CSHL Cancer Center - Cancer Genetics
The Cancer Genetics Program is focused on revealing the structure and landscape of cancer genomes. Such information provides insight into how cancer develops, progresses, and responds to therapy. The Program includes a diverse collection of faculty who are developing new technology that is changing how researchers across the globe study cancer. The Program currently has three main focus areas: experimental technology, bioinformatics, and cancer progression.
Garvin, T. and Aboukhalil, R. and Kendall, J. and Baslan, T. and Atwal, G. S. and Hicks, J. and Wigler, M. and Schatz, M. C. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods 12pp. 1058-1060.
Goodwin, S. and Gurtowski, J. and Ethe-Sayers, S. and Deshpande, P. and Schatz, M. C. and McCombie, W. R. (2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 25(11) pp. 1750-1756.
Pendleton, M. and Sebra, R. and Pang, A. W. and Ummat, A. and Franzen, O. and Rausch, T. and Stutz, A. M. and Stedman, W. and Anantharaman, T. and Hastie, A. and Dai, H. and Fritz, M. H. and Cao, H. and Cohain, A. and Deikus, G. and Durrett, R. E. and Blanchard, S. C. and Altman, R. and Chin, C. S. and Guo, Y. and Paxinos, E. E. and Korbel, J. O. and Darnell, R. B. and McCombie, W. R. and Kwok, P. Y. and Mason, C. E. and Schadt, E. E. and Bashir, A. (2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods 12(8) pp. 780-786.
Stephens, Z. D. and Lee, S. Y. and Faghri, F. and Campbell, R. H. and Zhai, C. and Efron, M. J. and Iyer, R. and Schatz, M. C. and Sinha, S. and Robinson, G. E. (2015) Big Data: Astronomical or Genomical?. PLoS Biol 13(7) pp. e1002195.
Wasik, K. A. and Tam, O. H. and Knott, S. R. and Falciatori, I. and Hammell, M. and Vagin, V. V. and Hannon, G. J. (2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev 29(13) pp. 1403-1415.
Wang, X. and Yu, X. and Zhu, W. and McCombie, W. R. and Antoniou, E. and Powers, R. S. and Davidson, N. O. and Li, E. and Williams, J. (2015) A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics 31(12) pp. 2040-2042.
Dos Santos, C. O. and Dolzhenko, E. and Hodges, E. and Smith, A. D. and Hannon, G. J. (2015) An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland. Cell Reports
Danko, C. G. and Hyland, S. L. and Core, L. J. and Martins, A. L. and Waters, C. T. and Lee, H. W. and Cheung, V. G. and Kraus, W. L. and Lis, J. T. and Siepel, A. (2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods 12(5) pp. 433-8.
Lyons, S. K. (2015) Imaging Mouse Models of Cancer. Cancer J 21(3) pp. 152-164.
Baslan, T. and Kendall, J. and Ward, B. and Cox, H. and Leotta, A. and Rodgers, L. and Riggs, M. and D'Italia, S. and Sun, G. and Yong, M. and Miskimen, K. and Gilmore, H. and Saborowski, M. and Dimitrova, N. and Krasnitz, A. and Harris, L. and Wigler, M. and Hicks, J. (2015) Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Research 25(5) pp. 714-724.
Teixeira, F. K. and Sanchez, C. G. and Hurd, T. R. and Seifert, J. R. and Czech, B. and Preall, J. B. and Hannon, G. J. and Lehmann, R. (2015) ATP synthase promotes germ cell differentiation independent of oxidative phosphorylation. Nature Cell Biology 17(5) pp. 689-696.
Wagenblast, E. and Soto, M. and Gutierrez-Angel, S. and Hartl, C. A. and Gable, A. L. and Maceli, A. R. and Erard, N. and Williams, A. M. and Kim, S. Y. and Dickopf, S. and Harrell, J. C. and Smith, A. D. and Perou, C. M. and Wilkinson, J. E. and Hannon, G. J. and Knott, S. R. (2015) A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis. Nature 520(7547) pp. 358-362.
Rye, I. H. and Lundin, P. and Maner, S. and Fjelldal, R. and Naume, B. and Wigler, M. and Hicks, J. and Borresen-Dale, A. L. and Zetterberg, A. and Russnes, H. G. (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.
Fuda, N. J. and Guertin, M. J. and Sharma, S. and Danko, C. G. and Martins, A. L. and Siepel, A. and Lis, J. T. (2015) GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters. Plos Genetics 11(3) pp. e1005108.
Marinov, Georgi K and Wang, Jie and Handler, Dominik and Wold, Barbara J and Weng, Zhiping and Hannon, Gregory J and Aravin, Alexei A and Zamore, Phillip D and Brennecke, Julius and Toth, Katalin Fejes (2015) Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified. Developmental Cell 32(6) pp. 765-771.
Lee, J. H. and Daugharthy, E. R. and Scheiman, J. and Kalhor, R. and Ferrante, T. C. and Terry, R. and Turczyk, B. M. and Yang, J. L. and Lee, H. S. and Aach, J. and Zhang, K. and Church, G. M. (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc 10(3) pp. 442-58.
Kirschner, K. and Samarajiwa, S. A. and Cairns, J. M. and Menon, S. and Perez-Mancera, P. A. and Tomimatsu, K. and Bermejo-Rodriguez, C. and Ito, Y. and Chandra, T. and Narita, M. and Lyons, S. K. and Lynch, A. G. and Kimura, H. and Ohbayashi, T. and Tavare, S. and Narita, M. (2015) Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet 11(3) pp. e1005053.
Stein, P. and Rozhkov, N. V. and Li, F. and Cardenas, F. L. and Davydenk, O. and Vandivier, L. E. and Gregory, B. D. and Hannon, G. J. and Schultz, R. M. (2015) Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. PLoS Genetics 11(2) pp. e1005013.
Jayaprakash, A. D. and Benson, E. K. and Gone, S. and Liang, R. and Shim, J. and Lambertini, L. and Toloue, M. M. and Wigler, M. and Aaronson, S. A. and Sachidanandam, R. (2015) Stable heteroplasmy at the single-cell level is facilitated by intercellular exchange of mtDNA. Nucleic Acids Research 43(4) pp. 2177-2187.
Ruiz, C. and Li, J. and Luttgen, M. S. and Kolatkar, A. and Kendall, J. T. and Flores, E. and Topp, Z. and Samlowski, W. E. and McClay, E. and Bethel, K. and Ferrone, S. and Hicks, J. and Kuhn, P. (2015) Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology 12(1) pp. 16008.
Church, D. M. and Schneider, V. A. and Steinberg, K. M. and Schatz, M. C. and Quinlan, A. R. and Chin, C. S. and Kitts, P. A. and Aken, B. and Marth, G. T. and Hoffman, M. M. and Herrero, J. and Mendoza, M. L. Z. and Durbin, R. and Flicek, P. (2015) Extending reference assembly models. Genome Biology 16pp. Article no. 13.
Patrick, P. S. and Rodrigues, T. B. and Kettunen, M. I. and Lyons, S. K. and Neves, A. A. and Brindle, K. M. (2015) Development of Timd2 as a reporter gene for MRI. Magn Reson Med
Narzisi, G. and Schatz, M. C. (2015) The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol 3pp. 8.Additional materials of the author at
CSHL Institutional Repository
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