1 "A novel role for p73 in supporting cellular growth through c-Jun-dependent AP-1 transactivation" Vikhansyaka, F., Toh, WH., Dulloo, I., Wu, Q., Boominathan, L., Ng, HH., Vousden, K., Sabapathy, K. (In Press) Nat. Cell. Biol, 2007

2 "Assessment of CASP7 structure predictions for template free targets." Ralf Jauch, Hock Chuan Yeo, Prasanna R. Kolatkar, and Neil D. Clarke (In Press) PROTEINS: Structure, Function, and Bioinformatics

3 "Computational analysis of genome-scale avidity distribution of TFBS in Chip-PER experiments " Kuznetsov, V.A*, Orlov, Yu.L., Wei Chia Lin, Ruan Y (In Press) Genome Informatics

4 "Computational analysis of genome-scale avidity distribution of TFBS in Chip-PER experiments " Kuznetsov, V.A*, Orlov, Yu.L., Wei Chia Lin, Ruan Y (In Press) Genome Informatics

5 "Data-driven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in Unreplicated 0-time Normalized Time-course Microarray Studies" Juntao Li, Jianhua Liu and R. Krishna Murthy Karuturi (In Press) Springer Verlag Lecture Notes in Bioinformatics series for ISBRA'07

6 "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 (In Press) PLoS Medicine, 2007

7 "Genome-wide mapping of RELA(p65) binding identifies E2F1 as a NF-κB-dependent transcriptional activator downstream of Toll-like receptor 4." Ching-Aeng Lim, Fei Yao, Joshy George, Han Xu, Kuo Ping Chiu, Wing-Kin Sung, Leonard Lipovich, Vinsensius B Vega, Joanne Chen, Atif Shahab, Xiao Dong Zhao, Martin Hibberd, Chia-Lin Wei, Bing Lim, Huck-Hui Ng, Yijun Ruan, Keh-Chuang Chin (In Press) Molecular Cell

8 "Genomewide Expression Analysis in Zebrafish mind bomb Mutants Identifies Putative Notch Signaling Responsive Genes Involved in Pancreas Development. " Ashok Hegde, Kenny Qi-Ye Tay, Nick Chuanxin Qiu, Joshy George, Steven Hao-Kee Ho, Felicia Soo Lee Ng, Kunde Ramamoorthy Govindarajan, Zhiyuan Gong, Sinnakaruppan Mathavan and Yun-Jin Jiang. (In Press) PLoS ONE

9 "Identification and Characterization of a Novel Mutation in the Carbonic Anhydrase IV Gene that Causes Retinitis Pigmentosa." Bernardo V. Alvarez, Eranga N. Vithana, Zhenglin Yang, Adrian H. Koh, Kit Yeung, Victor Yong, Haley J. Shandro, Yali Chen, Prasanna Kolatkar, Paaventhan Palasingam, Kang Zhang, Tin Aung and Joseph R. Casey (In Press) Investigative Opthalmology and Visual Science (IOVS)

10 "Identification of biomarkers, antiviral molecules and drug targetable pathways in dengue infection. " Joshua Fink, Feng Gu, Ling Ling, Thomas Tolfvenstam, Farzad Olfat, Keh Chuang Chin, Pauline Aw, Joshy George, Vladimir A. Kuznetsov, Mark Schreiber, Subhash G Vasudevan, Martin L Hibberd (In Press) PLoS

11 "Initial Sequence and Comparative Analysis of the Cat Genome. " Pontius JU, Mullikin JC, Smith D, Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schaeffer AA, Agarwala R, Narfstroem K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program and Stephen J. O’Brien SJ (2007) (In Press) Genome Res 17(11):1675-89

12 "Integration of Heterogeneous Cis-Antisense Gene Pair Data Sets Mapping onto the Human Genome " Orlov Y., Zhou J.T., Kuznetsov V (In Press) J. Integrative Bioinformatics

13 "Jmjd1a and Jmjd2c histone H3 lysine 9 demethylases regulate self-renewal in embryonic stem cells " Loh, YH., Zhang, W., Chen, X., George, J., Ng, HH (In Press) Genes Dev

14 "Recovering True Evolutionary Events on Phylogenetic Trees " Zhao H, Bourque G (In Press) In Proceedings of the 5th RECOMB Workshop on Comparative Genomics. San Diego, USA

15 "Review: Novel Applications of the Paired-End diTag (PET) Technology in Pharmacogenomics. " Chiu KP (In Press) Current Pharmacogenomics

16 "RPS27L, a p53-inducible modulator of cell fate in response to genotoxic stress. " Jingsong Li, Jing Tan, Li Zhuang, Birendranath Banerjee, Xiaojing Yang, Jenny Fung Ling Chau, Puay Leng Lee, Manoor Prakash Hande, Baojie Li and Qiang Yu (In Press) Cancer Research

17 "Significance Analysis and Improved Discovery of Disease Specific Differentially Co-expressed Gene Sets in Microarray Data " Haixia Li and R. Krishna Murthy Karuturi (Corresponding author) (In Press) Intl Jl of Data Mining and Bioinformatics

1 "A Comparative Synteny Map of Burkholderia Species Links Large-scale Genome Rearrangements to Fine-scale Nucleotide Variation in Prokaryotes. " Lin CH, Bourque G, Tan P (2007) Mol Biol Evol.

2 "A gene harvest revealing the archeology and complexity of human disease. " Petretto E, Liu ET, Aitman TJ (2007) Nature Genetics 39, 1299 - 1301 (2007) doi:10.1038/ng1107-1299

3 "A gene signature in breast cancer " Wennmalm K, Miller LD, Bergh J (2007) N Engl J Med. 356(18):1887-8

4 "Adaptive expression responses in the Pol-gamma null strain of S. pombe depleted of mitochondrial genome " Chu Z, Li J, Eshaghi M, Karuturi RK, Lin K, Liu J (2007) BMC Genomics 8(1):323 doi:10.1186/1471-2164-8-323

5 "An alternative approach to determining therapeutic choices in advanced non-small cell lung carcinoma (NSCLC): maximizing the diagnostic procedure and the use of low-volume lung biopsies " Lim EH, Zhang SL, Yu K, Nga ME, Ahmed DA, Agasthian T, Wong PS, Chua GC, Wong D, Tan L, Seto KY, Yap WS, Low SP, Khoo KL, Chang A, Ng A, Tan P. (2007) Journal of Thoracic Oncology 2(5):387-96.

6 "Analyzing genome rearrangements" Guillaume BOURQUE (2007) Bioinformatics: From Genomes to Therapies. Lengauer T. ed, Wiley-VCH

7 "Assessment of intramolecular contact predictions for CASP7 " Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND (2007) Proteins

8 "Association mapping via regularized regression analysis of single-nucleotide-polymorphism haplotypes in variable-sized sliding windows " Li Y, Sung WK, Liu JJ (2007) Am J Hum Genet 80(4):705-15

9 "Automated server predictions in CASP7 " Battey JN, Kopp J, Bordoli L, Read RJ, Clarke ND, Schwede T (2007) Proteins

10 "Baculoviral vector-mediated transient and stable transgene expression in human embryonic stem cells " Zeng J, Du J, Zhao Y, Palanisamy N, Wang S (2007) Stem Cells 25(4):1055-61

11 "BLIMP1 regulates cell growth through repression of p53 transcription" Yan J, Jiang J, Lim CA, Wu Q, Ng HH, Chin KC. (2007) Proc. Natl. Acad. Sci. (PNAS), 2007 Jan

12 "c-Myc overexpression sensitizes Bim-mediated Bax activation for apoptosis induced by histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) through regulating Bcl-2/Bcl-xL expression" Xia Jianga, Ying Hung Tsanga and Qiang Yu (2007) The International Journal of Biochemistry & Cell Biology doi:10.1016/j.biocel.2007.01.024, 2007 February 2 [Epub ahead of print]

13 "Catching bird flu in a droplet " Pipper J, Inoue M, Ng LF, Neuzil P, Zhang Y, Novak L (2007) Nat Med. 13(10):1259-63

14 "Cellular transcription modulator SMARCE1 binds to HBV core promoter containing naturally occurring deletions and represses viral replication " Pan H, Niu DD, Feng H, Ng LF, Ren EC, Chen WN (2007) Biochim Biophys Acta. 1772(9):1075-84

15 "Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution " Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström G PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y (2007) Nat Genet 39(9):1174 doi:10.1038/ng0907-1174b

16 "DengueInfo: A web portal to dengue information resources" Schreiber MJ, Ong SH, Holland RC, Hibberd ML, Vasudevan SG, Mitchell WP, Holmes EC (2007) Infect Genet Evol. 7(4):540-1.

17 "DengueInfo: A web portal to dengue information resources. " Schreiber MJ, Ong SH, Holland RC, Hibberd ML, Vasudevan SG, Mitchell WP, Holmes EC (2007) Infect Genet Evol. 7(4):540-1.

18 "Detection of generic spaced motifs using submotif pattern mining " Wijaya E, Rajaraman K, Yiu SM, Sung WK (2007) Bioinformatics 23(12):1476-85

19 "Domain definition and target classification for CASP7 " Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M (2007) Proteins

20 "Dopaminergic mutations: Within-family association and linkage in multiplex alcohol dependence families. " Hill SY, Hoffman EK, Zezza N, Thalamuthu A, Weeks DE, Matthews AG, Mukhopadhyay I. (2007) Am J Med Genet B Neuropsychiatr Genet.

21 "Evidence for a Novel Psoriasis Susceptibility Locus at 9q33-9q34 in Chinese Hans" Sun LD, Li W, Yang S, Fan X, Yan KL, Liang YH, Gao M, Cui Y, Xiao FL, Du WH, Zhang KY, Huang W, Liu J, Zhang XJ (2007) Journal of Investigative Dermatology doi:10.1038/sj.jid.5700671, 2007 Jan 4 [Epub ahead of print]

22 "Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine " Miller LD, Liu ET (2007) Breast Cancer Res. 9(2):206

23 "Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine" Miller LD, Liu ET (2007) Breast Cancer Res. 9(2):206, 2007 Mar 26 [Epub ahead of print]

24 "Finding linear motif pairs from protein interaction networks: a probabilistic approach. " Leung HC, Siu MH, Yiu SM, Chin FY, Sung KW. (2007) Comput Syst Bioinformatics Conf. 6:111-9.

25 "Foxo3 is required for the regulation of oxidative stress in erythropoiesis " Marinkovic D, Zhang X, Yalcin S, Luciano JP, Brugnara C, Huber T, Ghaffari S. (2007) J Clin Invest 117(8):2133-44

26 "Frequent decreased expression of candidate tumor suppressor gene, DEC1, and its anchorage-independent growth properties and impact on global gene expression in esophageal carcinoma. " Leung AC, Wong VC, Yang LC, Chan PL, Daigo Y, Nakamura Y, Qi RZ, Miller LD, Liu ET, Wang LD, Li JL, Law S, Tsao SW, Lung ML (2007) International Journal of Cancer. Volume 122, Issue 3 , Pages 587 - 594

27 "Functional validation of candidate oncogenes by high content screening." Soh, F.L., Liu, X., Han, B.L., Datta, A., Zhang, J., Miller, L.D. and Wong, C. W (2007) In: Proceedings of the Annual Meeting of the American Association for Cancer Research; AACR; 2007. p 901. Abstract nr 3798

28 "Fusion Transcripts and Transcribed Retrotransposed Loci Discovered through Comprehensive Transcriptome Analysis using Paired-End diTags (PETs)" Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL (2007) Genome Res. 17(6):828-38

29 "Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). " Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL (2007) Genome Res. 17(6):828-38

30 "Genetic variation in Northern Thailand Hill Tribes: origins and relationships with social structure and linguistic differences " Besaggio D, Fuselli S, Srikummool M, Kampuansai J, Castrì L, Tyler-Smith C, Seielstad M, Kangwanpong D, Bertorelle G (2007) BMC Evol Biol. 7 Suppl 2:S12

31 "Genome-wide association study identifies novel breast cancer susceptibility loci " Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, Wareham N, Ahmed S, Healey CS, Bowman R; SEARCH collaborators, Meyer KB, Haiman CA, Kolonel LK, Henderson BE, Le Marchand L, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Eccles D, Evans DG, Peto J, Fletcher O, Johnson N, Seal S, Stratton MR, Rahman N, Chenevix-Trench G, Bojesen SE, Nordestgaard BG, Axelsson CK, Garcia-Closas M, Brinton L, Chanock S, Lissowska J, Peplonska B, Nevanlinna H, Fagerholm R, Eerola H, Kang D, Yoo KY, Noh DY, Ahn SH, Hunter DJ, Hankinson SE, Cox DG, Hall P, Wedren S, Liu J, Low YL, Bogdanova N, Schürmann P, Dörk T, Tollenaar RA, Jacobi CE, Devilee P, Klijn JG, Sigurdson AJ, Doody MM, Alexander BH, Zhang J, Cox A, Brock IW, MacPherson G, Reed MW, Couch FJ, Goode EL, Olson JE, Meijers-Heijboer H, van den Ouweland A, Uitterlinden A, Rivadeneira F, Milne RL, Ribas G, Gonzalez-Neira A, Benitez J, Hopper JL, McCredie M, Southey M, Giles GG, Schroen C, Justenhoven C, Brauch H, Hamann U, Ko YD, Spurdle AB, Beesley J, Chen X; kConFab; AOCS Management Group, Mannermaa A, Kosma VM, Kataja V, Hartikainen J, Day NE, Cox DR, Ponder BA (2007) Nature 447(7148):1087-93

32 "Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. " Lim CA, Yao F, Wong JJ, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, Ng HH, Ruan Y, Chin KC (2007) Mol Cell 27(4):622-35

33 "Genomic and proteomic characterization of embryonic stem cells. " Stanton LW, Bakre MM (2007) Current Opinion in Chemical Biology 11(4):399-404

34 "Global profiling of DNA replication timing and efficiency reveals that efficient replication/firing occurs late during S-phase in S. pombe " Eshaghi M, Karuturi RK, Li J, Chu Z, Liu ET, Liu J (2007) PLoS ONE 2(1):e722

35 "Gut flora, Toll-Like-Receptors and Nuclear Receptors: a tripartite communication that tunes innate immunity in large intestine. " Lundin A, Bok CM, Aronsson L, Björkholm B, Gustafsson JA, Pott S, Arulampalam V, Hibberd M, Rafter J, Pettersson S. (2007) Cell Microbiol.

36 "Higher order structure in the cancer transcriptome and systems medicine" Liu ET, Lemberger T (2007) Mol Syst Biol 2007;3:94, 2007 Mar 13 [Epub ahead of print]

37 "Homeobox gene Sax2 deficiency causes an imbalance in energy homeostasis " Simon R, Lufkin T, Bergemann AD (2007) Dev Dyn. 236(10):2792-2799

38 "Host gene expression profiling of dengue virus infection in cell lines and patients. " Fink J, Gu F, Ling L, Tolfvenstam T, Olfat F, Chin KC, Aw P, George J, Kuznetsov VA, Schreiber M, Vasudevan SG, Hibberd ML. (2007) PLoS Negl Trop Dis. 1(2):e86

39 "HOXA1-stimulated oncogenicity is mediated by selective upregulation of components of the p44/42 MAP kinase pathway in human mammary carcinoma cells" Mohankumar KM, Xu XQ, Zhu T, Kannan N, Miller LD, Liu ET, Gluckman PD, Sukumar S, Emerald BS, Lobie PE (2007) Oncogene, 2007 Jan 8 [Epub ahead of print]

40 "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. " ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ (2007) Nature. 447(7146):799-816

41 "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." …, Chiu Kuo Ping, …, Vinsensius B. Vega, …, (Multi-center study) (2007) Nature. 447(7146):799-816

42 "Identification and Characterization of a Novel Mutation in the Carbonic Anhydrase IV Gene that Causes Retinitis Pigmentosa. " Bernardo V. Alvarez, Eranga N. Vithana, Zhenglin Yang, Adrian H. Koh, Kit Yeung, Victor Yong, Haley J. Shandro, Yali Chen, Prasanna Kolatkar, Paaventhan Palasingam, Kang Zhang, Tin Aung and Joseph R. Casey (2007) Investigative Opthalmology and Visual Science (IOVS)

43 "Identifying differentially expressed genes in time-course microarray experiment without replicate " Han X, Sung WK, Feng L (2007) J Bioinform Comput Biol. 5(2a):281-96

44 "Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer. " Lin CY, Ström A, Li Kong S, Kietz S, Thomsen JS, Tee JB, Vega VB, Miller LD, Smeds J, Bergh J, Gustafsson JA, Liu ET (2007) Breast Cancer Res. 9(2):R25 doi:10.1186/bcr1667

45 "Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer." Lin CY, Ström A, Li Kong S, Kietz S, Thomsen JS, Tee JB, Vega VB, Miller LD, Smeds J, Bergh J, Gustafsson JA, Liu ET (2007) Breast Cancer Res. 9(2):R25 doi:10.1186/bcr1667

46 "Initial Sequence and Comparative Analysis of the Cat Genome " Pontius JU, Mullikin JC, Smith D, Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schaeffer AA, Agarwala R, Narfstroem K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program and Stephen J. O’Brien SJ (2007) (2007) Genome Res

47 "Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. " Loh YH, Zhang W, Chen X, George J, Ng HH. (2007) Genes Dev. 21(20):2545-57.

48 "Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. " Loh YH, Zhang W, Chen X, George J, Ng HH. (2007) Genes Dev. 21(20):2545-57.

49 "Kruppel-like factor 5 modulates p53-independent apoptosis through Pim1 survival kinase in cancer cells. " Zhao Y, Hamza MS, Leong HS, Lim CB, Pan YF, Cheung E, Soo KC, Iyer NG. (2007) Oncogene. doi:10.1038/sj.onc.1210625

50 "Lack of association between interleukin-1 gene cluster polymorphisms and glaucoma in Chinese subjects " How AC, Aung T, Chew X, Yong VH, Lim MC, Lee KY, Toh JY, Li Y, Liu J, Vithana EN (2007) Invest Ophthalmol Vis Sci. 48(5):2123-6

51 "Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies " Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M (2007) Genome Res. 17(6):898-909

52 "MicroRNA-134 Modulates the Differentiation of Mouse Embryonic Stem Cells where it Causes Post-transcriptional Attenuation of Nanog and LRH1. " Tay YM, Tam WL, Ang YS, Gaughwin PM, Yang HH, Wang W, Liu R, George J, Ng HH, Perera RJ, Lufkin T, Rigoutsos I, Thomson AM, Lim B (2007) Stem Cells. doi: 10.1634/stemcells.2007-0295

53 "Modulation of cell cycle-specific gene expressions at the onset of S phase arrest contributes to the robust DNA replication checkpoint response in fission yeast. " Chu Z, Li J, Eshaghi M, Peng X, Karuturi RK, Liu J. (2007) Mol Biol Cell. 18(5):1756-67

54 "Modulation of Cell Cycle-specific Gene Expressions at the Onset of S-Phase Arrest Contributes to the Robust DNA Replication Checkpoint Response in Fission Yeast" Chu Z, Li J, Eshaghi M, Peng X, Karuturi RK, Liu J (2007) Mol Biol Cell, 2007 Mar 1 [Epub ahead of print]

55 "Molecular diagnostics in advanced NSCLC: trying to maximize a non-ideal situation " Lim EH, Tan P (2007) Journal of Thoracic Oncology 2(8):782

56 "Oct4 and Sox2 directly regulate expression of another pluripotency transcription factor Zfp206 in embryonic stem cells" Wang ZX, Teh CH, Kueh JL, Lufkin T, Robson P, Stanton LW (2007) Biol Chem, 2007 Mar 7 [Epub ahead of print]

57 "Oct4 and Sox2 directly regulate expression of another pluripotency transcription factor, Zfp206, in embryonic stem cells " Wang ZX, Teh CH, Kueh JL, Lufkin T, Robson P, Stanton LW (2007) J Biol Chem. 282(17):12822-30.

58 "On the usage of HWE for identifying genotyping errors " Teo YY, Fry AE, Clark TG, Tai ES, Seielstad M (2007) Ann Hum Genet. 71(Pt 5):701-3

59 "On the usage of HWE for identifying genotyping errors" Yik Y. Teo, Andrew E. Fry, Taane G. Clark, E.S. Tai, Mark Seielstad (2007) Annals of Human Genetics 71, 1-3, 2007

60 "Optimization and clinical validation of a pathogen detection microarray. " Wong CW, Heng CL, Wan Yee L, Soh SW, Kartasasmita CB, Simoes EA, Hibberd ML, Sung WK, Miller LD (2007) Genome Biology 8:R93 doi:10.1186/gb-2007-8-5-r93

61 "Optimization and clinical validation of a pathogen detection microarray." Wong CW, Heng CL, Wan Yee L, Soh SW, Kartasasmita CB, Simoes EA, Hibberd ML, Sung WK, Miller LD (2007) Genome Biology 8:R93 doi:10.1186/gb-2007-8-5-r93

62 "p73 supports cellular growth through c-Jun-dependent AP-1 transactivation " Vikhanskaya F, Toh WH, Dulloo I, Wu Q, Boominathan L, Ng HH, Vousden KH, Sabapathy K (2007) Nat Cell Biol. 9(6):698-705

63 "Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. " Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei CL, Sung WK (2007) BMC Cancer. 7(1):109

64 "Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes." Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei CL, Sung WK (2007) BMC Cancer. 7(1):109

65 "Pharmacologic disruption of Polycomb repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells" Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q (2007) Genes Dev. 21(9):1050-63 doi:10.1101/gad1524107

66 "Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. " Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q (2007) Genes Dev. 21(9):1050-63 doi:10.1101/gad1524107

67 "PI3 K/Akt/mTOR-mediated translational control regulates proliferation and differentiation of lineage-restricted RoSH stem cell lines " Que J, Lian Q, El Oakley RM, Lim B, Lim SK (2007) J Mol Signal. 2(1):9

68 "Pleiotrophin Enhances Clonal Growth and Long-term Expansion of Human Embryonic Stem Cells " Soh BS, Song CM, Vallier L, Li P, Choong C, Yeo BH, Lim EH, Pedersen RA, Yang HH, Rao M, Lim B (2007) Stem Cells

69 "Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution " Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB (2007) Genome Res. 17(6):839-51

70 "Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis " Orlov Yu.L., Zhou J. , Lipovich L.L. , Shahab A. , Kuznetsov V.A (2007) In Silico Biology 7, 0041

71 "Reconstructing recombination network from sequence data: the small parsimony problem " Nguyen CT, Nguyen NB, Sung WK, Zhang L (2007) IEEE/ACM Trans Comput Biol Bioinform 4(3):394-402

72 "Recovering True Evolutionary Events on Phylogenetic Trees " Zhao H, Bourque G (2007) In Proceedings of the 5th RECOMB Workshop on Comparative Genomics. San Diego, USA

73 "Ribosomal protein S27-like, a p53-inducible modulator of cell fate in response to genotoxic stress. " Li J, Tan J, Zhuang L, Banerjee B, Yang X, Chau JF, Lee PL, Hande MP, Li B, Yu Q. (2007) Cancer Res. 67(23):11317-26.

74 "Significance Analysis and Improved Discovery of Disease Specific Differentially Co-expressed Gene Sets in Microarray Data " Haixia Li and R. Krishna Murthy Karuturi (Corresponding author) (2007) Intl Jl of Data Mining and Bioinformatics

75 "Stromal effects in breast cancer. " Liu ET. (2007) N Engl J Med. 357(25):2537-8

76 "Targets of genome copy number reduction in primary breast cancers identified by integrative genomics" Chen W, Salto-Tellez M, Palanisamy N, Ganesan K, Hou Q, Tan LK, Sii LH, Ito K, Tan B, Wu J, Tay A, Tan KC, Ang E, Tan BK, Tan PH, Ito Y, Tan P (2007) Genes Chromosomes Cancer 46(3):288-301, 2007 Mar

77 "TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study " Plenge RM, Seielstad M, Padyukov L, Lee AT, Remmers EF, Ding B, Liew A, Khalili H, Chandrasekaran A, Davies LR, Li W, Tan AK, Bonnard C, Ong RT, Thalamuthu A, Pettersson S, Liu C, Tian C, Chen WV, Carulli JP, Beckman EM, Altshuler D, Alfredsson L, Criswell LA, Amos CI, Seldin MF, Kastner DL, Klareskog L, Gregersen PK (2007) N Engl J Med. 357(12):1199-209

78 "Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast specific regulation of the IGFBP4 gene. " Denger S, Bähr-Ivacevic T, Brand H, Reid G, Blake J, Seifert M, Lin CY, May K, Benes V, Liu ET, Gannon F (2007) Mol Endocrinol. doi: 10.1210/me.2007-0292

79 "Understanding ligand binding effects on the conformation of estrogen receptor alpha-DNA complexes: a combinational quartz crystal microbalance with dissipation and surface plasmon resonance study. " Peh WY, Reimhult E, Teh HF, Thomsen JS, Su X. (2007) Biophysical Journal. 92(12):4415-23

80 "Understanding ligand binding effects on the conformation of estrogen receptor alpha-DNA complexes: a combinational quartz crystal microbalance with dissipation and surface plasmon resonance study." Peh WY, Reimhult E, Teh HF, Thomsen JS, Su X. (2007) Biophysical Journal. 92(12):4415-23

81 "Using indirect protein interactions for the prediction of Gene Ontology functions " Chua HN, Sung WK, Wong L (2007) BMC Bioinformatics 8 Suppl 4:S8

82 "Whole-Genome Cartography of Estrogen Receptor alpha Binding Sites. " Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET (2007) PLoS Genet. 3(6):e87

83 "Whole-Genome Cartography of Estrogen Receptor alpha Binding Sites." Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET (2007) PLoS Genet. 3(6):e87

84 "Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells " Xiao Dong Zhao, Xu Han, Joon Lin Chew, Jun Liu, Kuo Ping Chiu, Andre Choo, Yuriy L. Orlov, Wing-Kin Sung, Atif Shahab, Vladimir A. Kuznetsov, Guillaume Bourque, Steve Oh, Yijun Ruan, Huck-Hui Ng, Chia-Lin Wei (2007) Cell Stem Cell Vol 1, 286-298

85 "Zfp206 Is a Transcription Factor That Controls Pluripotency of Embryonic Stem Cells. " Wang ZX, Kueh JL, Teh CH, Rossbach M, Lim L, Li P, Wong KY, Lufkin T, Robson P, Stanton LW (2007) Stem Cells 25(9):2173-2182

86 "Zic3 is required for maintenance of pluripotency in embryonic stem cells" Lim LS, Loh YH, Zhang W, Li Y, Chen X, Wang Y, Bakre M, Ng HH, Stanton LW (2007) Mol Biol Cell 18(4):1348-58, 2007 Jan 31 [Epub ahead of print]

1 "(2006) Genomic Patterns of Pathogen Evolution Revealed by Comparison of Burkholderia pseudomallei, the Causative Agent of Melioidosis, to Avirulent Burkholderia thailandensis" Yiting Yu, H. Stanley Kim, Hui Hoon Chua, Chi Ho Lin, Siew Hoon Sim, Daoxun Lin, Alan Derr, Reinhard Engels, David DeShazer, Bruce Birren, William C. Nierman, Patrick Tan (2006) BMC Microbiology 6(1):46, 2006 May 26 [Epub ahead of print]

2 "A Global Mapping of p53 Transcription Factor Binding Sites in the Human Genome" Chia Lin Wei, Qiang Wu, Vinsensius Vega, Kuo Ping Chiu, Patrick Ng, Tao Zhang, Atif Shahab, Azmi Ridwan, YuTao Fu, Zhiping Weng, Yen Ling Lee, Jian Jun Liu, Vladimir A. Kuznetsov, Ken Sung, Bing Lim, Edison T. Liu, Qiang Yu, Huck Hui Ng, and Yijun Ruan (2006) Cell (2006)

3 "A Machine Learning Strategy to Identify Exonic Candidate Binding Sites in Human Protein-coding Sequence" Thomas A. Down, Bernard Leong and Tim J. P. Hubbard (2006) BMC Bioinformatics 7:419, 2006 Sep 26 Epub ahead of print

4 "A Modular Analysis of Breast Cancer Reveals A Novel Low-Grade Molecular Signature in Estrogen Receptor Positive Tumors." Kun Yu, Kumaresan Ganesan, Lance D. Miller and Patrick Tan (2006) Clinical Cancer Research 12:3288-3296, 2006 Jun 1

5 "A pattern based method for the identification of microRNA binding sites and their corresponding heteroduplexes" Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. (2006) Cell, 2006 Sep 22

6 "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 (2006) BLOOD 107(7):2777-85, 2006 Apr 1

7 "Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network" Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung (2006) SIAM Journal of Computing 35(5):1098-1121, 2006 Apr

8 "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. (2006) Mov Disord, 2006 Apr 6 [Epub ahead of print]

9 "Apoptosis signal-regulating kinase 1 is a direct target of E2F1 and contributes to histone deacetylase inhibitor-induced apoptosis through positive feedback regulation of E2F1 apoptotic activity" Tan J, Zhuang L, Jiang X, Yang KK, Karuturi KM, Yu Q (2006) J Biol Chem. 281(15):10508-15, 2006 Apr 14

10 "Application of advanced technologies in ageing research" Lim CA, Ng HH (2006) Mech Ageing Dev, 2006 Nov 16 [Epub ahead of print]

11 "Bapx1 homeobox gene gain-of-function mice show preaxial polydactyly and activated Shh signaling in the developing limb" Tribioli, C., and T. Lufkin (2006) Developmental Dynamics 235, 2483-2492, 2006 Sep

12 "CD14 promoter polymorphisms have no functional significance and are not associated with atopic phenotypes" Liang X, Cheung W, Heng CK, Liu J, Li CW, Lim B, Wang DY (2006) Pharmacogenet Genomics 16(4):229-36, 2006 Apr

13 "Celecoxib reduces microvessel density in patients treated with nasopharyngeal carcinoma and induces changes in gene expression" Ross A. Soo, Jeanie Wu, Amit Aggarwal, Qian Tao, Wenson Hsieh, Thomas Putti, Kong B Tan, Wah L Soon, Yoke F Lai, Benjamin Mow, Stephen Hsu, Kwok S Loh, Luke Tan, Patrick Tan*, Boon-C Goh* (* equal contribution) (2006) Ann Oncol. 17(11):1625-30, 2006 Nov

14 "Combinational application of surface plasmon resonance spectroscopy and quartz crystal microbalance for studying nuclear hormone receptor-response element interactions" Su X, Lin CY, O'Shea SJ, Teh HF, Peh WY, Thomsen JS (2006) Anal Chem 78(15):5552-8, 2006 Aug 1

15 "Complex loci in mammalian genomes" Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng E, Batalov S, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, and Lipovich L. (2006) PLoS Genetics 2(4):e47, 2006 Apr

16 "Comprehensive analysis of the ATM, CHEK2 and ERBB2 genes in relation to breast tumour characteristics and survival: a population-based case-control and follow-up study" Einarsdottir K, Rosenberg LU, Humphreys K, Bonnard C, Palmgren J, Li Y, Li Y, Chia KS, Liu ET, Hall P, Liu J, Wedren S. (2006) Breast Cancer Res. 8(6):R67, 2006 Nov 28 [Epub ahead of print]

17 "Differential Friendly Neighbors algorithm for differential relationships-based gene selection and classification using Microarray data" Karuturi RKM, Wong S, Sung W-K, Miller LD. (2006) The Proc of the 2006 Intl Conf on Data Mining (DMIN’06), Jun 26-29, 2006

18 "Dlx homeobox gene control of mammalian limb and craniofacial development" Kraus, P., and T. Lufkin (2006) American J Medical Genetics 140, 1366-1374, 2006 Jul 11

19 "Dlx5 and Dlx6 homeobox genes are required for specification of the mammalian vestibular apparatus" Robledo, R.F., and T. Lufkin (2006) Genesis: J of Genetics and Development 44, 425-437, 2006 Sep

20 "Early Dengue infection and outcome study (EDEN) - study design and preliminary findings" Low JG, Ooi EE, Tolfvenstam T, Leo YS, Hibberd ML, Ng LC, Lai YL, Yap GS, Li CS, Vasudevan SG, Ong A. (2006) Ann Acad Med Singapore 35:783-9, 2006 Nov

21 "Effect of ATM, CHEK2 and ERBB2 tagSNPs and haplotypes on endometrial cancer risk" Einarsdottir K, Humphreys K, Bonnard C, Li Y, Li Y, Chia KS, Liu ET, Hall P, Liu J, Wedren S. (2006) Hum Mol Genet, 2006 Dec 12 [Epub ahead of print]

22 "Effect of raloxifene on bone mineral density in premenopausal women at increased risk of breast cancer" Eng-Wong J, Reynolds JC, Venzon D, Liewehr D, Gantz S, Danforth D, Liu ET, Chow C, Zujewski J. (2006) J Clin Endocrinol Metab. 91(10):3941-6, 2006 Jul 25 [Epub ahead of print]

23 "Embryonic stem cells as a module for systems biology" Thomson et al (2006) Systems Biology Vol 2 ed Rigoutsos & Stephanopolous, 2006 Sep 10

24 "Emergence of size-dependent networks on genome scale" Kuznetsov, VA (2006) Lecture Series on Computer and computational Sciences vol. 7, pp754-757, 2006

25 "Establishing Clonal Cell Lines with Endothelial-Like Potential from CD9hi, SSEA-1- Cells in Embryonic Stem Cell-Derived Embryoid Bodies" Lian, Q., Yeo, K., Que, J., Tan, E., Yu, F., Yin, Y., Salto-Tellez, M., Oakley, R. M., and Lim, S. K. (2006) PLoS ONE 1(1) e6. doi:10.1371/journal.pone.0000006, 2006 Dec 20

26 "Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions" Chua HN, Sung WK, Wong L. (2006) Bioinformatics 2006 Jul 1; 22(13):1623-30, 2006 Apr 21 [Epub ahead of print]

27 "Follow-Up Analysis of PSORS9 in 151 Chinese Families Confirmed the Linkage to 4q31-32 and Refined the Evidence to the Families of Early-Onset Psoriasis" KL Yan , W Huang, XJ Zhang, S Yang, YM Chen, FL Xiao, X Fan, M Gao, Y Cui, GL Zhang, LD Sun, PG Wang, JJ Chen, W Li, ZH Chen, ZM Wang, D Wang, KY Zhang, J Liu (2006) Journal of Investigative Dermatology doi:10.1038/sj.jid.5700506, 2006 Nov 30 [Epub ahead of print]

28 "Gene expression preferentially regulated by tamoxifen in breast cancer cells and correlations with clinical outcome" Frasor J, Chang EC, Komm B, Lin CY, Vega VB, Liu ET, Miller LD, Smeds J, Bergh J, Katzenellenbogen BS. (2006) Cancer Res 66(14):7334-40, 2006 Jul 15

29 "Genome-wide analysis of mammalian promoter architecture and evolution" Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y. (2006) Nat Genet. 38(6):626-35, 2006 Apr 28 [Epub ahead of print]

30 "Genome-wide Expression Profiling in the Zebrafish Embryo Identifies Target Genes Regulated by Hedgehog Signaling During Vertebrate Development" Xu, J., B.P. Srinivas, S.Y. Tay, A. Mak, X. Yu, S.G. Lee, H. Yang, K.R. Govindarajan, B. Leong, G. Bourgue, S. Mathavan and S. Roy (2006) Genetics 174: 735-752, 2006 Oct

31 "Global map of growth-regulated gene expression in Burkholderia pseudomallei, the causative agent of melioidosis" Fiona Rodrigues, Mitali Sarkar-Tyson, Sarah V Harding, Siew Hoon Sim, Hui Hoon Chua, Chi Ho Lin, Xu Han, R Krishna M Karuturi, Ken Sung, Kun Yu, Wei Chen, Timothy P Atkins, Richard W Titball, and Patrick Tan (2006) Journal of Bacteriology p. 8178-8188, Vol. 188, No. 23, 2006 Dec

32 "Global mapping of c-Myc binding sites and target gene networks in human B cells" 3. Karen I. Zeller, XiaoDong Zhao, Charlie W. H. Lee, Kuo Ping Chiu, Hong Sain Ooi, Fei Yao, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Vladimir A. Kuznetsov, Wing-Kin Sung, Yijun Ruan, Chi V. Dang, and Chia-Lin Wei (2006) Proc. Natl. Acad. Sci. USA 10.1073/pnas.0604129103, 2006 Nov 8

33 "HERC5 is a novel interferon-induced HECT-type E3 protein ligase that mediates Type I interferon-induced ISGylation of protein targets" Wong, J., Yuh-Fen Pung, Newamn Sze, and Keh-Chuang, Chin (2006) Proceedings of the National Academy of Sciences USA 103(28), 10735-10740, 2006

34 "High-throughput genomic technology in research and clinical management of breast cancer. Evolving landscape of genetic epidemiological studies" YL Low, S Wedrén and J Liu (2006) Breast Cancer Research 8(3):209, 2006 Jun 28 [Epub ahead of print]

35 "Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis: a cohort study" Hall P, Ploner A, Bjohle J, Huang F, Lin CY, Liu ET, Miller LD, Nordgren H, Pawitan Y, Shaw P, Skoog L, Smeds J, Wedren S, Ohd J, Bergh J. (2006) BMC Med. 4(1):16, 2006 Jun 30 [Epub ahead of print]

36 "Identification of Common Pathways Mediating Differentiation of Bone Marrow and Adipose Tissues Derived Human Mesenchymal Stem Cells (MSCs) into Three Mesenchymal Lineages" Liu TM, Martina M, Hutmacher DW, Hoi J, Hui P, Lee EH, Lim B. (2006) Stem Cells DOI: 10.1634/stemcells.2006-0394, 2006 Nov 9 [Epub ahead of print]

37 "Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients" Broet P, Kuznetsov VA, Bergh J, Liu E, Miller LD. (2006) Bioinformatics, 2006 Jun 15

38 "In the pursuit of complexity: systems medicine in cancer biology" Liu ET, Kuznetsov VA, Miller LD. (2006) Cancer Cell. 9(4):245-7, 2006 Apr

39 "Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression" Tang, L, Liu, X and Clarke, ND (2006) BMC Genomics 7: 215, 2006 Aug 22

40 "Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients" alza S, Hall P, Auer G, Bjohle J, Klaar S, Kronenwett U, Liu ET, Miller LD, Ploner A, Smeds J, Bergh J, Pawitan Y. (2006) Breast Cancer Res. 8(4):R34, 2006 Jul 17 [Epub ahead of print]

41 "Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, Wong JE, Liu ET, Bergh J, Kuznetsov VA, Miller LD." Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer (2006) Cancer Res. 66(21):10292-301, 2006 Nov 1

42 "Lian, Q., Lye, E., Yeo, K. S., Tan, E. K., Salto-Tellez, M., Liu, T. M., Palanisamy, N., El Oakley, R. M., Lee, E. H., Lim, B., and Lim, S. K." Derivation of Clinically Compliant MSCs from CD105+, CD24- Differentiated Human ESCs (2006) Stem Cells DOI: 10.1634/stemcells.2006-0420, 2006 Oct 19 [Epub ahead of print]

43 "Linkage disequilibrium mapping of CHEK2: common variation and breast cancer risk" Einarsdottir K, Humphreys K, Bonnard C, Palmgren J, Iles MM, Sjolander A, Li Y, Chia KS, Liu ET, Hall P, Liu J, Wedren S. (2006) PLoS Med. 3(6):e168, 2006 May 9 [Epub ahead of print]

44 "Liver X receptors regulate adrenal steroidogenesis and hypothalamic-pituitary-adrenal feedback" Nilsson M, Stulnig TM, Lin CY, Yeo AL, Nowotny P, Liu ET, Steffensen KR (2006) Mol Endocrinol 21(1):126-37, 2006 Sep 14 [Epub ahead of print]

45 "Long-term room temperature storage of high-quality embryonic stem cell genomic DNA extracted with a simple and rapid procedure" Tribioli C, Lufkin T (2006) Journal of Biomolecular Techniques 17:249-251, 2006 Sep

46 "LRRK2 G2019S founder haplotype in the Chinese population" Tan EK, Skipper L, Tan L, Liu JJ (2006) Mov Disord, 2006 Nov 2 [Epub ahead of print]

47 "Mice and men: promoter properties" Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, and Hayashizaki Y. (2006) PLoS Genetics. ; 2(4):e54, 2006 Apr

48 "Multi-platform genome-wide identification and modeling of functional human estrogen receptor binding sites" Vega VB, Lin CY, Lai KS, Kong SL, Xie M, Su X, Teh HF, Thomsen JS, Yeo AL, Sung WK, Bourque G, Liu ET. (2006) Genome Biol 7(9):R82, 2006 Sep 9

49 "Multiplex Sequencing of Paired-End Ditags (MS-PET): a Strategy for the Ultra-High-Throughput Analysis of Transcriptomes and Genomes" Ng, Patrick; Tan, Jack; Ooi, Hong Sain; Lee, Yen Ling; Chiu, Kuo Ping; Fullwood, Melissa; Srinivasan, Kandhadayar; Perbost, Clotilde; Du, Lei; Sung, Wing-Kin; Wei, Chia-Lin; Ruan, Yijun (2006) Nucleic Acids Research 34(12): e84 doi:10.1093/nar/gkl444, 2006, July 13

50 "MYBBP1a is a novel repressor of NF-kappaB" Owen HR, Elser M, Cheung E, Gersbach M, Kraus WL, Hottiger MO (2006) Journal of Molecular Biology 366(3):725-36, 2006 Dec 15

51 "MYBBP1a is a Novel Repressor of NF-kappaB" Owen HR, Elser M, Cheung E, Gersbach M, Kraus WL, Hottiger MO (2006) Journal of Molecular Biology doi:10.1016/j.jmb.2006.11.099, 2006 Dec 15 [Epub ahead of print]

52 "Paired-End diTagging for Transcriptome and Genome Analysis" Patrick Ng, Chia-Lin Wei, Yijun Ruan, Fred M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J.G. Seidman, John A. Smith, Kevin Struhl (eds.); Virginia B. Chanda (Series Editor) (2006) In Current Protocols in Molecular Unit 21.12, 2006 July

53 "Pareto-Gamma Statistics reveals global rescaling in transcriptomes of low and high aggressive breast cancer phenotypes" Chua A L-S, Ivshina AV, Kuznetsov VA (2006) Pattern Recognition in Bioinformatics (PRIB-2006) pp.49-59, 2006

54 "PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data" Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Ken Sung, and Yijun Ruan (2006) BMC Bioinformatics 7:390, 2006 Aug 25

55 "Polymorphisms in candidate genes: implications for the current treatment of Parkinson's disease" Skipper L, Liu J, Tan EK (2006) Expert Opinion on Pharmacotherapy Vol. 7, No. 7, Pages 849-855, 2006 May

56 "Power Laws, Maximal Efficiency and the Turnover of Sports Managers" Toke Aidt, Bernard Leong, Daniel Sgroi and William Saslaw (2006) Physica A 370(2):697-703, 2006

57 "Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster" Leonard LIPOVICH, Ravi Raj Vanisri, Say Li Kong, Chin-Yo Lin, Edison Tak-Bun LIU (2006) Journal of Molecular Evolution

58 "Quantitative Profiling of Drug-Associated Proteomic Alterations by Combined 2-Nitrobenzenesulfenyl Chloride (NBS) Isotope Labeling and 2DE/MS Identification" Keli Ou, Djohan Kesuma, Kumaresan Ganesan, Kun Yu, Sou Yen Soon, Suet Ying Lee, Xin Pei Goh, Michelle Hooi, Wei Chen, Hiroyuki Jikuya, Tetsuo Ichikawa, Hiroki Kuyama, Ei-ichi Matsuo, Osamu Nishimura, and Patrick Tan (2006) J Proteome Res 5(9); 2194 - 2206, 2006 Sept

59 "Recursive SVM feature selection and sample classification for proteomics mass-spectrometry data" Zhang, X, Lu, X, Shi, Q, Xu, X, Eastwood Hon-Chiu LEUNG, Miron, A, Liu, J.S, Wong, W.H (2006) BioMed Central Bioinformatics

60 "Restoring p53-mediated apoptosis in cancer cells: new opportunities for cancer therapy." Qiang Yu (2006) Drug Resistance Updates doi:10.1016/j.drup.2006.03.001, Online 2006 April 5

61 "Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells" Wu, Q., Chen, X., Zhang, J., Loh, YH., Low, TY, Zhang, W., Zhang, W., Sze, S., Lim, B., Ng, HH. (2006) J. Biol. Chem. 281(34):24090-4, 2006 Jul 13 (Accelerated Publication)

62 "Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1" J.Zhang, W-L.Tam, G.Q.Tong, Q.Wu, H-Y.Chan, B-S.Soh, Y.Lou, J.Yang, Y.Ma, L.Chai, H-H.Ng, T.Lufkin, P.Robson, B.Lim (2006) Nature Cell Biology doi:10.1038/ncb1481, 2006 Sep 17 [Epub ahead of print])

63 "Smads orchestrate specific histone modifications and chromatin remodeling to activate transcription" Ross S, Cheung E, Petrakis TG, Howell M, Kraus WL, Hill CS (2006) The EMBO Journal 25, 4490–4502, 2006 Sep 21

64 "Statistically Weighted Voting Analysis of Microarrays for Molecular Pattern Selection and Discovery Cancer Genotypes" V. A. Kuznetsov, O. V. Senko, L. D. Miller and Anna V. Ivshina (2006) Internet of computer sciences and network security (12) 73-83, 2006

65 "Statistics of the numbers of transcripts and protein sequences encoded in the genome" Kuznetsov, VA (2006) Computational and Statistical Methods to Genomics pp.160-208, 2006

66 "Systematic evaluation of association between the microsomal glutathione S-transferase 2 common variation and psoriasis vulgaris in Chinese population" Yang S, Yan KL, Zhang XJ, Xiao FL, Fan X, Gao M, Cui Y, Wang PG, Zhang GL, Sun LD, Wang ZM, Wang DZ, Zhang KY, Huang W, Liu J (2006) Arch Dermatol Res. 298(3):107-12, 2006 Jun 14 [Epub ahead of print]

67 "The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction" Bourque G., Tesler G., Pevzner P.A (2006) Genome Research. Accepted (2006)

68 "The LRRK2 Gly2385Arg variant is associated with Parkinson's disease: genetic and functional evidence" EK Tan, Y Zhao, Skipper L, MG Tan, A Di Fonzo, L Sun, S Fook-Chong, S Tang, E Chua, Y Yuen, L Tan, R Pavanni, MC Wong, P Kolatkar, CS Lu ,V Bonifati, JJ Liu (2006) Hum Genet, 2006 Sep 30 [Epub ahead of print]

69 "The molecular basis of ageing in stem cells" Tam WL, Ang YS, Lim B. (2006) Mech Ageing Dev. doi:10.1016/j.mad.2006.11.020, 2006 Nov 27 [Epub ahead of print]

70 "The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells" Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH (2006) Nat Genet. 2006 Apr;38(4):431-40, 2006 Apr

71 "The Oct4 and Nanog transcription network that regulates pluripotency in mouse embryonic stem cells" Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W. Sung, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin Wei, Yijun Ruan, Bing Lim, Huck-Hui Ng (2006) Nature Genetics 38, 431 - 440 (2006)

72 "The transcriptome of human oocytes" Kocabas AM, Crosby J, Ross PJ, Otu HH, Beyhan Z, Can H, Tam WL, Rosa GJ, Halgren RG, Lim B, Fernandez E, Cibelli JB (2006) Proc Natl Acad Sci U S A. 103(38):14027-32, 2006 Sep 19

73 "TLR3 ligation activates an antiviral response in human fetal astrocytes: a role for viperin/cig5" Rivieccio, M.A., Suh, H.S., Zhao, Y., Zhao, M.L., Chin, K. C., Lee, S.C., and Brosnan, C.F. (2006) Journal of Immunology 177, 4735-4741, 2006 Oct 1

74 "Topological and Functional Discovery in a Gene Co-expression Meta-Network of Gastric Cancer" Amit Aggarwal, Dong Li Guo, Yujin Hoshida, Siu Tsan Yuen, Kent-Man Chu, Samuel So, Alex Boussioutas, Xin Chen, David Bowtell, Hiroyuki Aburatani, Suet Yi Leung, and Patrick Tan (2006) Cancer Research

75 "Trancriptome Kinetics of Arsenic-induced Adaptive Response in Zebrafish Liver" Lam SH, Winata CL, Tong Y, Korzh S, Lim WS, Korzh V, Spitsbergen J, Mathavan S, Miller LD, Liu ET, Gong Z. (2006) Physiol Genomics 27: 351-361, 2006 Aug 1 [Epub ahead of print]

76 "Whole genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection" Liu, X, Lee, C-K, Granek, JA, Clarke, ND and Lieb, JD (2006) Genome Research 16:1517-1528, 2006 Dec 16

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 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

7 "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

8 "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

9 "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

10 "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

11 "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

12 "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)

13 "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

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

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

16 "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

17 "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

18 "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

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

20 "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]

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

22 "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

23 "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

24 "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

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

26 "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

27 "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

28 "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

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

30 "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]

31 "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

32 "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

33 "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

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

35 "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

36 "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

37 "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)

38 "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

39 "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

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

41 "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

42 "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

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

44 "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

45 "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

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

47 "Reciprocal Transcriptional Regulation of Pou5f1 and Sox2 Via the Oct4/Sox2 Complex in Embryonic Stem Cells" Joon-Lin Chew, Yuin-Han Loh, Paul ROBSON, Bing LIM, Ang Yen-Sin, Li Pin, Yeap Leng-Siew, Tam Wai-Leong, Chen Xi, Zhang Wensheng, Huck Hui NG (2005) Molecular & Cellular Biology. 25 . 6031-6046

48 "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)

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

50 "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

51 "SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis" Jianjun LIU, SL Lim, Yijun RUAN, Ling AE, Lisa Fong-Poh NG, C Drostein, Edison Tak-Bun LIU, Lawrence STANTON, Martin Lloyd HIBBERD (2005) PLoS Med. 2(2) . 162-168

52 "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

53 "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

54 "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

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

56 "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

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

58 "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

59 "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

60 "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