collins@cc.ucsf.edu
(415) 502-7065 (voice)
(415) 476-8218 (fax)

Box 0808, UCSF; San Francisco, CA 94143-0808

additional websites:

Collins Lab Website

Western New England College, Springfield, MA, B.S., 1982, Biology
San Francisco State Univ., San Francisco, CA, Certificate, 1985, Genetic Engineering
Univ. of British Columbia, Vancouver, Canada, Ph.D., 1993, Genetics
Univ. of California San Francisco, CA, Postdoc, 1993, Tumor Genetics

Pinkel, D., Landegent, J., Collins, C., Fuscoe, J., Segraves, R., Lucas, J., and Gray, J. (1988). Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of Trisomy 21 and translocations of chromosome 4. Proc. Natl. Acad. Sci. 85, 9138-9142.

Theilmann, J., Kanani, S., Shiang, R., Robbins, C., Quarrell, O., Huggins, M., Hedrick, A., Weber, B., Collins, C., Buetow, K., Murray, J., Hayden, M. (1989). Non random association between alleles detected by D4S95 and the Huntington disease gene. J. Med. Genet. 26: 676-681.

Fuscoe, J., Collins C., Pinkel, D., and Gray, J. (1989). An efficient method for selecting unique-sequence clones from DNA libraries and its application to fluorescent staining of human chromosome 21 using in situ hybridization. Genomics. 5, 100-109.

Fuscoe, J., McNinch, J., Collins, C., van Dekken, H., and Van Dilla, M. (1989). Human chromosome-specific DNA libraries: Construction and Purity Analysis. Cytogenet. Cell Genet., 50, 211-215.

Weber, B., Collins, C., Robbins, C., Magenis R., Delaney, A., Gray, J., and Hayden M. (1990). Characterization and organization of DNA sequences adjacent to the human telomere associated repeat (TTAGGG)n. Nucl. Acids Res., 18, 3353-3361.

Adam, S., Theilmann, J., Buetow, K., Hedrick, A., Collins, C., Weber, B., Huggins, M., and Hayden, M. (1990). Linkage Disequilibrium and Modification of Risk For Huntington Disease. Am. J. Hum. Gen. 48:595-603.

Weber, B., Hedrick, A., Andrew, S., Riess, O., Collins, C., Kowbel, D., and Hayden, M. (1991). Isolation and characterization of new highly polymorphic DNA markers from the Huntington disease region. Am. J. Hum. Gen. 50: 382-393.

Weber, B., Collins, C., Kowbel, D., Riess, O., and Hayden, M. (1991). Identification of multiple CpG islands and associated conserved sequences in a candidate region for the Huntington disease gene. Genomics 11, 1113-1124.

Collins, C., Kuo, W., Seagraves, R., Pinkel, D., Fuscoe, J., and Gray, J. (1991). Construction and characterization of human chromosome-specific plasmid libraries enriched in sequences from single human chromosomes. Genomics 11, 997-1006.

Riess, O., Noerremoelle, A., Collins, C., Mah, D., Weber, B., and Hayden, M. (1992). Exclusion of DNA changes in the beta subunit of the cGMP phosphodiesterase (PDEB) gene as the cause for Huntington disease. Nature (Genetics) 1, 104-108.

Weber B., Riess, O., Wolff, G., Andrew, S., Collins, C., Graham, R., Theilmann, J., and Hayden, M. (1992). Delineation of a 50 kilobase DNA segment containing the recombination site in a sporadic case of Huntington's disease. Nature (Genetics) 2, 216-222.

Collins, C., Hutchinson, G., Kowbel, D., Riess, O., Weber, B., and Hayden, M. (1992). The human b-subunit of rod photoreceptor cGMP phosphodiesterase: complete retinal cDNA sequence and evidence for expression in brain. Genomics 13, 1113-1124.

Collins, C., Schappert, K., and Hayden, M. (1992). The genomic organization of a novel regulatory myosin light chain that maps to chromosome 4p16.3 and shows different patterns of expression between primates. Human Molecular Genetics 1, 727-733.

Collins, C., Norremolle, A., Michaelis, E., Duff, C., Worton, R., and Hayden, M. (1993). Mapping of human NMDA receptor subunit (NMDAR1) and the proposed NMDA receptor glutamate-binding subunit (NMDARA1) to chromosomes 9q34.3 and 8 respectively. Genomics 17, 237-239.

Tanner, M., Tikkonen, M., Kallioniemi, A., Collins, C., Stokke, T., Karhu, R., Kowbel, D., Shadravan, F., Hintz, M., Kuo, W., Waldman, F., Isola, J., Gray, J., and Kallioniemi, O. (1994). Increased copy number at 20q13 in breast cancer: defining the critical region and exclusion of candidate genes. Cancer Res., 54: 4257-4260.

Weier, H., Rhein, A., Shadravan, F., Collins, C., Polikoff, D. (1995). Rapid physical mapping of the human trk proto-oncogene (NTRK1) gene to human chromosome 1q21-22 by P1 clone selection, fluorescence in situ hybridization (FISH) and computer-assisted microscopy. Genomics 26: 390-393.

Stokke, T., Collins, C., Kuo, W., Kowbel, D., Shadravan, F., Tanner, M., Kallioniemi, A., Kallioniemi, O., Pinkel, D., Deaven, L., and Gray, J. (1995). A physical map of chromosome 20 established using fluorescence in situ hybridization and digital image analysis. Genomics 26:134-137.

Tanner, M., Tirkkonen, M., Kallioniemi, A., Holli, K., Collins, C., Gray, J., Kallioniemi, O., and Isola, J. (1995). Amplification of chromosomal region 20q13 in invasive breast cancer: prognostic implications. Clinical Cancer Research 1:1455-1461.

Deng, G., Yu, M., Chen, L., Moore, D., Kurisu, W., Kallioniemi, A., Waldman, F., Collins, C., Smith H. (1996). Amplifications of oncogene erbB-2 and chromosome 20q in breast cancer determined by differentially competitive polymerase chain reaction. Breast Cancer Res Treat 40:271-281.

Tanner, M., Tirkkonen, M., Kallioniemi, A., Isola, J., Kuukasjarvai, T., Collins, C., Kowbel, D., Guan, X., Trent, J., Gray, J., Meltzer, P., and Kallioniemi, O. (1996). Independent amplification and frequent co-amplification of three non-syntentic regions of the long arm of chromosome 20 in human breast cancer. Cancer Research 56: 3441-3445.

Brzoska, P., Chen, H., Levin, N., Kuo, W., Collins, C., Fu, K., Gray, J., and Christman, M. (1997). Cloning, mapping, and in vivo localization of a human member of the PKCI-1 protein family (PRKCNH1. Genomics 36:151-156.

Nehlin, J., Hara, E., Kuo, W., Collins, C., Campisi, J. (1997). Genomic Organization, Sequence and Chromosomal Localization of the Human Helix-Loop-Helix Id1 Gene. BBRC 231, 628-634.

Collins, C., Nehlin, J., Stubbs, J., Kowbel, D., Kuo, W., and Parry, G. (1997). Mapping of a newly discovered human gene homologous to the apoptosis associated-murine mammary protein, MFG-E8, to chromosome 15q25. Genomics 39, 117-118.

Xie, J., Quinn, A., Zhang, X., Bare, J., Rothman, A., Collins, C., Cutone, S., Rutter, M., McCormick, M., Epstein, E. (1997). Physical mapping of the 5 Mb D9S196-D9S180 interval harboring the basal cell nevus syndrome gene and localization of six genes in this region. Genes Chromosomes Cancer 18:305-309.

Hwang, S., Kuo, W., Cochran, J., Guzman, R., Nandi, S. and Collins C. (1997). Assignment to 1q21 of the human homolog of the murine mammary transforming gene (HMAT1) associated with tumorigenesis. Genomics 42, 540-542.

Li, L., Krantz, I., Deng, Y., Genin, A., Banta, A., Collins, C., Qi, M., Trask, B., Kuo, W., Cochran, J., Costa, T., Pierpont, M., Rand, E., Piccoli, D., Hood, L., Spinner, N. (1997). Alagille syndrome is caused by mutations in human Jagged1, which encodes a ligand for Notch1. Nature Genet. 16: 243-251.

Chang, C., Scott, G., Kuo, W., Xiong, X., Suzdaltseva, Y., Park, J., Sayre, P., Erny, K., Collins C., Gray, J., Benz, C. (1997). ESX: a structurally unique Ets overexpressed early during human breast tumorigenesis. Oncogene 14:1617-1622.

Trask, B., Friedman, C., Martin-Gallardo, A., Rowen, L., Akinbami, C., Blankenship, J., Collins, C., Giorgi, D., Iadonato, S., Johnson, F., Kuo, W., Massa, H., Morrish, T., Naylor, S., Nguyen, O., Rouquier, S., Smith T., Wong, D., Youngblom, J., van den Engh, G. (1998). Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum. Molec. Genet. 7, 13-26.

Hiraguri, K., Godfrey, T., Nakamura, H., Graff, J., Collins, C., Shayesteh, L., Doggett, N., Johnson, K., Wheelock, M., Herman, J., Baylin, S., Pinkel, D., Gray, J. (1998). Mechanisms of inactivatin of E-Cadherin (CDH1) in breast cancer cell lines. Cancer Res. 58, 1972-1977.

Collins, C., Rommens, J., Kowbel, D., Godfrey, T., Tanner, M., Hwang., S., Polikoff, D., Nonet, G., Cochran, J., Myambo, K., Jay, K., Froula, J., Cloutier, T., Kuo, W.,Yaswen, P., Dairkee, S., Giovanola, J., Hutchinson, G., Isola, J., Kallioniemi., O., Palazzolo, M., Martin, C., Ericsson, C., Pinkel, D., Albertson, D., Li, W., and Gray, J. (1998). Positional Cloning of ZABC1 and AIBC1: Genes Amplified at 20q13.2 and Overexpressed In Breast Carcinoma. Proc. Natl. Acad. Sci. 8703-8708.

Ratziu, V., Wong, L., Dang, Q., Lalazar, A., Shaulian, E., Jensen, S., Collins, C. and Friedman, S. (1998). Zf9, a Novel Kruppel-like Transcription Factor, Regulates Gene Activation in Hepatic Wound Healing. Proc. Natl. Acad. Sci. 95, 9500-9505.

Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W., Chen, C., Zhai, Y., Dairkee, S., Lejung, B., Gray, J., and Albertson, D. (1998). Quantitative high resolution analysis of DNA copy number variation in breast cancer using comparative genomic hybridization to DNA microarrays. Nature Genetics 20:207-211.

Mears, A., Jordan, T., Mirzayans, F., Dubois, S., Kume, T., Parlee, M., Ritch, R. Koops, B., Kuo, W., Collins, C., Marshall, J., Gould, D., Carlsson, P., Pearce,W., Morissette, J., Battacharya,S., Hogan, B., Raymond, V., and Walter, M. (1998). Mutations of the forkhead/winged helix gene, FREAC3, in patients with glaucoma and anterior segment dysgenesis. American Journal of Human Genetics 63, 1316-1328.

Chen, L., Manjeshwar, S., Lu, Y., Moore, D., Ljung, B., Kuo, W., Dairkee, S., Wernick, M., Collins, C., Smith, H. (1998). The human homologue for the Caenorhabditis elegans cul-4 gene is amplified and overexpressed in primary breast cancers. Cancer Res. 58:3677-3683.

Korn, M., Yasutake, T., Kuo, W., Warren, R., Collins, C., Tomita, M., Gray, J., and Waldman, F. (1999). Chromosome Arm 20q Gains and Other Genomic Alterations in Colorectal Cancer Metastatic to Liver, as Analyzed by Comparative Genomic Hybridization and Fluorescence In Situ Hybridization. Genes Chromosomes & Cancer 25, 82-90.

Shayesteh, L., Yiling, L., Kuo, W., Collins, C., Yang-Feng, T., Pinkel, D., Mills, G., and Gray, J. (1999). PIK3CA is implicated as an oncogene in ovarian cancer. Nature Genetics 21, 99-102.

Gray, J., and Collins C. (2000). Genome changes and gene expression in human solid tumors. Carcinogenesis 21, 443-452.

Albertson, D., Ylstra, B., Segraves, R., Collins, C., Dairkee, S., Kowbel, D., Kuo, W., Gray, J., and Pinkel, D. (2000). Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nature Genetics 25, 144-146.

Nonet, G., Stampfer, M., Chin, K., Gray, J., Collins, C., and Yaswen, P. (2001). The ZNF217 Gene Amplified In Breast Cancers Promotes Immortalization Of Human Mammary Epithelial Cells. Cancer Research, 61, 1250-1254.

Collins, C., Volik, S., Kowbel, D., Ginzinger, D., Ylstra, B., Cloutier, T., Hawkins, T., Predki, P., Martin, C., Wernick, M., Kuo, W., and Gray, J. (2001). Comprehensive Genome Sequence Analysis of a Breast Cancer Amplicon. Genome Research 11, 1034-1042.

Mannino J., Wernick M., Braquet R., Collins C., Brown K. (2001). Evidence for alternative splicing within the mRNA transcript of the DNA damage-response kinase ATR. Gene 272, 35-43.

Thakur M., Wernick M., Collins C., Limoli C., Cleaver J. (2001). Genetic and functional analysis of polymerase eta in protection against UV sensitivity, apoptosis and chromosome instability. Genes, Chromosomes and Cancer 32, 222-235.

Hodgson G., Hager J., Wernick M., Collins C., Hanahan D., Gray J., (2001). Highly sensitive detection of single copy changes in murine tumor genomes using DNA microarrays. Nature Genetics 29, 459-464.

Anad N., Murthy S., Wernick M., Porter L., Cukier H., Collins C., Gray J., Lee J. (2002). Protein elongation factor eEf-12 involved in Ovarian Cancer. Nature Genetics. In press.

Zheng, L., Meng, Z., Chandrasekharan, R., Kuo, W., Collins, C., Gray., J., and Dairkee, S. (2002). Biallelic inactivation of the thyroid hormone receptor B1 gene in early stage breast cancer. Cancer Research 62, 1939-43.

Li, Z., Meng, Z., Chandrasekaran, R., Kuo, W., Collins, C., Gray J., Dairkee S. (2002). Biallelic inactivation of the thyroid hormone receptor beta1 gene in early stage breast cancer. Cancer Res. 62:1939-43.

Anand, N., Murthy, S., Amann, G., Wernick, M., Porter, L., Cukier, I., Collins, C., Gray J., Diebold, J., Demetrick, D., Lee, J. (2002). Protein elongation factor EEF1A2 is a putative oncogene in ovarian cancer. Nat Genet. 31: 301-5.

Zardo, G., Tiirikainen, M., Hong, C., Misra, A., Feuerstein, B., Volik, S., Collins, C., Lamborn, K., Bollen, A., Pinkel, D., Albertson, D., Costello, J. (2002). Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet. 32: 453-8.

Paris, P., Albertson, D., Alers, J., Andaya, A., Carroll, P., Fridlyand, J., Jain, A., Kamkar, S., Kowbel, D., Krijtenburg, P., Pinkel, D., Schröder, F., Vissers, K., Watson, V., Wildhagen, M., Collins, C., and van Dekken, H. (2003). High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. American Journal of Pathology 162: 763-770.

Volik, S., Zhao, S., Chin, K., Brebner, J., Herndon, D., Tao, Q., Kowbel, K., Huang,G., Lapuk, A., Kuo, W, Magrane, G., de Jong, P., Gray, J., and Collins, C. (2003). End Sequence Profiling: sequence-based analysis of aberrant genomes. PNAS 100: 7696-7701.

Raphael, B., Volik., S., Collins, C., and Pevzner, P. (2003). Reconstruction of the genomic architecture of a breast cancer tumor. Bioiformatics Suppl. II, 162-171.

Cleaver, J., Collins, C., Ellis, J., Volik, S. (2003). Genome sequence and splice site analysis of low fidelity DNA polymerases H& I involved in replication of damaged DNA. Genomics 82: 561-570.

Albertson, D., Collins C, McCormick, F., Gray, J. (2003). Chromosome aberrations in solid tumors. Nat Genet. 34: 369-76.

Beardsley, D., Kowbel, D., Lataxes, T., Mannino, J., Xin, H., Kim, W., Collins, C., Brown, K. (2003). Characterization of the novel amplified in breast cancer-1 (NABC1) gene product. Exp Cell Res. 290: 402-13.

van Dekken, H., Paris, P., Albertson, D., Alers, J., Andaya, A., Kowbel, D., van der Kwast, T., Pinkel, D., SchrsØder, F., Vissers, K., Wildhagen, M., and Collins, C. (2004) Evaluation of Genetic Patterns in Different Tumor Areas of Intermediate Grade Prostatic Adenocarcinomas by High-Resolution Genomic Array Analysis. Genes Chromosomes and Cancer, 39: 249-256.

Watson, J., Doggett, N., Albertson D., Andaya, A., Chinnaiyan, A., van Dekken, H., Ginzinger, D., Haqq, C., James, K., Kamkar, S., Kowbel, D., Paris, P., Pinkel, D., Schmitt, L., Simko, J., Volik, S., Weinberg, V., Collins, C. (2004). Identification of candidate tumor suppressor genes in prostate cancer through integration of high resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data. Oncogene 23: 3487-3494.

Paris, P., Andaya, A., Fridlyand, J., Jain, A., Weinberg, V., Kowbel, D., Brebner, J., Simko, J., Volik, S., Watson, J., Albertson, D., Pinkel, D., Febbo, P., Chinnayian, A., Carroll, P., Rubin, M., van Dekken, H. and Collins, C. (2004). Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Human Molecular Genetics. 13: 1303-1313.

Rubin, M., Varambally, S., Beroukhim, R., Tomlins, S., Rhodes, D., Paris, P., Hofer, M., Storz-Shweizer, M., Kuefer, R., Fletcher, J., Byrne, J., Collins, C, Sellers, W., Chinnayian, A., (2004). Overexpression, Amplification and Androgen-regulation of TPD52. Cancer Research. 64: 3814-3822.

Lapuk A, Volik S, Vincent R, Chin K, Kuo WL, de Jong P, Collins C, Gray JW. (2004) Computational BAC clone contig assembly for comprehensive genome analysis. Genes Chromosomes Cancer, 40:66-71.

Macoska, J., Paris, P., Collins, C., Beheshti, B., Chaib, H., Kant, R. Begley, L., MacDonald, J., and Squires, J. (2004). Evolution of 8p Loss in Transformed Human Prostate Epithelial Cells. Cancer Genetics and Cytogenetics. Cancer Genetics and Cytogenetics. Cancer Genetics and Cytogenetics 154:36-43.

McAlhany, S., Ayala, G., Frolov, A., Ressler, S., Wheeler, T., Watson, J., Collins, C., Rowley, D. (2004). Decreased Stromal Expression and Increased Epithelial Expression of WFDC1/ps20 in Prostate Cancer is Associated with Reduced Recurrence-free Survival. The Prostate 61:182-191..

Watson JEV, Kamkar S, James K, Kowbel D, Andaya A, Paris PL, Simko JP, Carroll PR, McAlhany SJ, Rowley DR, Collins C. (2004). Molecular Analysis of WFDC1/ps20 gene in prostate cancer. The Prostate. 61:192-199.

Paris PL, Weinberg V, Simko J, Andaya A, Albo G, Rubin MA, Carroll PR and Collins C. (2005) Preliminary Evaluation of Prostate Cancer Metastatic Risk Biomarkers. International Journal of Biomarkers. In Press.

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