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Selected Publications

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Developmental Therapeutics Clinic

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Home » Research

Molecular Targets and Developmental Therapeutics

SELECTED PUBLICATIONs

2007 2006 Earlier Publications

2007

  • Cheson BD.  Is BEACOPP superior to ABVD? Curr Hematol Malig Rep (in press).

  • Cheson BD.  Oblimersen for the treatment of patients with chronic lymphocytic leukemia.  Therapetuics and Clinical Risk Management (in press).

  • Cheson BD.  The International Harmonization Project for Response Criteria in Lymphoma Clinical Trials.  Hematol Oncol Clin North Amer (in press).

  • Czuczman M, Porcu P, Johnson J, Niedzwiecki D, Kelly M, His ED, Cook JR, Canellos G, Cheson BD.  Results of a phase II study of 506U78 in cutaneous T-cell lymphoma and peripheral T-cell lymphoma: CALGB 59901.  Leuk and Lymph (in press).

  • Deeken J, and Loscher W.  The blood-brain barrier and cancer:  transporters, treatment, and  Trojan Horses.  Clin Cancer Res.  2007.  In press. 

  • Deeken J, Figg W, Bates SE, and Sparreboom A.  Toward individualized treatment: Prediction of  anticancer drug disposition and toxicity with pharmacogenetics.   Anticancer Drugs.  2007 Feb;18(2):111-26.

  • Holst, J.P., Soldin, S.P., Tractenberg, R.E., Guo, T., Kundra, P., Verbalis, J.G., Jonklaas, J. Use of Steroid Profiles in Determining the Cause of Adrenal Insufficiency. Steroids 71-84, 2007.

  • Hu ZZ, Valencia JC, Huang H, Chi A, Shabanowitz J, Hearing VJ, Appella E, Wu CH. (2007) Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes. International Journal of Mass Spectrometry 259, 147-160.

  • Huang H, Shukla H, Saxena S, Wu CH. (2007) Challenges and solutions in proteomics. Current Genomics 8, (in press)

  • Janicic-Kahric, N., Soldin, S., Soldin, O., West, T., Gu, J., Jonklaas, J. Tandem mass spectrometry improves the accuracy of free thyroxine measurements during pregnancy. Thyroid, In Press,  2007.

  • Juweid ME, Stroobants S, Hoekstra OS, Mottaghy FM, Dietlein M, Guermazi A, Wiseman GA, Kostakoglu L, Scheidhauer K, Buck A, Naumann R, Spaepen K, Hicks R, Weber W, reske SN, Schwaiger M, Siegel BA, Cheson BD.  Use of positron eemission tomography (PET) for response assessment of lymphoma: consensus of the Imaging Subcommittee of the International harmonization Project (IHP) in lymphoma. J Clin Oncol 25:571-578, 2007.

  • Lai R, Bartlett NL, Mackey JR, Jung S-H, Johnson JL, Cook JR, Jones D, Cass CE, Young JD, Said J, Cheson BD, His ED.  High expression of nucleoside transporter hENT1 in Reed-Sternberg cells is associated with treatment failure in relapsed/refractory Hodgkin lymphoma patients treated with gemcitabine, vinorelbine, and liposomal doxorubicin: a CALGB 59804 correlative study (submitted for publication).

  • Morgan NP, Graves KD, Poggi EA, Cheson BD.  Implementing an expressive writing study in a cancer clinic.  J Health Psychol (in press).

  • Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, et al., Wu CH, Yeats C. (2007) New developments in the InterPro database. Nucleic Acids Res. 35(Database issue), D224-228.

  • Nie L, Convergence Rate of MLE in Generalized Linear and Nonlinear Mixed-Effects Models: Theory and   Applications, Journal of Statistical Planning and Inference,2007, 1787-1804, Vol 137.

  • Pirollo, K.F., Rait, A., Zhou, Q., Hwang, S-H., Dagata, J.A., Zon, G., Hogrefe, R., Palchick, G., and Chang, E.H.  Materializing the Potential of siRNA Via a Tumor-Targeting Nanodelivery System.  Cancer Research, In Press 2007.

  • Qiu P, Wang ZJ, Liu KJ, Hu ZZ, Wu CH. (2007) Dependence network modeling for biomarker identification. Bioinformatics 23, 198-206.

  • Robey RW, Polgar O, Deeken JF, To KW, and Bates SE. ABCG2:  determining its relevance in clinical drug resistance.  Cancer Metastasis Rev 2007.  In press. 

  • UniProt Consortium – Bairoch A, et al. (SIB), Apweiler R, et al. (EBI), Wu CH, et al. (PIR) (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res. 35(Database issue), D193-197

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2006

  • Abrishamchian, R. Kanhai, D. Zwets, E., Nie, L, Cardarelli,M. Low birth weight or diagnosis, which   is a higher risk? - a meta-analysis of observational studies, TOC Category: Congenital, Review   European Journal of Cardio-thoracic Surgery, 2006, 30, 700-5

  • Bach, G., Jonklaas, J. Use of Thyroid Medications during Pregnancy. Therapeutic Drug Monitoring 28: 431- 441, 2006.

  • Banovac F, Wilson E, Zhang H, Cleary K. Needle biopsy of anatomically unfavorable liver lesions with an electromagnetic navigation assist device in a computed tomography environment. J Vasc Interv Radiol, 2006. 17(10): 1671-5.

  • Bek M, Wang X, Asico LD, Zheng S, Jones JE, Li XX, Eisner GM, Grandy DK, Carey RM, Soares-da-Silva P, Jose PA. Angiotensin type I receptor-mediated hypertension in D4 dopamine receptor deficient mice. Hypertension Hypertension 47:288-95, 2006.

  • Binet J-L, Caligaris-Cappio F, Catovsky D, Cheson B, Davis T, Dighiero G, Döhner H, Hallek H, Hillmen P, Keating M, Montserrat E, Kipps TJ, Rai K.  Perspectives on the use of new diagnostic tools in the treatment of chronic lymphocytic leukemia.  Blood 107:859-861, 2006.

  • Blum KA, Johnson JL, Niedzwiecki D, Piro LD, Saven A, Peterson BA, Byrd JC, Cheson BD.  Prolonged follow-up after initial therapy with 2-chlorodeoxyadenosine in patients with indolent non-Hodgkin’s lymphoma: Results of CALGB study 9153.  Cancer 107:2817-2825, 2006.

  • Boulares H, Zoltoski A, Kandan S, Akbulut T, Yakovlev A, Oumouna M. Correlation between decreased sensitivity of the Daudi lymphoma cells to VP-16-induced apoptosis and deficiency in DNAS1L3 expression. Biochem Biophys Res Commun. 2006; 341(2):653-62.

  • Chen S, Crawford M, Day RM, Victorino R. Briones VR, Leader JE, Jose PA, Lechleider RJ. RhoA modulates SMAD signaling during transforming growth factor-induced smooth muscle differentiation. J Biol Chem 281:1765-70, 2006.

  • Cheson BD and Canellos GP.  The Cancer and Leukemia Group B Lymphoma Committee.  Clin Cancer Res 12 (11 part 2):3572s-3575s, 2006.

  • Cheson BD, Greenberg PL, Bennett JM, Lowenberg J, Wijermans PW, Nimer SD, Pinto A, Beran M, de Witte TM, Stone RM, Mittelman M, Sanz GF, Gore SD, Schiffer CA, Kantarjian H.  Clinical application and proposal for modification of the international working group (IWG) response criteria in myelodysplasia.  Blood 108:419-425, 2006.

  • Cheson BD.  CLL response criteria.  Clin Adv Hematol Oncol 4 (suppl 12):4-5, 2006.

  • Cheson BD.  Histone deacetylase inhibition: a novel approach to cancer treatment.  Br J Cancer 95 (suppl 1):S1, 2006.

  • Cheson BD.  Monoclonal antibody therapy for B-cell malignancies. Semin Oncol. 33(2 Suppl 5):2-14, 2006.

  • Cheson BD.  Monoclonal antibody therapy of chronic lymphocytic leukemia.  Cancer Immunol Immunother 55:188-196, 2006.

  • Cheson BD.  New drugs for peripheral T-cell lymphomas.  Haematologica Rep 2 (13) 42-45, 2006.

  • Cheson BD.  Radioimmunotherapy of Non-Hodgkin’s Lymphomas.  Curr Drug Targets 7:1293-1300, 2006.

  • Chi A, Valencia JC, Hu ZZ, Watabe H, Yamaguchi H, Mangini NJ, Huang H, Canfield VA, Cheng KC, Yang F, Abe R, Yamagishi S, Shabanowitz J, Hearing VJ, Wu CH, Appella E and Hunt DF. (2006) Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. Journal of Proteome Research 5, 3135-3144.

  • Cleary K, Melzer A, Watson V, Kronreif G, Stoianovici D. Interventional robotic systems: applications and technology state-of-the-art. Minim Invasive Ther Allied Technol, 2006. 15(2): 101-13.

  • Desulfovibriovulgaris: A multiple regression to identify sources of variations. Biochemical and   Biophysical Research Communications, 339 (2006) 603-610.

  • Di Giovanni S, Knights CD, Rao M, Yakovlev A, Beers J, Catania J, Avantaggiati ML, Faden AI. The tumor suppressor protein p53 is required for neurite outgrowth and axon regeneration. EMBO J. 2006; 25(17):4084-96.

  • Gary K., Ibanez L., Aylward S., Gobbi D., Blake B., Cleary K., IGSTK: An Open Source Software Toolkit for Image-Guided Surgery, IEEE Computer, 2006 39 (4): 46-53.

  • Han B, Obradovic Z, Hu ZZ, Wu CH, Vucetic S. (2006) Substring selection for biomedical document classification. Bioinformatics 22, 2136-2142.

  • He AR, Marshall JL. Clinical experiences with G17DT in gastrointestinal malignancies. Expert Rev Anticancer Ther. 2006 Apr; 6(4):487-92

  • Hodak, S.P., Huang, C., Burman, K.D., Clarke, D., Jonklaas, J., Janicic-Kharic, N. Intravenous Methimazole in the Treatment of Refractory Hyperthyroidism. Thyroid 16: 691-695, 2006.

  • Hodge JW, Greiner JW, Tsang KY, Sabzevari H, Kudo-Saito C, Grosenbach DW, Gulley JL, Arlen PM, Marshall JL, Panicali D, Schlom J. Costimulatory molecules as adjuvants for immunotherapy. Front Biosci. 2006 Jan 1;11:788-803.

  • Hogrefe, R.I., Lebedev, A.V., Zon, G., Pirollo, K.F., Rait, A. Zhou, Q., Yu, W., and Chang, E.H.  Chemically Modified Short Interfering Hybrids (siHybrids):  Nanoimmunoliposome Delivery In Vitro and In Vivo for RNAi of HER-2. Nucleosides Nucleotides Nucleic Acids, 25:889-907, 2006.

  • Hwang J, Marshall JL. Targeted therapy for colorectal cancer.
    Curr Opin Investig Drugs. 2006 Dec; 7(12):1062-6.

  • Hwang J, Marshall JL. Targeted therapy for colorectal cancer.
    Curr Opin Investig Drugs. 2006 Dec; 7(12):1062-6.

  • Jonklaas, J., Sarlis, N.J., Litofsky, D., Ain, K., Bigos, S., Brierley, J., D., Cooper, D.S., Haugen, B., Kim, P, Ladenson, P, Marks, P., Robbins, J., Skarulis, M., Maxon, H., Sherman, S.I.  The impact of initial therapy on differentiated thyroid cancer outcomes. Thyroid 16: 1245-1258, 2006.

  • Juweid M and Cheson BD.  Positron emission tomography (PET) in post-therapy assessment of cancer.  New Engl J Med 354:496-507, 2006.

  • Liu H., Hu ZZ, Manabu T, Wu CH, Friedman, C. (2006) Quantitative assessment of dictionary-based protein named entity tagging. J Am Med Inform Assoc. 13, 497-507.

  • Liu, H.F., Hu, Z.Z., Zhang, J., Wu CH. (2006) BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics 22, 103-105.

  • Lohmueller KE, Wong LJ, Mauney MM, Jiang L, Felder RA, Jose PA, Williams SM. Patterns of genetic variation in the hypertension candidate gene GRK4: ethnic variation and haplotype structure. Ann Hum Genet. 70:27-41, 2006.

  • Lou E, Marshall J, Aklilu M, Cole D, Chang D, Morse M: A phase II study of active immunotherapy with PANVAC or autologous, cultured dendritic cells infected with PANVAC after complete resection of hepatic metastases of colorectal cancer. Clinical Colorectal Cancer 5:368-71, 2006.

  • Manson K, Dolan KE, Marshall J, Kaufman H, Mazzara GP, Schuetz TJ: A novel non-HLA restricted cellular immune assay for monitoring patient response to targeted immunotherapeutics. ASCO 2006 #257.

  • Lewis N, Marshall J, Amelsberg A, Cohen RB, Stopfer P, Hwang J, Malik S: A Phase I dose escalation study of BIBW 2992, an irreversible dual EGFR/HER2 receptor tyrosine kinase inhibitor, in a 3 week on, 1 week off schedule in patients with advanced solid tumors. ASCO 2006 #3091.

  • Pishvaian MJ. Firozvi K, Hwang JJ, Marshall JL, Ramzi P, Malik S: A Phase I trial of bexarotene and docetaxel in patients with advanced solid tumors. ASCO 2006 #13085.

  • Hwang JJ, Marshall JL, Malik S, Chun H, Ahmed T, Pilla PA: A Q7D Phase I study of TPI 287, a novel taxane, in advanced malignancies: Imaging studies, pharmacokinetics, and circulating tumor cell quantitation. ASCO 2006 #12008.

  • Malik S, Hwang J, Marshall J, Ramzi P, Posey J, Ahn C, Lee Y: Phase I study of RX-0201 in patients with advanced or metastatic solid tumors. ASCO 2006 #13102.

  • He AR, Hwang J, Malik S, Park S, Schlom J, Marshall J: Randomized single institution pilot study of vaccinia-CEA(6D)-Tricom and Fowlpox-CEA(6D)-Tricom with GM-CSF in combination with docetaxel in patients with colorectal cancer. ASCO 2006 #13538.

  • Firozvi K, Hwang J, Hansen N, Malik S, Maclean M, Siu L, Marshall JL, Mendelson D, Kurucilla J: A Phase I study of the pan-Bcl2 family inhibitor GX15-070, administered as a 3-hour weekly infusion in patients with refractory solid tumors or lymphomas. ASCO 2006 #3081.

  • Fuchs C, Marshall J, Mitchell E, Wierzbicki R, Ganju V, Jeffrey M, Schultz J, Richards D, Wang B, Morrison M: A randomized trial of first-line irinotecan/fluoropyrimidine combinations with or without celecoxib in metastatic colorectal cancer (BICC-C). ASCO 2006 #3506.

  • Perez RP, Lewis LD, Cohen GI, Hwang J, Malik S, Marshall JL, Baker J, Phan AT, Yao JC, Ajani JA: First-in-human Phase I pharmacokinetic trial of NS-9, a liposomal poly(1):poly©, in patients with liver metastases from various primary tumors. ASCO 2006 #13016.

  • Miller AA, Murry DJ, Hollis DR, Owzar K, Lewis LD, Kindler HL, Marshall JL, Villaluna-Calero M, Edelman MJ, Ratain MJ: Phase I study of erlotinib for solid tumors in patients with hepatic or renal dysfunction: CALGB 60101. ASCO 2006 #3026.

  • Isaacs C, Wang A, Warren R, Wilkinson M, Grana G, Liu MC, Stearns V, Park VH, Novielli A: A Phase II study of weekly gemcitabine and docetaxel in first and second line metastatic breast cancer. ASCO 2006 #10668.

  • Hayes JH, Oh WK, Kantoff PW, Manola JB, Smith MR, Gelmann EP, Bubley G, Balk SP, Taplin M: Mifepristone (Ru-486) in androgen independent prostate cancer. ASCO 2006 #14508.

  • Van der Jagt RH, Cohen P, Cheson BD, Tulpule A, Herst JA, Lemieux B, Schwartzenberg LS, Robinson KS, Oliver JW, Williams ME: Phase II results of bendamustine in combination with rituximab in relapsed indolent and mantle-cell non-Hodgkin’s lymphoma. ASH 2006 #2710.

  • Forero-Torres A, Bernstein SH, Gopal A, Foss F, Leonard JP, Rosenblatt JD, Bartlett NL, Cheson BD, et al: SGN-30 (Anti-CD30 mAb) has a single-agent response rate of 21% in patients with refractory or recurrent systemic anaplastic large cell lymphoma. ASH 2006 # 2718.

  • Mavromatis BH, Kessler CM, Cheson BD, Sein A, Sharp SA: The impact of GM-CSF on arsenic trioxide therapy in patients with myelodysplastic syndrome: preliminary results of a Phase II study. ASH 2006 #4856.

  • Muntener M, Patriciu A, Petrisor D, Mazilu D, Bagga H, Kavoussi L, Cleary K, Stoianovici D. Magnetic resonance imaging compatible robotic system for fully automated brachytherapy seed placement. Urology, 2006. 68(6): 1313-7.

  • Natale DA, Arighi C, Barker WC, Blake J, Chang TC, Hu ZZ, Liu HF, Smith B,  Wu CH. (2006) Framework for a protein ontology. Proceedings of ACM First International Workshop on Text Mining in Bioinformatics, TMBIO 2006.

  • Nie L, Chu H and Cole S  A general approach for sample size and statistical power calculation   using a mixture model in the presence of detection limits. Contemporary clinical trails. 2006, 27(5), 483-491.

  • Nie L, Strong Consistency of the Maximum Likelihood Estimator in Generalized Linear and Nonlinear  Mixed-Effects Models, Metrika, Vol. 63, 2006, 123-143

  • Nie L, Wu G, Zhang W  Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis. Genetics 2006 Dec;174(4):2229-43.

  • Nie, L., Wu, G., Brockman, F.J., and Zhang, W.. Integrated analysis of transcriptomic and  proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict  abundance for undetected proteins. Bioinformatics, 2006 Jul 1;22(13):1641-7.

  • Nikolskaya AN, Arighi C., Huang H., Barker W.C., Wu CH. (2006) PIRSF family classification system for protein functional and evolutionary analysis. Evolutionary Bioinformatics Online 2, 209-221.

  • O’Leary M, Sheaffer J, Keller F, Shu X-O, Cheson B: Lymphomas and reticuloendothelial neoplasms. In: Bleyer A, O’Leary M, Barr R, Ries LAG (eds): Cancer epidemiology in older adolescents and young adults 15 to 29 years of age, including SEER incidence and survival: 1975-2000. National Cancer Institute, NIH Pub. No. 06-5767. Bethesda, MD 2006; pp. 25-38.

  • Petrova NV, Wu CH. (2006). Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinformatics 7, 312.

  • Pirollo, K.F., Zon, G., Rait, A., Zhou, Q., Yu, W., Hogrefe, R., and Chang, E.H.  Tumor Targeting Nanoimmunoliposome Complex For Short Interfering RNA Delivery. Human Gene Therapy 17:117-124 2006.

  • Rankin ML, Marinec PS, Cabrera DM, Wang Z, Jose PA, Sibley DR. The D1 dopamine receptor is constitutively phosphorylated by G protein-coupled receptor kinase 4: evidence for a novel mechanism of regulation. Mol Pharmacol 69:759-69, 2006.

  • Sanada H, Yatabe J, Midorikawa S, Hashimoto S, Watanabe H, Felder RA, Jose PA.  Single-nucleotide polymorphisms for diagnosis of salt-sensitive hypertension.. Clin Chem 52:352-60, 2006.

  • Smith SM, Johnson JL, Niedzwiecki D, Eder JP, Canellos G, Cheson BD, Bartlett NL.  Sequential doxorubicin and topotecan in relapsed/refractory aggressive non-Hodgkin’s lymphoma: Results of CALGB 59906.  Leuk Lymphoma 47:1511-1517, 2006.

  • Torii M, Liu HF, Hu ZZ, Wu CH. (2006) A comparison study of biomedical short form definition detection algorithms. Proceedings of ACM First International Workshop on Text Mining in Bioinformatics, TMBIO 2006.

  • Wu CH, Apweiler, R., Bairoch, A., Natale, D.A., Barker, W.C., Boeckmann, B., Ferro1, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Mazumder, R., O Donovan, C., Redaschi, N. and Suzek, B. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research, 34, D187-191.

  • Wu G, Nie L, Zhang W, Predicted highly expressed genes in Nocardia farcinica and the implication to its primary metabolism and nocardial virulence, Antonie van Leeuwenhoek International Journal of  General and Molecular Microbiolog, 2006 Jan; 89(1):135-46.

  • Xu S, Taylor RH, Fichtinger G, Cleary K. Lung deformation estimation and four-dimensional CT lung reconstruction. Acad Radiol, 2006. 13(9): 1082-92.

  • Yakovlev AG. BOK (BCL2-related ovarian killer). Atlas Genet Cytogenet Oncol Haematol. 2006.

  • Yang Z, Asico LD, Yu P, Wang Z, Jones JE, Escano CS, Wang X, Quinn MT, Sibley DR, Romero GG, Felder RA, Jose PA. D5 dopamine receptor regulation of reactive oxygen species production, NADPH oxidase, and blood pressure. Am J Physiol Regul Integr Comp Physiol 290:R96-R104, 2006. 

  • Yuan X, Hu ZZ, Wu HT, Torii M, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH. (2006) An online literature mining tool for protein phosphorylation. Bioinformatics 22, 1668-1669.

  • Zeng C, Wang Z, Yu P, Zheng S, Wu L, Asico LD, Hopfer U, Eisner GM, Felder RA, Jose PA. D3 dopamine receptor directly interacts with D1 dopamine receptor in immortalized renal proximal tubule cells. Hypertension 47:573-579, 2006.

  • Zhang H, Banovac F, Lin R, Glossop N, Wood BJ, Lindisch D, Levy E, Cleary K. Electromagnetic tracking for abdominal interventions in computer aided surgery. Comput Aided Surg, 2006. 11(4): 319-28.

  • Zhang, W, Culley, D, Nie, L, Brockman, F. DNA microarray analysis of anaerobic Methanosarcina barkeri, Journal of Industrial Microbiology & Biotechnology, 2006 Sep;33(9):784-90.

  • Zhang, W. Culley, D. Gritsenko,M. Moore, R. Nie, L, Scholten, J. Petritis, K. Strittmatter, E. Camp, D. Smith, R. Brockman, F.  LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Biochem Biophys Res Commun. 2006 349 (2006) 1412–1419.

  • Zhang, W. Culley, D. Gritsenko,M. Moore, R. Nie, L, Scholten, J. Petritis, K. Strittmatter, E. Camp, D. Smith,  R. Brockman, F. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid  chromatography coupled with tandem mass spectrometry. Proteomics 2006 Aug;6 (15):4286-99.

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Earlier Publications
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