Annual Book of World DNA Day. 1 . 294-295


  55. "SARS transmission pattern in Singapore reassessed by viral sequence variation analysis." Liu Jianjun, Lim Siew Lan, Ruan Yijun, Ling Ai Ee, Ng Lisa F P, Drosten Christian, Liu Edison T, Stanton Lawrence W, Hibberd Martin L (2005) PLoS Med. 2005 Feb ; 2(2) : e43


  56. "Scientists and societies. Horizons in molecular biology." Jauch Ralf (2005) Nature 2005 Feb 24 ; 433(7028) : 904


  57. "STAR: Multiplexed quantitative real time PCR platform for gene expression analysis and molecular diagnostics" Garcia EP, Dowding LA, Lawrence W. Stanton, and Slepnev, VI (2005) J. Molecular Diagnostics Oct;7(4):444-54


  58. "Structure of rhodocetin reveals non-covalently bound heterodimer interface" Palasingam Paaventhan, Chunguang Kong, Jeremiah S. Joseph, Max C. M. Chung and, Prasanna R KOLATKAR (2005) Protein Science. 14:169-175


  59. "Structures of Escherichia coli NAD synthetase with substrates and products reveal mechanistic rearrangements." Jauch Ralf, Humm Andreas, Huber Robert, Wahl Markus C (2005) J. Biol. Chem. 2005 Apr 15 ; 280(15) : 15131-40 Epub 2005 Feb 7


  60. "Systematic Deletion Analysis of Fission Yeast Protein Kinases" A. Bimbo, Y. Jia, S.L. Poh, Radha Krishna Murthy KARUTURI, N.d. Elzen, X. Peng, L. Zheng, M. O'Connell, Edison Tak-Bun LIU, M.K. Balasubramanian, Jianhua LIU (2005) Eukaryotic Cell 4: 799-813


  61. "Systems biology, integrative biology, predictive biology" Liu ET (2005) Cell. 121(4):505-6


  62. "The 350-fold compacted Fugu parkin gene is structurally and functionally similar to human Parkin" Wei-Ping Yu, Jeanne M.M. Tan, Katherine C.M., Chew, Tania Oh, Prasanna R KOLATKAR, Byrappa Venkatesh, Ted M. Dawson, Kah Leong Lim (2005) Gene. 346 . 97-104


  63. "The easy part is making the knockout" Thomas LUFKIN (2005) Developmental Dynamics. 233 . 1173-1174


  64. "The G2019S LRRK2 mutation is uncommon in an Asian cohort of Parkinson's disease patients" Tan EK, Shen H, Tan LC, Farrer M, Yew K, Chua E, Jamora RD, Puvan K, Puong KY, Zhao Y, Pavanni R, Wong MC, Yih Y, Skipper L, Jianjun LIU (2005) Neurosci Lett. 384(3) . 327-9


  65. "The nuclear kinase, Lsk1p, positively regulates the Septation Initiation Network and promotes the successful completion of cytokinesis in response to minor perturbation of the actomyosin ring" J. Karagiannis, A. Bimbo, S. Rajagopalan, Jianhua LIU, M.K. Balasubramanian (2005) Mol. Biol. Cell. 16(1) . 358-371


  66. "The Transcriptional Landscape of the Mammalian Genome" The FANTOM Consortium, P. Carninci, ..., Kuo Ping CHIU, Edison Tak-Bun LIU, Yijun RUAN, Chia Lin WEI, Leonard LIPOVICH, et al, RIKEN Genome Exploration Research Group, Genome Science Group - Genome Network Project Core Group (2005) Science. 309 . 1559-1563


  67. "THY1 is a candidate tumour suppressor gene with decreased expression in metastatic nasopharyngeal carcinoma" Lung HL, Bangarusamy DK, Xie D, Cheung AK, Cheng Y, Kumaran MK, Lance D MILLER, Edison Tak-Bun LIU, Guan XY, Sham JS, Fang Y, Li L, Wang N, Protopopov AI, Zabarovsky ER, Tsao SW, Stanbridge EJ, Lung ML (2005) Oncogene. Jun 20; [Epub ahead of print] 24(43):6525-32


  68. "Transcriptional regulation of nanog by OCT4 and SOX2." Rodda David J, Chew Joon-Lin, Lim Leng-Hiong, Loh Yuin-Han, Wang Bei, Ng Huck-Hui, Robson Paul (2005) J. Biol. Chem. 2005 Jul 1 ; 280(26) : 24731-7


  69. "Transcriptome analysis of zebrafish embryogenesis using microarrays." Mathavan Sinnakaruppan, Lee Serene G P, Mak Alicia, Miller Lance D, Murthy Karuturi Radha Krishna, Govindarajan Kunde R, Tong Yan, Wu Yi Lian, Lam Siew Hong, Yang Henry, Ruan Yijun, Korzh Vladi mir, Gong Zhiyuan, Liu Edison T, Lufkin Thomas (2005) PLoS Genet. 2005 Aug ; 1(2) : 260-76


  70. "Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state." Wei Chia Lin, Miura Takumi, Robson Paul, Lim Sai-Kiang, Xu Xiu-Qin, Lee Mathia Yu-Chuan, Gupta Sanjay, Stanton Lawrence, Luo Yongquan, Schmitt Jacqui, Thies Scott, Wang Wei, Khrebtukova Irina, Zhou Daixing, Liu Edison T, Ruan Yi Jun, Rao Mahendra, Lim Bing (2005) Stem Cells 2005 Feb ; 23(2) : 166-85


  71. "Transcriptome profiling of murine and human ES cells reveals divergent paths to maintenance of the stem cell state" Chia Lin WEI, Miura T, Paul ROBSON, Sai Kiang LIM, Xu XQ, Lee MY, Sanjay GUPTA, Lawrence STANTON, Luo Y, Schmitt J, Thies S, Wang W, Khrebtukova I, Zhou D, Edison Tak-Bun LIU, Yijun RUAN, Rao M, Bing LIM (2005) Stem Cells. 23 . 166-185


  72. "Wavelet Transformations of Tumor Expression Profiles Reveals a Pervasive Genome Wide Imprinting of Aneuploidy on the Cancer Transcriptome" Aggarwal Amit, Siew Hong Leong, Cheryl Lee, Oi Lian Kon, Patrick Boon Ooi TAN (2005) Cancer Research. 65 . 186-194


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