PUBLICATIONS
Original Articles
(peer reviewed) in:
Fridlyand J., Snijders
A., Pinkel, D., Albertson D. G. and Jain, A. N..
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) (Journal
Website) (Preprint)
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)
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, 2004, in press)
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).
Maldonado J. L., Timmerman L.,
Fridlyand J. and Bastian B. C.
Mechanisms of cell cycle arrest in
spitz nevi with constitutive activation of the
MAP-Kinase pathway. (American Journal of Pathology, May 2004, V.164(5), pp. 1783-7).
Fridlyand J. and Dudoit
S.
Bagging
to improve the accuracy of a clustering procedure. (Bioinformatics,
2003, vol. 19, No. 9). Dudoit and Fridlyand are joint first authors.
(Journal
website) (Technical report
#600)
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).
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). .
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)
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).
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).
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).
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).
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).
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). Dudoit and Fridlyand
are joint first authors. (Journal website)
(Technical
report #600)
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). Dudoit and Fridlyand are joint first authors. This
paper was listed among New Hot Papers in July 2003 by Thomson-ISI Web of
Science Database (http://esi-topics.com)
(Journal website) (Technical report
#576)
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).
International Human Genome Sequencing
Consortium.
Initial Sequencing
and Analysis of the Human Genome. (Nature , 860 - 921, 2001). Listed
as a member of JGI
sequencing team.
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.
(June,
2001)