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2006
MD-PhD program students in italics

Awad MM, Dalal D, Tichnell C, James C, Tucker A, Abraham T, Spevak PJ, Calkins H, Judge DP. Recessive arrhythmogenic right ventricular dysplasia due to novel cryptic splice mutation in PKP2. Hum Mutat. 2006 Nov;27(11):1157.

Awad MM, Dalal D, Tichnell C, James C, Tucker A, Abraham T, Spevak PJ, Calkins H, Judge DP. Recessive arrhythmogenic right ventricular dysplasia due to novel cryptic splice mutation in PKP2. Hum Mutat. 2006 Nov;27(11):1157.

Awad MM, Dalal D, Cho E, Amat-Alarcon N, James C, Tichnell C, Tucker A, Russell SD, Bluemke DA, Dietz HC, Calkins H, Judge DP. DSG2 mutations contribute to arrhythmogenic right ventricular dysplasia/cardiomyopathy. Am J Hum Genet. 2006 Jul;79(1):136-42. Epub 2006 Apr 28.

Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, Persaud D, Gallant JE, Cofrancesco J Jr, Quinn TC, Wilke CO, Ray SC, Siliciano JD, Nettles RE, Siliciano RF.  Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells. J Virol. 2006 Jul;80(13):6441-57

Lassen KG, Ramyar KX, Bailey JR, Zhou Y, Siliciano RF.  Nuclear retention of multiply spliced HIV-1 RNA in resting CD4+ T cells. PLoS Pathog. 2006 Jul;2(7):e68.

Bailey JR, Cymet TC.  Planning for the HPV vaccine and its impact on cervical cancer prevention.  Compr Ther. 2006 Summer;32(2):102-5.

Bailey JR, Williams TM, Siliciano RF, Blankson JN.  Maintenance of viral suppression in HIV-1-infected HLA-B*57+ elite suppressors despite CTL escape mutations. J Exp Med. 2006 May 15;203(5):1357-69. Epub 2006 May 8.

Bailey JR, Lassen KG, Yang HC, Quinn TC, Ray SC, Blankson JN, Siliciano RF.  Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy. J Virol. 2006 May;80(10):4758-70.

Blankson JN, Bailey JR, Siliciano RF.  Crosscurrents in HIV-1 evolution. Nat Immunol. 2006 Feb;7(2):121-2.

B. Barnett, DL Kraitchman, C. Lauzon, CA Magee, P. Walczak, WD Gilson, A Arepally, JW Bulte. Radiopaque alginate microcapsules as new diagnostic agents for visualization and immunoprotection of cellular therapeutics. Mol Pharm. 2006 Sep-Oct;3(5):531-8.

Arepally, P. Karmarkar, D. Qian, B. Barnett, E. Atalar. MR-guided porto-systemic shunts.  J Vasc Interv  Radiology 2006: 17: 1165-1173.

P. Walczak, D. Kedziorek, A. Gilad, S. Lin, B. Barnett,  J. Bulte. Instant MR labeling of stem cells using magnetoelectroporation. Nanomedicine 2 (2006) 89-94.

Siclari F, Burger I, Fasel J, Gailloud P. Developmental anatomy of the distal vertebral artery in relation to variants of the posterior and lateral spinal arterial systems. Am J Neuroradiol. 2006 Feb;27(2):317-20.

Johnson S, Burger I.  Limitations and Justifications for Analogical Reasoning.  American Journal of Bioethics. Nov-Dec; 6(6): 59-61 (2006)

Burger I, Murphy K, Jordan L, Tamargo R, Gailloud P. Safety of cerebral digital subtraction angiography (DSA) in children. Complication rate analysis in 241 cons. diagnostic angiograms. Stroke Oct; 37(10): 2535-9 (2006)

Burger I, Sugarman J, Goodman S.  Ethical Issues in Evidence-based Surgery. Surgical Clinics of North America. February: 86:151-168 (2006)

Gailloud P, O’Riordan, D, Burger I, Lehmann C. Confirmation of communication between deep venous drainage and the vein of galen after treatment of a vein of Galen aneurysmal malformation in an infant presenting with severe pulmonary hypertension. American Journal of Neuroradiology. Feb: 27:317-320 (2006)

Sampathkumar SG, Jones MB, Meledeo MA, Campbell CT, Choi SS, Hida K, Gomutputra P, Sheh A, Gilmartin T, Head SR, Yarema KJ. Targeting glycosylation pathways and the cell cycle: sugar-dependent activity of butyrate-carbohydrate cancer prodrugs. Chem Biol. 2006 Dec;13(12):1265-75.

Cheong R, Wilson RK, Cortese IC, Newman-Toker DE.  Mothball withdrawal encephalopathy-Case Report and Review of Paradichlorobenzene Neurotoxicity.”  Substance Abuse.  27(4):63-672006.

Cheong, R., Wilson R.K., Cortese, I.C.M., and Newman-Toker, D.E.Mothball withdrawal encephalopathy: case report and review of paradichlorobenzene neurotoxicity.  Substance Abuse, in press.

Kahn, J.D., Cheong, R., Mehta, R.A., Edelman, L.M., and Morgan, M.A. Flexibility and control of protein-DNA loops.  Biophysical Reviews and Letters, 1(4):327-341 (2006).

Cheong, R., Bergmann, A., Werner S.L., Regal, J., Hoffmann, A., and Levchenko A.  Transient IkappaB kinase activity mediates temporalNF-kappaB dynamics in response to a wide rage of tumor necrosis factor-alpha doses.  Journal of Biological Chemistry, 281(5):2945-2950(2006).

Chong CR, Chen X, Shi L, Liu JO, Sullivan DJ.  Identification of astermizole as an antimalarial agent by screening a clinical compound library.  Nature Chemical Biology 2006, 2:415.

Chen X, Chong CR, Shi L, Yoshimoto T, Sullivan DJ Jr, Liu Jo.  Inhibitors of Plasmodium falciparum methionine aminopeptidase 1b possess antimalarial activity.  Proceedings of the National Academy of Sciences USA 2006: 103:145-48.

Lu J, chong CR, Hu X, Liu JO.  Fumarranol, a rearranged fumagillin analogue that inhibits angiogenesis in vivo.  Journal of Medicinal Chemistry. 2006, 49:5645.

Allen MD, DiPilato LM, Rahdar M, Ren YR, Chong CR, Liu, JO, Zhang J.  Reading dynamic kinase activity in living cells for high-throughput screening.  ACS Chemical Biology 2006, 1(6):108.

Dang L, Yoon K, Wang M, Gaiano N. Notch3 signaling promotes radial glial/progenitor character in the Mammalian telencephalon. Dev Neurosci. 2006;28(1-2):58-69.   

Dang L, Fan X, Chaudhry A, Wang M, Gaiano N, Eberhart CG. Notch3 signaling initiates choroid plexus tumor formation. Oncogene. 2006 Jan 19;25(3):487-91.

Dowdy DW, Sweat MD, Holtgrave DR.  Country-wide distribution of the nnitrile female condom (FC2) in Brazil and South Africa: a cost-effectiveness analysis.  AIDS 2006; 20(6):2091-8.

Nachega JB, HislopM, Dowdy DW, Lo M, Omer SB, Regensberg L, Chaiison RE, Maartens G.  Adherence to highly active antiretroviral therapy assessed by pharmacy claims predicts survival in HIV-infected South African adults.  J Acquir Immune Defic Syndr. 2006; 43(1):78-84.

Dowdy DW, Eid MP, Dennison CR, Mendez-Tellez PA, Herridge MS, Guallar E, Pronovost PJ, Needham DM.  Quality of life after acute respiratory distress syndrome: a meta-analysis.  Intensive Care Med 2006; 32(8):1115-24.

Dowdy DW, Sweat MD, Holtgrave DR. Country-wide distribution of the nitrile female condom (FC2) in Brazil and South Africa: a cost-effectiveness analysis. AIDS. 2006 Oct 24;20(16):2091-8.

Nachega JB, Hislop M, Dowdy DW, Lo M, Omer SB, Regensberg L, Chaisson RE, Maartens G. Adherence to highly active antiretroviral therapy assessed by pharmacy claims predicts survival in HIV-infected South African adults. J Acquir Immune Defic Syndr. 2006 Sep;43(1):78-84.

Dowdy DW, Eid MP, Dennison CR, Mendez-Tellez PA, Herridge MS, Guallar E, Pronovost PJ, Needham DM. Quality of life after acute respiratory distress syndrome: a meta-analysis. Intensive Care Med. 2006 Aug;32(8):1115-24.

Dowdy DW. Partnership as an ethical model for medical research in developing countries: the example of the "implementation trial". J Med Ethics. 2006 Jun;32(6):357-60.

Dowdy DW, Chaisson RE, Moulton LH, Dorman SE. The potential impact of enhanced diagnostic techniques for tuberculosis driven by HIV: a mathematical model. AIDS. 2006 Mar 21;20(5):751-62.

Needham DM, Dennison CR, Dowdy DW, Mendez-Tellez PA, Ciesla N, Desai SV, Sevransky J, Shanholtz C, Scharfstein D, Herridge MS, Pronovost PJ. Study protocol: The Improving Care of Acute Lung Injury Patients (ICAP) study. Crit Care. 2006 Feb;10(1):R9.

Castanon Holguin AM, Congdon N, Patel N, Ratcliffe A, Esteso P, Toledo Flores S, Gilbert D, Pereyra Rito MA, Munoz B. Factors associated with spectacle-wear compliance in school-aged Mexican children. Invest Ophthalmol Vis Sci. 2006 Mar;47(3):925-8.

Frank CJ and Greider CW. Regulation of telomere elongation by the cyclin-dependent kinase Cdk1. Mol Cell. 2006 Nov 3;24(3):423-32.

Palapattu GS, Meeker A, Harris T, Collector MI, Sharkis SJ, DeMarzo AM, Warlick C, Drake CG, Nelson WG. Epithelial architectural destruction is necessary for bone marrow derived cell contribution to regenerating prostate epithelium. J Urol. 2006 Aug;176(2):813-8.

Weil ZM, Huang AS, Beigneux A, Kim PM, Mllover ME, Blacksway S, Young SH, Nelson RJ, Snyder SH.  Behaviorial alterations in male mice lacking the gene for D-aspartate oxidase.  Behav Brain Res 2006; 171(2):295-302.

Levinson NM, Kuchment O, Shen K, Young MA, Koldobskiy M, Karplus M, Cole PA, Kuriyan J.  A Src-like inactive conformation in the abl tyrosine kinase domain.  PLoS Biol. 2006 May;4(5):e144. Epub 2006 May

Bera, T., Saint Fluer, A., Lee Y., Kydd A., Hahn Y, Popescu NC, Zimonjic DB, Lee B, Pastan I.  POTE Paralogs are Induced and Differentially Expressed in Many Cancers.  Cancer Res.,2006; 66: 52-56.

Parmigiani G, Lin J, Sjoblom T, Kinzler K, Vogelstein B, Velculescu VE.  Significant of candidate cancer genes assessed by the CaMP score.  JHU Department of Biostatistics Working Papers 2006, 126.

Lin J, Bettegowda C, Huang X, Cheong I, Kohli M, Szabo S, Zhang X, Diaz D, Velculescu V, Parmigiani G, Kinzler K, Vogelstein B, Zhou S.  The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.  Nat Biotechnol. 2006, December 24(12):1573-80.

Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N,Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopulos N, Vogelstein B, Kinzler KW, Velculescu VE.  The consensus coding sequences of human breast and colorectal cancers.  Science. 2006, October 13; 314(1597):268-74.

Yu X, Lin J, Zack DJ, Qian J.Computatioinal analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues.  Nucleic Acids Res. 2006; 34(17):4925-36.

Yu X, Lin J, Zack DJ, Qian J.  Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res. 2006;34(17):4925-36.

Qian J, Lin J, Zack DJ. Characterization of binding sites of eukaryotic transcription factors. Genomics Proteomics Bioinformatics. 2006 May;4(2):67-79.

Yu X, Lin J, Masuda T, Esumi N, Zack DJ, Qian J.  Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res. 2006 Feb 6;34(3):917-27.

Lin J, Bettegowda C, Huang X, Cheong I, Kohli M, Szabo SA, Zhang X, Diaz LA Jr, Velculescu VE, Parmigiani G, Kinzler KW, Vogelstein B, Zhou S. The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT. Nat Biotechnol. 2006 Nov 19.

Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The consensus coding sequences of human breast and colorectal cancers. Science. 2006 Oct 13;314(5797):268-74.

Yu X, Lin J, Masuda T, Esumi N, Zack DJ, Qian J. Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res. 2006 Feb 6;34(3):917-27.

Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Siloliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE.  The consensus coding sequences of human breast and colorectal cancers.  Science 2006, 314:268-74.

Hikida, T.*, Mustafa, A.K.*, Oby, L., Snyder, S.H., Kenji, H. and Sawa, A., Modulation of D-Serine in brains of mice lacking PICK1, Biological Psychiatry, 2006 (in review)

Chakraborty, A, Sixt, K., Mustafa, A.K., Koldobskiy, M. and Snyder, S.H., Heat shock protein-90 inhibition of Inositolhexakisphosphate Kinase-2-mediated apoptosis, Molecular Cell, 2006 (in review)

Fujii K, Maeda K, Hikida T, Mustafa AK, Balkissoon R, Xia J, Yamada T, Ozeki Y, Kawahara R, Okawa M, Huganir RL, Ujike H, Snyder SH, Sawa A. Serine racemase binds to PICK1: potential relevance to schizophrenia. Mol Psychiatry. 2006 Feb;11(2):150-7.

Sdrulla AD, Linden DJ. Dynamic imaging of cerebellar Purkinje cells reveals a population of filopodia which cross-link dendrites during early postnatal development. Cerebellum. 2006;5(2):105-15.

Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, Persaud D, Gallant JE, Cofrancesco J Jr, Quinn TC, Wilke CO, Ray SC, Siliciano JD, Nettles RE, Siliciano RF.  Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells.  J Virol 2006, July 80(13):6441-57.

Steinberg, J.P.,* Takamiya, K.,* Shen, Y., Xia, J., Rubio, M.E., Yu, S., Jin, W., Thomas, G.M., Linden, D.J., and Huganir, R.L. (2006). Targeted in vivo mutations of the AMPA receptor subunit GluR2 and its interacting protein PICK1 eliminate cerebellar long-term depression.  Neuron 49, 845-860.

Janak SL, Taylor MS, Floudas CA, Burka M, Mountziaris TJ.  Novel and effective integer optimization approach for the NSF panel-assignment problem: a multiresource and preference-constrained generalized assignment problem.  Industrial and Engineering Chemistry Research, 2006; 45:258-65

Sjoblom T*, Jones S*, Wood LD*, Parsons DW*, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE.  The consensus coding sequences of human breast and colorectal cancers.  Science. 2006 Oct 13; 314(5797):268-74.  (*equal authorship)

Wood LD, Calhoun ES, Silliman N, Ptak J, Szabo S, Powell SM, Riggins GJ, Wang TL, Yan H, Gazdar A, Kern SE, Pennacchio L, Kinzler KW, Vogelstein B, Velculescu VE.  Somatic mutations of GUCY2F, EPHA3, and NTRK3 in human cancers.  Human Mutation.  2006 Oct; 27(10):1060