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Publications |
Publications
2008, 2007, 2006, 2005, 2004, 2003, 2001, 2000 Cheng Li (2008) Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics. 9:231. (PubMed) Ming
Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung
Wong*, and Cheng Li*
(2004) dChipSNP: Significance
Curve and Clustering of SNP-Array-Based Loss-of-Heterozygosity Data. Bioinformatics.
20: 1233-1240. (PubMed,
Journal,
Data and Software,
dChip usage) Sheng
Zhong, Cheng Li* and Wing Hung Wong* (2003) ChipInfo: Software for Extracting
Gene Annotation and Gene Ontology Information for Microarray Analysis. Nucleic
Acids Research. Vol. 31, 3483-3486. (PubMed, Journal,
Software, dChip
usage) Cheng Li and Wing Hung Wong
(2003) DNA-Chip Analyzer (dChip).
In The analysis of gene expression data: methods and software. Edited
by G Parmigiani, ES Garrett, R Irizarry and SL Zeger. Springer, New York.
120-141. (Book site) Cheng Li and Wing Hung Wong (2001b) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application, Genome Biology 2(8): research0032.1-0032.11 (PubMed) Cheng Li and Wing Hung Wong (2001a) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl. Acad. Sci. Vol. 98, 31-36. (PubMed, Journal) *Joint corresponding authors 2008 (Top) Cheng Li, Samir Amin (2008) Analysis of cancer genome alterations using single nucleotide polymorphism (SNP) microarrays. In New developments in biostatistics and bioinformatics. Edited by Jianqing Fan, Xihong Lin and Jun Liu. In press. 2007 (Top) Yuhyun Park†, Sean
R. Downing†,
Dohyun Kim, William C. Hahn, Cheng Li,
Philip W. Kantoff, L.J. Wei (2007) Simultaneous
and exact interval estimates for the contrast of two groups based on an
extremely high dimensional variable: Application to Mass Spec data. Bioinformatics. 23(12):1451-1458. (PubMed, †Joint first authors) Vallat LD, Park Y, Li C, Gribben JG. (2007) Temporal genetic program following B-cell receptor cross-linking: altered balance between proliferation and death in healthy and malignant B cells. Blood. 109(9):3989-97. (PubMed) George RE, Attiyeh EF, Li S, Moreau LA, Neuberg D, Li C, Fox EA, Meyerson M, Diller L, Fortina P, Look AT, Maris JM (2007) Genome-Wide Analysis of Neuroblastomas using High-Density Single Nucleotide Polymorphism Arrays. PLoS ONE 2(2): e255. (PubMed) Bae J, Mitsiades C, Tai YT, Bertheau R, Shammas M, Batchu RB, Li C, Catley L, Prabhala R, Anderson KC, Munshi NC. (2007) Phenotypic and functional effects of heat shock protein 90 inhibition on dendritic cell. J Immunol. 178(12):7730-7. (PubMed) Wong YF, Cheung TH, Lo KW, Yim SF, Siu NS, Chan SC, Ho TW, Wong KW, Yu MY, Wang VW, Li C, Gardner GJ, Bonome T, Johnson WB, Smith DI, Chung TK, Birrer MJ. (2007) Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling. Oncogene. 26:1971-82. (PubMed) 2006 (Top) BA Walker, PE Leone, MW Jenner, C Li, D Gonzalez, DC
Johnson, FM Ross, FE Davies, GJ Morgan (2006) Integration of global SNP-based mapping
and expression arrays reveals key regions, mechanisms, and genes important in
the pathogenesis of multiple myeloma. Blood
108: 1733-1743. (PubMed) Juszczynski P, Kutok JL, Li C, Mitra J, Aguiar RC, Shipp MA. (2006) BAL1 and BBAP are regulated by a gamma interferon-responsive bidirectional promoter and are overexpressed in diffuse large B-cell lymphomas with a prominent inflammatory infiltrate. Mol Cell Biol. 26(14):5348-59. (PubMed) Moran JL, Bolton AD, Tran PV, Brown A, Dwyer ND, Manning DK, Bjork BC, Li C, Montgomery K, Siepka SM, Vitaterna MH, Takahashi JS, Wiltshire T, Kwiatkowski DJ, Kucherlapati R, Beier DR. (2006) Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse. Genome Res. 16:436-440. (PubMed) 2005 (Top) Garraway
LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy
S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL,
Meyerson ML, Fisher DE, Sellers WR (2005) Integrative genomic analyses
identify MITF as a lineage survival oncogene amplified in malignant melanoma.
Nature. 436(7047):117-22. (PubMed, GEO
data) Wang V, Li C, Lin M, Welch W, Bell D, Wong YF, Berkowitz R, Mok SC, Bandera CA (2005) Ovarian cancer is a heterogeneous disease. Cancer Genet Cytogene. 161(2):170-3. Goodison S, Yuan J, Sloan D, Kim R, Li C, Popescu NC, Urquidi V (2005) The RhoGAP protein DLC-1 functions as a metastasis suppressor in breast cancer cells. Cancer Res. 65(14):6042-53. (Abstract)
T LaFramboise, BA Weir, X Zhao, R Beroukhim, C Li, D Harrington, WR Sellers, M Meyerson (2005) Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis. PLoS Comput Biol 1(6): e65. (Abstract, R package) PLM Dahia, KN Ross, ME Wright, CY Hayashida, S Santagata, M Barontini, AL Kung, G Sanso, JF Powers, AS Tischler, R Hodin, S Heitritter, F Moore, R Dluhy, JA Sosa, IT Ocal, DE Benn, DJ Marsh, BG Robinson, K Schneider, J Garber, SM Arum, M Korbonits, A Grossman, P Pigny, SPA Toledo, V Nosé, C Li, CD Stiles (2005) A HIF1α Regulatory Loop Links Hypoxia and Mitochondrial Signals in Pheochromocytomas. PLoS Genet. 1(1): e8. Tang D, Khaleque MA, Jones EL,
Theriault JR, Li C, Wong WH, Stevenson MA, Calderwood SK (2005) Expression of
heat shock proteins and heat shock protein messenger ribonucleic acid in
human prostate carcinoma in vitro and in tumors in vivo. Cell Stress
Chaperones. 10(1):46-58. (Abstract) Wang Z, Neuburg D, Li C, Su L, Kim JY, Chen JC, Christiani
DC (2005) Global
gene expression profiling in whole-blood samples from individuals exposed to
metal fumes. Environ Health Perspect. 113(2):233-41. 2004 (Top)
X Zhao, C Li, JG Paez, K Chin, PA Jänne, TH Chen, L Girard, J Minna, D Christiani, C Leo, JW Gray, WR Sellers, M Meyerson (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Research. 64:3060-3071. (Abstract, Data) Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ, Gabriel S, Herman P, Sasaki H, Altshuler D, Li C, Meyerson M, Sellers WR (2004) Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Research. 32(9):e71. (Abstract) ZC Wang, M Lin, LJ Wei, C Li, A Miron, G Lodeiro, L Harris, S Ramaswamy, DM Tanenbaum, M Meyerson, JD Iglehart, A Richardson (2004) Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers. Cancer Research. 64(1): 64-71. (Abstract, Data) RM Bachoo†, RS Kim†, KL Ligon, EA Maher, C Brennan, N Billings, S Chan, C Li, DH Rowitch, WH Wong and RA DePinho (2004) Molecular diversity of astrocytes with implications for neurological disorders. Proc. Natl. Acad. Sci. 101(22):8384-9. (Abstract, †Joint first authors) Munshi NC, Hideshima T, Carrasco D, Shammas M, Auclair D, Davies F, Mitsiades N, Mitsiades C, Kim RS, Li C, Rajkumar SV, Fonseca R, Bergsagel L, Chauhan D, Anderson KC (2004) Identification of genes modulated in multiple myeloma using genetically identical twin samples. Blood. 103(5):1799-806. (Abstract) Ke Hao, Cheng Li, Carsten Rosenow, Wing H. Wong (2004) Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10K array . European Journal of Human Genetics. 12:1001-1006. (Abstract,
Highlight)
Ke Hao, Cheng Li, Carsten Rosenow, Wing Hung Wong (2004) Estimation of Genotype Error Rate Using Samples with Pedigree Information -- An application on GeneChip Mapping 10K array. Genomics. 84: 623-630. (Abstract) Dring AM, Davies
FE, Fenton JA, Roddam PL, Scott K, Gonzalez D, Rollinson S, Rawstron AC,
Rees-Unwin KS, Li C, Munshi NC, Anderson KC, Morgan GJ (2004) A Global
Expression-based Analysis of the Consequences of the t(4;14) Translocation in
Myeloma. Clin Cancer Res. 10(17):5692-701. (PubMed) DJ Willis, JA Kalish, C Li, ER Deutsch, MA Contreras, FW LoGerfo and WC Quist (2004) Temporal gene expression following prosthetic arterial grafting. Journal of Surgical Research. 120(1):27-36 (Abstract) Kalish JA, Willis DJ, Li C, Link JJ, Deutsch ER, Contreras MA, Quist WC, Logerfo FW (2004) Temporal genomics of vein bypass grafting through oligonucleotide microarray analysis. Journal of Vascular Surgery. 39(3):645-54. (Abstract) Zhou X, Li C, Mok SC, Chen Z, Wong DT (2004) Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) array. Cancer Genet Cytogenet. 151(1):82-4. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5(10):R80. (PubMed) Zhong S, Tian L, Li C, Storch FK and Wong WH (2004) Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework. Proc. IEEE Comp Systems Bioinformatics. 425-435. (Abstract, Software) Hui Han, C. Lee Giles, Hongyuan Zha, Cheng Li, and Kostas Tsioutsiouliklis
(2004) Two Supervised Learning Approaches for Name Disambiguation in Author
Citations. Proceedings of ACM/IEEE Joint Conference on Digital Libraries
(JCDL 2004). 296-305. (Abstract) 2003 (Top) Cheng Li, George C. Tseng and Wing Hung Wong (2003) Model-based analysis of oligonucleotide arrays and issues in cDNA microarray analysis. In Statistical analysis of gene expression microarray data. Edited by Terry Speed. CRC Press. 1-34. (Amazon; consists of 3 previous papers: 1, 2, 3)
Chauhan D, Li G, Auclair D, Hideshima T, Richardson P, Podar K, Mitsiades N, Mitsiades C, Li C, Kim RS, Munshi N, Chen LB, Wong W, Anderson KC (2003) Identification of genes regulated by 2-methoxyestradiol (2ME2) in multiple myeloma cells using oligonucleotide arrays. Blood. 101(9):3606-14. FE Davies, AM Dring, C Li, AC Rawstron, MA Shammas, SM O'Connor, JA Fenton, T Hideshima, D Chauhan, IT Tai, E Robinson, D Auclair, K Rees, D Gonzalez, AJ Ashcroft, R Dasgupta, C Mitsiades, N Mitsiades, LB Chen, WH Wong, NC Munshi, GJ Morgan and KC Anderson (2003) Insights into the multistep transformation of MGUS to myeloma using microarray expression analysis. Blood. 102(13):4504-11. (Abstract) Schoenberg, F.P., Ferguson, T., and Li, C. (2003). Inverting
Dirichlet tessellations. The Computer Journal 46(1), 76-83.
(Abstract,
C code) 2001 (Top) Hakak Y, Walker JR, Li C, Wong WH, Davis KL, Buxbaum JD, Haroutunian V and Fienberg AA (2001) Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc. Natl. Acad. Sci. Vol. 98, 4746-4751. (Abstract; dChip Compare samples, Gene clustering and Sample classification by LDA) Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ and Meyerson M (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc. Natl. Acad. Sci. USA, Vol. 98, 13790-13795 (Abstract, Supplement, Data) Eric E. Schadt, Cheng Li, Byron Ellis and Wing H.
Wong (2001) Feature extraction
and normalization algorithms for high-density oligonucleotide gene expression
array data. Journal of Cellular Biochemistry. Supplement 37,
120-125. (Abstract) Schoenberg, F., Berk, R., Fovell, R., Li, C., Lu, R., and Weiss, R. (2001). Approximation and inversion of a complex meteorological system via local linear filters. Journal of Applied Meteorology, 40(3), 446--458. 2000
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