fridlyand.jane@gene.com

University of California Berkeley, Berkeley, CA, BA, 1995, Applied Mathematics
University of California Berkeley, Berkeley, CA, MA, 1996, Statistics
University of California Berkeley, Berkeley, CA, PhD, 2001, Statistics

International Human Genome Sequencing Consortium. Initial Sequencing and Analysis of the Human Genome. (Nature , 860 Ð 921, 2001). Listed as a member of JGI sequencing team.

Symons, R. C. A., Daly, M. J., Fridlyand, J., Speed, T. P., Cook, W. D., Gerondakis, S., Harris, A. W. and Foote, S. J. Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in Emu-v-abl transgenic mice. (PNAS, 2002, No. 99).

Fridlyand J., Dudoit S. and Speed, T.P. Comparison of Discrimination Methods for the Classification of Tumors using Gene Expression Data. (Journal of American Statistical Association, March 2002, Vol. 97, No. 457). First two authors contributed equally

Fridlyand J. and Dudoit S. A prediction-based resampling method to estimate the number of clusters in a dataset. (Genome Biology, 2002, Vol. 3, No. 7). Both authors contributed equally

Veltman, J. A., Fridlyand, J., Pejavar, S., Olshen, A. B., Korkola, J. E., DeVries, S., Carroll, P., Kuo, W. , Pinkel, D., Albertson, D., Cordon-Cardo, C., Jain, A. N. and Waldman, F. W. Array- based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors (Cancer Research, 2003, Vol, 63, No. 11).

Paris, P. L., Albertson, D. G., Alers, J. C., Andaya, A., Carroll, P., Fridlyand, J., Jain, A. N., Kamkar, S., Kowbel, D., Krijtenburg, P. J., Pinkel, D., Schroder, F. H., Vissers, K. J., Watson, V. J., Wildhagen, M.F., Collins, C. and Van Dekken, H. High-resolution analysis of paraffin- embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays . (American Journal of Pathology, 2003, Vol. 162, No. 3).

Snijders, A. M., Nowee, M. E., Fridlyand, J., Piek, J. M. J., Dorsman, J. C., Jain, A. J., Pinkel, D., van Diest, P. J., Verheijen, R. H. and Albertson D. G. Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in Falopian tuba carcinoma. (Oncogene, 2003, Vol. 22, No. 27).

Snijders, A. M., Fridlyand, J., Mans, D., Segraves, R., Jain, A. N., Pinkel, D. and Albertson D. G. Shaping of tumors and drug-resistant genomes by instability and selection. ( Oncogene, 2003, Vol. 22, No. 28).

Hackett, C. S, Hodgson, G., Law, M. E., Fridlyand, J., Osoegawa, K., de Jong, P. L., Nowak, N. J., Pinkel, D., Alberston, D. G., Jain, A. N., Jenkins, R., Gray, J. W. and Weiss, W. A. Genome- wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. (Cancer Research, 2003, Vol. 63, No. 17).

Korkola, J. E., DeVries, H., Fridlyand, J., Hwang, E. S., Estep, A. I. H., Chen, Y., Dairkee, S. H., Jensen, R. M. and Waldman, F. M. Differentiation of lobular vs ductal breast carcinoma by expression microarray analysis. (Cancer Research, 2003, Vol. 63, No. 21)

Maldonado J.L., Fridlyand J., Patel H., Jain A. N., Busam K., Kageshita T., Ono T., Albertson D. G., Pinkel D. and Bastian B. C. Determinants of BRAF mutations in primary melanomas. (Journal of National Cancer Institute, 2003, Vol. 95, No. 24).

Nelson, D. O. and Fridlyand, J. Designing meaningful measures of read length for data produced by DNA sequencers. (IMS Lecture Notes -- Monograph Series, 2003, Vol. 40).

Fridlyand J. and Dudoit S. Bagging to improve the accuracy of a clustering procedure. (Bioinformatics, 2003, vol. 19, No. 9). Both authors contributed equally.

Maldonado J. L., Timmerman L., Fridlyand J. and Bastian B. C. Mechanisms of cell cycle arrest in spitz nevi with constitutive activation od the MAP-Kinase pathway. (American Journal of Pathology, May 2004, V.164(5), pp. 1783-7).

Hager, J. H., Hodgson, G., Fridlyand, J., Hariono, S., Gray, J. W. and Hanahan D. Oncogene expression and genetic background influence the frequency od DNA copy abnormalities in mouse pancreatic islet cell carcinomas. (Cancer Research, 2004, Vol. 64 No. 7).

Nakao, K., Mehta, K. R., Fridlyand, J., Moore, D. H., Jain, A. N., Lafuente, A., Wiencke, J. W., Terdiman, J. P. and Waldman, F. M. High resolution analysis of colorectal cancer by array- based comparative genomic hybridization. (Carcinogenesis, Aug; 2004, V. 25(8), pp. 1345-57)

Paris, P. L., Andaya , A., Fridlyand, J., Jain, A. N., Weinberg, V., Kowbel, D., Brebner, J. H., Simko, J., Watson, J.E., Volik, S., Albertson, D. G., Pinkel, D., Alers, J.C., Van Der Kwast, T. H., Vissers, K. J., Schroder, F. H., Wildhagen, M. F., Febbo, P. G., Chinnaiyan, A. M., Pienta, K. J. , Carroll, P. R. , Rubin, M. A., Collins, C. , Van Dekken, H. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. (Hum Mol Genet., Jul 2004 Jul 1, V. 13, pp. 1303-13)

Fridlyand J., Snijders A., Pinkel, D., Albertson D. G. and Jain, A. Application of Hidden Markov Models to the analysis of the array CGH data. (Special Genomic Issue of Journal of Multivariate Analysis, June 2004, V. 90, pp. 132-153)

Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. (Genome Research, 2005 Feb;15(2):302-11)

Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RC, Albertson DG. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. (Oncogene. 2005 Jun 16;24(26):4232-42.)

Ching T-T; Maunakea AK; Jun P; Hong C; Zardo G; Pinkel D; Albertson DG; Fridlyand J; Mao J- H; Shchors K; Weiss WA; Costello JF. Epigenome analyses using BAC microarrays identifies evolutionary conservation of tissue-specific methylation of SHANK3. (Nature Genetics, 37(6), 645-51, 2005,)

Willenbrock H. and Fridlyand J. A comparison study: applying segmentation to array CGH data for downstream analysis. (Bioinformatics, 21(22):4084-91,2005). Fridlyand is a senior author

Curtin JA, Fridlyand J, Kageshita T, Patel H, Busam K, Kutzner H, Cho KH, Aiba S, Brocker EB, LeBoit PE, Pinkel D and Bastian BC. Distinct sets of genetic alterations in melanoma. ( New England Journal of Medicine, 353(20):2135-47, 2005)

Blaveri E., Brewer J. L., Roydsgupta R., Fridlyand J., DeVries S., Koppie T., Pejevar S., Mejat K., Carroll P., Simko JP and Waldman FM . Bladder cancer stage and outcome defined by array based comparative genomic hybridization. ( Clinical Cancer Research, 11 (19 Pt 1), 7012-22, 2005)

Chao RC, Pyzel U., Fridlyand J., Teel L., Haaga J., Borowsky A., Horvai A., Kogan S., Bonfias J., Huey B., Jacks TE, Albertson D., Shannon K. Therapy induced malignant neoplasms in Nf1 mutant mice. (Cancer Cell, 2005, 8(4):337-48, 2005)

Rubinstein J., Fridlyand J., Shen A., Aldape K., Ginzinger D., Batchelor T., Treseler P., Bergere M., McDermott M., Prados M., Krach J., Okada C., Hyun W., Parikh S., Haqq C., Shuman M. Gene expression and angiotropism in primary CNS lymphoma. (Blood, Jan 2006)

Albertson DG, Snijders AM, Fridlyand J, Jordan R, Pinkel D, Schmidt B. .Comprehensive analysis of tumors by array comparative genomic hybridization: more is better. (Cancer Research, 66(7):3955-6, 2006)

Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen AB, Segraves R, Dairkee S, Tokuyasu TA, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6:96, 2006. First three authors contributed equally

Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay, Kouros Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tohon G, Roschke A, Gehlahaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Molecular Cancer Therapy 5(4):853-67, 2006.

Reynolds PA, Sigaroudinia M, Zardo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello JF, Tlsty TD. Tumor suppressor P16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells. Journal of Biological Chemistry, 2006 Aug 25;281(34):24790-802.

Book Chapters

Dudoit, S. and Fridlyand, J. Classification in microarray experiments. (Analysis of microarray experiments, Chapman & Hall/CRC, 2003, edited by T. P. Speed).

Dudoit, S. and Fridlyand, J. Classification in microarray experiments (Understanding and Using Microarrays Analysis Techniques: A Practical Guide, Kluwer, 2003, edited by D. Berrar, W. Dubitzky and M. Grnazow).

Ph.D Dissertation

Fridlyand, J. Resampling methods for variable selection and classification: applications to genomics. (http://www.stat.berkeley.edu/users/janef/index.html, June 2001)

Abstracts

Fridlyand J. , Snijders A., Pinkel, D., Albertson D. G. and Jain, A. N. Statistical issues in the analysis of the array CGH data. (Computations Systems Bioinformatics 2003 Conference Proceedings, IEEE Computer Society).

9/24/07