1. Lin KI, Tam CS, Keating MJ, Wierda WG, O'Brien S, Lerner S, Coombes KR, Schlette E, Ferrajoli A, Barron LL, Kipps TJ, Rassenti L, Faderl S, Kantarjian H, Abruzzo LV. Relevance of the immunoglobulin VH somatic mutation status in patients with chronic lymphocytic leukemia treated with fludarabine, cyclophosphamide, and rituximab (FCR) or related chemoimmunotherapy regimens. (2008) Blood. :.
  2. Gunn SR, Bolla AR, Barron LL, Gorre ME, Mohammed MS, Bahler DW, Mellink CH, van Oers MH, Keating MJ, Ferrajoli A, Coombes KR, Abruzzo LV, Robetorye RS. Array CGH analysis of chronic lymphocytic leukemia reveals frequent cryptic monoallelic and biallelic deletions of chromosome 22q11 that include the PRAME gene. (2008) Leuk Res. :.
  3. Deus HF, Stanislaus R, Behrens C, Wistuba I, Minna JD, Garner HR, Swisher SG, Roth J, Correa A, Broom B, Coombes K, Almeida JS. Data Driven Semantic Integration of Translational Lung Cancer Research at MDAnderson Cancer Center. (2008) AMIA Annu Symp Proc. :927.
  4. Kornblau SM, Tibes R, Qiu Y, Chen W, Kantarjian HM, Andreeff M, Coombes KR, Mills GB. Functional proteomic profiling of AML predicts response and survival. (2008) Blood. :.
  5. Park HS, Park WS, Bondaruk J, Tanaka N, Katayama H, Lee S, Spiess PE, Steinberg JR, Wang Z, Katz RL, Dinney C, Elias KJ, Lotan Y, Naeem RC, Baggerly K, Sen S, Grossman HB, Czerniak B. Quantitation of Aurora kinase A gene copy number in urine sediments and bladder cancer detection. (2008) J Natl Cancer Inst. 100(19):1401-11. Epub 2008 Sep 23.
  6. Zuo X, Morris JS, Shureiqi I. Chromatin modification requirements for 15-lipoxygenase-1 transcriptional reactivation in colon cancer cells. (2008) J Biol Chem. 283(46):31341-7. Epub 2008 Sep 17.
  7. Deus HF, Stanislaus R, Veiga DF, Behrens C, Wistuba II, Minna JD, Garner HR, Swisher SG, Roth JA, Correa AM, Broom B, Coombes K, Chang A, Vogel LH, Almeida JS. A Semantic Web management model for integrative biomedical informatics. (2008) PLoS ONE. 3(8):e2946.
  8. Andreeff M, Ruvolo V, Gadgil S, Zeng C, Coombes K, Chen W, Kornblau S, Barón AE, Drabkin HA. HOX expression patterns identify a common signature for favorable AML. (2008) Leukemia. 22(11):2041-7. Epub 2008 Jul 31.
  9. Colella S, Richards KL, Bachinski LL, Baggerly KA, Tsavachidis S, Lang JC, Schuller DE, Krahe R. Molecular signatures of metastasis in head and neck cancer. (2008) Head Neck. 30(10):1273-83.
  10. Gold D, Mallick B, Coombes K. Real-time gene expression: statistical challenges in design and inference. (2008) J Comput Biol. 15(6):611-23.
  11. Murph MM, Smith DL, Hennessy B, Lu Y, Joy C, Coombes KR, Mills GB. Individualized molecular medicine: linking functional proteomics to select therapeutics targeting the PI3K pathway for specific patients. (2008) Adv Exp Med Biol. 622:183-95. Review.
  12. Robinson CJ, Swift S, Johnson DD, Almeida JS. Prediction of pelvic organ prolapse using an artificial neural network. (2008) Am J Obstet Gynecol. 199(2):193.e1-6. Epub 2008 Jun 4.
  13. Suzuki H, Morris JS, Li Y, Doll MA, Hein DW, Liu J, Jiao L, Hassan MM, Day RS, Bondy ML, Abbruzzese JL, Li D. Interaction of the cytochrome P4501A2, SULT1A1 and NAT gene polymorphisms with smoking and dietary mutagen intake in modification of the risk of pancreatic cancer. (2008) Carcinogenesis. 29(6):1184-91. Epub 2008 May 21.
  14. Hennessy BT, Murph M, Nanjundan M, Carey M, Auersperg N, Almeida J, Coombes KR, Liu J, Lu Y, Gray JW, Mills GB. Ovarian cancer: linking genomics to new target discovery and molecular markers--the way ahead. (2008) Adv Exp Med Biol. 617:23-40. Review.
  15. Cheung HC, Baggerly KA, Tsavachidis S, Bachinski LL, Neubauer VL, Nixon TJ, Aldape KD, Cote GJ, Krahe R. Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays. (2008) BMC Genomics. 9:216.
  16. Majewski T, Lee S, Jeong J, Yoon DS, Kram A, Kim MS, Tuziak T, Bondaruk J, Lee S, Park WS, Tang KS, Chung W, Shen L, Ahmed SS, Johnston DA, Grossman HB, Dinney CP, Zhou JH, Harris RA, Snyder C, Filipek S, Narod SA, Watson P, Lynch HT, Gazdar A, Bar-Eli M, Wu XF, McConkey DJ, Baggerly K, Issa JP, Benedict WF, Scherer SE, Czerniak B. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy. (2008) Lab Invest. 88(7):694-721. Epub 2008 May 5.
  17. Tordai A, Wang J, Andre F, Liedtke C, Yan K, Sotiriou C, Hortobagyi GN, Symmans WF, Pusztai L. Evaluation of biological pathways involved in chemotherapy response in breast cancer. (2008) Breast Cancer Res. 10(2):R37. Epub 2008 Apr 29.
  18. Vilela M, Chou IC, Vinga S, Vasconcelos AT, Voit EO, Almeida JS. Parameter optimization in S-system models. (2008) BMC Syst Biol. 2:35.
  19. Arthur JM, Janech MG, Varghese SA, Almeida JS, Powell TB. Diagnostic and prognostic biomarkers in acute renal failure. (2008) Contrib Nephrol. 160:53-64. Review.
  20. Wu Y, Fang B, Yang XQ, Wang L, Chen D, Krasnykh V, Carter BZ, Morris JS, Shureiqi I. Therapeutic molecular targeting of 15-lipoxygenase-1 in colon cancer. (2008) Mol Ther. 16(5):886-92. Epub 2008 Mar 18.
  21. Koch N, Newhauser WD, Titt U, Gombos D, Coombes K, Starkschall G. Monte Carlo calculations and measurements of absorbed dose per monitor unit for the treatment of uveal melanoma with proton therapy. (2008) Phys Med Biol. 53(6):1581-94. Epub 2008 Feb 25.
  22. Sun M, Estrov Z, Ji Y, Coombes KR, Harris DH, Kurzrock R. Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells. (2008) Mol Cancer Ther. 7(3):464-73.
  23. Baggerly KA, Coombes KR, Neeley ES. Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. (2008) J Clin Oncol. 26(7):1186-7; author reply 1187-8.
  24. Gutstein HB, Morris JS, Annangudi SP, Sweedler JV. Microproteomics: analysis of protein diversity in small samples. (2008) Mass Spectrom Rev. 27(4):316-30. Review.
  25. McDonnell TJ, Chari NS, Cho-Vega JH, Troncoso P, Wang X, Bueso-Ramos CE, Coombes K, Brisbay S, Lopez R, Prendergast G, Logothetis C, Do KA. Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer. (2008) BMC Med Genomics. 1:1.
  26. Zuo X, Shen L, Issa JP, Moy O, Morris JS, Lippman SM, Shureiqi I. 15-Lipoxygenase-1 transcriptional silencing by DNA methyltransferase-1 independently of DNA methylation. (2008) FASEB J. 22(6):1981-92. Epub 2008 Jan 15.
  27. Morris JS, Clark BN, Gutstein HB. Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. (2008) Bioinformatics. 24(4):529-36. Epub 2008 Jan 14.
  28. Garzon R, Volinia S, Liu CG, Fernandez-Cymering C, Palumbo T, Pichiorri F, Fabbri M, Coombes K, Alder H, Nakamura T, Flomenberg N, Marcucci G, Calin GA, Kornblau SM, Kantarjian H, Bloomfield CD, Andreeff M, Croce CM. MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. (2008) Blood. 111(6):3183-9. Epub 2008 Jan 10.
  29. Stanislaus R, Arthur JM, Rajagopalan B, Moerschell R, McGlothlen B, Almeida JS. An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis. (2008) BMC Bioinformatics. 9:4.
  30. Bekele BN, Ji Y, Shen Y, Thall PF. Monitoring late-onset toxicities in phase I trials using predicted risks. (2008) Biostatistics. 9(3):442-57. Epub 2007 Dec 14.
  31. Kassouf W, Black PC, Tuziak T, Bondaruk J, Lee S, Brown GA, Adam L, Wei C, Baggerly K, Bar-Eli M, McConkey D, Czerniak B, Dinney CP. Distinctive expression pattern of ErbB family receptors signifies an aggressive variant of bladder cancer. (2008) J Urol. 179(1):353-8. Epub 2007 Nov 19.
  32. Morris JS, Brown PJ, Herrick RC, Baggerly KA, Coombes KR. Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models. (2008) Biometrics. 64(2):479-89. Epub 2007 Sep 20.


  1. Deus HF, Sousa MA, Carrico JA, Lencastre H, Almeida JS. Adapting experimental ontologies for molecular epidemiology. (2007) AMIA Annu Symp Proc. :935.
  2. Esteva FJ, Wang J, Lin F, Mejia JA, Yan K, Altundag K, Valero V, Buzdar AU, Hortobagyi GN, Symmans WF, Pusztai L. CD40 signaling predicts response to preoperative trastuzumab and concomitant paclitaxel followed by 5-fluorouracil, epirubicin, and cyclophosphamide in HER-2-overexpressing breast cancer. (2007) Breast Cancer Res. 9(6):R87.
  3. Coombes KR, Wang J, Baggerly KA. Microarrays: retracing steps. (2007) Nat Med. 13(11):1276-7; author reply 1277-8.
  4. Gutstein HB, Morris JS. Laser capture sampling and analytical issues in proteomics. (2007) Expert Rev Proteomics. 4(5):627-37. Review.
  5. Vinga S, Almeida JS. Local Renyi entropic profiles of DNA sequences. (2007) BMC Bioinformatics. 8:393.
  6. Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. (2007) Bioinformatics. 23(21):2903-9. Epub 2007 Oct 5.
  7. Ji Y, Li Y, Nebiyou Bekele B. Dose-finding in phase I clinical trials based on toxicity probability intervals. (2007) Clin Trials. 4(3):235-44.
  8. Vilela M, Borges CC, Vinga S, Vasconcelos AT, Santos H, Voit EO, Almeida JS. Automated smoother for the numerical decoupling of dynamics models. (2007) BMC Bioinformatics. 8:305.
  9. Lee S, Jeong J, Majewski T, Scherer SE, Kim MS, Tuziak T, Tang KS, Baggerly K, Grossman HB, Zhou JH, Shen L, Bondaruk J, Ahmed SS, Samanta S, Spiess P, Wu X, Filipek S, McConkey D, Bar-Eli M, Issa JP, Benedict WF, Czerniak B. Forerunner genes contiguous to RB1 contribute to the development of in situ neoplasia. (2007) Proc Natl Acad Sci U S A. 104(34):13732-7. Epub 2007 Aug 16.
  10. Nakamura T, Kuwai T, Kitadai Y, Sasaki T, Fan D, Coombes KR, Kim SJ, Fidler IJ. Zonal heterogeneity for gene expression in human pancreatic carcinoma. (2007) Cancer Res. 67(16):7597-604.
  11. Abruzzo LV, Barron LL, Anderson K, Newman RJ, Wierda WG, O'brien S, Ferrajoli A, Luthra M, Talwalkar S, Luthra R, Jones D, Keating MJ, Coombes KR. Identification and validation of biomarkers of IgV(H) mutation status in chronic lymphocytic leukemia using microfluidics quantitative real-time polymerase chain reaction technology. (2007) J Mol Diagn. 9(4):546-55. Epub 2007 Aug 9.
  12. Zhu R, Ji Y, Xiao L, Matin A. Testicular germ cell tumor susceptibility genes from the consomic 129:MOLF-Chr19 mouse strain. (2007) Mamm Genome. 18(8):584-95. Epub 2007 Aug 2.
  13. Jenny MJ, Chapman RW, Mancia A, Chen YA, McKillen DJ, Trent H, Lang P, Escoubas JM, Bachere E, Boulo V, Liu ZJ, Gross PS, Cunningham C, Cupit PM, Tanguy A, Guo X, Moraga D, Boutet I, Huvet A, De Guise S, Almeida JS, Warr GW. A cDNA microarray for Crassostrea virginica and C. gigas. (2007) Mar Biotechnol (NY). 9(5):577-91. Epub 2007 Aug 1.
  14. Hu J, He X, Baggerly KA, Coombes KR, Hennessy BT, Mills GB. Non-parametric quantification of protein lysate arrays. (2007) Bioinformatics. 23(15):1986-94. Epub 2007 Jun 28.
  15. Sun X, Zhang W, Ramdas L, Stivers DN, Jones DM, Kantarjian HM, Estey EH, Vadhan-Raj S, Medeiros LJ, Bueso-Ramos CE. Comparative analysis of genes regulated in acute myelomonocytic leukemia with and without inv(16)(p13q22) using microarray techniques, real-time PCR, immunohistochemistry, and flow cytometry immunophenotyping. (2007) Mod Pathol. 20(8):811-20. Epub 2007 Jun 15.
  16. Bohn A, Zippel B, Almeida JS, Xavier JB. Stochastic modeling for characterisation of biofilm development with discrete detachment events (sloughing). (2007) Water Sci Technol. 55(8-9):257-64.
  17. Wu C, Zhao H, Baggerly K, Carta R, Zhang L. Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays. (2007) Bioinformatics. 23(19):2566-72. Epub 2007 May 30.
  18. Hu J, He X. Enhanced quantile normalization of microarray data to reduce loss of information in gene expression profiles. (2007) Biometrics. 63(1):50-9.
  19. Hu J, Wright FA. Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance model. (2007) Biometrics. 63(1):41-9.
  20. Dubrovinsky L, Dubrovinskaia N, Crichton WA, Mikhaylushkin AS, Simak SI, Abrikosov IA, de Almeida JS, Ahuja R, Luo W, Johansson B. Noblest of all metals is structurally unstable at high pressure. (2007) Phys Rev Lett. 98(4):045503. Epub 2007 Jan 25.
  21. Hernández-Blanco C, Feng DX, Hu J, Sánchez-Vallet A, Deslandes L, Llorente F, Berrocal-Lobo M, Keller H, Barlet X, Sánchez-Rodríguez C, Anderson LK, Somerville S, Marco Y, Molina A. Impairment of cellulose synthases required for Arabidopsis secondary cell wall formation enhances disease resistance. (2007) Plant Cell. 19(3):890-903. Epub 2007 Mar 9.
  22. Varghese SA, Powell TB, Budisavljevic MN, Oates JC, Raymond JR, Almeida JS, Arthur JM. Urine biomarkers predict the cause of glomerular disease. (2007) J Am Soc Nephrol. 18(3):913-22. Epub 2007 Feb 14.
  23. Wolf G, Almeida JS, Crespo JG, Reis MA. An improved method for two-dimensional fluorescence monitoring of complex bioreactors. (2007) J Biotechnol. 128(4):801-12. Epub 2007 Jan 16.
  24. Pinto FR, Carriço JA, Ramirez M, Almeida JS. Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. (2007) BMC Bioinformatics. 8:44.
  25. Chen X, Che Y, Zhang L, Putman AH, Damaj I, Martin BR, Kendler KS, Miles MF. RhoA, encoding a Rho GTPase, is associated with smoking initiation. (2007) Genes Brain Behav. 6(8):689-97. Epub 2006 Dec 20.
  26. Nakamura T, Fidler IJ, Coombes KR. Gene expression profile of metastatic human pancreatic cancer cells depends on the organ microenvironment. (2007) Cancer Res. 67(1):139-48.
  27. He J, Pan Y, Hu J, Albarracin C, Wu Y, Dai JL. Profile of Ets gene expression in human breast carcinoma. (2007) Cancer Biol Ther. 6(1):76-82.
  28. Shureiqi I, Zuo X, Broaddus R, Wu Y, Guan B, Morris JS, Lippman SM. The transcription factor GATA-6 is overexpressed in vivo and contributes to silencing 15-LOX-1 in vitro in human colon cancer. (2007) FASEB J. 21(3):743-53. Epub 2006 Dec 13.
  29. Robalino J, Almeida JS, McKillen D, Colglazier J, Trent HF 3rd, Chen YA, Peck ME, Browdy CL, Chapman RW, Warr GW, Gross PS. Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge. (2007) Physiol Genomics. 29(1):44-56. Epub 2006 Dec 5.
  30. Karpievitch YV, Hill EG, Smolka AJ, Morris JS, Coombes KR, Baggerly KA, Almeida JS. PrepMS: TOF MS data graphical preprocessing tool. (2007) Bioinformatics. 23(2):264-5. Epub 2006 Nov 22.
  31. Mancia A, Lundqvist ML, Romano TA, Peden-Adams MM, Fair PA, Kindy MS, Ellis BC, Gattoni-Celli S, McKillen DJ, Trent HF, Chen YA, Almeida JS, Gross PS, Chapman RW, Warr GW. A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions. (2007) Dev Comp Immunol. 31(5):520-9. Epub 2006 Sep 20.
  32. Gold DL, Coombes KR, Wang J, Mallick B. Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL. (2007) Brief Bioinform. 8(2):71-7. Epub 2006 Oct 31.
  33. Kupferman ME, Patel V, Sriuranpong V, Amornphimoltham P, Jasser SA, Mandal M, Zhou G, Wang J, Coombes K, Multani A, Pathak S, Silvio Gutkind J, Myers JN. Molecular analysis of anoikis resistance in oral cavity squamous cell carcinoma. (2007) Oral Oncol. 43(5):440-54. Epub 2006 Sep 15.


  1. Broom BM, McDonnell TJ, Subramanian D. Predicting altered pathways using extendable scaffolds. (2006) Int J Bioinform Res Appl. 2(1):3-18.
  2. Almeida JS, Vinga S. Computing distribution of scale independent motifs in biological sequences. (2006) Algorithms Mol Biol. 1:18.
  3. Yin G, Li Y, Ji Y. Bayesian dose-finding in phase I/II clinical trials using toxicity and efficacy odds ratios. (2006) Biometrics. 62(3):777-84.
  4. Almeida JS, Chen C, Gorlitsky R, Stanislaus R, Aires-de-Sousa M, Eleutério P, Carriço J, Maretzek A, Bohn A, Chang A, Zhang F, Mitra R, Mills GB, Wang X, Deus HF. Data integration gets 'Sloppy'. (2006) Nat Biotechnol. 24(9):1070-1.
  5. Rohatgi PR, Mansfield PF, Crane CH, Wu TT, Sunder PK, Ross WA, Morris JS, Pisters PW, Feig BW, Gunderson LL, Ajani JA. Surgical pathology stage by American Joint Commission on Cancer criteria predicts patient survival after preoperative chemoradiation for localized gastric carcinoma. (2006) Cancer. 107(7):1475-82.
  6. Vega F, Coombes KR, Thomazy VA, Patel K, Lang W, Jones D. Tissue-specific function of lymph node fibroblastic reticulum cells. (2006) Pathobiology. 73(2):71-81.
  7. Bland AM, D'Eugenio LR, Dugan MA, Janech MG, Almeida JS, Zile MR, Arthur JM. Comparison of variability associated with sample preparation in two-dimensional gel electrophoresis of cardiac tissue. (2006) J Biomol Tech. 17(3):195-9.
  8. Carriço JA, Silva-Costa C, Melo-Cristino J, Pinto FR, de Lencastre H, Almeida JS, Ramirez M. Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. (2006) J Clin Microbiol. 44(7):2524-32.
  9. Spurgers KB, Gold DL, Coombes KR, Bohnenstiehl NL, Mullins B, Meyn RE, Logothetis CJ, McDonnell TJ. Identification of cell cycle regulatory genes as principal targets of p53-mediated transcriptional repression. (2006) J Biol Chem. 281(35):25134-42. Epub 2006 Jun 23.
  10. Ji Y, Coombes K, Zhang J, Wen S, Mitchell J, Pusztai L, Symmans WF, Wang J. RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms. (2006) Appl Bioinformatics. 5(2):89-98.
  11. Kolonin MG, Sun J, Do KA, Vidal CI, Ji Y, Baggerly KA, Pasqualini R, Arap W. Synchronous selection of homing peptides for multiple tissues by in vivo phage display. (2006) FASEB J. 20(7):979-81. Epub 2006 Mar 31.
  12. Karpievitch YV, Almeida JS. mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code. (2006) BMC Bioinformatics. 7:139.
  13. Mueller M, Wagner CL, Annibale DJ, Knapp RG, Hulsey TC, Almeida JS. Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants. (2006) BMC Med Inform Decis Mak. 6:11.
  14. Chen YA, Chou CC, Lu X, Slate EH, Peck K, Xu W, Voit EO, Almeida JS. A multivariate prediction model for microarray cross-hybridization. (2006) BMC Bioinformatics. 7:101.
  15. Xu H, Cheepala S, McCauley E, Coombes K, Xiao L, Fischer SM, Clifford JL. Chemoprevention of skin carcinogenesis by phenylretinamides: retinoid receptor-independent tumor suppression. (2006) Clin Cancer Res. 12(3 Pt 1):969-79.
  16. Mueller LN, de Brouwer JF, Almeida JS, Stal LJ, Xavier JB. Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP. (2006) BMC Ecol. 6:1.
  17. Zhang J, Ren H, Yuan P, Lang W, Zhang L, Mao L. Down-regulation of hepatoma-derived growth factor inhibits anchorage-independent growth and invasion of non-small cell lung cancer cells. (2006) Cancer Res. 66(1):18-23.
  18. Zhang J, Zhang L, Coombes KR. Gene sequence signatures revealed by mining the UniGene affiliation network. (2006) Bioinformatics. 22(4):385-91. Epub 2005 Dec 8.
  19. Giri U, Ashorn CL, Ramdas L, Stivers DN, Coombes K, El-Naggar AK, Ang KK, Story MD. Molecular signatures associated with clinical outcome in patients with high-risk head-and-neck squamous cell carcinoma treated by surgery and radiation. (2006) Int J Radiat Oncol Biol Phys. 64(3):670-7. Epub 2005 Nov 10.
  20. Zuo X, Wu Y, Morris JS, Stimmel JB, Leesnitzer LM, Fischer SM, Lippman SM, Shureiqi I. Oxidative metabolism of linoleic acid modulates PPAR-beta/delta suppression of PPAR-gamma activity. (2006) Oncogene. 25(8):1225-41.


  1. Almeida JS, McKillen DJ, Chen YA, Gross PS, Chapman RW, Warr G. Design and calibration of microarrays as universal transcriptomic environmental biosensors. (2005) Comp Funct Genomics. 6(3):132-7.
  2. Mato R, Sanches IS, Simas C, Nunes S, Carriço JA, Sousa NG, Frazão N, Saldanha J, Brito-Avô A, Almeida JS, Lencastre HD. Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal. (2005) Microb Drug Resist. 11(4):309-22.
  3. Shureiqi I, Wu Y, Chen D, Yang XL, Guan B, Morris JS, Yang P, Newman RA, Broaddus R, Hamilton SR, Lynch P, Levin B, Fischer SM, Lippman SM. The critical role of 15-lipoxygenase-1 in colorectal epithelial cell terminal differentiation and tumorigenesis. (2005) Cancer Res. 65(24):11486-92.
  4. Bast RC Jr, Badgwell D, Lu Z, Marquez R, Rosen D, Liu J, Baggerly KA, Atkinson EN, Skates S, Zhang Z, Lokshin A, Menon U, Jacobs I, Lu K. New tumor markers: CA125 and beyond. (2005) Int J Gynecol Cancer. 15 Suppl 3:274-81. Review.
  5. Oates JC, Varghese S, Bland AM, Taylor TP, Self SE, Stanislaus R, Almeida JS, Arthur JM. Prediction of urinary protein markers in lupus nephritis. (2005) Kidney Int. 68(6):2588-92.
  6. Ramaswamy A, Lin E, Chen I, Mitra R, Morrisett J, Coombes K, Ju Z, Kapoor M. Application of protein lysate microarrays to molecular marker verification and quantification. (2005) Proteome Sci. 3:9.
  7. Carriço JA, Pinto FR, Simas C, Nunes S, Sousa NG, Frazão N, de Lencastre H, Almeida JS. Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis. (2005) J Clin Microbiol. 43(11):5483-90.
  8. Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Hung MC, Kuerer HM. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. (2005) Proteomics. 5(16):4107-17.
  9. Yokoi K, Shih LC, Kobayashi R, Koomen J, Hawke D, Li D, Hamilton SR, Abbruzzese JL, Coombes KR, Fidler IJ. Serum amyloid A as a tumor marker in sera of nude mice with orthotopic human pancreatic cancer and in plasma of patients with pancreatic cancer. (2005) Int J Oncol. 27(5):1361-9.
  10. Garcia SP, Almeida JS. Multivariate phase space reconstruction by nearest neighbor embedding with different time delays. (2005) Phys Rev E Stat Nonlin Soft Matter Phys. 72(2 Pt 2):027205.
  11. Wang X, Gorlitsky R, Almeida JS. From XML to RDF: how semantic web technologies will change the design of 'omic' standards. (2005) Nat Biotechnol. 23(9):1099-103.
  12. Marquez RT, Baggerly KA, Patterson AP, Liu J, Broaddus R, Frumovitz M, Atkinson EN, Smith DI, Hartmann L, Fishman D, Berchuck A, Whitaker R, Gershenson DM, Mills GB, Bast RC Jr, Lu KH. Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon. (2005) Clin Cancer Res. 11(17):6116-26.
  13. Hu J, Kapoor M, Zhang W, Hamilton SR, Coombes KR. Analysis of dose-response effects on gene expression data with comparison of two microarray platforms. (2005) Bioinformatics. 21(17):3524-9. Epub 2005 Aug 4.
  14. Gold DL, Wang J, Coombes KR. Inter-gene correlation on oligonucleotide arrays: how much does normalization matter? (2005) Am J Pharmacogenomics. 5(4):271-9.
  15. Stec J, Wang J, Coombes K, Ayers M, Hoersch S, Gold DL, Ross JS, Hess KR, Tirrell S, Linette G, Hortobagyi GN, Fraser Symmans W, Pusztai L. Comparison of the predictive accuracy of DNA array-based multigene classifiers across cDNA arrays and Affymetrix GeneChips. (2005) J Mol Diagn. 7(3):357-67.
  16. Abruzzo LV, Wang J, Kapoor M, Medeiros LJ, Keating MJ, Edward Highsmith W, Barron LL, Cromwell CC, Coombes KR. Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays. (2005) J Mol Diagn. 7(3):337-45.
  17. Liu ZH, Anderson JA, Hu J, Friesen TL, Rasmussen JB, Faris JD. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. (2005) Theor Appl Genet. 111(4):782-94. Epub 2005 Jul 15.
  18. Wolf G, Almeida JS, Reis MA, Crespo JG. Modelling of the extractive membrane bioreactor process based on natural fluorescence fingerprints and process operation history. (2005) Water Sci Technol. 51(6-7):51-8.
  19. Koomen JM, Li D, Xiao LC, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. (2005) J Proteome Res. 4(3):972-81.
  20. Abruzzo LV, Lee KY, Fuller A, Silverman A, Keating MJ, Medeiros LJ, Coombes KR. Validation of oligonucleotide microarray data using microfluidic low-density arrays: a new statistical method to normalize real-time RT-PCR data. (2005) Biotechniques. 38(5):785-92.
  21. Hu J, Zou F, Wright FA. Practical FDR-based sample size calculations in microarray experiments. (2005) Bioinformatics. 21(15):3264-72. Epub 2005 Jun 2.
  22. Lahad JP, Mills GB, Coombes KR. Stem cell-ness: a "magic marker" for cancer. (2005) J Clin Invest. 115(6):1463-7.
  23. Wolf G, Almeida JS, Reis MA, Crespo JG. Non-mechanistic modelling of complex biofilm reactors and the role of process operation history. (2005) J Biotechnol. 117(4):367-83. Epub 2005 Mar 25.
  24. Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. (2005) Rapid Commun Mass Spectrom. 19(12):1624-36.
  25. Tuziak T, Jeong J, Majewski T, Kim MS, Steinberg J, Wang Z, Yoon DS, Kuang TC, Baggerly K, Johnston D, Czerniak B. High-resolution whole-organ mapping with SNPs and its significance to early events of carcinogenesis. (2005) Lab Invest. 85(5):689-701.
  26. Garcia SP, Almeida JS. Nearest neighbor embedding with different time delays. (2005) Phys Rev E Stat Nonlin Soft Matter Phys. 71(3 Pt 2B):037204.
  27. Mikhitarian K, Gillanders WE, Almeida JS, Hebert Martin R, Varela JC, Metcalf JS, Cole DJ, Mitas M. An innovative microarray strategy identities informative molecular markers for the detection of micrometastatic breast cancer. (2005) Clin Cancer Res. 11(10):3697-704.
  28. Almeida JS, Meletti PC, Martinez CB. Acute effects of sediments taken from an urban stream on physiological and biochemical parameters of the neotropical fish Prochilodus lineatus. (2005) Comp Biochem Physiol C Toxicol Pharmacol. 140(3-4):356-63.
  29. Esteva FJ, Sahin AA, Cristofanilli M, Coombes K, Lee SJ, Baker J, Cronin M, Walker M, Watson D, Shak S, Hortobagyi GN. Prognostic role of a multigene reverse transcriptase-PCR assay in patients with node-negative breast cancer not receiving adjuvant systemic therapy. (2005) Clin Cancer Res. 11(9):3315-9.
  30. Hu J, Coombes KR, Morris JS, Baggerly KA. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. (2005) Brief Funct Genomic Proteomic. 3(4):322-31. Review.
  31. Beach R, Chan AO, Wu TT, White JA, Morris JS, Lunagomez S, Broaddus RR, Issa JP, Hamilton SR, Rashid A. BRAF mutations in aberrant crypt foci and hyperplastic polyposis. (2005) Am J Pathol. 166(4):1069-75.
  32. Mitas M, Almeida JS, Mikhitarian K, Gillanders WE, Lewin DN, Spyropoulos DD, Hoover L, Graham A, Glenn T, King P, Cole DJ, Hawes R, Reed CE, Hoffman BJ. Accurate discrimination of Barrett's esophagus and esophageal adenocarcinoma using a quantitative three-tiered algorithm and multimarker real-time reverse transcription-PCR. (2005) Clin Cancer Res. 11(6):2205-14.
  33. Kim JH, Tuziak T, Hu L, Wang Z, Bondaruk J, Kim M, Fuller G, Dinney C, Grossman HB, Baggerly K, Zhang W, Czerniak B. Alterations in transcription clusters underlie development of bladder cancer along papillary and nonpapillary pathways. (2005) Lab Invest. 85(4):532-49.
  34. Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics profiling--a young technology begins to mature. (2005) Nat Biotechnol. 23(3):291-2.
  35. Abba MC, Hu Y, Sun H, Drake JA, Gaddis S, Baggerly K, Sahin A, Aldaz CM. Gene expression signature of estrogen receptor alpha status in breast cancer. (2005) BMC Genomics. 6(1):37.
  36. McKillen DJ, Chen YA, Chen C, Jenny MJ, Trent HF 3rd, Robalino J, McLean DC Jr, Gross PS, Chapman RW, Warr GW, Almeida JS. Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. (2005) BMC Genomics. 6(1):34.
  37. Tan FK, Hildebrand BA, Lester MS, Stivers DN, Pounds S, Zhou X, Wallis DD, Milewicz DM, Reveille JD, Mayes MD, Jin L, Arnett FC Jr. Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease. (2005) Arthritis Rheum. 52(3):865-76.
  38. Frazão N, Brito-Avô A, Simas C, Saldanha J, Mato R, Nunes S, Sousa NG, Carriço JA, Almeida JS, Santos-Sanches I, de Lencastre H. Effect of the seven-valent conjugate pneumococcal vaccine on carriage and drug resistance of Streptococcus pneumoniae in healthy children attending day-care centers in Lisbon. (2005) Pediatr Infect Dis J. 24(3):243-52.
  39. Nunes S, Sá-Leão R, Carriço J, Alves CR, Mato R, Avô AB, Saldanha J, Almeida JS, Sanches IS, de Lencastre H. Trends in drug resistance, serotypes, and molecular types of Streptococcus pneumoniae colonizing preschool-age children attending day care centers in Lisbon, Portugal: a summary of 4 years of annual surveillance. (2005) J Clin Microbiol. 43(3):1285-93.
  40. Almeida JS, Stanislaus R, Krug E, Arthur JM. Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics. (2005) Proteomics. 5(5):1242-9.
  41. Almeida JS, Nowotny H. The emergence of the ERC. (2005) Science. 307(5713):1200; author reply 1200.
  42. Chirieac LR, Swisher SG, Ajani JA, Komaki RR, Correa AM, Morris JS, Roth JA, Rashid A, Hamilton SR, Wu TT. Posttherapy pathologic stage predicts survival in patients with esophageal carcinoma receiving preoperative chemoradiation. (2005) Cancer. 103(7):1347-55.
  43. Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. (2005) J Natl Cancer Inst. 97(4):307-9.
  44. Madoff DC, Abdalla EK, Gupta S, Wu TT, Morris JS, Denys A, Wallace MJ, Morello FA Jr, Ahrar K, Murthy R, Lunagomez S, Hicks ME, Vauthey JN. Transhepatic ipsilateral right portal vein embolization extended to segment IV: improving hypertrophy and resection outcomes with spherical particles and coils. (2005) J Vasc Interv Radiol. 16(2 Pt 1):215-25.
  45. Ji Y, Wu C, Liu P, Wang J, Coombes KR. Applications of beta-mixture models in bioinformatics. (2005) Bioinformatics. 21(9):2118-22. Epub 2005 Feb 15.
  46. Koomen JM, Shih LN, Coombes KR, Li D, Xiao LC, Fidler IJ, Abbruzzese JL, Kobayashi R. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. (2005) Clin Cancer Res. 11(3):1110-8.
  47. Pawlik TM, Fritsche H, Coombes KR, Xiao L, Krishnamurthy S, Hunt KK, Pusztai L, Chen JN, Clarke CH, Arun B, Hung MC, Kuerer HM. Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry. (2005) Breast Cancer Res Treat. 89(2):149-57.
  48. Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. (2005) Bioinformatics. 21(9):1764-75. Epub 2005 Jan 26.
  49. Stanislaus R, Chen C, Franklin J, Arthur J, Almeida JS. AGML Central: web based gel proteomic infrastructure. (2005) Bioinformatics. 21(9):1754-7. Epub 2005 Jan 12.
  50. Coombes KR. Analysis of mass spectrometry profiles of the serum proteome. (2005) Clin Chem. 51(1):1-2.
  51. Ji Y, Tsui KW, Kim K. A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples. (2005) Bioinformatics. 21(7):1055-61. Epub 2004 Oct 28.
  52. Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS. Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method. (2005) Bioinformatics. 21(7):1037-45. Epub 2004 Oct 27.
  53. Le XF, Lammayot A, Gold D, Lu Y, Mao W, Chang T, Patel A, Mills GB, Bast RC Jr. Genes affecting the cell cycle, growth, maintenance, and drug sensitivity are preferentially regulated by anti-HER2 antibody through phosphatidylinositol 3-kinase-AKT signaling. (2005) J Biol Chem. 280(3):2092-104. Epub 2004 Oct 25.


  1. Baggerly KA, Edmonson SR, Morris JS, Coombes KR. High-resolution serum proteomic patterns for ovarian cancer detection. (2004) Endocr Relat Cancer. 11(4):583-4; author reply 585-7.
  2. Chen YA, McKillen DJ, Wu S, Jenny MJ, Chapman R, Gross PS, Warr GW, Almeida JS. Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. (2004) BMC Bioinformatics. 5:191.
  3. Kuerer HM, Coombes KR, Chen JN, Xiao L, Clarke C, Fritsche H, Krishnamurthy S, Marcy S, Hung MC, Hunt KK. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. (2004) Surgery. 136(5):1061-9.
  4. Hu Y, Sun H, Drake J, Kittrell F, Abba MC, Deng L, Gaddis S, Sahin A, Baggerly K, Medina D, Aldaz CM. From mice to humans: identification of commonly deregulated genes in mammary cancer via comparative SAGE studies. (2004) Cancer Res. 64(21):7748-55.
  5. Vinga S, Almeida JS. Rényi continuous entropy of DNA sequences. (2004) J Theor Biol. 231(3):377-88.
  6. Baggerly KA, Deng L, Morris JS, Aldaz CM. Overdispersed logistic regression for SAGE: modelling multiple groups and covariates. (2004) BMC Bioinformatics. 5:144.
  7. Koomen JM, Zhao H, Li D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using proteolytic peptide targeting and identification. (2004) Rapid Commun Mass Spectrom. 18(21):2537-48.
  8. Du M, Irani RA, Stivers DN, Lee SJ, Travis EL. H2-Ea deficiency is a risk factor for bleomycin-induced lung fibrosis in mice. (2004) Cancer Res. 64(19):6835-9.
  9. Abba MC, Drake JA, Hawkins KA, Hu Y, Sun H, Notcovich C, Gaddis S, Sahin A, Baggerly K, Aldaz CM. Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression. (2004) Breast Cancer Res. 6(5):R499-513.
  10. Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. (2004) Bioinformatics. 20(17):3166-78. Epub 2004 Jul 1.
  11. Rohrer B, Pinto FR, Hulse KE, Lohr HR, Zhang L, Almeida JS. Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling. (2004) J Biol Chem. 279(40):41903-10. Epub 2004 Jun 24.
  12. Yin G, Hu J. Two simulation methods for constructing confidence bands under the additive risk model. (2004) J Biopharm Stat. 14(2):389-402.
  13. Sinicrope FA, Half E, Morris JS, Lynch PM, Morrow JD, Levin B, Hawk ET, Cohen DS, Ayers GD, Stephens LC; Familial Adenomatous Polyposis Study Group. Cell proliferation and apoptotic indices predict adenoma regression in a placebo-controlled trial of celecoxib in familial adenomatous polyposis patients. (2004) Cancer Epidemiol Biomarkers Prev. 13(6):920-7.
  14. Zhang L, Wu C, Carta R, Baggerly K, Coombes KR. Response to Preprocessing of oligonucleotide array data. (2004) Nat Biotechnol. 22(6):658.
  15. Lu KH, Patterson AP, Wang L, Marquez RT, Atkinson EN, Baggerly KA, Ramoth LR, Rosen DG, Liu J, Hellstrom I, Smith D, Hartmann L, Fishman D, Berchuck A, Schmandt R, Whitaker R, Gershenson DM, Mills GB, Bast RC Jr. Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis. (2004) Clin Cancer Res. 10(10):3291-300.
  16. Mueller M, Wagner CL, Annibale DJ, Hulsey TC, Knapp RG, Almeida JS. Predicting extubation outcome in preterm newborns: a comparison of neural networks with clinical expertise and statistical modeling. (2004) Pediatr Res. 56(1):11-8. Epub 2004 May 5.
  17. Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ, Symmans WF, Wagner P, Hortobagyi GN, Laronga C, Semmes OJ, Wright GL Jr, Drake RR, Vlahou A. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. (2004) Cancer. 100(9):1814-22.
  18. Stanislaus R, Jiang LH, Swartz M, Arthur J, Almeida JS. An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. (2004) BMC Bioinformatics. 5:9.
  19. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. (2004) Bioinformatics. 20(5):777-85. Epub 2004 Jan 29.
  20. Vinga S, Gouveia-Oliveira R, Almeida JS. Comparative evaluation of word composition distances for the recognition of SCOP relationships. (2004) Bioinformatics. 20(2):206-15.
  21. Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, Koo JS, Kapoor M. A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays. (2004) BMC Genomics. 5(1):2.
  22. Spurgers KB, Coombes KR, Meyn RE, Gold DL, Logothetis CJ, Johnson TJ, McDonnell TJ. A comprehensive assessment of p53-responsive genes following adenoviral-p53 gene transfer in Bcl-2-expressing prostate cancer cells. (2004) Oncogene. 23(9):1712-23.


  1. Almeida JS, Voit EO. Neural-network-based parameter estimation in S-system models of biological networks. (2003) Genome Inform. 14:114-23.
  2. Freitas F, Temudo M, Almeida JS, Reis MA. Nutrient removal in a sequencing batch reactor operated with short anaerobic/aerobic cycles. (2003) Commun Agric Appl Biol Sci. 68(2 Pt A):85-92.
  3. Morris JS, Wang N, Lupton JR, Chapkin RS, Turner ND, Hong MY, Carroll RJ. Understanding the relationship between carcinogen-induced DNA adduct levels in distal and proximal regions of the colon. (2003) Adv Exp Med Biol. 537:105-16.
  4. Mueller M, Wagner CL, Annibale DJ, Hulsey TC, Knapp RG, Almeida JS. Web-based prediction of extubation outcome in premature infants on mechanical ventilation using an artificial neural network. (2003) AMIA Annu Symp Proc. :945.
  5. Morris JS, Baggerly KA, Coombes KR. Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE. (2003) Biometrics. 59(3):476-86.
  6. Pawlik TM, Izzo F, Cohen DS, Morris JS, Curley SA. Combined resection and radiofrequency ablation for advanced hepatic malignancies: results in 172 patients. (2003) Ann Surg Oncol. 10(9):1059-69.
  7. Kerns RT, Zhang L, Miles MF. Application of the S-score algorithm for analysis of oligonucleotide microarrays. (2003) Methods. 31(4):274-81.
  8. Coombes KR, Fritsche HA Jr, Clarke C, Chen JN, Baggerly KA, Morris JS, Xiao LC, Hung MC, Kuerer HM. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. (2003) Clin Chem. 49(10):1615-23.
  9. Baggerly KA, Morris JS, Wang J, Gold D, Xiao LC, Coombes KR. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. (2003) Proteomics. 3(9):1667-72.
  10. Hong MY, Chapkin RS, Davidson LA, Turner ND, Morris JS, Carroll RJ, Lupton JR. Fish oil enhances targeted apoptosis during colon tumor initiation in part by downregulating Bcl-2. (2003) Nutr Cancer. 46(1):44-51.
  11. Baggerly KA, Deng L, Morris JS, Aldaz CM. Differential expression in SAGE: accounting for normal between-library variation. (2003) Bioinformatics. 19(12):1477-83.
  12. Shureiqi I, Jiang W, Zuo X, Wu Y, Stimmel JB, Leesnitzer LM, Morris JS, Fan HZ, Fischer SM, Lippman SM. The 15-lipoxygenase-1 product 13-S-hydroxyoctadecadienoic acid down-regulates PPAR-delta to induce apoptosis in colorectal cancer cells. (2003) Proc Natl Acad Sci U S A. 100(17):9968-73. Epub 2003 Aug 8.
  13. Blehert DS, Palmer RJ Jr, Xavier JB, Almeida JS, Kolenbrander PE. Autoinducer 2 production by Streptococcus gordonii DL1 and the biofilm phenotype of a luxS mutant are influenced by nutritional conditions. (2003) J Bacteriol. 185(16):4851-60.
  14. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. (2003) Biotechniques. 35(1):146-50.
  15. Pusztai L, Ayers M, Stec J, Clark E, Hess K, Stivers D, Damokosh A, Sneige N, Buchholz TA, Esteva FJ, Arun B, Cristofanilli M, Booser D, Rosales M, Valero V, Adams C, Hortobagyi GN, Symmans WF. Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors. (2003) Clin Cancer Res. 9(7):2406-15.
  16. Goy A, Ramdas L, Remache YK, Gu J, Fayad L, Hayes KJ, Coombes KR, Barkoh BA, Katz R, Ford R, Cabanillas F, Gilles F. Establishment and characterization by gene expression profiling of a new diffuse large B-cell lymphoma cell line, EJ-1, carrying t(14;18) and t(8;14) translocations. (2003) Lab Invest. 83(6):913-6.
  17. Udtha M, Lee SJ, Alam R, Coombes K, Huff V. Upregulation of c-MYC in WT1-mutant tumors: assessment of WT1 putative transcriptional targets using cDNA microarray expression profiling of genetically defined Wilms' tumors. (2003) Oncogene. 22(24):3821-6.
  18. Zhang L, Miles MF, Aldape KD. A model of molecular interactions on short oligonucleotide microarrays. (2003) Nat Biotechnol. 21(7):818-21. Epub 2003 Jun 8.
  19. Cowart LA, Okamoto Y, Pinto FR, Gandy JL, Almeida JS, Hannun YA. Roles for sphingolipid biosynthesis in mediation of specific programs of the heat stress response determined through gene expression profiling. (2003) J Biol Chem. 278(32):30328-38. Epub 2003 May 9.
  20. Wolf G, Almeida JS, Crespo JG, Reis MA. Monitoring of biofilm reactors using natural fluorescence fingerprints. (2003) Water Sci Technol. 47(5):161-7.
  21. Xavier JB, White DC, Almeida JS. Automated biofilm morphology quantification from confocal laser scanning microscopy imaging. (2003) Water Sci Technol. 47(5):31-7.
  22. Madoff DC, Hicks ME, Abdalla EK, Morris JS, Vauthey JN. Portal vein embolization with polyvinyl alcohol particles and coils in preparation for major liver resection for hepatobiliary malignancy: safety and effectiveness--study in 26 patients. (2003) Radiology. 227(1):251-60. Epub 2003 Feb 28.
  23. Wang J, Hu L, Hamilton SR, Coombes KR, Zhang W. RNA amplification strategies for cDNA microarray experiments. (2003) Biotechniques. 34(2):394-400.
  24. McCarthy H, Wierda WG, Barron LL, Cromwell CC, Wang J, Coombes KR, Rangel R, Elenitoba-Johnson KS, Keating MJ, Abruzzo LV. High expression of activation-induced cytidine deaminase (AID) and splice variants is a distinctive feature of poor-prognosis chronic lymphocytic leukemia. (2003) Blood. 101(12):4903-8. Epub 2003 Feb 13.


  1. Coombes KR, Zhang L, Bueso-Ramos C, Brisbay S, Logothetis C, Roth J, Keating MJ, McDonnell TJ. TAD: a web interface and database for tissue microarrays. (2002) Appl Bioinformatics. 1(3):155-8.
  2. Morris JS, Wang N, Lupton JR, Chapkin RS, Turner ND, Hong M, Carroll RJ. A Bayesian analysis of colonic crypt structure and coordinated response to carcinogen exposure incorporating missing crypts. (2002) Biostatistics. 3(4):529-46.
  3. Lin E, Morris JS, Ayers GD. Effect of celecoxib on capecitabine-induced hand-foot syndrome and antitumor activity. (2002) Oncology (Williston Park). 16(12 Suppl No 14):31-7.
  4. Buchholz TA, Stivers DN, Stec J, Ayers M, Clark E, Bolt A, Sahin AA, Symmans WF, Hess KR, Kuerer HM, Valero V, Hortobagyi GN, Pusztai L. Global gene expression changes during neoadjuvant chemotherapy for human breast cancer. (2002) Cancer J. 8(6):461-8.
  5. Schwacke J, Almeida JS. Efficient Boolean implementation of universal sequence maps (bUSM). (2002) BMC Bioinformatics. 3:28.
  6. Coombes KR, Highsmith WE, Krogmann TA, Baggerly KA, Stivers DN, Abruzzo LV. Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. (2002) J Comput Biol. 9(4):655-69.
  7. Hu L, Wang J, Baggerly K, Wang H, Fuller GN, Hamilton SR, Coombes KR, Zhang W. Obtaining reliable information from minute amounts of RNA using cDNA microarrays. (2002) BMC Genomics. 3(1):16. Epub 2002 Jun 21.
  8. Zhang L, Wang L, Ravindranathan A, Miles MF. A new algorithm for analysis of oligonucleotide arrays: application to expression profiling in mouse brain regions. (2002) J Mol Biol. 317(2):225-35.
  9. Almeida JS, Vinga S. Universal sequence map (USM) of arbitrary discrete sequences. (2002) BMC Bioinformatics. 3:6. Epub 2002 Feb 5.
  10. Barton MC, Stivers DN. Microarray analysis of hepatic-regulated gene expression: specific applications and nonspecific problems. (2002) Hepatology. 35(3):727-9.
  11. Almeida JS. Predictive non-linear modeling of complex data by artificial neural networks. (2002) Curr Opin Biotechnol. 13(1):72-6. Review.
  12. Chan AO, Issa JP, Morris JS, Hamilton SR, Rashid A. Concordant CpG island methylation in hyperplastic polyposis. (2002) Am J Pathol. 160(2):529-36.
  13. Arap W, Kolonin MG, Trepel M, Lahdenranta J, Cardó-Vila M, Giordano RJ, Mintz PJ, Ardelt PU, Yao VJ, Vidal CI, Chen L, Flamm A, Valtanen H, Weavind LM, Hicks ME, Pollock RE, Botz GH, Bucana CD, Koivunen E, Cahill D, Troncoso P, Baggerly KA, Pentz RD, Do KA, Logothetis CJ, Pasqualini R. Steps toward mapping the human vasculature by phage display. (2002) Nat Med. 8(2):121-7.


  1. Freitas F, Pires T, Barqueiro R, Almeida JS, Reis MA. Carbon, nitrogen and phosphorus removal in a sequential batch reactor operated with high frequency oxygen oscillations. (2001) Meded Rijksuniv Gent Fak Landbouwkd Toegep Biol Wet. 66(3a):155-8.
  2. Silva CP, Terra WR, de Sá MF, Samuels RI, Isejima EM, Bifano TD, Almeida JS. Induction of digestive alpha-amylases in larvae of Zabrotes subfasciatus (Coleoptera: Bruchidae) in response to ingestion of common bean alpha-amylase inhibitor 1. (2001) J Insect Physiol. 47(11):1283-1290.
  3. Baggerly KA, Coombes KR, Hess KR, Stivers DN, Abruzzo LV, Zhang W. Identifying differentially expressed genes in cDNA microarray experiments. (2001) J Comput Biol. 8(6):639-59.
  4. Ramdas L, Coombes KR, Baggerly K, Abruzzo L, Highsmith WE, Krogmann T, Hamilton SR, Zhang W. Sources of nonlinearity in cDNA microarray expression measurements. (2001) Genome Biol. 2(11):RESEARCH0047. Epub 2001 Oct 18.
  5. Hong MY, Chapkin RS, Morris JS, Wang N, Carroll RJ, Turner ND, Chang WC, Davidson LA, Lupton JR. Anatomical site-specific response to DNA damage is related to later tumor development in the rat azoxymethane colon carcinogenesis model. (2001) Carcinogenesis. 22(11):1831-5.
  6. Hess KR, Zhang W, Baggerly KA, Stivers DN, Coombes KR. Microarrays: handling the deluge of data and extracting reliable information. (2001) Trends Biotechnol. 19(11):463-8. Review.
  7. Baggerly KA. Probability binning and testing agreement between multivariate immunofluorescence histograms: extending the chi-squared test. (2001) Cytometry. 45(2):141-50.
  8. Xavier JB, Schnell A, Wuertz S, Palmer R, White DC, Almeida JS. Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images. (2001) J Microbiol Methods. 47(2):169-80.
  9. Ramdas L, Wang J, Hu L, Cogdell D, Taylor E, Zhang W. Comparative evaluation of laser-based microarray scanners. (2001) Biotechniques. 31(3):546, 548, 550, passim.
  10. Di Gennaro JA, Siew N, Hoffman BT, Zhang L, Skolnick J, Neilson LI, Fetrow JS. Enhanced functional annotation of protein sequences via the use of structural descriptors. (2001) J Struct Biol. 134(2-3):232-45.
  11. Rashid A, Shen L, Morris JS, Issa JP, Hamilton SR. CpG island methylation in colorectal adenomas. (2001) Am J Pathol. 159(3):1129-35.
  12. Thibault C, Wang L, Zhang L, Miles MF. DNA arrays and functional genomics in neurobiology. (2001) Int Rev Neurobiol. 48:219-53. Review.
  13. Zhang W, Labordé PM, Coombes KR, Berry DA, Hamilton SR. Cancer genomics: promises and complexities. (2001) Clin Cancer Res. 7(8):2159-67. Review.
  14. Taylor E, Cogdell D, Coombes K, Hu L, Ramdas L, Tabor A, Hamilton S, Zhang W. Sequence verification as quality-control step for production of cDNA microarrays. (2001) Biotechniques. 31(1):62-5.
  15. Shureiqi I, Xu X, Chen D, Lotan R, Morris JS, Fischer SM, Lippman SM. Nonsteroidal anti-inflammatory drugs induce apoptosis in esophageal cancer cells by restoring 15-lipoxygenase-1 expression. (2001) Cancer Res. 61(12):4879-84.
  16. Almeida JS, Carriço JA, Maretzek A, Noble PA, Fletcher M. Analysis of genomic sequences by Chaos Game Representation. (2001) Bioinformatics. 17(5):429-37.
  17. Johnson DH, Gruner CM, Baggerly K, Seshagiri C. Information-theoretic analysis of neural coding. (2001) J Comput Neurosci. 10(1):47-69.
  18. Wolf G, Almeida JS, Pinheiro C, Correia V, Rodrigues C, Reis MA, Crespo JG. Two-dimensional fluorometry coupled with artificial neural networks: a novel method for on-line monitoring of complex biological processes. (2001) Biotechnol Bioeng. 72(3):297-306.


  1. Lewohl JM, Wang L, Miles MF, Zhang L, Dodd PR, Harris RA. Gene expression in human alcoholism: microarray analysis of frontal cortex. (2000) Alcohol Clin Exp Res. 24(12):1873-82.
  2. Almeida JS, Noble PA. Neural computing in microbiology. (2000) J Microbiol Methods. 43(1):1-2.
  3. Hong MY, Lupton JR, Morris JS, Wang N, Carroll RJ, Davidson LA, Elder RH, Chapkin RS. Dietary fish oil reduces O6-methylguanine DNA adduct levels in rat colon in part by increasing apoptosis during tumor initiation. (2000) Cancer Epidemiol Biomarkers Prev. 9(8):819-26.
  4. Davidson LA, Brown RE, Chang WC, Morris JS, Wang N, Carroll RJ, Turner ND, Lupton JR, Chapkin RS. Morphodensitometric analysis of protein kinase C beta(II) expression in rat colon: modulation by diet and relation to in situ cell proliferation and apoptosis. (2000) Carcinogenesis. 21(8):1513-9.
  5. Tan FK, Reveille JD, Arnett FC, Stivers DN, Tsao BP. Poly(ADP)-ribose polymerase and susceptibility to systemic lupus erythematosus and primary antiphospholipid syndrome: comment on the article by Delrieu et al. (2000) Arthritis Rheum. 43(6):1421-3.
  6. Neves AR, Ramos A, Shearman C, Gasson MJ, Almeida JS, Santos H. Metabolic characterization of Lactococcus lactis deficient in lactate dehydrogenase using in vivo 13C-NMR. (2000) Eur J Biochem. 267(12):3859-68.
  7. Zhou X, Tan FK, Stivers DN, Arnett FC. Microsatellites and intragenic polymorphisms of transforming growth factor beta and platelet-derived growth factor and their receptor genes in Native Americans with systemic sclerosis (scleroderma): a preliminary analysis showing no genetic association. (2000) Arthritis Rheum. 43(5):1068-73.
  8. Do KA, Broom BM, Kuhnert P, Duffy DL, Todorov AA, Treloar SA, Martin NG. Genetic analysis of the age at menopause by using estimating equations and Bayesian random effects models. (2000) Stat Med. 19(9):1217-35.
  9. Cruz PE, Almeida JS, Murphy PN, Moreira JL, Carrondo MJ. Modeling retrovirus production for gene therapy: (1) Determination Of optimal bioreaction mode and harvest strategy. (2000) Biotechnol Prog. 16(2):213-21.
  10. Noble PA, Almeida JS, Lovell CR. Application of neural computing methods for interpreting phospholipid fatty acid profiles of natural microbial communities. (2000) Appl Environ Microbiol. 66(2):694-9.


  1. Hong MY, Chapkin RS, Wild CP, Morris JS, Wang N, Carroll RJ, Turner ND, Lupton JR. Relationship between DNA adduct levels, repair enzyme, and apoptosis as a function of DNA methylation by azoxymethane. (1999) Cell Growth Differ. 10(11):749-58.
  2. Lopes MF, Pereira CI, Rodrigues FM, Martins MP, Mimoso MC, Barros TC, Figueiredo Marques JJ, Tenreiro RP, Almeida JS, Barreto Crespo MT. Registered designation of origin areas of fermented food products defined by microbial phenotypes and artificial neural networks. (1999) Appl Environ Microbiol. 65(10):4484-9.
  3. Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. (1999) Electrophoresis. 20(8):1682-96. Review.
  4. Tan FK, Stivers DN, Arnett FC, Chakraborty R, Howard R, Reveille JD. HLA haplotypes and microsatellite polymorphisms in and around the major histocompatibility complex region in a Native American population with a high prevalence of scleroderma (systemic sclerosis). (1999) Tissue Antigens. 53(1):74-80.
  5. Palmqvist E, Almeida JS, Hahn-Hägerdal B. Influence of furfural on anaerobic glycolytic kinetics of Saccharomyces cerevisiae in batch culture. (1999) Biotechnol Bioeng. 62(4):447-54.


  1. Zhang L, Godzik A, Skolnick J, Fetrow JS. Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. (1998) Fold Des. 3(6):535-48.
  2. Tan FK, Stivers DN, Foster MW, Chakraborty R, Howard RF, Milewicz DM, Arnett FC. Association of microsatellite markers near the fibrillin 1 gene on human chromosome 15q with scleroderma in a Native American population. (1998) Arthritis Rheum. 41(10):1729-37.
  3. Zhang L, Skolnick J. What should the Z-score of native protein structures be? (1998) Protein Sci. 7(5):1201-7.
  4. Zhang L, Skolnick J. How do potentials derived from structural databases relate to "true" potentials? (1998) Protein Sci. 7(1):112-22.


  1. Stivers DN, Chakraborty R. A test of allelic independence based on distributions of allele size differences at microsatellite loci. (1997) Hum Hered. 47(2):66-75.
  2. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. (1997) Proc Natl Acad Sci U S A. 94(3):1041-6.


  1. Sijbesma WF, Almeida JS, Reis MA, Santos H. Uncoupling effect of nitrite during denitrification by Pseudomonas fluorescens: An in vivo (31)P-NMR study. (1996) Biotechnol Bioeng. 52(1):176-82.
  2. Stivers DN, Kimmel M, Axelrod DE. A discrete-time, multi-type generational inheritance branching process model of cell proliferation. (1996) Math Biosci. 137(1):25-50.
  3. Chakraborty R, Stivers DN, Zhong Y. Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci. (1996) Mutat Res. 354(1):41-8.
  4. Chakraborty R, Stivers DN. Paternity exclusion by DNA markers: effects of paternal mutations. (1996) J Forensic Sci. 41(4):671-7.
  5. Chakraborty R, Stivers DN, Deka R, Yu LM, Shriver MD, Ferrell RE. Segregation distortion of the CTG repeats at the myotonic dystrophy locus. (1996) Am J Hum Genet. 59(1):109-18.
  6. Kimmel M, Chakraborty R, Stivers DN, Deka R. Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsatellite loci. (1996) Genetics. 143(1):549-55.
  7. Zhang L, Hermans J. Hydrophilicity of cavities in proteins. (1996) Proteins. 24(4):433-8.
  8. Deka R, Majumder PP, Shriver MD, Stivers DN, Zhong Y, Yu LM, Barrantes R, Yin SJ, Miki T, Hundrieser J, Bunker CH, McGarvey ST, Sakallah S, Ferrell RE, Chakraborty R. Distribution and evolution of CTG repeats at the myotonin protein kinase gene in human populations. (1996) Genome Res. 6(2):142-54.


  1. Almeida JS, Reis MA, Carrondo MJ. Competition between nitrate and nitrite reduction in denitrification by Pseudomonas fluorescens. (1995) Biotechnol Bioeng. 46(5):476-84.
  2. Almeida JS, Júlio SM, Reis MA, Carrondo MJ. Nitrite inhibition of denitrification by Pseudomonas fluorescens. (1995) Biotechnol Bioeng. 46(3):194-201.


  1. Axelrod DE, Baggerly KA, Kimmel M. Gene amplification by unequal sister chromatid exchange: probabilistic modeling and analysis of drug resistance data. (1994) J Theor Biol. 168(2):151-9.
  2. Kimmel M, Stivers DN. Time-continuous branching walk models of unstable gene amplification. (1994) Bull Math Biol. 56(2):337-57.


  1. Zhang L, Hermans J. Calculation of the pitch of the alpha-helical coiled coil: an addendum. (1993) Proteins. 17(2):217-8.
  2. Zhang L, Hermans J. Molecular dynamics study of structure and stability of a model coiled coil. (1993) Proteins. 16(4):384-92.


  1. Reis MA, Almeida JS, Lemos PC, Carrondo MJ. Effect of hydrogen sulfide on growth of sulfate reducing bacteria. (1992) Biotechnol Bioeng. 40(5):593-600.


  1. White RA, Terry NH, Baggerly KA, Meistrich ML. Measuring cell proliferation by relative movement: (I) Introduction and in vitro studies. (1991) Cell Prolif. 24(3):257-70.


  1. Crespo JP, Almeida JS, Moura MJ, Carrondo MJ. Modeling of immobilized cell reactor for propionic acid fermentation. (1990) Biotechnol Bioeng. 36(7):705-16.
  2. McCoy-Pardington D, Judd WJ, Knafl P, Abruzzo LV, Coombes KR, Butch SH, Oberman HA. Blood use during extracorporeal membrane oxygenation. (1990) Transfusion. 30(4):307-9.

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