Publications from 2007
  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 constrained polynomial regression procedure for estimating the local False Discovery Rate." Dalmass o Cyril, Bar-Hen Avner, Broët Philippe (2007) BMC Bioinformatics 2007 ; 8 : 229


  3. "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


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


  5. "A Mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosis." Khor CC, Chapman SJ, Vannberg FO, Dunne A, Murphy C, Ling EY, Frodsham AJ, Walley AJ, Kyrieleis O, Khan A, Aucan C, Segal S, Moore CE, Knox K, Campbell SJ, Lienhardt C, Scott A, Aaby P, Sow OY, Grignani RT, Sillah J, Sirugo G, Peshu N, Williams TN, Maitland K, Davies RJ, Kwiatkowski DP, Day NP, Yala D, Crook DW, Marsh K, Berkley JA, O\'Neill LA, Hill AV (2007) Nat Genet 2007 Apr ; 39(4) : 523-8 Epub 2007 Feb 25


  6. "A mixture model approach to multiple testing for the genetic analysis of gene expression." Dalmasso Cyril, Pickrell Joseph, Tuefferd Marianne, Génin Emmanuelle, Bourgain Catherine, Broët Philippe (2007) 2007 ; 1 Suppl 1 : S141


  7. "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


  8. "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.


  9. "An efficient strategy for extensive integration of diverse biological data for protein function prediction." Chua Hon Nian, Sung Wing-Kin, Wong Limsoon (2007) ics 2007 Dec 15 ; 23(24) : 3364-73


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


  11. "Application of advanced technologies in ageing research." Lim Ching-Aeng, Ng Huck-Hui (2007) Mech. Ageing Dev. 2007 Jan ; 128(1) : 149-60


  12. "Assessment of CASP7 structure predictions for template free targets." Jauch Ralf, Yeo Hock Chuan, Kolatkar Prasanna R, Clarke Neil D (2007) Proteins 2007 ; 69 Suppl 8 : 57-67


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


  14. "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


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


  16. "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


  17. "BLIMP1 regulates cell growth through repression of p53 transcription." Yan Junli, Jiang Jianming, Lim Ching Aeng, Wu Qiang, Ng Huck-Hui, Chin Keh-Chuang (2007) Proc. Natl. Acad. Sci. U.S.A. 2007 Feb 6 ; 104(6) : 1841-6


  18. "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]


  19. "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


  20. "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


  21. "Chromosome classification using dynamic time warping" Benoıˆt Legrand, C.S. Chang, S.H. Ong, Soek-Ying Neo, Nallasivam Palanisamy (2007) ScienceDirect


  22. "Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments." Kuznetsov Vladimir A, Orlov Yuriy L, Wei Chia Lin, Ruan Yijun (2007) Genome Inform. 2007;19:83-94.


  23. "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


  24. "DengueInfo: A web portal to dengue information resources." Schreiber Mark J, Ong Swee Hoe, Holland Richard C G, Hibberd Martin L, Vasudevan Subhash G, Mitchell Wayne P, Holmes Edward C (2007) Infect. Genet. Evol. 2007 Jul ; 7(4) : 540-1


  25. "Detection of generic spaced motifs using submotif pattern mining." Wijaya Edward, Rajaraman Kanagasabai, Yiu Siu-Ming, Sung Wing-Kin (2007) Bioinformatics 2007 Jun 15 ; 23(12) : 1476-85


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


  27. "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.


  28. "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]


  29. "Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine." Miller Lance D, Liu Edison T (2007) Breast Cancer Res. 2007 ; 9(2) : 206


  30. "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.


  31. "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


  32. "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


  33. "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


  34. "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


  35. "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


  36. "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


  37. "Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation." Lim Ching-Aeng, Yao Fei, Wong Joyce Jing-Yi, George Joshy, Xu Han, Chiu Kuo Ping, Sung Wing-Kin, Lipovich Leonard, Vega Vinsensius B, Chen Joanne, Shahab Atif, Zhao Xiao Dong, Hibberd Martin, Wei Chia-Lin, Lim Bing, Ng Huck-Hui, Ruan Yijun, Chin Keh-Chuang (2007) Mol. Cell 2007 Aug 17 ; 27(4) : 622-35


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


  39. "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 2007 ; 2(1) : e722


  40. "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.


  41. "High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons." McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, Hillson NJ, Hu P, Shapiro L, McAdams HH (2007) Nat Biotechnol 2007 May ; 25(5) : 584-92 Epub 2007 Apr 1


  42. "Higher order structure in the cancer transcriptome and systems medicine." Liu Edison T, Lemberger Thomas (2007) Mol. Syst. Biol. 2007 ; 3 : 94


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


  44. "Host gene expression profiling of dengue virus infection in cell lines and patients." Fink Joshua, Gu Feng, Ling Ling, Tolfvenstam Thomas, Olfat Farzad, Chin Keh Chuang, Aw Pauline, George Joshy, Kuznetsov Vladimir A, Schreiber Mark, Vasudevan Subhash G, Hibberd Martin L (2007) PLoS Negl Trop Dis 2007 ; 1(2) : e86


  45. "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]


  46. "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


  47. "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)


  48. "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


  49. "IkappaB genetic polymorphisms and invasive pneumococcal disease." Chapman SJ, Khor CC, Vannberg FO, Frodsham A, Walley A, Maskell NA, Davies CW, Segal S, Moore CE, Gillespie SH, Denny P, Day NP, Crook DW, Davies RJ, Hill AV (2007) Am J Respir Crit Care Med 2007 Jul 15 ; 176(2) : 181-7 Epub 2007 Apr 26


  50. "Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer." Lin Chin-Yo, Ström Anders, Li Kong Say, Kietz Silke, Thomsen Jane S, Tee Jason B S, Vega Vinsensius B, Miller Lance D, Smeds Johanna, Bergh Jonas, Gustafsson Jan-Ake, Liu Edison T (2007) Breast Cancer Res. 2007 ; 9(2) : R25


  51. "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


  52. "Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells." Loh Yuin-Han, Zhang Weiwei, Chen Xi, George Joshy, Ng Huck-Hui (2007) Genes Dev. 2007 Oct 15 ; 21(20) : 2545-57


  53. "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


  54. "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


  55. "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


  56. "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


  57. "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


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


  59. "Oct4 and Sox2 directly regulate expression of another pluripotency transcription factor, Zfp206, in embryonic stem cells." Wang Zheng-Xu, Teh Christina Hui-Leng, Kueh Jacqueline L L, Lufkin Thomas, Robson Paul, Stanton Lawrence W (2007) J. Biol. Chem. 2007 Apr 27 ; 282(17) : 12822-30


  60. "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


  61. "Optimization and clinical validation of a pathogen detection microarray." Wong Christopher W, Heng Charlie Lee Wah, Wan Yee Leong, Soh Shirlena W L, Kartasasmita Cissy B, Simoes Eric A F, Hibberd Martin L, Sung Wing-Kin, Miller Lance D (2007) Genome Biol. 2007 ; 8(5) : R93


  62. "p73 supports cellular growth through c-Jun-dependent AP-1 transactivation." Vikhanskaya Faina, Toh Wen Hong, Dulloo Iqbal, Wu Qiang, Boominat han Lakshmanane, Ng Huck Hui, Vousden Karen H, Sabapathy Kanaga (2007) Nat. Cell Biol. 2007 Jun ; 9(6) : 698-705


  63. "Paired-end diTagging for transcriptome and genome analysis." Ng P, Wei CL, Ruan Y (2007) Curr Protoc Mol Biol 2007 Jul ; Chapter 21 : Unit 21.12


  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. "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


  67. "Pleiotrophin enhances clonal growth and long-term expansion of human embryonic stem cells." Soh Boon Seng, Song Chun Meng, Vallier Ludovic, Li Pin, Choong Cleo, Yeo Boon Huat, Lim Elaine Hsuen, Pedersen Roger A, Yang Henry He, Rao Mahendra, Lim Bing (2007) Stem Cells 2007 Dec ; 25(12) : 3029-37


  68. "Positive replication and linkage disequilibrium mapping of the chromosome 21q22.1 malaria susceptibility locus." Khor CC, Vannberg FO, Chapman SJ, Walley A, Aucan C, Loke H, White NJ, Peto T, Khor LK, Kwiatkowski D, Day N, Scott A, Berkley JA, Marsh K, Peshu N, Maitland K, Williams TN, Hill AV (2007) Genes Immun 2007 Oct ; 8(7) : 570-6 Epub 2007 Aug 16


  69. "Possible involvement of ActVI-ORFA in transcriptional regulation of actVI tailoring-step genes for actinorhodin biosynthesis." Taguchi T, Okamoto S, Lezhava A, Li A, Ochi K, Ebizuka Y, Ichinose K (2007) FEMS Microbiol Lett 2007 Apr ; 269(2) : 234-9 Epub 2007 Jan 15


  70. "Power to detect risk alleles using genome-wide tag SNP panels." Eberle MA, Ng PC, Kuhn K, Zhou L, Peiffer DA, Galver L, Viaud-Martinez KA, Lawley CT, Gunderson KL, Shen R, Murray SS (2007) PLoS Genet 2007 Oct ; 3(10) : 1827-37 Epub 2007 Aug 22


  71. "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


  72. "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


  73. "Rapid detection of epidermal growth factor receptor mutations in lung cancer by the SMart-Amplification Process." Hoshi K, Takakura H, Mitani Y, Tatsumi K, Momiyama N, Ichikawa Y, Togo S, Miyagi T, Kawai Y, Kogo Y, Kikuchi T, Kato C, Arakawa T, Uno S, Cizdziel PE, Lezhava A, Ogawa N, Hayashizaki Y, Shimada H (2007) Clin Cancer Res 2007 Sep 1 ; 13(17) : 4974-83


  74. "Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology." Mitani Y, Lezhava A, Kawai Y, Kikuchi T, Oguchi-Katayama A, Kogo Y, Itoh M, Miyagi T, Takakura H, Hoshi K, Kato C, Arakawa T, Shibata K, Fukui K, Masui R, Kuramitsu S, Kiyotani K, Chalk A, Tsunekawa K, Murakami M, Kamataki T, Oka T, Shimada H, Cizdziel PE, Hayashizaki Y (2007) Nat Methods 2007 Mar ; 4(3) : 257-62 Epub 2007 Feb 18


  75. "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


  76. "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


  77. "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.


  78. "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


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


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