Center for Bioinformatics & Molecular Biostatistics http://biostat.ucsf.edu/cbmb/pubs.html
UCSF
Center for Bioinformatics & Molecular Biostatistics

Publications

For links to publication lists for individual CBMB members, see People.

'Limited Access' publication links require institutional authorization or personal membership/payment.

2009

  1. Wrensch M, Jenkins RB, Chang JS, Yeh R-F, Xiao Y, et al. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nature Genetics, in press. (2009) CBMB Working Paper.
  2. Xiao Y, Segal MR. Identification of yeast transcriptional regulation networks using multivariate random forests. (2009) CBMB Working Paper.
  3. Segal MR. A Novel Topology for Representing Protein Folds. (2009) In Protein Science  CBMB Working Paper  Limited Access.

2008

  1. Bacchetti P, McCulloch CE, Segal MR. (2008) Simple, defensible sample sizes based on cost efficiency. Biometrics, 64:577-85; discussion 586-94. Limited Access
  2. C.S. Chan and J.S. Song. CTCF Confines the Distal Action of Estrogen Receptor. Cancer Research 68 (2008) 9041–9.
  3. K.A. Holmes, J.S. Song, X.S. Liu, M. Brown, and J.S. Carroll. NKX3-1 and LEF-1 function as transcriptional inhibitors of Estrogen Receptor activity. Cancer Research 68 (2008) 7380–7385.
  4. D.S. Johnson, W. Li, D.B. Gordon, A. Bhattacharjee, B. Curry, J. Ghosh, L. Brizuela, J.S. Carroll, M. Brown, P. Flicek, C.M. Koch, I. Dunham, M. Bieda, X. Xu, P.J. Farnham, P. Kapranov, D.A. Nix, T.R. Gingeras, X. Zhang, H. Holster, N. Jiang, R.D. Green, J.S. Song, S.A. McCuine, E. Anton, L. Nguyen, N.D. Trinklein, Z. Ye, K. Ching, D. Hawkins, B. Ren, P.C. Scacheri, J. Rozowsky, A. Karpikov, G. Euskirchen, S. Weissman, M. Gerstein, M. Snyder, A. Yang, Z. Moqtaderi, H. Hirsch, H.P. Shulha, Y. Fu, Z. Weng, K. Struhl, R.M. Myers, J.D. Lieb, and X.S. Liu, Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research 18(3) (2008) 393-403.
  5. McKay JK, Richards JH, Nemali KS, Sen S, Mitchell-Olds T, Boles S, Stahl EA, Wayne T, Juenger TE. (2008) Genetics of drought adaptation in Arabidopsis thaliana II: QTL analysis of a new mapping population, Kas-1xTsu-1. Evolution, in press.
  6. F. Ozsolak, L.L. Poling, Z. Wang, H. Liu, X.S. Liu, R.G. Roeder, X. Zhang, J.S. Song* and D.E. Fisher* (* co-corresponding authors). Chromatin Structure Analyses Identify miRNA Promoters. Genes & Development 22 (2008) 3172–3183.
  7. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. (2008) A genome-wide approach to indentifying novel-imprinted genes. Human Genetics, 122(6):625-634. Open access
  8. Segal MR. Prediction of RNA splice signals. (2008) In Statistical Advances in Biomedical Sciences: State of Art and Future Directions. A Biswas, S Datta, J Fine and MR Segal, Editors. Wiley, 443-463. Publisher details
  9. Segal MR. (2008) Re-cracking the nucleosome positioning code. Statistical Applications in Genetics and Molecular Biology 7: Article 14. Open Access   CBMB Working Paper
  10. Segal MR. (2008) On E-values for tandem MS scoring schemes. Bioinformatics, 24:1652-3. Limited Access   CBMB Working Paper
  11. Seibold MA, Wang B, Eng C, Kumar G, Beckman KB, Sen S, Choudhry S, Meade K, Lenoir M, Watson HG, Thyne S, Williams LK, Kumar R, Weiss KB, Grammer LC, Avila PC, Schleimer RP, Burchard EG, Brenner R. (2008) An African-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severity. Human Molecular Genetics, in press.
  12. Sen S, Johannes F, Broman KW. (2008) Selective genotyping and phenotyping strategies in a complex trait context. CBMB Working Paper
  13. J.S. Song*, X. Liu*, X.S. Liu, and X. He (*co-first authors). A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Research 18 (2008) 1064–1072.
  14. Xiao Y, Segal MR. (2008) Biological sequence classification utilizing positive and unlabeled data. Bioinformatics, 24:1198-1205. Limited Access
  15. Xiao Y, Segal MR, Houseman EA, Wiemels J, Wiencke J, Zheng S, Wrensch M, Christensen B, Marsit C, Kelsey K,Nelson H, Karagas M, Yeh R-F. (2008) Analysis of high-throughput DNA methylation bead arrays utilizing Bayesian genotyping algorithms. Proceedings of The International Conference on BioMedical Engineering and Informatics (BMEI2008), Volume 1, 447-452.
  16. Y. Zhang, H. Shin, J.S. Song, Y. Lei, and X.S. Liu. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 9 (2008) 537.

2007

  1. Busch K, Keller T, Fuchs U, Yeh RF, Harbott J, Klose I, Wiemels J, Novosel A, Reiter A, Borkhardt A. (2007) Identification of two distinct MYC breakpoint clusters and their association with various IGH breakpoint regions in the t(8;14) translocations in sporadic Burkitt-lymphoma. Leukemia, Epub May 31.
  2. Byrd KN, Huey B, Roydasgupta R, Fridlyand J, Snijders AM, Albertson DG. (2007) FBXW7 and DNA copy number instability. Breast Cancer Research and Treatment. Epub.
  3. Cascio M, Xing Y, Gong D, Popovich J, Eger EI, Sen S, Peltz G, Sonner JM. (2007) Mouse chromosome 7 harbors a quantitative trait locus for isoflurane minimum alveolar concentration. Anesthesia and Analgesia. 105:381-385.
  4. Climent J, Dimitrow P, Fridlyand J, Palacios J, Siebert R, Albertson DG, Gray JW, Pinkel D, Lluch A, Martinez-Climent JA. (2007) Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancer. Cancer Research. 67(2):818-26.
  5. Coro ES, Chang WLW, Doucett VP, Xiao Y, Erle DJ, Baumgarth N. (2007) Type I interferon directly activates B cells for maximal early antibody response to influenza virus infection. Journal of Immunology. 178(3):1457-1467.
  6. Dreszer TR, Wall GD, Haussler D, Pollard KS. (2007) Biased clustered substitutions in the human genome: the footprints of male driven biased gene conversion. Genome Research, 17:1420-1430. Open access
  7. Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG. (2007) Genome position and gene amplification. Genome Biology. 8(6):R120.
  8. Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. (2007) Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Systems Biology, 1:56. Open access
  9. Lindquist K, Sen S, Cauley JA, Ferrell RE, Penninx B, Harris T, Li R, Cummings SR, Yaffe K. (2007) Estrogen receptor genotype and risk of cognitive impairment in elders: Findings from the Health ABC study. Neurobiology of Aging, in press.
  10. Magalhaes TR, Palmer J, Tomancak P, Pollard KS. (2007) Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach, BMC Neuroscience, 8:59. Open access
  11. Manichaikul A, Palmer A, Sen S, Broman KW. (2007) Significance thresholds for quantitative trait locus mapping under selective genotyping. Genetics, in press.
  12. F. Ozsolak* , J.S. Song* , X.S. Liu, D.E. Fisher (* co-first authors). High-throughput mapping of the chromatin structure of human promoters. Nature Biotech 25 (2007) 244–248.
  13. Satagopan JM, Sen S, Churchill GA. (2007) Sequential quantitative trait locus mapping in experimental crosses. Statistical Applications in Genetics and Molecular Biology, 6: Article 12.
  14. Sen S, Satagopan JM, Broman, KW, and Churchill GA. (2007) R/qtlDesign: Inbred line cross experimental design. Mammalian Genome. 18:87-93. CBMB Working Paper
  15. J.S. Song*, W.E. Johnson*, X. Zhu*, X. Zhang, W. Li, A.K. Manrai, J.S. Liu, R. Chen, and X.S. Liu (*co-first authors). Model-based analysis of two-color arrays (MA2C). Genome Biol 8(8) (2007) R178.
  16. J.S. Song*, K. Maghsoudi*, W. Li, E. Fox, J. Quackenbush, and X. Shirley Liu (*co-first authors). Microarray blob-defect removal improves array analysis. Bioinformatics 23(8) (2007) 966-71.
  17. Y.S. Song and J.S. Song. Analytic Computation of the Expectation of the Linkage Disequilibrium Coe?cient r2 . Theoretical Population Biology 71 (2007) 49-60.
  18. Taylor SL, Temple Lang D, Pollard KS. (2007) Improvements to the multiple testing package multtest. R News, 7(3):52-55. Open access
  19. Thorns C, Bastian B, Pinkel D, Roydasgupta R, Fridlyand J, Merz H, Krokowski M, Bernd HW, Feller AC. (2007) Chromosomal aberrations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma unspecified: A matrix-based CGH approach. Genes, Chromosomes and Cancer. 46(1):37-44.
  20. Ware ML, Hirose Y, Scheithauer BW, Yeh RF, Mayo MC, Smith JS, Chang S, Cha S, Tihan T, Feuerstein BG. (2007) Genetic aberrations in gliomatosis cerebri. Neurosurgery. 60(1):150-8.
  21. Williams EO, Xiao Y, Sickles H, Shafer P, Yona G, Yang JYH and Lin DM. (2007) Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers. BMC Developmental Biology. 16;7:48.
  22. Xiao Y, Segal MR, Yang YH, Yeh RF. (2007) A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics. 23(12):1459-1467. Open Access
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2006

  1. Albertson DG, Snijders AM, Fridlyand J, Jordan R, Pinkel D, Schmidt B. (2006) Comprehensive analysis of tumors by array comparative genomic hybridization: more is better. Cancer Research. 66(7):3955-3956.
  2. Barbour JD, Hecht FM, Little SJ, Markowitz M, Daar ES, Kelleher AD, Kaldor J, Routy JP, Campbell TB, Rosenberg E, Schafer K, Wood K, Segal MR, Weidler J, Bates M, Grant RM. (2006) Greater CD4+ T cell responses during anti-retroviral therapy associates with lower viral pol replication capacity. AIDS. 20(16):2123-5.
  3. 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. (2006) Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Molecular Cancer Therapeutics. 5(4):853-867.
  4. J. Carroll, C. Meyer, J.S. Song, W. Li, T.R. Geistlinger, J. Eeckhoute, A.S. Brodsky, E.K. Keeton, K.C. Fertuck, G.F. Hall, Q. Wang, S. Bekiranov, V. Sementchenko, E.A. Fox, P.A. Silver, T.R. Gingeras, X.S. Liu, and M. Brown. Genome Wide Analysis of Estrogen Receptor Binding Sites. Nature Genetics 38 (2006) 1289–1297.
  5. Chen Y, Toland AE, McLennan J, Fridlyand J, Crawford B, Costello JF, Ziegler JL. (2006) Lack of germline promoter methylation in BRCA1 negative families with familial breast cancer. Genetic Testing. 10(4):281-4.
  6. Chin K., DevVries S., Fridlyand J., Spellman P., Roydasgupta R., Kuo WL, Lapuk A, Neve R, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng S, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson D, Waldman F, Gray JW. (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 10(6):529-41.
  7. Fridlyand J*, Snijders AM*, Ylstra B* (*equal authorship), 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. (2006) Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 6:96.
  8. Hoopes RR, Middleton FA, Sen S, Hueber PA, Reid R, Bushinsky DA, Scheinman SJ. (2006) Isolation and confirmation of calcium excretion QTL on chromosome 1 in GHS congenic rats. Journal of the American Society of Nephrology. 17(5):1292-304.
  9. X. Ji, W. Li, J. Song, L. Wei, and X.S. Liu. CEAS: cis-regulatory element annotation system. Nucleic Acids Res 34 (2006) W551-4.
  10. Manichaikul A, Dupuis J, Sen S, Broman KW. (2006) Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus. Genetics. 174(1):481-9.
  11. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 10(6):515-27.
  12. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genetics, 2(10). Details of accelerated regions   Open access
  13. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443:167-172. Limited Access   UC Davis Press Release
  14. Reynolds PA, Sigaroudinia M, Zrdo G, Wilson MB, Benton GM, Miller CJ, Hong C, Fridlyand J, Costello JF, Tlsty TD. (2006) Tumor suppressor P16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells. Journal of Biological Chemistry. 281(34):24790-802.
  15. Rubenstein 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. (2006) Gene expression and angiotropism in primary CNS lymphoma. Blood. 107(9):3716-3723.
  16. Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. (2006) The UCSC Archaeal Genome Browser. Nucleic Acids Research, 34, Database issue: D407-D410. Open access
  17. Segal MR. (August 16, 2006) Chess, chance and conspiracy. Statistical Science. In Press. CBMB Working Paper
  18. Segal MR. (2006) Microarray gene expression data with linked survival phenotypes: Diffuse large-B-cell lymphoma revisited. Biostatistics. 7:268-285. CBMB Working Paper
  19. Segal MR. (2006) Validation in Genomics: CpG Island Methylation Revisited. Statistical Applications in Genetics and Molecular Biology. 5(1):Article 29. CBMB Working Paper
  20. Siepel A, Pollard KS, Haussler D. (2006) New methods for detecting lineage-specific selection. Proceedings of the 10th International Conference on Research in Computational Molecular Biology, 190-205. Open access
  21. Trautmann K, Terdiman JP, French AJ, Roydasgupta R, Sein N, Kakar S, Fridlyand J, Snijders AM, Albertson DG, Thibodeau SN, Waldman FM. (2006) Chromosomal instability in microsatellite-unstable and stable colon cancer. Clinical Cancer Research 12(21):6379-85.
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2005

  1. Birkner MD, Pollard KS, Dudoit S, van der Laan MJ. (2005) Multiple testing procedures and applications to genomics. UC Berkeley Division of Biostatistics Working Paper Series, No. 168. Working Paper
  2. Blaveri E, Brewer JL, Roydasgupta R, Fridlyand J, DeVries S, Koppie T, Pejevar S, Mejat K, Carroll P, Simko JP and Waldman FM . (2005) Bladder cancer stage and outcome defined by array based comparative genomic hybridization. Clinical Cancer Research. 11(19 Pt 1):7012-7022.
  3. 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. (2005) Therapy induced malignant neoplasms in Nf1 mutant mice. Cancer Cell. 8(4):337-348.
  4. The Chimpanzee Sequencing and Analysis Consortium. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437:69-87. Open access   Press Release
  5. 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. (2005) Epigenome analyses using BAC microarrays identifies evolutionary conservation of tissue-specific methylation of SHANK3. Nature Genetics. 37(6):645-51.
  6. Collin GB, Maddatu TP, Sen S, and Naggert JK. (2005) Genetic modifiers interact with Cpefat to affect body weight, adiposity, and hyperglycemia. Physiological Genomics. 22:182-190.
  7. Curtin JA, Fridlyand J, Kageshita T, Patel H, Busam K, Kutzner H, Cho KH, Aiba S, Brocker EB, LeBoit PE, Pinkel D, Bastian BC. (2005) Distinct sets of genetic alterations in melanoma. New England Journal of Medicine. 353(20):2135-2147.
  8. Fernald GH, Yeh RF, Hauser SL, Oksenberg JR, Baranzini SE. (2005) Mapping gene activity in complex disorders: Integration of expression and genomic scans for multiple sclerosis. Journal of Neuroimmunology. 167(1-2):157-69.
  9. Hausmann N, Juenger TE, Sen S, Stowe KA, Dawson TE, Simms EL. (2005) Quantitative trait loci (QTL) affecting δ13C and response to differential water availability in Arabidopsis thaliana. Evolution. 59:81-96.
  10. Juenger TE, McKay JK, Hausmann N, Keurentjes J, Sen S, Stowe KA, Dawson TE, Simms EL, Richards JH. (2005) Identification and characterization of QTL underlying whole-plant physiology in Arabidopsis thaliana: δ13C, stomatal conductance, and transpiration efficiency. Plant, Cell, and the Environment. 28:697-708.
  11. Juenger TE, Sen S, Stowe KA, Simms EL. (2005) Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana. Genetica. 123:87-105.
  12. Mistry AR, Felix CA, Whitmarsh R, Mason A, Reiter A, Cassinat B, Parry A, Walz C, Wiemels JL, Segal MR, Ades L, Blair IA, Osheroff N, Littlewood TJ, Lafage-Pochitaloff M, Cross NCP, Chomienne C, Solomon E, Fenaux P, Grimwade D. (2005) Genomic breakpoint cloning and a functional assay of DNA topoisomerase II cleavage reveals translocation mechanism underlying formation of t(15;17) chromosomal translocation in therapy-related acute promyelocytic leukaemia. New England Journal of Medicine. 352:1529-1538.
  13. Pollard KS, Dudoit S, van der Laan MJ. (2005) Multiple Testing Procedures: R multtest Package and Applications to Genomics. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, Editors. Springer Statistics for Biology and Health Series, 251-272. Amazon.com  Working Paper
  14. Pollard KS, van der Laan MJ. (2005) Cluster Analysis of Genomic Data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, Editors. Springer Statistics for Biology and Health Series, 209-229. Amazon.com   Working Paper
  15. Pollard KS, Birkner MD, Dudoit S, van der Laan MJ. (2005) Test statistics null distributions in multiple testing: simulation studies and applications to genomics. Numéro double spécial Statistique et Biopuces, Journal de la Société Française de Statistique, 146(1-2):77-115. Working Paper
  16. Salomonis NG, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. (2005) Identifying genetic networks underlying myometrial transition to labor. Genome Biology, 6:R12. Open access
  17. Sen S. (July 15, 2005) Cluster Computing: When Many Hands Make Light Work. CBMB Working Paper
  18. Sen S, Satagopan JM, and Churchill GA. (2005) Quantitative trait locus study design from an information perspective. Genetics. 170:447-464. PDF See the supplementary information page for code used to generate the figures in the paper and for results derived using symbolic computation.
  19. Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao J-H, Jain AN, Jones SJM, Marra M, Balmain A, Pinkel D, Albertson DG. (2005) Detection and mapping of segmental and sequence variations among genomes of laboratoty mice using BAC array CGH. Genome Research . 15(2):302-11.
  20. Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RC, Albertson DG. (2005) Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene. 24(26):4232-4242.
  21. Willenbrock H and Fridlyand J. (2005) A comparison study: applying segmentation to array CGH data for downstream analysis. Bioinformatics. 21(22):4084-91.
  22. Xiao Y, Segal MR. (September 16, 2005) Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation. Statistical Applications in Genetics and Molecular Biology 4(1):Article 25. CBMB Working Paper
  23. Xiao Y, Segal MR, Yang YH. (2005) Stepwise Normalization of Two-Channel Spotted Microarrays. Statistical Applications in Genetics and Molecular Biology. 4(1): Article 4. CBMB Working Paper
  24. Xiao Y, Yang YH, Burckin TA, Shiue L, Hartzog GA, Segal MR. (2005) Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing. PLoS Computational Biology. 1(4):e39. CBMB Working Paper
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2004

  1. Arrasate M, Mitra S, Schweitzer E, Segal MR, Finkbeiner S. (2004) Inclusion body formation reduces mutant huntingtin levels and the risk of polyglutamine-dependent death in neurons. Nature. 431:805-810.
  2. Barbour JD, Hecht FM, Wrin T, Liegler TJ, Ramstead CA, Busch MP, Segal MR, Petropoulos CJ, Grant RM. (2004) Persistence of primary drug resistance among recently HIV-1 infected adults. AIDS. 18:1683-1689.
  3. Barbour JD, Hecht FM, Wrin T, Segal MR, Spotts GE, Warmerdam MS, Hellman NS, Petropoulos CJ, Grant RM. (2004) Higher CD4+ T cell counts associated with low viral pro/pol replication capacity among treatment naive adults in early HIV-1 infection. Journal of Infectious Diseases. 190:251-256.
  4. Bouxsein ML, Uchiyama T, Rosen CJ, Schultz KL, Donahue LR, Turner CH, Sen S, Churchill GA, Muller R, Beamer WG. (2004) Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in mice. Journal of Bone and Mineral Research. 19:587-99.
  5. Cummings MP, Segal MR. (2004) Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis. BMC Bioinformatics. 5:137.
  6. Dudoit S, van der Laan MJ, Pollard KS. (2004) Multiple testing. Part I. Single-step procedures for control of general type I error rates. Statistical Applications in Genetics and Molecular Biology, 3(1): article 13. Open access
  7. Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB. (2004) RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Research. 32:W187-90.
  8. Fridlyand J, Snijders AM, Pinkel D, Albertson DG and Jain AN. (2004) Hidden Markov models approach to the analysis of array CGH data. Special Genomic Issue of the Journal of Multivariate Analysis. 90(1):132-153.
  9. Gui J, Li H. (March 1, 2004) Penalized Cox Regression Analysis in the High-Dimensional and Low-sample Size Settings, with Applications to Microarray Gene Expression Data. CBMB Working Paper
  10. Hager JH, Hodgson JG, Fridlyand J, Hariono S, Gray JW, Hanahan D. (2004) Oncogene expression and genetic background influence the frequency of DNA copy number abnormalities in mouse pancreatic islet cell carcinomas. Cancer Research. 64(7):2406-2410.
  11. Hong F, Li H. (November 10, 2004) Functional Empirical Bayes Methods for Identifying Genes with Different Time-course Expression Profiles. CBMB Working Paper
  12. Korstanje R, Eriksson P, Samnegard A, Olsson PG, Forsman-Semb K, Sen S, Churchill GA, Rollins J, Harris S, Hamsten A, Paigen B. (2004) Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humans. Atherosclerosis. 177:443-50.
  13. Li H, Gui J. (March 1, 2004) Partial Cox Regression Analysis for High-Dimensional Microarray Gene Expression Data. CBMB Working Paper
  14. Li L, Li H. (February 1, 2004) Dimension Reduction Methods for Microarrays with Application to Censored Survival Data. CBMB Working Paper
  15. Maldonado JL, Timmerman L, Fridlyand J, Bastian BC. (2004) Mechanisms of cell-cycle arrest in Spitz nevi with constitutive activation of the MAP-kinase pathway. American Journal of Pathology. 164(5):1783-1787.
  16. Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM. (2004) High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis. 25(8):1345-1357.
  17. Paris PL, Andaya A, Fridlyand J, et al. (2004) Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Human Molecular Genetics. 13(13):1303-1313.
  18. Rabert D, Xiao Y, Yiangou Y, Kreder D, Sangameswaran L, Segal MR, Hunt CA, Birch R, Anand P. (2004) Plasticity of gene expression in injured human dorsal root ganglia revealed by GeneChip oligonucleotide microarrays. Journal of Clinical Neuroscience. 11:289-299.
  19. Segal MR. (April 14, 2004) Machine Learning Benchmarks and Random Forest Regression. CBMB Working Paper
  20. Segal MR, Barbour JD, Grant RM. (2004) Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests. Statistical Applications in Genetics and Molecular Biology 3(1):Article 2. PDF
  21. Sen S, Ferdig M. (2004) QTL analysis for discovery of genes involved in drug responses. Current Drug Targets Infectious Disorders. 4:53-63.
  22. Sun W, Li H. (2004) Ascertainment-Adjusted Maximum Likelihood Estimation for the Additive Genetic Gamma Frailty Model. Lifetime Data Analysis. 10:229-45. Limited Access
  23. van der Laan MJ, Dudoit S, Pollard KS. (2004) Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Statistical Applications in Genetics and Molecular Biology, 3(1): article 15. Open access
  24. van der Laan MJ, Dudoit S, Pollard KS. (2004) Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Statistical Applications in Genetics and Molecular Biology, 3(1): article 14. Open access
  25. Yang YH, Xiao Y, Segal MR. (2004) Identifying Differentially Expressed Genes from Microarray Experiments via Statistic Synthesis. Bioinformatics 21:1084-93, 2005. CBMB Working Paper
  26. Zhang C, Chen K, Seldin MF, Li H. (2004) A Hidden Markov Modeling Approach for Admixture Mapping Based on Case-Control Data. Genetic Epidemiology. 27:225-39. CBMB Working Paper
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2003

  1. Broman KW, Wu H, Sen S, Churchill GA. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics. 19:889-890.
  2. Bureau A, Shiboski SC, Hughes JP. (2003) Applications of continuous time hidden Markov models to the study of misclassified disease outcomes. Statistics in Medicine. 22(3):441-62.
  3. Dudoit S*, Fridlyand J* (equal authorship). (2003) Bagging to improve the accuracy of a clustering procedure. Bioinformatics. 19(9):1090-9.
  4. Glidden DV, Liang K-Y, Chiu Y-F, Pulver AE. (2003) Multipoint affected sibpair linkage methods for localizing susceptibility genes for complex diseases. Genetic Epidemiology. 24:107-177.
  5. Hackett CS, Hodgson JG, Law ME, Fridlyand J, Osoegawa K, de Jong PJ, Nowak NJ, Pinkel D, Albertson DG, Jain A, Jenkins R, Gray JW, Weiss WA. (2003) Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Research. 63(17):5266-73.
  6. Hoopes RR, Reid R, Sen S, Szpirer C, Dixon P, Pannet A, Thakker RV, Bushinsky DA, Scheinman SJ. (2003) Quantitative trait loci for hypercalciuria in a rat model of kidney stone disease. Journal of the American Society of Nephrology. 14:1844-1850.
  7. Korkola JE, DeVries S, Fridlyand J, Hwang ES, Estep AL, Chen YY, Chew KL, Dairkee SH, Jensen RM, Waldman FM. (2003) Differentiation of lobular vs ductal breast carcinoma by expression microarray analysis. Cancer Research. 63(21):7167-75.
  8. Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC. (2003) Determinants of BRAF mutations in primary melanomas. Journal of the National Cancer Institute. 95(24):1878-1890.
  9. Nelson DO and Fridlyand J. (2003) Designing meaningful measures of read length for data produced by DNA sequencers. IMS Lecture Notes - Monograph Series, Vol. 40.
  10. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schroder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, 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(3):763-70.
  11. Pollard KS, van der Laan MJ. (2003) Multiple testing for gene expression data: an investigation of null distributions with consequences for the permutation test. Proceedings of the 2003 International MultiConference in Computer Science and Engineering, METMBS'03 Conference, 3-9. PDF
  12. Segal MR, Dahlquist KD, Conklin BR. (2003) Regression approaches for microarray data analysis. Journal of Computational Biology. 10:961-980. PDF
  13. Snijders AM, Nowee ME, Fridlyand J, Piek JM, Dorsman JC, Jain AN, Pinkel D, van Diest PJ, Verheijen RH, Albertson DG. (2003) Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene. 22(27):4281-6.
  14. Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG. (2003) Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene. 22(28):4370-9.
  15. van der Laan MJ, Pollard KS, Bryan J. (2003) A new partitioning around medoids algorithm. Journal of Statistical Computation and Simulation, 73(8):575-584. Working Paper
  16. van der Laan MJ, Pollard KS. (2003) Hybrid clustering of gene expression data with visualization and the bootstrap. Journal of Statistical Planning and Inference, 117:275-303. Working Paper
  17. Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM. (2003) Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Research. 63(11):2872-80.
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2002

  1. Barbour JD, Wrin T, Grant RM, Martin JN, Segal MR, Petropoulos CJ, Deeks SG. (2002) Evolution of phenotypic drug susceptibility and viral replication capacity during long-term virologic failure of protease inhibitor therapy in human immunodeficiency virus-infected adults. Journal of Virology. 76:11104-12.
  2. Bryan J, Pollard KS, van der Laan MJ. (2002) Paired and unpaired comparison and clustering with gene expression data. Statistica Sinica, 12(1):87-110. Working Paper
  3. Dudoit S*, Fridlyand J* (*equal authorship). (2002) A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biology. 3(7):0036.1-0036.21.
  4. Dudoit S*, Fridlyand J* (*equal authorship), Speed TP. (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. Journal of the American Statistical Association. 97:77-87.
  5. Fridlyand J, Dudoit S. (2002) Classification in microarray experiments. In Understanding and Using Microarrays Analysis Techniques: A Practical Guide. Kluwer Academic Press.
  6. Glidden DV. (2002) Rejoinder to the discussion of P.R. Burton and M.P. Epstein. Genetic Epidemiology. 23:219-20.
  7. Glidden DV, Liang K-Y. (2002) Ascertainment adjustment in complex diseases (with discussion). Genetic Epidemiology. 23:201-208.
  8. Keles S*, Segal MR* (*equal authorship). (2002) Residual-based tree-structured survival analysis. Statistics in Medicine. 21:313-326.
  9. Li H, Zhong X. (2002) Multivariate survival models induced by genetic frailties, with application to linkage analysis. Biostatistics. 3(1):57-75.
  10. Ormoneit D, Sen S. (2002) Kernel based reinforcement learning. Machine Learning. 49:161-178.
  11. Pollard KS, van der Laan MJ. (2002) Resampling-based multiple testing: Asymptotic control of type I error and applications to gene expression data. Journal of Statistical Planning and Inference, 125:85-100. Working Paper
  12. Pollard KS, van der Laan MJ. (2002) New methods for identifying significant clusters in gene expression data. 2002 Proceedings of the American Statistical Association, Biometrics Section [CD-ROM]. PDF
  13. Pollard KS, van der Laan MJ. (2002) A method to identify significant clusters in gene expression data. Proceedings of SCI 2002, Vol. II: 318-325. Working Paper
  14. Pollard KS, van der Laan MJ. (2002) Statistical inference for simultaneous clustering of gene expression data. In Nonlinear Estimation and Classification. Denison DD, Hansen MH, Holmes C, Mallick B, Yu B, Editors. Springer-Verlag, 305-320. Amazon.com  PDF
  15. Pollard KS, van der Laan MJ. (2002) Statistical inference for simultaneous clustering of gene expression data. Mathematical Biosciences, 176(1):99-121. Working Paper
  16. Segal MR, Wiemels JL. (2002) Clustering of translocation breakpoints. Journal of the American Statistical Association. 97:66-76.
  17. Symons RC, Daly MJ, Fridlyand J, Speed TP, Cook WD, Gerondakis S, Harris AW, and Foote SJ. (2002) Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E(mu)-v-abl transgenic mice. Proceedings of the National Academy of Science. 99(17):11299-304.
  18. Wiemels JL, Leonard BC, Wang Y, Segal MR, Hunger SP, Smith MT, Crouse V, Ma X, Buffler PA, Pine SR. (2002) Site-specific translocation and evidence of postnatal origin of the t(1;19) E2A-PBX1 fusion in childhood acute lymphoblastic leukemia. Proceedings of the National Academy of Sciences. 99:15101-15106.
  19. Xiao Y*, Segal MR* (*equal authorship), Rabert D, Ahn AH, Anand P, Sangameswaran L, Hu D, Hunt AC. (2002) Application of resampling-based multiple testing in the analysis of gene expression in human peripheral nerve injury. BMC Genomics. 3:1-29.
  20. Yang YH, Buckley MJ, Dudoit S, Speed TP. (2002) Comparison of methods for image analysis of cDNA microarray data. Journal of Computational and Graphical Statistics. 11:108-136.
  21. Yang YH, Speed T. (2002) Design issues for cDNA microarray experiments. Nature Reviews. 3:579-589.
  22. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research. 30(4):e15.
  23. Yeh R-F*, Fairbrother WG* (*equal authorship), Sharp PA, Burge CB. (2002) Predictive identification of exonic splicing enhancers in human genes. Science Express. (10.1126/science.1073774). Limited Access
  24. Yeh R-F, Speed TP, Waterman MS, Li X. (October 11, 2002) Predicting Progress in Shotgun Sequencing with Paired Ends. CBMB Working Paper
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2001

  1. Beamer WG, Shultz KL, Donahue LR, Churchill GA, Sen S, Wergedal JR, Baylink DJ, and Rosen CJ. (2001) Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3H/HeJ inbred strains of mice. Journal of Bone and Mineral Research. 16:1195-1206.
  2. Kim JH, Sen S, Avery CS, Simpson EM, Churchill GA, Nishina PM, Naggert JK. (2001) Genetic analysis of a new mouse model for non-insulin-dependent diabetes. Genomics. 74:273-286.
  3. International Human Genome Sequencing Consortium. (2001) Initial Sequencing and Analysis of the Human Genome. Nature. 409:860-921. (J Fridlyand listed as a member of JGI sequencing team.)
  4. Li H, Hong F. (2001) Cluster-Rasch models for microarray gene expression data. Genome Biology. 2(8):research0031.1-0031.13.
  5. Segal MR, Cummings MP, Hubbard AE. (2001) Relating amino acid sequence to phenotype: Analysis of peptide binding data. Biometrics. 57:632-43. PDF
  6. Segal MR, Wiemels JL. (2001) Clustering of translocation breakpoints. Journal of the American Statistical Association. 97:66-76. PDF
  7. Sen S. (June 1, 2001) A note on the mating scheme used by the Mutagenesis Project. CBMB Working Paper
  8. Sen S, Churchill G. (2001) A statistical framework for quantitative trait mapping. Genetics. 159:371-387. PDF | Pseudomarker software | QTL Archive
  9. Xiao Z, Greaves MF, Buffler P, Smith MT, Segal MR, Dicks BM, Wiencke JK, Wiemels JL. (2001) Genomic structure of t(8;21) AML1-ETO fusions in childhood acute myeloid leukemia indicate etiologic clues to translocation formation. Leukemia. 15:1906-1913.
  10. Yang YH, Buckley MJ, Speed TP. (2001) Analysis of cDNA microarray images. Briefings in Bioinformatics. 2(4):341-9.
  11. Yeh R-F, Lim L, Burge CB. (2001) Computational inference of homologous gene structures in the human genome. Genome Research. 11:803-816.
Top.

2000

  1. Bureau A, Hughes JP, Shiboski S. (2000) An S-PLUS implementation of hidden Markov models in continuous time. Journal of Computational and Graphical Statistics. 9(4):621-32.
  2. Li H, Hsu L. (2000) Effects of Ages at Onset on the Power of the Affected Sib Pair and Transmission/Disequilibrium Tests. Annals of Human Genetics. 64:239-54.
  3. Segal MR, Salamon H, Small PM. (2000) Comparing DNA fingerprints of infectious organisms. Statistical Science. 15:27-45.
  4. Sen S, Seburn K. (June 1, 2000) An algorithm for detecting phenotypic mutants for the JAX neuroscience mutagenesis facility. CBMB Working Paper