Items where Community is "Hicks lab"

Paper

Anaparthy, N., Ho, Y. J., Martelotto, L., Hammell, M., Hicks, J. (January 2019) Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (10). ISSN 2157-1422

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (July 2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res, 28 (9). pp. 1353-1363. ISSN 1088-9051

Wolff, R. A., Wang-Gillam, A., Alvarez, H., Tiriac, H., Engle, D., Hou, S., Groff, A. F., Lucas, A. S., Bernard, V., Allenson, K., Castillo, J., Kim, D., Mulu, F., Huang, J., Stephens, B., Wistuba, I. I., Katz, M., Varadhachary, G., Park, Y., Hicks, J., Chinnaiyan, A., Scampavia, L., Spicer, T., Gerhardinger, C., Maitra, A., Tuveson, D., Rinn, J., Lizee, G., Yee, C., Levine, A. J. (March 2018) Dynamic changes during the treatment of pancreatic cancer. Oncotarget, 9 (19). pp. 14764-14790. ISSN 1949-2553

Rodriguez-Lee, M., Kolatkar, A., McCormick, M., Dago, A. D., Kendall, J., Carlsson, N. A., Bethel, K., Greenspan, E. J., Hwang, S. E., Waitman, K. R., Nieva, J. J., Hicks, J., Kuhn, P. (February 2018) Effect of Blood Collection Tube Type and Time to Processing on the Enumeration and High-Content Characterization of Circulating Tumor Cells Using the High-Definition Single-Cell Assay. Arch Pathol Lab Med, 142 (2). pp. 198-207. ISSN 0003-9985

Baslan, T., Hicks, J. (August 2017) Unravelling biology and shifting paradigms in cancer with single-cell sequencing. Nat Rev Cancer, 17 (9). pp. 557-569. ISSN 1474-175x

Martelotto, L. G., Baslan, T., Kendall, J., Geyer, F. C., Burke, K. A., Spraggon, L., Piscuoglio, S., Chadalavada, K., Nanjangud, G., Ng, C. K., Moody, P., D'Italia, S., Rodgers, L., Cox, H., da Cruz Paula, A., Stepansky, A., Schizas, M., Wen, H. Y., King, T. A., Norton, L., Weigelt, B., Hicks, J. B., Reis-Filho, J. S. (March 2017) Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nat Med, 23 (3). pp. 376-385. ISSN 1546-170X (Electronic)1078-8956 (Linking)

Pal, D., Pertot, A., Shirole, N. H., Yao, Z., Anaparthy, N., Garvin, T., Cox, H., Chang, K., Rollins, F., Kendall, J., Edwards, L., Singh, V. A., Stone, G. C., Schatz, M. C., Hicks, J., Hannon, G., Sordella, R. (January 2017) TGF-beta reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. Elife, 6. ISSN 2050-084X (Electronic)2050-084X (Linking)

Piscuoglio, S., Ng, C. K., Murray, M. P., Guerini-Rocco, E., Martelotto, L. G., Geyer, F. C., Bidard, F. C., Berman, S., Fusco, N., Sakr, R. A., Eberle, C., De Mattos-Arruda, L., Macedo, G. S., Akram, M., Baslan, T., Hicks, J., King, T. A., Brogi, E., Norton, L., Weigelt, B., Hudis, C. A., Reis-Filho, J. S. (March 2016) The Genomic Landscape of Male Breast Cancers. Clin Cancer Res, 22 (16). pp. 4045-56. ISSN 1078-0432 (Electronic)1078-0432 (Linking)

Martelotto, L. G., Baslan, T., Kendall, J., Rodgers, L., Cox, H., King, T. A., Weigelt, B., Hicks, J., Reis, J. S. (February 2016) Single cell sequencing analysis of formalin-fixed paraffin-embedded ductal carcinomas in situ and invasive breast cancers reveals clonal selection in the progression from in situ to invasive disease. Cancer Research, 76 (Supple). Abstract P2-05. ISSN 0008-5472

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (November 2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking) (Public Dataset)

Velasco, C. R., Stepansky, A., Dago, A., Carlson, A., Kolatkar, A., Kendall, J., Hicks, J., Kuhn, P. (August 2015) Single-cell molecular profiling of fluid biopsies of epithelial ovarian cancer. Clinical Cancer Research, 21. ISSN 1078-0432

Somlo, George, Barlow, William, Moore, Halle, Gralow, Julie, Schott, Anne, Hayes, Daniel, Kuhn, Peter, Hicks, James, Lew, Danika, Tripathy, Debu, Hortobagyl, Gabriel (May 2015) Fulvestrant alone versus fulvestrant and everolimus versus fulvestrant, everolimus and anastrozole: A Phase III randomized, placebo-controlled trial in postmenopausal patients with hormone-receptor-positive stage IV breast cancer: SWOG-Clinical Trials Ini. Cancer Research, 75 (9 Supp). OT2-1. ISSN 1538-7445

Baslan, T., Kendall, J., Ward, B., Cox, H., Leotta, A., Rodgers, L., Riggs, M., D'Italia, S., Sun, G., Yong, M., Miskimen, K., Gilmore, H., Saborowski, M., Dimitrova, N., Krasnitz, A., Harris, L., Wigler, M., Hicks, J. (May 2015) Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Research, 25 (5). pp. 714-724. ISSN 1088-9051

Piscuoglio, S., Murray, M., Ng, C. K. Y., Rocco, E. G., Martelotto, L. G., Bidard, F. C., Eberle, C. A., Fusco, N., Sakr, R. A., De Mattos-Arruda, L., Lim, R., Baslan, T., Hicks, J., King, T. A., Brogi, E., Norton, L., Weigelt, B., Hudis, C. A., Reis, J. S. (May 2015) The genomic landscape of male breast cancers. Cancer Research, 75 (9 Supp). ISSN 0008-5472

Rye, I. H., Lundin, P., Maner, S., Fjelldal, R., Naume, B., Wigler, M., Hicks, J., Borresen-Dale, A. L., Zetterberg, A., Russnes, H. G. (April 2015) Quantitative multigene FISH on breast carcinomas identifies der(1;16)(q10;p10) as an early event in luminal A tumors. Genes, Chromosomes & Cancer, 54 (4). pp. 235-48. ISSN 1045-2257

Ruiz, C., Li, J., Luttgen, M. S., Kolatkar, A., Kendall, J. T., Flores, E., Topp, Z., Samlowski, W. E., McClay, E., Bethel, K., Ferrone, S., Hicks, J., Kuhn, P. (February 2015) Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology, 12 (1). 016008. ISSN 1478-3967

Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S, Hicks, James, Wigler, Michael, Schatz, Michael (2015) Interactive analysis and quality assessment of single-cell copy-number variations. Nature Methods, 12. pp. 1058-1060. ISSN 15487091 (ISSN)

Pratt, E. D., Stepansky, A., Hicks, J., Kirby, B. J. (November 2014) Single-cell copy number analysis of prostate cancer cells captured with geometrically enhanced differential immunocapture microdevices. Analytical Chemistry, 86 (22). pp. 11013-7. ISSN 0003-2700

Dago, A. E., Stepansky, A., Carlsson, A., Luttgen, M., Kendall, J., Baslan, T., Kolatkar, A., Wigler, M., Bethel, K., Gross, M. E., Hicks, J., Kuhn, P. (August 2014) Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PLoS One, 9 (8). e101777. ISSN 1932-6203

Baslan, T., Hicks, J. (July 2014) Single cell sequencing approaches for complex biological systems. Curr Opin Genet Dev, 26c. pp. 59-65. ISSN 0959-437x

Miething, C., Scuoppo, C., Bosbach, B., Appelmann, I., Nakitandwe, J., Ma, J., Wu, G., Lintault, L., Auer, M., Premsrirut, P. K., Teruya-Feldstein, J., Hicks, J., Benveniste, H., Speicher, M. R., Downing, J. R., Lowe, S. W. (May 2014) PTEN action in leukaemia dictated by the tissue microenvironment. Nature, 510 (7505). p. 402. ISSN 0028-0836

Crockford, A., Jamal-Hanjani, M., Hicks, J., Swanton, C. (January 2014) Implications of intratumour heterogeneity for treatment stratification. Journal of Pathology, 232 (2). pp. 264-273. ISSN 00223417 (ISSN)

Cowell, Catherine F., Weigelt, Britta, Sakr, Rita A., Ng, Charlotte K. Y., Hicks, James, King, Tari A., Reis-Filho, Jorge S. (July 2013) Progression from ductal carcinoma in situ to invasive breast cancer: Revisited. Molecular Oncology. ISSN 1574-7891

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R. (June 2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research, 23 (10). pp. 1651-1662. ISSN 10889051 (ISSN)

Kuhn, P., Dago, A. E., Stepansky, A., Carlsson, A., Felch, N., Luttgen, M., Kolatkar, A., Hicks, J., Gross, M. E. (April 2013) Sequential monitoring of single-cell copy number variation in metastatic prostate cancer. Cancer Research, 73 (8 (Sup). p. 4599. ISSN 0008-5472

Donnenberg, A. D., Hicks, J. B., Wigler, M., Donnenberg, V. S. (January 2013) The Cancer Stem Cell: Cell Type or Cell State? Cytometry Part A, 83A (SI 1). pp. 5-7. ISSN 1552-4922

Baslan, T., Kendall, J. T., Rodgers, L., Cox, H., Riggs, M., Stepansky, A., Troge, J. E., Ravi, K., Esposito, D., Lakshmi, B., Wigler, M., Navin, N. E., Hicks, J. B. (May 2012) Genome-wide copy number analysis of single cells. Nat Protoc, 7 (6). pp. 1024-41. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., Zhang, J., Luo, W. J., Hicks, J., Zender, L., Wang, X. W., Powers, S., Wigler, M., Lowe, S. W. (May 2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109 (21). pp. 8212-8217. ISSN 0027-8424

Mazurek, A., Luo, W., Krasnitz, A., Hicks, J., Powers, R. S., Stillman, B. (2012) DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells. Cancer Discovery, 2 (9). pp. 812-825. ISSN 21598274 (ISSN)

Tang, M. H., Varadan, V., Kamalakaran, S., Zhang, M. Q., Dimitrova, N., Hicks, J. (2012) Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Frontiers in Oncology, 2. p. 197. ISSN 2234-943X (Electronic)2234-943X (Linking)

Tafe, L. J., Janjigian, Y. Y., Zaidinski, M., Hedvat, C. V., Hameed, M. R., Tang, L. H., Hicks, J. B., Shah, M. A., Barbashina, V. (November 2011) Human epidermal growth factor receptor 2 testing in gastroesophageal cancer: Correlation between immunohistochemistry and fluorescence in situ hybridization. Archives of Pathology and Laboratory Medicine, 135 (11). pp. 1460-1465. ISSN 00039985 (ISSN)

Shakya, R., Reid, L. J., Reczek, C. R., Cole, F., Egli, D., Lin, C. S., DeRooij, D. G., Hirsch, S., Ravi, K., Hicks, J. B., Szabolcs, M., Jasin, M., Baer, R., Ludwig, T. (October 2011) BRCA1 tumor suppression depends on BRCT phosphoprotein binding, but not its E3 ligase activity. Science, 334 (6055). pp. 525-528. ISSN 00368075 (ISSN)

Russnes, H. G., Navin, N., Hicks, J. B., Borresen-Dale, A. L. (October 2011) Insight into the heterogeneity of breast cancer through next-generation sequencing. Journal of Clinical Investigation, 121 (10). pp. 3810-3818. ISSN 0021-9738

Navin, N. E., Hicks, J. B. (June 2011) Corrigendum to "Tracing the tumor lineage" [Mol. Oncol. 4 (2010) 267-283]. Molecular Oncology, 5 (3). p. 302. ISSN 1574-7891

Navin, N., Hicks, J. B. (May 2011) Future medical applications of single-cell sequencing in cancer. Genome Medicine, 3 (5). ISSN 1756994X (ISSN)

Png, K. J., Yoshida, M., Zhang, X. H. F., Shu, W., Lee, H., Rimner, A., Chan, T. A., Comen, E., Andrade, V. P., Kim, S. W., King, T. A., Hudis, C. A., Norton, L., Hicks, J. B., Massagué, J., Tavazoie, S. F. (February 2011) MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes and Development, 25 (3). pp. 226-231. ISSN 08909369

Kamalakaran, S., Varadan, V., Giercksky Russnes, H. E., Levy, D., Kendall, J. T., Janevski, A., Riggs, M., Banerjee, N., Synnestvedt, M., Schlichting, E., Kåresen, R., Shama Prasada, K., Rotti, H., Rao, R., Rao, L., Eric Tang, M. H., Satyamoorthy, K., Lucito, R., Wigler, M. H., Dimitrova, N., Naume, B., Borresen-Dale, A. L., Hicks, J. B. (February 2011) DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Molecular Oncology, 5 (1). pp. 77-92.

Navin, N. E., Kendall, J. T., Troge, J. E., Andrews, P., Rodgers,  L., McIndoo, J., Cook, K., Stepansky,  A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. B., Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472 (7341). pp. 90-94. ISSN 00280836 (ISSN)

Tang, M. H. E., Varadan, V., Kamalakaran, S., Zhang, M. Q., Dimitrova, N., Hicks, J. (2011) A method for finding novel associations between genome-wide copy number and dna methylation patterns. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). pp. 78-82.

Russnes, H. G., Vollan, H. K. M., Lingjærde, O. C., Krasnitz, A., Lundin, P., Naume, B., Sørlie, T., Borgen, E., Rye, I. H., Langerød, A., Chin, S. F., Teschendorff, A. E., Stephens, P. J., Månér, S., Schlichting, E., Baumbusch, L. O., Kåresen, R., Stratton, M. P., Wigler, M. H., Caldas, C., Zetterberg, A., Hicks, J. B., Børresen-Dale, A. L. (June 2010) Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Science Translational Medicine, 2 (38).

Hicks, J. B., Navin, N. E., Kendall, J. T., Levy, D., Wigler, M. H. (May 2010) Tracing Tumor Lineage and Progression through Genomic Copy Number Profiling at the Single Cell Level. Annals of Oncology, 21 (S4). iv49. ISSN 0923-7534

Floer, M., Wang, X., Prabhu, V., Berrozpe, G., Narayan, S., Spagna, D., Alvarez, D., Kendall, J. T., Krasnitz, A., Stepansky,  A., Hicks, J. B., Bryant, G. O., Ptashne, M. (April 2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell, 141 (3). pp. 407-418.

Navin, N. E., Krasnitz, A., Rodgers, L., Cook, K., Meth, J. L., Kendall, J. T., Riggs, M., Eberling, Y., Troge, J. E., Grubor, V., Levy, D., Lundin, P., Månér, S., Zetterberg, A., Hicks, J. B., Wigler, M. H. (January 2010) Inferring tumor progression from genomic heterogeneity. Genome Research, 20 (1). pp. 68-80.

Harris, L. N., Parker, J., Broadwater, G., Schulz, V., Halligan, K., Geyda, K., Seidman, A., Berry, D., Winer, E., Hudis, C., Krasnitz, A., Hicks, J., Tuck, D. P., Perou, C. (December 2009) Genome-Wide Profiling of Archived Material from CALGB 9840 and 9342 for Paclitaxel (P) and Trastuzumab (T) Response Biomarkers Using Gene Expression and Copy Number Analysis. Cancer Research, 69 (24 (S3). 716S-717S. ISSN 0008-5472

Smith, A. D., Chung, W. Y., Hodges, E., Kendall, Jude T., Hannon, G. J., Hicks, J. B., Xuan, Z., Zhang, M. Q. (November 2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25 (21). pp. 2841-2842.

Bric, A., Miething, C., Bialucha, C. U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M. H., Hicks, J. B., McCombie, W. R., Hemann, M. T., Hannon, G. J., Powers, S., Lowe, S. W. (October 2009) Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell, 16 (4). pp. 324-35. ISSN 1535-6108

Hodges, E., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (September 2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

McArthur, H. L., Brogi, E., Patil, S., Wigler, M. H., Norton, L., Hicks, J. B., Hudis, C. A. (September 2009) High resolution microarray copy number analysis (array CGH) suggests that determination of HER2 amplification by FISH (FISH plus ) is inaccurate in human breast cancer specimens that are HER2 2+by immunohistochemistry (IHC2+). European Journal of Cancer Supplements, 7 (2). p. 88. ISSN 1359-6349

Kamalakaran, S., Kendall, J. T., Zhao, X., Tang, C., Khan, S., Ravi, K., Auletta, T., Riggs, M., Wang, Y., Helland, A., Naume, Bj., Dimitrova, N., Borresen-Dale, A.. L., Hicks, J. B., Lucito, R. (July 2009) Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation. Nucl. Acids Res., 37 (12). e89.

Hicks, J. B., McArthur, H., Tan, L. K., Patil, S., Wigler, M. H., Hudis, C., Norton, L. (May 2009) Topo2a and Her2 Co-Amplification Is Uncommon by High Resolution Representational Oligonucleotide Microarray Analysis (Roma) in Human Breast Cancer. Annals of Oncology, 20 (S2). ii22-23. ISSN 0923-7534

Russnes, H. G., Vollan, H. K. M., Sorlie, T., Krasnitz, A., Zetterberg, A., Naume, B., Borgen, E., Nesland, J. M., Wigler, M. H., Borresen-Dale, A. L., Hicks, J. B. (March 2009) Molecular subclassification of breast carcinomas based on aCGH reveals two major groups of tumors with common genomic, transcriptomic and clinicopathological characteristics. APMIS, 117 (3). pp. 238-239. ISSN 0903-4641

McArthur, H. L., Tan, L. K., Patil, S., Wigler, M. H., Hudis, C. A., Hicks, J. B., Norton, L. (January 2009) High resolution representational oligonucleotide microarray analysis (ROMA) suggests that TOPO2 and HER2 co-amplification is uncommon in human breast cancer. Cancer Res, 69 (2, Sup). 163S-163S. ISSN 0008-5472

Zender, L., Xue, W., Zuber, J., Semighini, C. P., Krasnitz, A., Ma, B., Zender, P., Kubicka, S., Luk, J. M., Schirmacher, P., McCombie, W. R., Wigler, M. H., Hicks, J. B., Hannon, G. J., Powers, S., Lowe, S. W. (November 2008) An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer. Cell, 135 (5). pp. 852-864. ISSN 0092-8674

Xiang, B., Chatti, K., Qiu, H., Lakshmi, B., Krasnitz, A., Hicks, J. B., Yu, M., Miller, W. T., Muthuswamy, S. K. (August 2008) Brk is coamplified with ErbB2 to promote proliferation in breast cancer. Proc Natl Acad Sci U S A, 105 (34). pp. 12463-8.

Baumbusch, L. O., Aaroe, J., Johansen, F. E., Hicks, J. B., Sun, H., Bruhn, L., Gunderson, K., Naume, B., Kristensen, V. N., Liestol, K., Borresen-Dale, A. L., Lingjaerde, O. C. (August 2008) Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics, 9. p. 379.

Russnes, H. G., Sorlie, T., Krasnitz, A., Zetterberg, A., Naume, B., Borgen, E., Nesland, J. M., Wigler, M. H., Borresen-Dale, A. L., Hicks, J. B. (July 2008) Molecular subclassification of breast carcinomas based on aCGH, gene expression, IHC and ploidy - relevance for clinical outcome. European Journal of Cancer Supplements, 6 (9). p. 9. ISSN 1359-6349

Haakensen, V. D., Helland, A., Holmen, M. M., Hicks, J. B., Børresen-Dale, A. L. (September 2007) No genomic changes in mammographically dense breast. European Journal of Cancer Supplements, 5 (4). p. 99. ISSN 1359-6349

Sebat, J., Lakshmi, B., Malhotra, D., Troge, J. E., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J. T., Leotta, A., Pai, D., Zhang, R., Lee, Y. H., Hicks, J. B., Spence, S. J., Lee, A. T., Puura, K., Lehtimaki, T., Ledbetter, D., Gregersen, P. K., Bregman, J., Sutcliffe, J. S., Jobanputra, V., Chung, W., Warburton, D., King, M. C., Skuse, D., Geschwind, D. H., Gilliam, T. C., Ye, K., Wigler, M. H. (April 2007) Strong Association of De Novo Copy Number Mutations with Autism. Science, 316 (5823). pp. 445-449.

Pelham, R. J., Rodgers, L., Hall, I. M., Lucito, R., Nguyen, K. C. Q., Navin, N. E., Hicks, J. B., Mu, D., Powers, S., Wigler, M. H., Botstein, D. (December 2006) Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A, 103 (52). pp. 19848-19853. ISSN 0027-8424

Hicks, J. B., Krasnitz, A., Lakshmi, B., Navin, N. E., Riggs, M., Leibu, E., Esposito, D., Alexander, J., Troge, J. E., Grubor, V., Yoon, S., Wigler, M. H., Ye, K., Borresen-Dale, A. L., Naume, B., Schlicting, E., Norton, L., Hagerstrom, T., Skoog, L., Auer, G., Månér, S., Lundin, P., Zetterberg, A. (December 2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Research, 16 (12). pp. 1465-79. ISSN 1088-9051

Navin, N. E., Grubor, V., Hicks, J. B., Leibu, E., Thomas, E., Troge, J., Riggs, M., Lundin, P., Månér, S., Sebat, J., Zetterberg, A., Wigler, M. H. (October 2006) PROBER: oligonucleotide FISH probe design software. Bioinformatics, 22 (19). pp. 2437-8. ISSN 1460-2059 (Electronic)

Hicks, J. B., Muthuswamy, L., Krasnitz, A., Navin, N. E., Riggs, M., Grubor, V., Esposito, D., Alexander, J., Troge, J. E., Wigler, M. H., Maner, S., Lundin, P., Zetterberg, A. (2005) High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol, 70. pp. 51-63. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Sebat, J., Lakshmi, B., Troge, J. E., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M., Navin, N. E., Lucito, R., Healy, J., Hicks, J. B., Ye, K., Reiner, A., Gilliam, T. C., Trask, B., Patterson, N., Zetterberg, A., Wigler, M. H. (July 2004) Large-scale copy number polymorphism in the human genome. Science, 305 (5683). pp. 525-8. ISSN 1095-9203 (Electronic)

Loughney, K., Martins, T. J., Harris, E. A. S., Sadhu, K., Hicks, J. B., Sonnenburg, W. K., Beavo, J. A., Ferguson, K. (1996) Isolation and characterization of cDNAs corresponding to two human calcium, calmodulin-regulated, 3′,5′-cyclic nucleotide phosphodiesterase. Journal of Biological Chemistry, 271 (2). pp. 796-806. ISSN 00219258 (ISSN)

Coghlan, V. M., Perrino, B. A., Howard, M., Langeberg, L. K., Hicks, J. B., Gallatin, W. M., Scott, J. D. (1995) Association of protein kinase A and protein phosphatase 2B with a common anchoring protein. Science, 267 (5195). pp. 108-111. ISSN 00368075 (ISSN)

Escarceller, M., Hicks, J., Gudmundsson, G., Trump, G., Touati, D., Lovett, S., Foster, P. L., McEntee, K., Goodman, M. F. (1994) Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation. Journal of Bacteriology, 176 (20). pp. 6221-6228. ISSN 00219193 (ISSN)

McEachern, M. J., Hicks, J. B. (1993) Unusually large telomeric repeats in the yeast Candida albicans. Molecular and Cellular Biology, 13 (1). pp. 551-560. ISSN 02707306 (ISSN)

Polacheck, I., Lebens, G., Hicks, J. B. (1992) Development of DNA probes for early diagnosis and epidemiological study of cryptococcosis in AIDS patients. Journal of Clinical Microbiology, 30 (4). pp. 925-930. ISSN 00951137 (ISSN)

Sadhu, C., Hoekstra, D., McEachern, M. J., Reed, S. I., Hicks, J. B. (1992) A G-protein α subunit from asexual Candida albicans functions in the mating signal transduction pathway of Saccharomyces cerevisiae and is regulated by the a1-α2 repressor. Molecular and Cellular Biology, 12 (5). pp. 1977-1985. ISSN 02707306 (ISSN)

Hinnen, A., Hicks, J. B., Fink, G. R. (1992) Transformation of yeast. 1978. Biotechnology (Reading, Mass.), 24. pp. 337-341. ISSN 07407378 (ISSN)

Miyasaki, S. H., Hicks, J. B., Greenspan, D., Polacheck, I., MacPhail, L. A., White, T. C., Agabian, N., Greenspan, J. S. (1992) The identification and tracking of Candida albicans isolates from oral lesions in HIV-seropositive individuals. Journal of Acquired Immune Deficiency Syndromes, 5 (10). pp. 1039-1046. ISSN 08949255 (ISSN)

Wickes, B. L., Hicks, J. B., Merz, W. G., Kwon-Chung, K. J. (1992) The molecular analysis of synonymy among medically important yeasts within the genus Candida. Journal of General Microbiology, 138 (5). pp. 901-907. ISSN 00221287 (ISSN)

McEachern, M. J., Hicks, J. B. (1991) Dosage of the smallest chromosome affects both the yeast-hyphal transition and the white-opaque transition of Candida albicans WO-1. Journal of Bacteriology, 173 (23). pp. 7436-7442. ISSN 00219193 (ISSN)

Tang, Y., Hicks, J. B., Hilvert, D. (1991) In vivo catalysis of a metabolically essential reaction by an antibody. Proceedings of the National Academy of Sciences of the United States of America, 88 (19). pp. 8784-8786. ISSN 00278424 (ISSN)

Sherman, F., Hicks, J. (1991) Micromanipulation and dissection of asci. Methods in Enzymology, 194. pp. 21-37. ISSN 00766879 (ISSN)

Stone, E. M., Swanson, M. J., Romeo, A. M., Hicks, J. B., Sternglanz, R. (1991) The SIR1 gene of Saccharomyces cerevisiae and its role as an extragenic suppressor of several mating-defective mutants. Molecular and Cellular Biology, 11 (4). pp. 2253-2262. ISSN 02707306 (ISSN)

Sadhu, C., McEachern, M. J., Rustchenko-Bulgac, E. P., Schmid, J., Soll, D. R., Hicks, J. B. (1991) Telomeric and dispersed repeat sequences in Candida yeasts and their use in strain identification. Journal of Bacteriology, 173 (2). pp. 842-850. ISSN 00219193 (ISSN)

Bowdish, K., Tang, Y., Hicks, J. B., Hilvert, D. (1991) Yeast expression of a catalytic antibody with chorismate mutase activity. Journal of Biological Chemistry, 266 (18). pp. 11901-11908. ISSN 00219258 (ISSN)

Rustchenko-Bulgac, E. P., Sherman, F., Hicks, J. B. (1990) Chromosomal rearrangements associated with morphological mutants provide a means for genetic variation of Candida albicans. Journal of Bacteriology, 172 (3). pp. 1276-1283. ISSN 00219193 (ISSN)

Kwon-Chung, K. J., Hicks, J. B., Lipke, P. N. (1990) Evidence that Candida stellatoidea type II is a mutant of Candida albicans that does not express sucrose-inhibitable α-glucosidase. Infection and Immunity, 58 (9). pp. 2804-2808. ISSN 00199567 (ISSN)

Livi, G. P., Hicks, J. B., Klar, A. J. S. (1990) The sum1-1 mutation affects silent mating-type gene transcription in Saccharomyces cerevisiae. Molecular and Cellular Biology, 10 (1). pp. 409-412. ISSN 02707306 (ISSN)

Kwon-Chung, K. J., Riggsby, W. S., Uphoff, R. A., Hicks, J. B., Whelan, W. L., Reiss, E., Magee, B. B., Wickes, B. L. (1989) Genetic differences between type I and type II Candida stellatoidea. Infection and Immunity, 57 (2). pp. 527-532. ISSN 00199567 (ISSN)

Soll, D. R., Galask, R., Isley, S., Rao, T. V. G., Stone, D., Hicks, J., Schmid, J., Mac, K., Hanna, C. (1989) Switching of Candida albicans during successive episodes of recurrent vaginitis. Journal of Clinical Microbiology, 27 (4). pp. 681-690. ISSN 00951137 (ISSN)

Soll, D. R., Staebell, M., Langtimm, C., Pfaller, M., Hicks, J., Rao, T. V. G. (1988) Multiple Candida strains in the course of a single systemic infection. Journal of Clinical Microbiology, 26 (8). pp. 1448-1459. ISSN 00951137 (ISSN)

Strathern, J., Shafer, B., Hicks, J., McGill, C. (1988) a/α-Specific repression by MATα2. Genetics, 120 (1). pp. 75-81. ISSN 00166731 (ISSN)

Marshall, M., Mahoney, D., Rose, A., Hicks, J. B., Broach, J. R. (1987) Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Molecular and Cellular Biology, 7 (12). pp. 4441-4452. ISSN 02707306 (ISSN)

Soll, D. R., Langtimm, C. J., McDowell, J., Hicks, J., Galask, R. (1987) High-frequency switching in Candida strains isolated from vaginitis patients. Journal of Clinical Microbiology, 25 (9). pp. 1611-1622. ISSN 00951137 (ISSN)

Hicks, J. B. (1987) Mechanisms of differentiation. Nature, 326 (6112). pp. 444-445. ISSN 00280836 (ISSN)

Ivy, J. M., Klar, A. J. S., Hicks, J. B. (1986) Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Molecular and Cellular Biology, 6 (2). pp. 688-702. ISSN 02707306 (ISSN)

Ivy, J. M., Hicks, J. B., Klar, A. J. (December 1985) Map positions of yeast genes SIR1, SIR3 and SIR4. Genetics, 111 (4). pp. 735-44. ISSN 0016-6731 (Print)0016-6731 (Linking)

Klar, A. J. S., Kakar, S. N., Ivy, J. M., Hicks, J. B., Livi, G. P., Miglio, L. M. (1985) SUM1, an apparent positive regulator of the cryptic mating-type loci in Saccharomyces cerevisiae. Genetics, 111 (4). pp. 745-748. ISSN 00166731 (ISSN)

Strathern, J., Klar, A. J. S., McGill, C., Abraham, J., Weisbrod, S. T., Kelly, M., Stephens, C., Hicks, J. B. (March 1984) Initiation and Resolution of Mating Type Switching in Yeast. Journal of Cellular Biochemistry - Supplement, 26 (S8B S). p. 125. ISSN 1097-4644

Dellaporta, S. L., Chomet, P. S., Mottinger, J. P., Wood, J. A., Yu, S. M., Hicks, J. B. (1984) Endogenous transposable elements associated with virus infection in maize. Cold Spring Harbor Symposia on Quantitative Biology, 49. pp. 321-328. ISSN 00917451 (ISSN)

Feldman, J. B., Hicks, J. B., Broach, J. R. (1984) Identification of sites required for repression of a silent mating type locus in yeast. Journal of Molecular Biology, 178 (4). pp. 815-834. ISSN 00222836 (ISSN)

Abraham, J., Nasmyth, K. A., Strathern, J. N., Klar, A. J. S., Hicks, J. B. (1984) Regulation of mating-type information in yeast. Negative control requiring sequences both 5′ and 3′ to the regulated region. Journal of Molecular Biology, 176 (3). pp. 307-331. ISSN 00222836 (ISSN)

Hicks, J., Strathern, J., Klar, A., Ismail, S., Broach, J. (1984) Structure of the SAD mutation and the location of control sites at silent mating type genes in Saccharomyces cerevisiae. Molecular and Cellular Biology, 4 (7). pp. 1278-1285. ISSN 02707306 (ISSN)

Strathern, J., Klar, A., Hicks, J., Abraham, J., Ivy, J., Kelly, M., Weisbrod, S., Stephens, C. (March 1983) Mechanism of Mating Type Cassette Switching. Journal of Cellular Biochemistry , 21 (S7B). pp. 89-90. ISSN 1097-4644

Klar, A. J. S., Strathern, J. N., Hicks, J. B., Prudente, D. (1983) Efficient production of a ring derivative of chromosome III by the mating-type switching mechanism in Saccharomyces cerevisiae. Molecular and Cellular Biology, 3 (5). pp. 803-810. ISSN 02707306 (ISSN)

Kassir, Y., Hicks, J. B., Herskowitz, I. (1983) SAD mutation of Saccharomyces cerevisiae is an extra a cassette. Molecular and Cellular Biology, 3 (5). pp. 871-880. ISSN 02707306 (ISSN)

Dellaporta, S. L., Wood, J., Hicks, J. B. (1983) A plant DNA minipreparation: Version II. Plant Molecular Biology Reporter, 1 (4). pp. 19-21. ISSN 07359640 (ISSN)

Kostriken, R., Strathern, J. N., Klar, A. J. S., Hicks, J. B., Heffron, F. (1983) A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae. Cell, 35 (1). pp. 167-174. ISSN 00928674 (ISSN)

Klar, A. J. S., Hicks, J. B., Strathern, J. N. (1982) Directionality of yeast mating-type interconversion. Cell, 28 (3). pp. 551-561. ISSN 00928674 (ISSN)

Strathern, J. N., Klar, A. J. S., Hicks, J. B., Abraham, J. A., Ivy, J. M., Nasmyth, K. A., McGill, C. (1982) Homothallic switching of yeast mating type cassettes is initiated by a double-stranded cut in the MAT locus. Cell, 31 (1). pp. 183-192. ISSN 00928674 (ISSN)

Broach, J. R., Li, Y. Y., Feldman, J., Jayaram, M., Abraham, J., Nasmyth, K. A., Hicks, J. B. (1982) Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harbor Symposia on Quantitative Biology, 47 (2). pp. 1165-1173. ISSN 00917451 (ISSN)

Abraham, J., Feldman, J., Nasmyth, K. A., Strathern, J. N., Klar, A. J., Broach, J. R., Hicks, J. B. (1982) Sites required for position-effect regulation of mating-type information in yeast. Cold Spring Harbor Symposia on Quantitative Biology, 47 (2). pp. 989-998. ISSN 00917451 (ISSN)

Strathern, J., Hicks, J., Herskowitz, I. (1981) Control of cell type in yeast by the mating type locus. The α1-α2 hypothesis. Journal of Molecular Biology, 147 (3). pp. 357-372. ISSN 00222836 (ISSN)

Klar, A. J., Hicks, J. B., Strathern, J. N. (1981) Irregular transpositions of mating-type genes in yeast. Cold Spring Harbor Symposia on Quantitative Biology, 45 Pt . pp. 983-990. ISSN 00917451 (ISSN)

Klar, A. J. S., Strathern, J. N., Broach, J. R., Hicks, J. B. (1981) Regulation of transcription in expressed and unexpressed mating type cassettes of yeast. Nature, 289 (5795). pp. 239-244. ISSN 00280836 (ISSN)

Klar, A. J. S., Strathern, J. N., Hicks, J. B. (1981) A position-effect control for gene transposition: State of expression of yeast mating-type genes affects their ability to switch. Cell, 25 (2). pp. 517-524.

Klar, A. J., McIndoo, J., Strathern, J. N., Hicks, J. B. (1980) Evidence for a physical interaction between the transposed and the substituted sequences during mating type gene transposition in yeast. Cell, 22 (1 I). pp. 291-298.

Klar, A. J. S., McIndoo, J., Hicks, J. B., Strathern, J. N. (1980) Precise mapping of the homothallism genes HML and HMR in Saccharomyces cerevisiae. Genetics, 96 (2). pp. 315-320. ISSN 00166731 (ISSN)

Broach, J. R., Hicks, J. B. (1980) Replication and recombination functions associated with the yeast plasmid, 2μ circle. Cell, 21 (2). pp. 501-508.

Strathern, J. N., Spatola, E., McGill, C., Hicks, J. B. (1980) Structure and organization of transposable mating type cassettes in Saccharomyces yeasts. Proceedings of the National Academy of Sciences of the United States of America, 77 (5 I). pp. 2839-2843. ISSN 00278424 (ISSN)

Hicks, J., Klar, A. J. S., Strathern, J. N. (1979) Control of Mating Type in Yeast. Journal of Supramolecular Structure, 8 (SUPPL.). p. 35.

Strathern, J. N., Newlon, C. S., Herskowitz, I., Hicks, J. B. (1979) Isolation of a circular derivative of yeast chromosome III: Implications for the mechanism of mating type interconversion. Cell, 18 (2). pp. 309-319.

Hicks, J. B., Hinnen, A., Fink, G. R. (1979) Properties of yeast transformation. Cold Spring Harbor Symposia on Quantitative Biology, 43 (2). pp. 1305-1313. ISSN 00917451 (ISSN)

Broach, J. R., Strathern, J. N., Hicks, J. B. (1979) Transformation in yeast: Development of a hybrid cloning vector and isolation of the CAN1 gene. Gene, 8 (1). pp. 121-133. ISSN 03781119 (ISSN)

Hicks, J., Strathern, J. N., Klar, A. J. S. (1979) Transposable mating type genes in Saccharomyces cerevisiae. Nature, 282 (5738). pp. 478-483. ISSN 00280836 (ISSN)

Rine, J., Strathern, J. N., Hicks, J. B., Herskowitz, I. (1979) A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: Evidence for and identification of cryptic mating-type loci. Genetics, 93 (4). pp. 877-901. ISSN 00166731 (ISSN)

Hicks, J., Strathern, J. N. (1978) Interconversion of mating type in S cervisiae and the cassette model for gene transfer. Brookhaven symposia in biology, No. 29. pp. 233-242.

Hinnen, A., Hicks, J. B., Fink, G. R. (1978) Transformation of yeast. Proceedings of the National Academy of Sciences of the United States of America, 75 (4). pp. 1929-1933. ISSN 00278424 (ISSN)

Hicks, J. B., Herskowitz, I. (March 1977) Interconversion of Yeast Mating Types II. Restoration of Mating Ability to Sterile Mutants in Homothallic and Heterothallic Strains. Genetics, 85 (3). pp. 373-93. ISSN 0016-6731 (Print)0016-6731 (Linking)

Hicks, J. B., Strathern, J. N., Herskowitz, I. (March 1977) Interconversion of Yeast Mating Types III. Action of the Homothallism (HO) Gene in Cells Homozygous for the Mating Type Locus. Genetics, 85 (3). pp. 395-405. ISSN 0016-6731 (Print)0016-6731 (Linking)

Hicks, J., Fink, G. R. (1977) Identification of chromosomal location of yeast DNA from hybrid plasmid pYeleu10. Nature, 269 (5625). pp. 265-267. ISSN 00280836 (ISSN)

Hicks, J. B., Herskowitz, I. (June 1976) Interconversion of Yeast Mating Types I. Direct Observations of the Action of the Homothallism (HO) Gene. Genetics, 83 (2). pp. 245-58. ISSN 0016-6731 (Print)0016-6731 (Linking)

Hicks, J. B., Herskowitz, I. (1976) Evidence for a new diffusible element of mating pheromones in yeast. Nature, 260 (5548). pp. 246-248. ISSN 00280836 (ISSN)

Book Section

Hicks, J. B., Ivy, J. M., Strathern, J. N., Klar, A. J. (1985) Sex in budding yeast: How and Why. In: The Origin and Evolution of Sex. Alan R. Liss Incorporated, pp. 97-111. ISBN 9780845122068

Hicks, J. B., Strathern, J. N., Klar, A. J. (1982) Cloning by complementation in yeast: the mating type genes. In: Genetic engineering: principles and methods. Plenum Press, New York, pp. 219-248.

Hicks, J., Klar, A., Strathern, J. N., Newlon, C. S. (1979) Control of Mating Type in Yeast Saccharomyces. In: Eucaryotic gene regulation. UCLA Symposium onEucaryotic Gene Regulation (Keystone : 1979). Icn-Ucla Symposia on Molecular and Cellular Biology, 14 (ED.). Academic Press, New York, pp. 27-42. ISBN 0120683504

Book

Sherman, F., Fink, G., Hicks, J. (1987) Methods in Yeast Genetics: A Laboratory Course Manual. Cold Spring Harbor Laboratory Press. ISBN 9780879691974

Hicks, J.B. (1986) Yeast cell biology. A.R. Liss. ISBN 9780845126325

Klar, A. J., Strathern, J. N., Hicks, J. B. (1984) Developmental Pathways in Yeast. 1984 . CSHL Press.

Video

Hicks, J. B. (November 2012) Talk from Jim Hicks at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Dataset

Hicks, J. B. (2006) Data file sw.dip.amps.txt for deletions. [Dataset] (Unpublished)