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Publications |
Publications
2008, 2007, 2006, 2005, 2004, 2003, 2001, 2000 2009 Li C, Kim SW, Rai D, Bolla AR, Adhvaryu S, Kinney MC, Robetorye RS, Aguiar RC. Copy number abnormalities, MYC activity and the genetic fingerprint of normal B-cells mechanistically define the microRNA profile of DLBCL. Blood. 2009. 113(26):6681-90. (PubMed, GEO) Li C, Amin S. 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. World
Scientific Publishing Co. 2009; 209-237. (Book site, Amazon) Avet-Loiseau H, Li C, Magrangeas F, Gouraud W, Charbonnel C, Harousseau JL, Attal M, Marit G, Mathiot C, Facon T, Moreau P, Anderson KC, Campion L, Munshi NC, Minvielle S. Prognostic Significance of Copy-Number Alterations in Multiple Myeloma. J Clin Oncol. 2009. 27(27):4585-90 (PubMed, PDF, GEO) Volchenboum SL, Li
C, Li S, Attiyeh EF, Reynolds CP, Maris JM, Look AT, George RE. Comparison
of Primary Neuroblastoma Tumors and Derivative Early-Passage Cell Lines Using
Genome-Wide Single Nucleotide Polymorphism Array Analysis. Cancer Res. 2009; 69(10):4143-9. (PubMed) Li J, Milbury
CA, Li C, Makrigiorgos GM. Two-round coamplification at lower
denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a
novel spectrum of low-level mutations in lung adenocarcinoma. Hum
Mutat. 2009. (PubMed) Heinrichs S, Kulkarni RV, Bueso-Ramos CE, Levine RL, Loh
ML, Li C, Neuberg D, Kornblau SM,
Issa JP, Gilliland DG, Garcia-Manero G, Kantarjian HM, Estey EH, Look AT.
Accurate detection of uniparental disomy and microdeletions by SNP array
analysis in myelodysplastic syndromes with normal cytogenetics. Leukemia.
2009. 23(9):1605-13. (PubMed) Shammas MA, Shmookler Reis RJ, Koley H, Batchu RB, Li C, Munshi NC. Dysfunctional
homologous recombination mediates genomic instability and progression in
myeloma. Blood. 2009; 113(10):2290-7. (PubMed) 2008 (Top) Li C. Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics. 2008; 9:231. (PubMed, PDF) Loerch PM†, Lu T†, Dakin KA,
Vann JM, Isaacs A, Geula C, Wang J, Pan Y, Gabuzda DH, Li C, Prolla TA, Yankner BA. Evolution
of the aging brain transcriptome and synaptic regulation. PloS ONE. 2008; 3(10):e3329. (PubMed, Journal,
PDF) Luo B, Cheung HW, Subramanian A, Sharifnia T, Okamoto M, Yang X, Hinkle G, Boehm JS, Beroukhim R, Weir BA, Mermel C, Barbie DA, Awad T, Zhou X, Nguyen T, Piqani B, Li C, Golub TR, Meyerson M, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE. Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci. 2008; 105(51):20380-5. (PubMed) 2007 (Top) Park Y†, Downing SR†, Kim D, Hahn WC, Li C, Kantoff PW, Wei LJ. Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: Application to Mass Spec data. Bioinformatics. 2007; 23(12):1451-1458. (†Joint first authors, PubMed, PDF) 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, PDF) 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) Walker BA, Leone PE, Jenner MW, Li C, Gonzalez D, Johnson DC, Ross FM, Davies FE, Morgan GJ.
Integration of global SNP-based mapping and expression arrays reveals key
regions, mechanisms, and genes important in the pathogenesis of multiple
myeloma. Blood.
2006;108: 1733-1743. (PubMed, PDF) 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, PDF, GEO
data) Fang X, Li C, Wong WH. Low-level analysis of oligonucleotide expression arrays. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons. 2005. (Abstract) 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 Cytogenet. 161(2):170-3. (PDF) 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) Dahia PL, Hao K, Rogus J, Colin C, Pujana MA, Ross K, Magoffin
D, Aronin N, Cascon A, Hayashida CY, Li
C, Toledo SP, Stiles CD; Familial Pheochromocytoma Consortium. LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M. (2005) Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis. PLoS Comput Biol 1(6): e65. (Abstract, R package) Dahia PL, Ross KN, Wright ME, Hayashida CY, Santagata S, Barontini M, Kung AL, Sanso G, Powers JF, Tischler AS, Hodin R, Heitritter S, Moore F, Dluhy R, Sosa JA, Ocal IT, Benn DE, Marsh DJ, Robinson BG, Schneider K, Garber J, Arum SM, Korbonits M, Grossman A, Pigny P, Toledo SP, Nosé V, Li C, Stiles CD. (2005) A HIF1α Regulatory Loop Links Hypoxia and Mitochondrial Signals in Pheochromocytomas. PLoS Genet. 1(1): e8. (Journal) 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. (Journal) 2004 (Top) Lin M, Wei LJ, Sellers WR, Lieberfarb M,
Wong WH*, Li C*. (2004) dChipSNP: Significance Curve and
Clustering of SNP-Array-Based Loss-of-Heterozygosity Data. Bioinformatics.
20: 1233-1240. (PubMed,
PDF, Journal,
Data and Software,
dChip usage)
Zhao X, Li C, Paez JG, Chin K, Jänne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M. (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, PDF, 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, PDF) Wang ZC, Lin M, Wei LJ, Li C, Miron A, Lodeiro G, Harris L, Ramaswamy S, Tanenbaum DM, Meyerson M, Iglehart JD, Richardson A. (2004) Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers. Cancer Research. 64(1): 64-71. (Abstract, PDF, Data) Bachoo RM†, Kim RS†, Ligon KL, Maher EA, Brennan C, Billings N, Chan S, Li C, Rowitch DH, Wong WH, DePinho RA. (2004) Molecular diversity of astrocytes with implications for neurological disorders. Proc. Natl. Acad. Sci. 101(22):8384-9. (†Joint first authors, Abstract, PDF) 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) Hao K, Li C,
Rosenow C, Wong WH. Detect and adjust for population stratification in
population-based association study using genomic control markers: an
application of Affymetrix Genechip Human Mapping 10K array. Eur J Hum Genet.
2004;12:1001-1006. (Abstract,
PDF,
Highlight)
Hao K, Li C, Rosenow C, Wong WH. (2004) Estimation of Genotype Error Rate Using Samples with Pedigree Information -- An application on GeneChip Mapping 10K array. Genomics. 84: 623-630. (Abstract, PDF) 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) Willis DJ, Kalish JA, Li C, Deutsch ER, Contreras MA, LoGerfo FW, Quist WC. (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. (PDF) 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, PDF, Software) Han H, Giles CL, Zha H, Li C, Tsioutsiouliklis K (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) Shammas MA, Koley H, Beer DG, Li
C, Goyal RK, Munshi NC. Growth arrest, apoptosis, and telomere shortening
of Barrett's-associated adenocarcinoma cells by a telomerase inhibitor. Gastroenterology.
2004; 126(5):1337-46. (PubMed) 2003 (Top) Zhong S, Li C*, Wong WH*. ChipInfo: Software for Extracting Gene Annotation and Gene Ontology Information for Microarray Analysis. Nucleic Acids Research. 2003; 31:3483-3486. (PubMed, PDF, Journal, Software, dChip usage; *Joint corresponding authors) Li
C and Wong WH (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. (PDF,
Book site) Li C, Tseng GC and Wong WH (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) Lieberfarb ME†, Lin M†, Lechpammer M, Li
C, Tanenbaum DM, Febbo PG, Wright RL, Shim J, Kantoff PW, Loda M,
Meyerson M, Sellers WR. 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. (Journal) Davies FE, Dring AM, Li C, Rawstron AC, Shammas MA, O'Connor SM, Fenton JA, Hideshima T, Chauhan D, Tai IT, Robinson E, Auclair D, Rees K, Gonzalez D, Ashcroft AJ, Dasgupta R, Mitsiades C, Mitsiades N, Chen LB, Wong WH, Munshi NC, Morgan GJ, Anderson KC. Insights into the multistep transformation of MGUS to myeloma using microarray expression analysis. Blood. 2003; 102(13):4504-11. (PubMed, PDF) Schoenberg FP, Ferguson T, and Li C. (2003). Inverting Dirichlet tessellations. The
Computer Journal 46(1), 76-83. (Abstract,
PDF, C code) 2001 (Top) Li C and Wong WH (2001a) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl. Acad. Sci. Vol. 98, 31-36. (PubMed, PDF, Journal) Li C and Wong WH (2001b) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application, Genome Biology 2(8): research0032.1-0032.11 (PubMed, PDF) 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, PDF, dChip functions: 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, PDF, Supplement, Data) Schadt EE, Li C, Ellis B and
Wong WH (2001) Feature extraction and normalization algorithms for
high-density oligonucleotide gene expression array data. Journal of
Cellular Biochemistry. Supplement 37, 120-125. (Abstract,
PDF) 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. (PDF) 2000 (Top) |
