We attempt to maintain an up-do-date list of publications based on your research using ACCRE that results in journal articles or conference proceedings. This list is only current if researchers provide us with their publication information. If you have work at least partially accomplished using ACCRE facilities, we will list your accomplishment here and provide links to your work. To submit updated or new information please use the update form.
Please refer to the list below to see what sort of information we wish to include for your article, along with any electronic public links. We are glad to also list articles submitted or in press, and ask that you please let us know when the articles finally appear in print.
When possible, we would also greatly appreciate an acknowledgement of ACCRE in presentations and publications. Follow this link to our suggested text.
Journal Articles: | Submitted | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |
Conference Proceedings: | 2007 |2006 | 2005 | 2004 | 2003 | 2002 | 2001 |
C.F. Aliferis, A. Statnikov, I. Tsamardinos, J.S. Schildcrout, B.E. Shepherd, and F.E. Harrell
Gene Expression Microarrays Do Predict Clinical Outcomes, submitted (2007)
L. Boucher, T. Palmeri, G.D. Logan, and J.D. Schall
Inhibitory Control in Mind and Brain: An Interactive Race Model of Countermanding Saccades. Psych. Rev., in press (2007)
P. Bisegna, G. Caruso, D. Andreucci, L. Shen, V.V. Gurevich, H. E. Hamm, and E. DiBenedetto
Diffusion of the Second Messengers in the Cytoplasm Acts as a Variability Suppressor of the Single Photon Response in Vertebrate Phototransduction, Biophysical Journal, submitted.
L.D. Bozulic, D.W. Powell, A. Nanez, A.J. Link, K.S. Ramos, and W.L. Dean
Plasma membrane Ca2+-ATPase associates with the actin cytoskeleton via CLP36 in human platelets, in revision.
A. Bulusu and D.G. Walker
Modeling of thermoelectric properties of semiconductor thin films with quantum and scattering effects, Journal of Heat Transfer, in press.
W.S. Bush, T.A. Thornton-Wells, and M.D. Ritchie
Association Rule Discovery Has the Ability to Model Complex Genetic Effects, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, in press.
C.R. Camalier, A. Gotler, A. Murthy, K.G. Thompson, G.D. Logan, T.J. Palmeri, and J.D. Schall
Dynamics of Saccade Target Selection: Race Model Analysis of Double Step and Search Step Saccade Production in Human and Macaque., under review at Vision Research.
E.R. Chan, A. Striolo, C. McCabe, S.C. Glotzer, and P.T. Cummings
A Coarse-Grained Force Field for Simulating Polymer-Tethered Silsesquioxane Self-Assembly in Solution, Journal of Physical Chemistry B, submitted (2006)
D.K. Chen, R.D. Schrimpf, D.M. Fleetwood, K.F. Galloway, S.T. Pantelides, A. Dimoulas, G. Mavrou, A. Sotiropoulos, and Y. Panayiotatos
Total Dose Response of Ge MOS Capacitors with HfO2/Dy2O3 Gate Stacks, IEEE Trans. Nucl. Sci., in press (2007)
D.M. Dilts and S.D. Pathak
A methodology for modeling supply network evolution. Journal of Operations Management, submitted (2007)
G.X. Ding, D.M. Duggan, and C.W. Coffey
Characteristics of kilovoltage x-ray beam used for cone-beam computed tomography in radiation therapy. Phys Med Biol, in press (2007)
Friedman DB, Wang SE, Whitwell CW, Caprioli RM, Arteaga CL
Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling, Mol Cell Proteomics, 6(1):150-69 (2007)
Gerbasi, V. R. and Link, A. J.
The myotonic dystrophy type-2 gene ZNF9 promotes cap-independent translation,Mol Cell Proteomics, in press.
P. Hinow and E.M. Boczko
Molecular Seismology: An Inverse Problem in Nanobiology, J. Theor. Biol., in press.
J. Jeon, N.R. Alexander, and P.T. Cummings
Migration of a Model Lamellipodium by Actin Polymerization: A Molecular Dynamics Simulation Approach, Phys. Rev. E, submitted.
V.N. Koparde and P.T. Cummings
A molecular dynamics simulation of adsorption of water molecules on anatase and rutile nanoparticles, J. Phys. Chem. B., submitted.
V.N. Koparde and P.T. Cummings
Molecular dynamics study of water adsorption on TiO2 nanoparticles, J. Phys. Chem. B., submitted.
Y.S. Leng, P.J. Dyer, P.S. Krsti, R.J. Harrison, and P.T. Cummings
Calibration of chemical bonding between benzenedithiolate and gold: the effects of geometry and size of gold clusters, Molecular Simulation, accepted for publication.
T.S. LeBlanc, K.G. Stassun, & E.L.N Jensen
Monte-carlo SED Models of Young Stars in the Taurus-Auriga Region, in prep.
C. Li, et al.
A Practical Evaluation of Genome-Wide Association Studies, in preparation.
C. Li, M. Li, E.M. Lange, and R.M. Watanabe
Prioritized Subset Analysis: Improving Power in Genome-wide Association Studies. Submitted to Genetic Epidemiology, Genetic Epidemiology, submitted.
H.C. Li, C.Y. Lee, C. McCabe, A. Striolo, and M. N Neurock
Evaluation of the Structural Properties of Alkane Silsesquioxanes Using Ab Initio Methods, Journal of Physical Chemistry A submitted.
M.L. Mack, A.C.-N. Wong, I. Gauthier, J.W. Tanaka, and T.J. Palmeri
Unraveling the Time-course of Perceptual Categorization: Does Fastest Mean First?, submitted.
E. Mamontov, L. Vlcek, D.J. Wesolowski, P.T. Cummings, W. Wang, L.M. Anovitz, J. Rosenqvist, C.M. Brown, and V.G. Sakai
Diffusion dynamics of hydration water in nano-powder rutile and cassiterite on pico- to nano-second time scale studied by quasielastic neutron scattering and molecular dynamics simultions, Journal of Physical Chemistry B, in press.
M.P. McDonald, S.D. Pathak, and S. Mahadevan
An evolutionary agent based model of a traffic super network with epistemic uncertainties. Management Science, in prep.
H.D. McInvale, S.D. Pathak, and S. Mahadevan
Investigating decision making under epistemic uncertainties in the Military Logistics Supply Networks. Management Science, in prep.
E.J. Montes, R.A. Reed, J.A. Pellish, M.L. Alles, R.D. Schrimpf, R.A. Weller, M. Varadharajaperumal,G. Niu, A.K. Sutton, R. Diestelhorst, G. Espinel, R.Krithivasan, J.P. Comeau, J.D. Cressler, P.W Marshall, and G.Vizkelethy
Single Event Usept Mechanisms for Low-Energy-deposition Events in SiGe HBTs, IEEE Trans.. " Nucl.Sci. , in press
M'Koma AE, Blum DL, Norris JL, Koyama T, Billheimer D, Motley S, Ghiassi M, Ferdowsi N, Bhowmick I, Chang SS, Fowke JH, Caprioli RM, Bhowmick NA
Detection of pre-neoplastic and neoplastic prostate disease by MALDI profiling of urine, Biochem Biophys Res Commun, 353(3):829-34 (2007)
E.J. Montes, R.A. Reed, J.A. Pellish, M.L. Alles, R.D. Schrimpf, R.A. Weller, M. Varadharajaperumal, G. Niu, A.K. Sutton, R. Diestelhorst, G. Espinel, R. Krithivasan, J.P. Comeau, J.D. Cressler, P.W. Marshall, and G. Vizkelethy
Single Event Upset Mechanisms for Low-Energy-Deposition Events in SiGe HBTs, IEEE Trans. Nucl. Sci., in press (2007)
A.A. Motsinger, D.M. Reif, S.M. Dudek, and M.D. Ritchie
Dissecting the Evolutionary Process of Grammatical Evolution Optimized Neural Networks, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, in press.
A. Nair and S.D. Pathak
Modeling evolutionary co-petition in a buyer-supplier diad. Journal of Operations Management, in prep.
V.E. Oberacker, A. Blazkiewicz, and A.S. Umar
Skyrme-HFB calculations in coordinate space for the Krypton isotopes up to the two-neutron dripline. Submitted invited paper for special issue of Romanian Reports in Physics.
S.D. Pathak and D.M. Dilts
Competing Supply Networks. Decision Sciences, in prep.
S.D. Pathak and D.M. Dilts
Implications of policy decisions, predator-prey relations and evolution of healthcare Supply Networks. Health Affairs, in prep.
S.D. Pathak, D.M. Dilts, and G.Biswas
On the evolutionary dynamics of supply network topologies. IEEE Transactions on Engineering Management, in press.
S.D. Pathak, D.M. Dilts, and G. Karsai
Analyzing the dynamics of supply network evolution. International Journal of Production Research, in prep.
S.D. Pathak and A. Nair
Models of evolutionary co-opetition in diverse Supply Networks. Journal of Operations Management, in prep.
C.M. Payne, X. Zhao, and P.T. Cummings
Molecular Simulation of DNA Transport in Solution, Molecular Simulation, in press.
J. Pierce, S.D. Pathak, and S. Mahadevan
Developing a methodology for System of Systems Engineering. Journal of Systems Engineering, in prep.
Q. Pu, Y.S. Leng, L. Tsetseris, H. Park, S. Pantelides, and P. T. Cummings
Molecular dynamics simulations of stretched gold nanowires- the relative utility of different semi-empirical potentials, J. Chem. Phys, submitted.
B. Reddy, T. Wacherhausen, J.A. Smith, A. Malmendal, and W.J. Chazin
Inclusion of Calcium Ions in NMR Structures of EF-hand Calcium-Binding Proteins Without Using Artificial Restraints., in preparation.
R.A. Reed, J.A. Pellish, R.A. Weller, M. Porter, J. Wilkinson, K.M. Warren, B. Sierawski, P.W. Marshall, and R.D. Schrimpf
Applications of Heavy Ion Microprobe for Single Event Effects Analysis, Nucl. Inst. Meth. B, submitted (2007)
K. Ryckman, L. Jiang, C. Li, J. Haines, and S.M. Williams
Redefining the null hypothesis for Hardy Weinberg equilibrium, Am. J. Human Genetics, in revision.
R.D. Schrimpf, R.A. Weller, M.H. Mendenhall, R.A. Reed, and L.W. Massengill
Physical Mechanisms of Single Event Effects in Advanced Microelectronics, Nucl. Inst. Meth. B, submitted (2007)
A. Statnikov, E. Kasparova, and C.F. Aliferis
Applying Decision Support Models in the Presence of Incomplete Evidence, submitted (2006).
M.A. Stremler
Fluid Mixing, Chaotic Advection, and Microarray Analysis, CISM Courses & Lectures, L. Cortelezzi & I. Mezic, eds., Springer-Wein, in review.
A. Striolo, C. McCabe, P.T. Cummings, E.R. Chan, and S.C. Glotzer
Aggregation of POSS monomers in Liquid Hexane: A Molecular-simulation Study, Journal of Physical Chemistry B, submitted.
D.R. Velez, B. White, A.A. Motsinger, W.S. Bush, M.D. Ritchie, S.M. Williams, and J.H. Moore
A Balanced Accuracy Metric for Epistasis Modeling in Imbalanced Datasets using Multifactor Dimensionality Reduction, Genetic Epidemiology, in press.
G. Vizkelethy, R.A. Reed, P.W. Marshall, and J.A. Pellish
Ion beam induced charge (IBIC) studies of silicon-germanium heterojunction bipolar transistors (HBTs), Nucl. Instr. And Meth. B, in press.
L. Vlcek, Z. Zhang, M.L. Machesky, P. Fenter, J. Rosenqvist, D.J. Wesolowski, L.M. Anovitz, and P.T. Cummings
Electric Double Layer at Metal Oxide Surfaces: Static Properties of the Cassiterite - Water Interface, Langmuir, in press.
R.A. Weller, R.D. Schrimpf, R.A. Reed, A.L. Sternberg, A.S. Kobayashi, M.H. Mendenhall, L.W. Massengill, and D.M. Fleetwood
Modeling Semiconductor Device Response using Detailed Radiation Event Simulations, J. Rad. Effects: Research and Engineering, in press (2007)
A. Xu, D. Li, Y. Leng, and Y. Chen
Molecular Dynamics Simulation of Ion Distribution in Nanochannels, Appl. Phys. Lett., submitted.
Y.A. Yi, C. Li, and A.L. George, Jr.
Strategy for Comparison and Alignment of Gene Expression Signatures, Nucleic Acids Research, submitted.
Cho, Y.-J.,, Jacob, J., Voehler, M., Kim, H.-Y., Kozekov, I., Harris, T.M., & Stone, M.P.
Stereochemistry Modulates the Stability of Reduced Interstrand Cross-Links Arising from R- and S--CH3--OH-1,N2-Propano-2'-deoxyguanosine in the 5'-CpG-3' DNA Sequence. Biochemistry 46: in press (2007)
C.H. Chung, S. Levy, P. Chaurand, and D.P. Carbone
Genomics and proteomics: emerging technologies in clinical cancer research, Crit Rev Oncol Hematol, 61(1):1-25 (2007)
D. Riley, X. Koutsoukos, and K. Riley
Safety Analysis of Sugar Cataract Development Using Stochastic Hybrid Systems, Hybrid Systems: Computation and Control 2007, LNCS 4416:758-761 (2007)
Elmquist, C.E., Wang, F., Stover, J.S., Stone, M.P., & Rizzo, C.J.
Site-specific Synthesis and Conformation of Oligonucleotides Containing the C8-Deoxyguanosine Adduct of the Dietary Mutagen 2-Amino-3-methylimidazo[4,5-f]quinoline (2007)
Kikuchi T, Carbone DP.
Proteomics analysis in lung cancer: challenges and opportunities, Respirology, 12(1):22-8, review article (2007)
Hughes, A. L., Powell, D. W., Bard, M., Eckstein, J., Barbuch, R., Link, A. J., Espenshade, P. J.
Dap1/PGRMC1 binds and regulates cytochrome P450 enzymes, Cell Metabolism, 5:143-149.
Lapierre LA, Avant KM, Caldwell CM, Ham AJ, Hill S, Williams JA, Smolka AJ, Goldenring JR.
Characterization of immunoisolated human gastric parietal cells tubulovesicles: identification of regulators of apical recycling, Am J Physiol Gastrointest Liver Physiol, in press (2007)
A.A. Motsinger, D. Brassat, S.C. Caillier, H.A. Erlich, K. Walker, L.L. Steiner, L. Barcellos, M.A. Pericak-Vance, S. Schmidt, S. Gregory, S.L. Hauser, J.L. Haines, J.R. Oksenberg, and M.D. Ritchie
Complex Gene-Gene Interactions in Multiple Sclerosis: A Multi-factorial Approach Reveals Associations with Inflammatory Genes, Neurogenetics, 8:11-20 (2007).
M.D. Ritchie, A.A. Motsinger, W.S. Bush, C.S. Coffey, and J.H. Moore
Genetic Programming Neural Networks: A Powerful Bioinformatics Tool for Human Genetics, Applied Soft Computing, 7:471-479 (2007).
Tabb DL, Fernando CG, Chambers MC.
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis, J Proteome Res, 6(2):654-61 (2007)
Tallman KA, Kim HY, Ji JX, Szapacs ME, Yin H, McIntosh TJ, Liebler DC, Porter NA.
Phospholipid-protein adducts of lipid peroxidation: synthesis and study of new biotinylated phosphatidylcholines, Chem Res Toxicol, 20(2):227-34 (2007)
K.M. Warren, B.D. Sierawski, R.A. Weller, R.A. Reed, M.H. Mendenhall, J.A. Pellish, R.D. Schrimpf, L.W. Massengill, M.E. Porter, and J.D. Wilkinson
Predicting Thermal Neutron Induced Soft Errors in Static Memories Using TCAD and Physics-Based Monte-Carlo SimulationTools, IEEE Electron Device Letters, 28:180-182 (2007)
J. Xu, M. Does, and J. Gore
Numerical study of water diffusion in biological tissues using an improved finite difference method, Phys. Med. Biol., 52:N111-N126 (2007).
Xu, W., Merritt, W.K., Nechev, L.V., Harris,T.M., Harris, C.M., Lloyd, R.S., & Stone, M .P.
Solution Structure of the 1,4-Bis(2'-Deoxyadenosin-N6-yl)-2S,3S-butanediol Crosslinked Adduct Arising from B
utadiene Diepoxide in the Human N-ras Codon 61 Sequence. Chem. Res. Toxicol. 20: in press (2007)
Yin H, Chacon A, Porter NA, Yin H, Masterson DS.
Free Radical-Induced Site-Specific Peptide Cleavage in the Gas Phase: Low-Energy Collision-Induced Dissociation in ESI- and MALDI Mass Spectrometry, J Am Soc Mass Spectrom, in press (2007)
A.M. Albadri, R.D. Schrimpf, K.D. Galloway, D.G. Walker
Single-event burnout in power diodes: mechanisms and models, Microelectronics Reliability, 46(2-4):317-325 (2006).
G. Anumanthan, S.K. Halder, D.B. Friedman, P.K. Datta
Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism, Cancer Res, 66(22):10824-32 (2006)
O.A. Amusan, A.F. Witulski, L.W. Massengill, B.L. Bhuva, P.R. Fleming, M.L. Alles, A.L. Sternberg, J.D. Black, and R.D. Schrimpf
Charge Collection and Charge Sharing in a 130 nm CMOS Technology, IEEE Trans. Nucl. Sci., 53:3253-3258 (2006)
A. Balasubramanian, A.L. Sternberg, B.L. Bhuva, and L.W. Massengill
Crosstalk Effects Caused by Single Event Hits in Deep Sub-Micron CMOS Technologies, IEEE Trans. Nucl. Sci., 53:3306-3311 (2006)
M.P. Baze, J. Wert, J.W. Clement, M.G. Hubert, A. Witulski, O.A. Amusan, L. Massengill, and D. McMorrow
Propagating SET Characterization Technique for Digital CMOS Libraries, IEEE Trans. Nuclear Science, 53:3472-3478 (2006)
D. Brassat, Motsinger AA, Caillier SJ, Erlich HA, Walker K, Steiner LL, Cree BA, Barcellos LF, Pericak-Vance MA, Schmidt S, Gregory S, Hauser SL, Haines JL, Oksenberg JR, Ritchie MD
Multifactor dimensionality reduction reveals gene-gene interactions associated with multiple sclerosis susceptibility in African Americans, Genes Immun, 7(4):310-5 (2006).
D. Brassat, A.A. Motsinger, K. Walker, L.L. Steiner, H.A. Erlich, L. Barcellos, M.A. Pericak-Vance, S.L. Hauser, J.L. Haines, J.R. Oksenberg, and M.D. Ritchie
Multifactor Dimensionality Reduction Reveals Gene-Gene Interactions Associated with Multiple Sclerosis in African Americans. Genes and Immunity, 7:310-315.
Brown, K.L., Iyer, R.S., Iyer, L.G., Deng, J.Z., Voehler, M. W., Stone, M.P., Harris, C.M., & Harris, T.M.
Unraveling the Aflatoxin-FAPY Conundrum: Structural Basis for Differential Replicative Processing of Isomeric Forms of the Formamidopyrimidine-type DNA Adduct of Aflatoxin B1. J. Am. Chem. Soc. 128:15188-15199 (2006)
W.S. Bush, S.M. Dudek, and M.D. Ritchie
Parallel Multifactor Dimensionality Reduction: A tool for the large scale analysis of gene-gene interactions, Bioinformatics, 22:2173-4 (2006).
Busler VJ, Torres VJ, McClain MS, Tirado O, Friedman DB, Cover TL
Protein-protein interactions among Helicobacter pylori cag proteins, J Bacteriol, 188(13):4787-800 (2006)
M.C. Casey, B.L. Bhuva, J.D. Black, L.W. Massengill, O.A. Amusan, and A.F. Witulski
Single-Event Tolerant Latch Using Cascode-Voltage Switch Logic Gates, IEEE Trans. Nucl. Sci., 53:3386-3391 (2006)
Cho, Y.-J., Jacob, J., Voehler, M., Kim, H.-Y., Kozekov, I., Harris, T.M., & Stone, M.P.
Orientation of the Crotonaldehyde-Derived N2-(3-oxo-1(S)-methyl-propyl)-dG DNA Adduct Hinders Interstrand Cross-Link Formation in the 5'-CpG-3' Sequence. Chem. Res. Toxicol. 19:1019-1029 (2006)
Cho, Y.-J., Kim, H.-Y., Huang, H., Wang, H., Kozekov, I.D., Jacob, J., Voehler, M., Harris. T.M., Lloyd, R.S., Rizzo, C.J., and Stone, M.P.
Stereospecific Formation of Interstrand Carbinolamine Crosslinks by R- and S-a-CH3-g-OH-1,N2-Propano-2'-deoxyguanosine Adducts in 5'-CpG-3' DNA Sequences. Chem. Res. Toxicol. 19:195-208 (2006)
Dennehy MK, Richards KA, Wernke GR, Shyr Y, Liebler DC.
Cytosolic and nuclear protein targets of thiol-reactive electrophiles, Chem Res Toxicol, 19(1):20-9 (2006)
Fleischer, T. C., Weaver, C. M., McAfee, K. J., Jennings, J. L., Link, A. J.
Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic translation complexes, Genes and Dev., 20:1294-1307.
Friedman DB, Stauff DL, Pishchany G, Whitwell CW, Torres VJ, Skaar EP.
Staphylococcus aureus redirects central metabolism to increase iron availability, PLoS Pathog, 2(8):e87 (2006)
Gold, B., Marky, L.M., Stone, M.P., & Williams, L.D. (2006)
The Role of the Sequence-Dependent Electrostatic Landscape in DNA Alkylation Patterns, Chem. Res. Toxicol. 19:1402-1414 (2006)
D.W. Hahs, McCauley JL, Crunk AE, McFarrland LL, Gaskell PC, Jiang L, Slifer SH, Vance JM, Scott WK, Welsh-Bohmer KA, Johnson SR, Jackson CE, Pericak-Vance MA, Haines JL
A genome-wide linkage analysis of dementia in the Amish, Am J Med Genet B Neuropsychiatr Genet, 141(2):160-6 (2006).
J.L. Haines, Schnetz-Boutaud N, Schmidt S, Scott WK, Agarwal A, Postel EA, Olson L, Kenealy SJ, Hauser M, Gilbert JR, Pericak-Vance MA
Functional candidate genes in age-related macular degeneration: significant association with VEGF, VLDLR, and LRP6, Invest Ophthal mol Vis Sci, 47(1):329-35 (2006).
Holt GE, Schwartz HS, Caldwell RL.
Proteomic profiling in musculoskeletal oncology by MALDI mass spectrometry, Clin Orthop Relat Res, 450:105-10 (2006)
S.J. Kenealy, Herrel LA, Bradford Y, Schnetz-Boutaud N, Oksenberg JR, Hauser SL, Barcellos LF, Schmidt S, Gregory SG, Pericak-Vance MA, Haines JL
Examination of seven candidate regions for multiple sclerosis: strong evidence of linkage to chromosome 1q44, Genes Immun., 7(1):73-6 (2006).
X. Liang, Schnetz-Boutaud N, Kenealy SJ, Jiang L, Bartlett J, Lynch B, Gaskell PC, Gwirtsman H, McFarland L, Bembe ML, Bronson P, Gilbert JR, Martin ER, Pericak-Vance MA, Haines JL
Covariate analysis of late-onset Alzheimer disease refines the chromosome 12 locus, Mol Psychiatry, 11(3):280-5 (2006).
P.I. Lin, Martin ER, Bronson PG, Browning-Large C, Small GW, Schmechel DE, Welsh-Bohmer KA, Haines JL, Gilbert JR, Pericak-Vance MA
Exploring the association of glyceraldehyde-3-phosphate dehydrogenase gene and Alzheimer disease, Neurology, 67(1):64-8 (2006).
T.D. Loveless, L.W. Massengill, B.L. Bhuva, W.T. Holman, A.F. Witulski and Y. Boulghassoul
A Hardened-by-Design Technique for RF Digital Phase-Locked Loops, IEEE Trans. Nucl. Sci., 53:3432-3438 (2006)
McAfee, K. J., Duncan, D. T., Assink, M., Link, A. J.
Analyzing proteomes and protein function using graphical comparative analysis of tandem mass spectrometry results, Mol. Cell. Proteomics., 5:1497-1513.
J.L. McCauley, Hahs DW, Jiang L, Scott WK, Welsh-Bohmer KA, Jackson CE, Vance JM, Pericak-Vance MA, Haines JL
Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish, BMC Med Genet. 7(1):19 (2006).
A.A. Motsinger, M.D. Ritchie
The Effect of Alternative Cross-Validation Strategies on the Performance of Multifactor Dimensionality Reduction. Genetic Epidemiology, 30:546-555.
J.A. Pellish, R.A. Reed, R.D. Schrimpf, M.L. Alles, M. Varadharajaperumal, G. Niu, A.K. Sutton, R.M. Diestelhorst, G. Espinel, R. Krithivasan, J.P. Comeau, J.D. Cressler, G. Vizkelethy, P.W. Marshall, R.A. Weller, M.H. Mendenhall and E.J. Montes
Substrate engineering concepts to mitigate charge collection in deep trench isolation tecnologies, IEEE Trans. Nucl. Sci., 53:3298-3305 (2006)
Peng, R., Hawkins, I., Link, A. J., Patton, J. G.
The Splicing Factor PSF is part of a large complex that assembles in the absence of pre-mRNA and contains all 5 snRNPs, RNA Biology., 3:69-76.
Powell, D. W., Merchant, M. L., Link, A. J.
Discovery of Regulatory Molecular Events and Biomarkers Using Two-Dimensional Capillary Chromatography and Mass Spectrometry, Expert Rev. Proteomics, 3:63-74.
R.A. Reed, R.A. Weller, R.D. Schrimpf, M.H. Mendenhall, K.M. Warren, and L.W. Massengill
Implications of Nuclear Reactions for Single Event Effects Test Methods and Analysis, IEEE Trans. Nucl. Sci., 53:3356-3362 (2006)
R.L .Shuler, A. Balasubramanian, B. Narasimham, B.L. Bhuva, P.M. O' Neill, and C. Kouba
The Effectiveness of TAG or Guard-Gates in SET Suppression Using Delay and Dual-Rail Configurations at 0.35 µm, IEEE Trans. Nucl. Sci., 53:3428-3431 (2006)
A.K. Sutton, A.P. Gnana Prakash, B. Jun, E. Zhao, M. Bellini, J.A. Pellish, R.M. Diestelhorst, M. Carts, A. Phan, R. Ladbury, J.D. Cressler, P.W. Marshall, C.J. Marshall, R.A. Reed, R.D. Schrimpf and D.M. Fleetwood
An investigation of dose rate and source dependent effects in 200 GHz SiGe HBTs, IEEE Trans. Nucl. Sci., 53:3166-3174 (2006)
A.D. Tipton, J.A. Pellish, R.A. Reed, R.D. Schrimpf, R.A. Weller, M.H. Mendenhall, B. Sierawski, A.K. Sutton, R.M. Diestelhorst, G. Espinel, J.D. Cressler, P.W. Marshall, and G. Vizkelethy
Multiple-Bit Upset in 130 nm CMOS Technology, IEEE Trans. Nucl. Sci., 53:3259-3264 (2006)
Venkov, C. D, Link, A. J., Jennings, J. L., Plieth, D., Inoue, Nagai, K., Xu, C., Dimitrova, Y. N., Rauscher III, F. J., Neilson, E. G.
A new proximal activator of transcription in epithelial-mesenchymal transition, J. Clin. Invest., 117:482-491.
Wilkins M.R., Appel R.D., Van Eyk J.E., Chung M.C., Gorg A., Hecker M., Huber L.A., Langen H., Link A.J., Paik Y.K., Patterson S.D., Pennington S.R., Rabilloud T., Simpson R.J., Weiss W., Dunn M.J.
Guidelines for the next 10 years of proteomics, Proteomics, 6:4-8.
Yoon, H.-J., Feoktistova, A., Jennings, J. L., Link, A. J., Gould, K. L.
Role of Hcn1 and its phosphorylation in fission yeast APC/C function, J. Biol. Chem., 281:32284-32293.
J.E. Cygler, E. Heath, G.X. Ding, and J. Seunjens
Monte Carlo Systems in pre-clinical and clinical treatment planning: Pitfalls and triumphs. Editors: B. Curran, J. Balter and I. Chetty,, ISBN: 10-930524-33-1, Medical Physics Publishing, Madison, WI (2006).
G.X. Ding, D.M. Duggan, C.W. Coffey, P. Shokrani, and J.E. Cygler
First Macro Monte Carlo based commercial dose calculation module for electron beam treatment planning - new issues for clinical consideration. Phys Med Biol 51:2781-99 (2006).
G.X. Ding, D.M. Duggan, and C.W. Coffey
Commissioning Stereotactic Radiosurgery Beams Using both Experimental and Theoretical Methods, Phys Med Biol. 51:2549-66 (2006).
P.J.Dyer and P.T. Cummings
Hydrogen bonding and induced dipole moments in water: Predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics. Journal of Chemical Physics, 125 #144519 (2006).
FOCUS Collaboration
New measurement of BR(D + → ρ 0μ+ν) / BR(D + → K∗0μ+ν) Branching Ratio, Phys. Lett. B 637:32-38 (2006).
[arXiv:hep-ex/0511022]. CITATION = HEP-EX 0511022
FOCUS Collaboration
Study of the Decay Asymmetry Parameter and CP Violation Parameter in the Lambda/c+ $\to$ Lambda pi+ Decay, Phys. Lett. B 634:165-172 (2006).
[arXiv:hep-ex/0509042]. CITATION = HEP-EX 0509042
FOCUS Collaboration
A Non-parametric Approach to the D+ $\to$ anti-K*0 mu+ nu Form Factors, Phys. Lett. B 633:183-189 (2006).
[arXiv:hep-ex/0509027]. CITATION = HEP-EX 0509027
D.W. Haas, D.E. Geraghty, J. Andersen, J. Mar, A.A. Motsinger, R.T. D'Aquila, D. Unutmaz, C.A. Benson, M.D. Ritchie, and A. Landay
Immunogenetics of CD4 Lymphocyte Recovery during Antiretroviral Therapy: An AIDS Clinical Trials Group Study. Journal of Infectious Disease 194:1098-1107 (2006).
E.M. Hadac, E.S. Dawson, J.W. Darrow, E.E. Sugg, T.P. Lybrand, and L.J. Miller
Novel Benzodiazepine Photoaffinity Probe Stereoselectively Labels a Site Deep within the Membrane-Spanning Domain of the Cholecystokinin Receptor. Journal of Medicinal Chemistry 49:850-863.
T.C. Ionescu, F. Qi, C. McCabe, A. Striolo, J. Kieffer, and P.T. Cummings
Evaluation of Force Fields for Molecular Simulation of Polyhedral Oligomeric Silsesquioxanes, Journal of Physical Chemistry B 110:2502-2510 (2006).
N.A. Lakomek, T Carlomagno, S. Becker, C. Griesinger, and J. Meiler
A thorough dynamic interpretation of residual dipolar couplings in ubiquitin, J Biomol NMR 34:101-115 (2006).
Y.S. Leng and P.T. Cummings
Shear dynamics of hydration layers . Journal of Chemical Physics, 125 #104701 (2006). Also selected for Virtual Journal of Nanoscale Science and Technology (2006 Sept).
Y.S. Leng and P.T. Cummings
Hydration structure of water confined between mica surfaces. Journal of Chemical Physics, 124 #074711 (2006).
E.R. Martin, M.D. Ritchie, S. Kang, L. Hahn, and J.H. Moore
A Novel Method to Identify Potential Interactions in Nuclear Families: The MDR-PDT. Genetic Epidemiology 30(2):111-23 (2006).
B.A. McKinney, N. Barney, P.S. Crooke, J.E. Crowe Jr., and J.H. Moore
Hybrid Grammar-based Approach to Nonlinear Dynamical System Identification from Biological Time Series, Physical Review E 73, 021912 (2006).
B.A. McKinney, D.M. Reif, M.T. Rock, K.N. Edwards, S.F. Kingsmore, J.H. Moore, and J.E. Crowe Jr.
Cytokine Expression Patterns Associated with Systemic Adverse Events following Smallpox Immunization. Journal of Infectious Disease 194(4):444-453 (2006).
J. Meiler and D. Baker
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility, Proteins, 65:538-548 (2006).
R. Menon, D.R. Velez, H. Simhan, K. Ryckman, L. Jiang, P. Thorsen, I. Vogel, B. Jacobsson, S.M. Williams, and S.J. Fortunato
Multilocus Interactions at Maternal TNF-, IL-6 and IL-6R Genes Predict Spontaneous Preterm Labor in European-American Women, Am. Journ. Ob. Gyn., 194:1616-1624 (2006).
A.A. Motsinger, S.M. Dudek, L.W. Hahn, and M.D. Ritchie
Comparison of Neural Network Optimization Approaches for Studies of Human Genetics. Lecture Notes in Computer Science 3907:103-114 (2006). [BibTeX]
A.A. Motsinger, S.L. Lee, G. Mellick, and M.D. Ritchie
Power of Genetic Programming Neural Networks for Detecting High-order Gene-gene Interactions in Association Studies of Human Disease and an Application in Parkinson’s Disease. BMC Bioinformatics, 7:39 (2006).
A.A. Motsinger, M.D. Ritchie, R.W. Shafer, G.K. Robbins, G.D. Morse, L. Labbe, G.R. Wilkinson, D.B. Clifford, R.T. D'Aquila, V.A. Johnson, V. De Gruttola, R.B. Pollard, T.C. Merigan, M.S. Hirsch, J.P. Donahue, R.B. Kim, and D.W. Haas
Multilocus Gene-Gene Interactions and Response to Efavirenz-Containing Regimens: An Adult AIDS Clinical Trials Group Study, Pharmacogenetics and Genomics, 16:837-845 (2006).
M.D. Ritchie, D.W. Haas, A.A. Motsinger, J.P. Donahue, H. Erdem, S. Raffanti, P. Rebiero, A.L. George, R.B. Kim, J.L. Haines, and T.R. Sterling
Drug Transporter and Metabolizing Enzyme Gene Variants and Non-Nucleoside Reverse Transcriptase Inhibitor Hepatotoxicity, Clinical Infectious Diseases, 43:779-82 (2006).
R. Pattanayek, D.R. Williams, S. Pattanayek, Y. Xu, T. Mori, C.H. Johnson, P.L. Stewart, and M. Egli
Analysis of KaiA-KaiC Protein Interactions in the Cyanobacterial Circadian Clock using Hybrid Structural Methods. EMBO J. 25:2017-2028 (2006).
P. Pouget, E.E. Emeric, M. Leslie, J.D. Schall
Dynamic relationship between spikes and field potentials in supplementary eye field of macaque monkeys during saccade countermanding. Abstract; Society for Neuroscience (2006).
S.D. Saban, M. Silvestry, G.R. Nemerow, and P.L. Stewart
Visualization of α-Helices in a 6-Ångstrom Resolution Cryoelectron Microscopy Structure of Adenovirus Allows Refinement of Capsid Protein Assignments. J. Virol. 80:12049-12059 (2006). (Cover article and JVI Spotlight article)
H. Sanada, J. Yatabe, S. Midorikawa, S. Hashimoto, T. Watanabe, J.H. Moore, M.D. Ritchie, S.M. Williams, J.C. Pezzullo, G.M. Eisner, P.A. Jose, and R.A. Felder
Salt Sensitivity and G-protein-coupled Receptor Kinase Type 4 Polymorphisms. Clinical Chemistry, 52:352-60 (2006).
J. Shi, H.A. Koteiche, H.S. Mchaourab, and P.L. Stewart
Cryoelectron Microscopy and EPR Analysis of Engineered Symmetric and Polydisperse Hsp16.5 Assemblies Reveals Determinants of Polydispersity and Substrate Binding. J. Biol. Chem. 281:40420-40428 (2006).
M.G. Stabin, T.E. Peterson, G.E. Holburn, and M.A. Emmons
Voxel-Based Mouse and Rat Models for Internal Dose Calculations. J. Nucl. Med. 47:655-659 (2006).
M.A. Stremler and B.A. Cola
A Maximum Entropy Approach to Optimal Mixing in a Pulsed Source-sink Flow. Physics of Fluids 18, 011701 (2006).
A. Striolo, C. McCabe, P.T. Cummings
Organic-Inorganic Telechelic Molecules: Solution Properties from Simulations. Journal of Chemical Physics, 125 #104904 (2006).
A. Striolo, A.A. Chialvo, K.E. Gubbins, P.T. Cummings
Simulated water adsorption in chemically heterogeneous carbon nanotubes. Journal of Chemical Physics, 124 #074710 (2006).
T.A. Thornton-Wells, J.H. Moore, J.L. Haines
Comparison of Three Clustering Methods for Dissecting Trait Heterogeneity in Genotypic Data, BMC Bioinformatics 7:204 (2006).
Tsamardinos, L.E. Brown, C.F. Aliferis
The Max-Min Hill-Climbing Bayesian Network Structure Learning Algorithm, Machine Learning, (2006).
Voehler. M., Collier, G., Young, J., Stone, M.P., & Germann, M.W.
Performance of Cryogenic Probes as a Function of Ionic Strength and Sample Tube Geometry. J. Magn. Reson. 183:102-109 (2006)
Wang, F., Elmquist, C.E., Stover, J.S., Rizzo, C.J., & Stone, M.P.
Base-Displaced Intercalated Structure of the Food Mutagen 2-Amino-3-methylimidazo[4,5-f]quinoline (IQ) in the Recognition Sequence of the NarI Restriction Enzyme, a Hotspot for -2 bp Deletions. J. Am. Chem. Soc. 128:10085-10095 (2006)
Y.V. White, X. Lu, R. Pasternak, N.H. Tolk, A. Chatterjee, R.D. Schrimpf, D.M. Fleetwood, A. Ueda, and R. Mu
Studies of Charge Carrier Trapping and Recombination Processes in Si/SiO2/MgO Structures Using Second-harmonic Generation, Appl. Phys. Lett. 88, 062102, pp. 1-3 (2006).
Yarbrough WG, Slebos RJ, Liebler D.
Proteomics: clinical applications for head and neck squamous cell carcinoma, Head Neck, 28(6):549-58, review article (2006)
A. Zanghellini, L. Jiang, A.M. Wollacott, G. Cheng, J. Meiler, E.A. Althoff, D. Rothlisberger, and D. Baker
New algorithms and an in silico benchmark for computational enzyme design, Protein Sci 15:2785-2794 (2006).
PHENIX Collaboration (S.S. Adler et al.)
Azimuthal angle correlations for rapidity separated hadron pairs in d + Au Collisions at s(NN)**(1/2) = 200-GeV,, Phys.Rev.Lett, 96:222301(2006)
PHENIX Collaboration (S.S. Adler et al.)
Nuclear effects on hadron production in d+Au and p+p collisions at s(NN)**(1/2) = 200-GeV,, Phys.Rev.C,74:024904 (2006)
PHENIX Collaboration (S.S. Adler et al.)
Improved measurement of double helicity asymmetry in inclusive midrapidity pi0 production for polarized p+p collisions at s**(1/2) = 200-GeV,, Phys.Rev.D,73:091102(2006)
PHENIX Collaboration (S.S. Adler et al.)
Common suppression pattern of eta and pi0 mesons at high transverse momentum in Au+Au collisions at S(NN)**(1/2) = 200-GeV,Phy.Rev.Lett.,96:202301(2006).
PHENIX Collaboration (S.S. Adler et al.)
Nuclear modification of electron spectra and implications for heavy quark energy loss in Au+Au collisions at s(NN)**(1/2) - 200-GeV, Phys.Rev.Lett., 96:032301 (2006).
PHENIX Collaboration (S.S. Adler et al.)
Jet structure from dihadron correlations in d+Au collisions at s(NN)**(1/2) = 200-GeV,Phys.Rev.C, 73:054903 (2006).
PHENIX Collaboration (S.S. Adler et al.)
Measurement of identified pi0 and inclusive photon v(2) and implication to the direct photon production in s(NN)**1/2 = 200-GeV Au+Au collisions, Phys.Rev.Lett.,96:032302 (2006).
PHENIX Collaboration (S.S. Adler et al.)
Single electrons from heavy flavor decays in p+p collisions at s**(1/2) = 200-GeV, Phys.Rev.Lett, 96:032001(2006).
PHENIX Collaboration (S.S. Adler et al.)
J/psi production and nuclear effects for d+Au and p+p collisions at s(NN)**(1/2) = 200-GeV, Phys.Rev.Lett, 96:012304(2006).
PHENIX Collaboration (S.S. Adler et al.)
Modifications to di-jet hadron pair correlations in Au+Au collisions at s(NN)**(1/2) = 200-GeV, Phys.Rev.Lett, 97:052301(2006).
A.M. Albadri, R.D. Schrimpf, D.G. Walker, S.V. Mahajan
Coupled electrothermal simulations of single-event burnout in power diodes, IEEE Transaction on Nuclear Science, 52(6.1): 2194-2199 (2005).
D.G. Walker, C.T. Harris, T.S. Fisher and J.L. Davidson
Estimation of Parameters in Thermal-Field Emission from Diamond, Diamond and Related Materials, 14(1):113-120 (2005).
M.L. Alles, D.R. Ball, R.D. Schrimpf, D.M. Fleetwood, R.A. Reed, and B. Jun
Recent Radiation Issues in Silicon-on-Insulator Devices, Silicon-on-Insulator Technology and Devices XII, PV2005-03:87-98, G. K. Celler, Ed. Quebec City, Canada: Electrochemical Society (2005) (Invited Article)
R.R. Allingham, Wiggs JL, Hauser ER, Larocque-Abramson KR, Santiago-Turla C, Broomer B, Del Bono EA, Graham FL, Haines JL, Pericak-Vance MA, Hauser MA
Early adult-onset POAG linked to 15q11-13 using ordered subset analysis, Invest Ophthalmol Vis Sci., 6:2002-5 (2005).
A.E. Ashley-Koch, Shao Y, Rimmler JB, Gaskell PC, Welsh-Bohmer KA, Jackson CE, Scott WK, Haines JL, Pericak-Vance MA
An autosomal genomic screen for dementia in an extended Amish family, Neuroscience Letters, 379:199-204 (2005).
Caprioli RM.
Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy, Cancer Res, 65(23):10642-5, review article (2005)
Cho, Y.-J., Kim, H.-Y., Huang, H., Slutzky, A., Minko, I.G., Wang, H., Nechev, L.V., Kozekov, I.D., Kozekova, A., Tamura, P., Jacob, J., Voehler, M., Harris, T.M., Lloyd, R.S., Rizzo, C.J., and Stone, M.P.
Spectroscopic Characterization of Interstrand Carbinolamine Crosslinks Formed in the 5'-CpG-3' Sequence by the Acrolein-Derived g-OH-1,N2-Propano-2'-deoxyguanosine DNA Adduct. J. Am. Chem. Soc. 127:17686-17696 (2005)
Dong, J., Lai, R., Jennings, J. L., Link, A. J., Hinnebusch, A. G.
The novel ATP-binding cassette protein ARB1 is a shuttling factor that stimulates 40S and 60S ribosome biogenesis, Mol. Cell. Biol., 25:9859-9873.
Duncan, D. T., Craig, R., Link, A. J.
Parallel Tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem, J. of Proteome Research, 4:1842-1847.
M.N. Ellingham and C. Stephens
Triangular embeddings of complete graphs (neighborly maps) with 12 and 13 vertices, J. Combinatorial Designs, 13: 336-344 (2005).
J.L. Haines, Hauser MA, Schmidt S, Scott WK, Olson LM, Gallins P, Spencer KL, Kwan SY, Noureddine M, Gilbert JR, Schnetz-Boutaud N, Agarwal A, Postel EA, Pericak-Vance MA
Complement factor H variant increases the risk of Age-related Macular Degeneration, Science, 308:419-421 (2005).
C.L. Howe, R.A. Weller, R.A. Reed, R.D. Schrimpf, L.W. Massengill, K.M. Warren, D.R. Ball, M.H. Mendenhall, K.A. LaBel, J.W. Howard Jr.
Monte Carlo Study of Radiation-Induced Energy Deposition in Scaled Microelectronic Structures, IEEE Trans. Nucl. Sci., 53:2182-2188 (2005)
Hu X, Friedman D, Hill S, Caprioli R, Nicholson W, Powers AC, Hunter L, Limbird LE.
Proteomic exploration of pancreatic islets in mice null for the alpha2A adrenergic receptor, J Mol Endocrinol, 35(1):73-88 (2005)
A.S. Kobayashi, D.R. Ball, R.A. Reed, K.M. Warren, M.H. Mendenhall, R.D. Schrimpf, R.A. Weller
The Effect of Metallization Layers on Single Event Susceptibility, IEEE Trans. Nucl. Sci., 53:2189-2193 (2005)
Link, A. J., Fleischer, T. C., Weaver, C. M., Gerbasi, V. R., Jennings, J. L.
Purifying protein complexes for mass spectrometry: applications to protein translation, Methods., 35:274-290.
Lominadze, G., Powell, D. W., Luerman, G. C., Link, A. J., Ward, R. A., McLeish, K. R.
Proteomic Analysis of Human Neutrophil Granules, Mol. Cell. Proteomics, 4:1503-1521.
J.L. McCauley, Li C, Jiang L, Olson LM, Crockett G, Gainer K, Folstein SE, Haines JL, Sutcliffe JS
Genome-wide and Ordered-Subset linkage analyses provide support for autism loci on 17q and 19p with evidence of phenotypic and interlocus genetics correlates, BMC Med Genet, 6(1) (2005).
Merritt, W.K., Nechev, L.V., Scholdberg, T.A., Dean, S.M., Kiehna, S.E., Chang, J.C., Harris, T.M., Harris, C.M., Lloyd, R.S., and Stone, M.P.
Structure of the 1,4-Bis(2'-deoxyadenosin-N6-yl)-2R,3R-Butanediol Crosslink Arising from Alkylation of the Human N-ras Codon 61 by Butadiene Diepoxide. Biochemistry 44:3327-3337 (2005)
Merritt, W.K., Kowalczyk, A., Scholdberg, T.A., Dean, S.M., Harris, T.M., Harris, C.M., Lloyd, R.S., and Stone, M.P.
Dual Roles of Stereochemical Configuration and Glycosyl Torsion Angle Conformation Upon trans-Lesion Replication of Butadiene Oxide-Derived N1 b-Hydroxyalkyl Deoxyinosine Adducts: A Structural Perspective. Chem. Res. Toxicol. 18:1098-1107 (2005)
Meyerson M, Carbone D.
Genomic and proteomic profiling of lung cancers: lung cancer classification in the age of targeted therapy, J Clin Oncol, 23(14):3219-26, review article (2005)
Moulaei, T., Maehigashi, T., Lountos, G., Komeda, S., Watkins, D., Stone, M.P., Marky, L., Li, J.-S., Gold, B., & Williams, L.D.
Structure of B-DNA with Cations Tethered in the Major Groove. Biochemistry 44:7458-7468 (2005)
B.D. Olson, D.R. Ball, K.M. Warren, L.W. Massengill, N.F. Haddad, S.E. Doyle, and D. McMorrow
Simultaneous Single Event Charge Sharing and Parasitic Bipolar Conduction in Highly-Scaled SRAM Design, IEEE Trans. Nuclear Science, 52:2132-2136 (2005)
J.C. Pickel, R.A. Reed, R.A. Weller, M.H. Mendenhall, R.D. Schrimpf, R. Ladbury, G. Gee, B. Fodness, P.W. Marshall, T.M. Jordan, M. McKelvey, R. McMurray, K. Ennico, C. McCreight, A. Waczynski, E. Polidan, S. Johnson
Transient Radiation Effects in Ultra-Low Noise HgCdTe IR Detector Arrays for Space-based Astronomy, IEEE Trans. Nucl. Sci., 53:2657-2663 (2005)
Rahman SM, Shyr Y, Yildiz PB, Gonzalez AL, Li H, Zhang X, Chaurand P, Yanagisawa K, Slovis BS, Miller RF, Ninan M, Miller YE, Franklin WA, Caprioli RM, Carbone DP, Massion PP.
Proteomic patterns of preinvasive bronchial lesions, Am J Respir Crit Care Med, 172(12):1556-62 (2005)
S. Sawcer, Ban M, Maranian M, Yeo TW, Compston A, Kirby A, Daly MJ, De Jager PL, Walsh E, Lander ES, Rious JD, Hafler DA, Ivinson A, Rimmler J, Gregory SG, Schmidt S, Pericak-Vance MA, Akesson E, Hillert J, Datta P, Oturai A, Ryder LP, Harbo HF, Spurkland A, Myhr KM, Laaksonen M, Booth D, Heard R, Stewart G, Lincoln R, Barcellos LF, Hauser SL, Oksenberg JR, Kenealy SJ, Haines JL
for the International Multiple Sclerosis Genetics Consortium, A high-density screen for linkage in multiple sclerosis, Am J Hum Genet, 77(3):454-67 (2005).
Scholdberg, T.A., Nechev, L.V., Merritt, W.K., Harris, T.M., Harris, C.M., Lloyd, R.S., & Stone, M.P.
Mispairing of a Site-Specific Major Groove (2S,3S)-N6-(2,3,4-Trihydroxybutyl)-2'-deoxyadenosyl DNA Adduct of Butadiene Diol Epoxide with Deoxyguanosine: Formation of a dA(anti)dG(anti) Pairing Interaction. Chem. Res. Toxicol. 18:145-153 (2005)
Scholdberg, T.A., Merritt, W.K., Dean, S.M., Kowalcyzk, A., Harris, C.M., Harris, T.M., Lloyd, R.S., & Stone, M.P.
Structure of an Oligodeoxynucleotide Containing a Butadiene Oxide-Derived N1 -Hydroxyalkyl Deoxyinosine Adduct in the Human N-ras Codon 61 Sequence. Biochemistry 44:3327-3337 (2005)
Schwartz SA, Weil RJ, Thompson RC, Shyr Y, Moore JH, Toms SA, Johnson MD, Caprioli RM.
Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry, Cancer Res, 65(17):7674-81 (2005)
Strange K.
The end of "naive reductionism": rise of systems biology or renaissance of physiology?, Am J Physiol Cell Physiol, 288(5):C968-74, review article (2005)
Sung, U., Jennings, J. L., Link, A. J., Blakely, R. D.
Proteomic analysis of human norepinephrine transporter complexes reveals associations with protein phosphatase 2A anchoring subunit and 14-3-3 proteins, Biochemical and Biophysical Research Communications, 333:671-678.
Delhommelle, J., Cummings, P. T.
Simulation of Friction in Nanoconfined Fluids for an Arbitrarily Low Shear Rate. Physical Review B 72, 172201 (2005).
Delhommelle, J., Cummings, P. T., Petravic, J.
Conductivity of Molten Sodium Chloride in an Arbitrarily Weak DC Electric Field. Journal of Chemical Physics 123, 114505 (2005).
T. Hulgan, D.W. Haas, J.L. Haines, M.D. Ritchie, G.K. Robbins, R.W. Shafer, D.B. Clifford, A. Kallianpur, M. Summar, and J.A. Canter
Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an Adult AIDS Clinical Trials Group Study, AIDS, 19:1341-1349. (2005).
Koparde, V. N., Cummings, P. T.
Molecular Dynamics Simulation of Titanium Dioxide Nanoparticle Sintering. Journal of Physical Chemistry B, 109 (51), 24280-24287 (2005).
N.A. Lakomek, C. Fares, S. Becker, T. Carlomagno, J. Meiler, and C. Griesinger
Side-chain orientation and hydrogen-bonding imprint supra-tauc motion on the protein backbone of ubiquitin, Angew Chem Int Ed Engl 44:7776-7778 (2005).
Leng, Y. S., Cummings, P. T.
Fluidity of Hydration Layers Nanoconfined Between Mica Surfaces [Erratum]. Physical Review Letters 94(2), 026101 (2005).
Leng, Y. S., Krstic, P. S., Wells, J. C., Cummings, P. T., Dean, D. J.
Interaction Between Benzenedithiolate and Gold: Classical Force Field for Chemical Bonding. Journal of Chemical Physics 122, 244721 (2005).
J. Meiler, and D. Baker
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy, J Magn Reson 173:310-316 (2005).
Naicker, P. K., Cummings, P. T., Zhang, H. Z., Banfield, J. F.
Characterization of Titanium Dioxide Nanoparticles Using Molecular Dynamics Simulations. Journal of Physical Chemistry B, 109 (32), 15243-15249 (2005).
Paricaud, P., Predota, M., Chialvo, A. A., Cummings, P. T.
From Dimer to Condensed Phases at Extreme Conditions: Accurate Predictions of the Properties of Water by a Gaussian Charge Polarizable Model. Journal of Chemical Physics 122, 244511 (2005).
M.D. Ritchie and A.A. Motsinger
Multifactor Dimensionality Reduction for Detecting Gene-Gene and Gene-Environment Interactions in Pharmacogenomics Studies, Pharmacogenomics, 6:823-34 (2005).
V.M. Sanchez-Pedregal, M. Reese, J. Meiler, M.J. Blommers, C. Griesinger, and T. Carlomagno
The INPHARMA Method: Protein-Mediated Interligand NOEs for Pharmacophore Mapping, Angew Chem Int Ed Engl 44:4172-4175 (2005).
A. Striolo, A.A. Chialvo, K.E. Gubbins, P.T. Cummings
Water in Carbon Nanotubes: Adsorption Isotherms and Thermodynamic Properties from Molecular Simulation. Journal of Chemical Physics 122, 234712 (2005).
A. Striolo, K.E. Gubbins, A.A. Chialvo, P.T. Cummings
The Effect of Pore Connectivity on Water Adsorption Isotherms in Non-activated Graphitic Nanopores. Adsorption-Journal of the International Adsorption Society 11, 337-341 (2005).
A. Striolo, C. McCabe, P.T. Cummings
Effective Interactions Between Polyhedral Oligomeric Sislesquioxanes Dissolved in Normal Hexadecane from Molecular Simulation. Macromolecules, 38:8950-8959 (2005).
A. Striolo, C. McCabe, P.T. Cummings
Thermodynamic and Transport Properties of Polyhedral Oligomeric Sislesquioxanes in Poly(dimethylsiloxane). Journal of Physical Chemistry B, 109:14300-14307 (2005).
Striolo, A., Naicker, P. K., Chialvo, A. A., Cummings, P. T., Gubbins, K. E.
Simulated Water Adsorption Isotherms in Hydrophilic and Hydrophobic Cylindrical Nanoporesi. Adsorption-Journal of the International Adsorption Society 11, 397-401 (2005).
L. Tsetseris, X. J. Zhou, D. M. Fleetwood, R. D. Schrimpf, and S. T. Pantelides
Hysical Mechanisms of Negative-bias Temperature Instability. Appl. Phys. Lett. 86, 142103 (2005).
X.J. Zhou, D.M. Fleetwood, J.A. Felix, E.P. Gusev, and C. D’Emic
Bias-temperature Instabilities and Radiation Effects in MOS Devices. IEEE Trans. Nucl. Sci. 52, 2231-2238 (2005).
M.P. Rodgers, D.M. Fleetwood, R.D. Schrimpf, I.G. Batyrev, S. Wang, and S.T. Pantelides
The Effects of Aging on MOS Irradiation and Annealing Response. IEEE Trans. Nucl. Sci. 52, 2642-2648 (2005).
L. Tsetseris, R.D. Schrimpf, D.M. Fleetwood, R.L. Pease, and S.T. Pantelides
Common Origin for Enhanced Low-dose-rate Sensitivity and Bias Temperature Instability Under Negative Bias. IEEE Trans. Nucl. Sci. 52, 2265-2271 (2005).
A.P. Karmarkar, B.D. White, D. Buttari, D.M. Fleetwood, R.D. Schrimpf, R.A. Weller, L.J. Brillson, and U.K. Mishra
Proton-induced Damage in GaN-based Schottky Diodes. IEEE Trans. Nucl. Sci. 52, 2239-2244 (2005).
R.R. Cizmarik, R.D. Schrimpf, D.M. Fleetwood, K.F. Galloway, D.G. Platteter, M.R. Shaneyfelt, R.L. Pease, J. Boch, D.R. Ball, J.D. Rowe, and M.C. Maher
The Impact of Mechanical Stress on the Total-dose Response of Linear Bipolar Transistors with Various Passivation Layers. IEEE Trans. Nucl. Sci. 52, 1513-1517 (2005).
Buchner, S., Campbell, A.B., Sternberg, A., Massengill, L., McMorrow, D., Dyer, C.
Validity of Using a Fixed Analog Input for Evaluating the SEU Sensitivity of a Flash Analog-to-digital Converter. IEEE Trans. Nucl. Sci. 52, 462–467 (2005).
Saban SD, Nepomuceno RR, Gritton LD, Nemerow GR, Stewart PL
CryoEM Structure at 9 Å Resolution of an Adenovirus Vector Targeted to Hematopoietic Cells. J. Mol. Biol., 349:526-537 (2005). (Cover article)
J.M. Sherwood, P. Pouget, K. Thompson, S. Chenchal Rao, J.D. Schall
Evidence for Ensemble Coding in the Macaque Frontal Eye Field Revealed Through Particle-clustering Analysis. Program No. 590.7. 2005 Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience (2005). Online.
A. Blazkiewicz, V.E. Oberacker, and A.S. Umar
2-D Lattice HFB Calculations for Neutron-Rich Zirconium Isotopes. Eur. Phys. J. A 25, s1.543-s1.544 (2005)
A. Blazkiewicz, V.E. Oberacker, A.S. Umar, and M. Stoitsov
Coordinate Space Hartree-Fock-Bogoliubov Calculations for the Zirconium Isotope Chain up to the Two-neutron Dripline. Phys. Rev. C 71, 054321 (2005).
Soares, M.L., Coelho, T., Sousa, A., Ritchie, M.D., Williams, S.M., Batalov, S., Conceição, I., de Lurdes, M., Luís, S., Saraiva , M.J., Buxbaum, J.N.
Susceptibility and Modifier Genes in Familial Amyloid Polyneuropathy Type I. Human Molecular Genetics 14:543-553 (2005).
Bush, W.S., Motsinger A.A., Dudek, S.M., Ritchie, M.D.
Can Neural Network Constraints in GP Provide Power to Detect Genes Associated with Human Disease? Lecture Notes in Computer Science 3449:44-53 (2005).
A. Statnikov, C.F. Aliferis, I. Tsamardinos, D. Hardin, and S. Levy
A Comprehensive Evaluation of Multicategory Classification Methods for Microarray Gene Expression Cancer Diagnosis. Bioinformatics 21(5):631-643 (2005).
Schwartz, S.A., Weil, R.J, Thompson, R.C., Shyr, Y., Moore, J.H., Toms S.A., Johnson, M.D., Caprioli, R.C.
Proteomic-based Prognosis of Brain Tumor Patients Using Direct-tissue Matrix-assisted Laser Desorption Ionization Mass Spectrometry. Cancer Research 65(17):7674-7681 (2005).
FOCUS Collaboration
Measurement of the Branching Ratio of the Decay {$D^0 \to \pi^- \mu^+ \nu$} Relative to {$D^0 \to K^-\mu^+\nu$}. Phys. Lett. B 607:51-58 (2005).
FOCUS Collaboration
A Study of {$D^0 \to K^0_S K^0_S X$} Decay Channels. Phys. Lett. B 607:59-66 (2005).
FOCUS Collaboration
Analysis of the Semileptonic Decay {$D^0 \to \bar{K}^0 \pi^- \mu^+\nu$}. Phys. Lett. B 607:67-77 (2005).
FOCUS Collaboration
Measurements of the {$q^2$} Dependence of the {$D^0 \to K^- \mu^+ \nu$} and {$D^0 \to \pi^- \mu^+ \nu$} Form Factors. Phys. Lett. B 607:233-242 (2005).
FOCUS Collaboration
Study of the decay mode $D^0 \to K^- K^+ \pi^- \pi^+$. Phys. Lett. B 610:225-234 (2005).
FOCUS Collaboration
Measurement of the Doubly {Cabibbo} Suppressed Decay $D^0 \to K^+ \pi^-$ and a Search for Charm Mixing. Phys. Lett. B 618:23-33 (2005).
FOCUS Collaboration
Hadronic Mass Spectrum Analysis of $D^+ \to K^- \pi^+ \mu^+ \nu$ Decay and Measurement of the {$K^*(892)^0$} Mass and Width. Phys. Lett. B 621:72-80 (2005).
FOCUS Collaboration
Application of Genetic Programming to High Energy Physics Event Selection. Nucl. Instrum. Meth. A 551:504-527 (2005).
FOCUS Collaboration
Search for a Strongly Decaying Neutral Charmed Pentaquark. Phys. Lett. B 622:229-238 (2005).
FOCUS Collaboration
Search for \emph{{T}} Violation in Charm Meson Decays. Phys. Lett. B 622:239-248 (2005).
FOCUS Collaboration
Study of $\Lambda_c^+$ Cabibbo Favored Decays Containing a $\Lambda$ Baryon in the Final State. Phys. Lett. B 624:22-30 (2005).
FOCUS Collaboration
Search for $\Lambda_c^+ \to p K^+ \pi^-$ and $D_s^+ \to K^+ K^+ \pi^-$ Using Genetic Programming Event Selection. Phys. Lett. B 624:166-172 (2005).
FOCUS Collaboration
Measurement of the $D_s^+$ Lifetime. Phys. Rev. Lett. 95, 052003 (2005).
Wardwell NR, Massion PP.
Novel strategies for the early detection and prevention of lung cancer, Semin Oncol, 32(3):259-68, review article (2005)
K.M. Warren, R.A. Weller, M.H. Mendenhall, R.A. Reed, D.R. Ball, C.L. Howe, B.D. Olson, M.L. Alles, L.W. Massengill, R.D. Schrimpf, N.F. Haddad, S.E. Doyle, D. McMorrow, J.S. Melinger, and W.T. Lotshaw
The Contribution of Nuclear Reactions to Heavy Ion Single Event Upset Cross-Section Measurements in a High-Density SEU Hardened SRAM, IEEE Trans. Nucl. Sci., 52:2125-2131 (2005)
Xie L, Xu BJ, Gorska AE, Shyr Y, Schwartz SA, Cheng N, Levy S, Bierie B, Caprioli RM, Moses HL.
Genomic and proteomic analysis of mammary tumors arising in transgenic mice, J Proteome Res, 4(6):2088-98 (2005)
Xu BJ, Shyr Y, Liang X, Ma LJ, Donnert EM, Roberts JD, Zhang X, Kon V, Brown NJ, Caprioli RM, Fogo AB.
Proteomic patterns and prediction of glomerulosclerosis and its mechanisms, J Am Soc Nephrol, 16(10):2967-75 (2005)
Zhang YQ, Friedman DB, Wang Z, Woodruff E 3rd, Pan L, O'donnell J, Broadie K.
Protein expression profiling of the drosophila fragile X mutant brain reveals up-regulation of monoamine synthesis, Mol Cell Proteomics, 4(3):278-90 (2005)
Zimmerman LJ, Wernke GR, Caprioli RM, Liebler DC.
Identification of protein fragments as pattern features in MALDI-MS analyses of serum, J Proteome Res, 4(5):1672-80 (2005)
PHENIX Collaboration (S.S. Adler et al.)
Measurement of transverse single-spin asymmetries for mid-rapidity production of neutral pions and charged hadrons in polarized p+p collisions at s**(1/2) = 200-GeV, Phys.Rev.Lett., 95:20200 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Measurement of single electron event anisotropy in Au+Au collisions at s(NN)**(1/2) = 200-GeV,Phys.Rev.C, 72:024901 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Mid-rapidity direct-photon production in p+p collisions at s**(1/2) = 200-GeV, Phys.Rev.D, 71:071102 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Nuclear modification factors for hadrons at forward and backward rapidities in deuteron-gold collisions at s(NN)**(1/2) = 200-GeV, Phys.Rev.Lett.,94:082302 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Saturation of azimuthal anisotropy in Au+Au collisions at s(NN)**(1/2) 62-GeV to 200-GeV, Phys.Rev.Lett.,94:232302 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Production of phi mesons at mid-rapidity in s(NN)**(1/2) = 200- GeV Au+Au collisions at RHIC,Phys.Rev.C,72:014903 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Centrality dependence of charm production from single electrons measurement in Au+Au collisions at s(NN)**(1/2) = 200-GeV, Phys.Rev.Lett., 94:082301 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Systematic studies of the centrality and s(NN)**(1/2) dependence of the d E(T) / d eta and d (N(ch) / d eta in heavy ion collisions at mid-rapidity,Phys.Rev.C, 71:034908,2005, Erratum-ibid.C71:049901 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Jet structure of baryon excess in Au+Au collisions at s(NN)**(1/2) = 200-GeV,Phys.Rev.C,71:051902 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Deuteron and antideuteron production in Au+Au collisions at s(NN)**(1/2) = 200-GeV,Phys.Rev.Lett.,94:122302 (2005).
PHENIX Collaboration (S.S. Adler et al.)
Centrality dependence of direct photon production in s(NN)**(1/ 2) = 200-GeV Au+Au collisions, Phys.Rev.Lett.,94:232301 (2005).
PHENIX Collaboration (K. Adcox et al.)
Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX collaboration,Nucl.Phys.A,757:184-283 (2005).
S. V. Greene and the PHENIX collaboration
Highlights from the PHENIX Experiment, Part I, Nucl. Phys. A,774, 93 (2005).
PHENIX Collaboration (Debsankar Mukhopadhyay for the collaboration)
Phi meson production in Au+Au collisions at s(NN)**(1/2) = 200-GeV, J.Phys.G,31:S187-S194 (2005).
D. Pal and the PHENIX collaboration
Nuclear modification and elliptic flow measurements for phi mesons at s(NN)**(1/2) = 200-GeV d+Au and Au+Au collisions by PHENIX, Nucl. Phys. A, 774, 489 (2005).
An, H., Morrell, J. L., Jennings, J. L., Link, A. J., Gould, K.L.
Requirements of Fission Yeast Septins for Complex Formation, Localization and Function, Mol. Biol. Cell., 15:5551-5564.
Chaurand P, Sanders ME, Jensen RA, Caprioli RM.
Proteomics in diagnostic pathology: profiling and imaging proteins directly in tissue sections, Am J Pathol, 165(4):1057-68, review article (2004)
Daikoku T, Tranguch S, Friedman DB, Das SK, Smith DF, Dey SK.
Proteomic analysis identifies immunophilin FK506 binding protein 4 (FKBP52) as a downstream target of Hoxa10 in the periimplantation mouse uterus, Mol Endocrinol, 19(3):683-97 (2004)
Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Coffey RJ, Caprioli RM.
Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry, Proteomics, 4(3):793-811 (2004)
Gerbasi, V. R., Weaver, C. M., Hill, S., Friedman, D. B., Link, A. J.
Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression, Mol. Cell. Bio., 24:8276-8287.
Gould, K. L., Ren, L., Feoktistova, A. S., Jennings, J. L., Link, A. J.
Methods. Tandem affinity purification and identification of protein complex components, Methods, 33:239-244.
Hachey DL, Chaurand P.
Proteomics in reproductive medicine: the technology for separation and identification of proteins, J Reprod Immunol, 63(1):61-73, review article (2004)
Hashim, M.F., Riggins, J.N., Schnetz-Boutaud, N., Voehler, M., Stone. M.P., & Marnett, L.J.
In Vitro Bypass of Malondialdehyde-Deoxyguanosine Adducts: Base Selection During Extension by the Klenow Fragment of DNA Polymerase I is the Critical Determinant of Replication Outcome. Biochemistry 43:11828-11835 (2004)
S.J. Kenealy, Babron MC, Bradford Y, Schnetz-Boutaud N, Haines JL, Rimmler JB, Schmidt S, Pericak-Vance MA, Barcellos LF, Lincoln RR, Oksenberg JR, Hauser SL, Clanet M, Brassat D, Edan G, Yaouanq J, Semana G, Cournu-Rebeix I, Lyon-Caen O, Fontaine B
American-French Multiple Sclerosis Genetics Group. A second-generation genomic screen for multiple sclerosis, Am J Hum Genet, 75(6):1070-8 (2004).
Kobor, M. S., Venkatasubrahmanyam, S., Meneghini, M. D., Gin, J. W., Jennings, J. L., Link, A. J., Madhani, H. D., Rine, J.
A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin, PLoS Biology, 2:587-599.
Lewis, P. W., Beall, E. L., Fleischer, T. C., Georlette, D., Link, A. J., Botchan, M. R.
Identification of a Drosophila Myb-E2F2/RBF complex that represses transcription, Genes and Dev., 18:2929-2940.
Link, A. J.
Complex Mixture Analysis, In The Encyclopedia of Mass Spectrometry (M. L. Gross and R. Caprioli, eds), Elsevier Science, New York. Volume 2, pg 274-289.
J.L. McCauley, L.M. Olson, M. Dowd, T. Amin, A. Steele, R.D. Blakely, S.E. Folstein, J.L. Haines, and J.S. Sutcliffe
Linkage and Association Analysis at the Serotonin Transporter (SLC6A4) Locus in a Rigid-Compulsive Subset of Autism, American Journal of Medical Genetics Part B (Neuropsychiatric Genetics), 127B:104-112 (2004).
Merritt, W.K., Nechev, L.N., Scholdberg, T.A., Harris, C.M., Harris, T.M., Lloyd, R.S., & Stone, M.P.
Stereospecific Structural Perturbations Arising from Adenine N6 Butadiene Triol Adducts in Duplex DNA. Chem. Res. Toxicol. 17:1007-1019 (2004)
Morrell, J. L, Tomlin, G. C., Venkatram, S., Rajagopalan, S., Feoktistova, A. S., Tasto, J. J., Mehta, S., Jennings, J. L., Link, A. J., Balasubramanian, M. K., Gould, K. L.
Sid4p-Cdc11p assemble the septation initiation network and its regulators a the S. pombe SPB, Curr. Biol., 14:579-584.
Powell, D. W., Weaver, C. M., Jennings, J. L., Mcafee, K. J., He, Y., Weil, P. A., and Link, A. J.
Cluster analysis of mass spectrometry data reveals a novel component of SAGA, Mol. Cell. Bio., 24:7249-7259.
Reyzer ML, Caldwell RL, Dugger TC, Forbes JT, Ritter CA, Guix M, Arteaga CL, Caprioli RM
Early changes in protein expression detected by mass spectrometry predict tumor response to molecular therapeutics, Cancer Res, 64(24):9093-100 (2004)
Sattlegger, E., Swanson, M. J., Ashcraft, E. A., Jennings, J. L., Fekete, R. A., Link, A. J., Hinnebusch, A. G.
YIH1 is an actin-binding protein that inhibits protein kinase GCN2 and impairs general amino acid control when overexpressed, J. Biol. Chem., 279:29952-29962.
Venkatram, S., Tasto, J. J., Feoktistova, A. S., Jennings, J. L., Link, A. J., Gould K. L.
Identification and characterization of two novel proteins affecting fission yeast gamma-tubulin complex function, Mol. Biol. Cell, 15:2287-2301.
H. D. Xiong, D. M. Fleetwood, and J. R. Schwank
Low-frequency Noise and Radiation Response of Buried Oxides in SOI nMOS Transistors. IEE Proc. Circuits, Devices & Systems 151(2):118-124 (2004).
X. J. Zhou, L. Tsetseris, S. N. Rashkeev, D. M. Fleetwood, R. D. Schrimpf, S. T. Pantelides, J. A. Felix, E. P. Gusev, and C. D'Emic
Negative Bias-temperature Instabilities in MOS Devices with SiO2 and SiOxNy/HfO2 Gate Dielectrics. Appl. Phys. Lett. 84, (22) 4394-4396 (2004).
J. A. Felix, H. D. Xiong, D. M. Fleetwood, E. P. Gusev, R. D. Schrimpf, A. L. Sternberg, and C. D'Emic
Interface Trapping Properties of nMOSFETs with Al2O3/SiOxNy/Si (100) Gate Dielectric Stacks after Exposure to Ionizing Radiation. Microelectron. Engrg. 72, 50-54 (2004).
J. A. Felix, J. R. Schwank, C. R. Cirba, R. D. Schrimpf, M. R. Shaneyfelt, D. M. Fleetwood, and P. E. Dodd
Influence of Total-dose Radiation on the Electrical Characteristics of SOI MOSFETs. Microelectron. Engrg. 72, 332-341 (2004).
J. R. Schwank, D. M. Fleetwood, H. D. Xiong, M. R. Shaneyfelt, and B. L. Draper
Generation of Metastable Electron Traps in the Near Interfacial Region of SOI Buried Oxides by Ion Implantation and their Effect on Device Properties. Microelectron. Engrg. 72, 362-366 (2004).
Scholdberg, T.A., Nechev, L.N., Merritt, W.K., Harris, T.M., Harris, C.M., Lloyd, R.S., & Stone, M.P.
Structure of the Site-Specific Major Groove (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2-deoxyadenosyl Adenine N6 Adduct of Butadiene Diol Epoxide. Chem. Res. Toxicol. 17:717-730 (2004).
X. Hu, B. K. Choi, H. J. Barnaby, D. M. Fleetwood, R. D. Schrimpf, S. C. Lee, S. Shojah-Ardalan, R. Wilkins, U. K. Mishra, and R. Dettmer
The Energy Dependence of Proton-Induced Degradation in AlGaN/GaN High Electron Mobility Transistors. IEEE Trans. Nucl. Sci. 51, 293-297 (2004). [also in RADECS2002 Workshop Proc., pp. 17-20, 2002].
J. A. Felix, J. R. Schwank, D. M. Fleetwood, M. R. Shaneyfelt, and E. P. Gusev
Effects of Radiation and Charge Trapping on the Reliability of High-Rate Dielectrics. Microelectron. Reliab. 44(4):563-575 (2004).
S. N. Rashkeev, D. M. Fleetwood, R. D. Schrimpf, and S. T. Pantelides
Hydrogen at the Si/SiO2 Interface: From Atomic-Scale Calculations to Engineering Models. in Radiation Effects and Soft Errors in Integrated Circuits and Electronic Devices, edited by R. D. Schrimpf and D. M. Fleetwood (World Scientific, Singapore, 2004), pp. 291-296.
J. Boch, F. Saigne, R. D. Schrimpf, D. M. Fleetwood, R. Cizmarik, and D. Zander
Elevated Temperature Irradiation at High dose Rate of Commercial Linear Bipolar ICs. IEEE Trans. Nucl. Sci. 51, 2903-2907 (2004).
J. Boch, F. Saigne, R. D. Schrimpf, D. M. Fleetwood, S. Ducret, L. Dusseau, J. P. David, J. Fesquet, J. Gasiot, and R. Ecoffet
Effect of Switching from High to Low Dose Rate on Linear Bipolar Technology Radiation Response. IEEE Trans. Nucl. Sci. 51, 2896-2902 (2004).
B. Jun, M. Fouillat, R. D. Schrimpf, D. M. Fleetwood, and S. Cristoloveanu
Total Dose Radiation Effects in Partially-depleted SOI Transistors with Ultrathin Gate Oxide. Proceeedings IEEE SOI Conference, Charleston SC, October 4-7, 2004, pp. 30-31.
B. Jun, Y. V. White, R. D. Schrimpf, D. M. Fleetwood, F. Brunier, N. Bresson, S. Cristoloveanu, and N. H. Tolk
Characterization of Multiple Si/SiO2 Interfaces in Silicon-on-insulator Materials via Second-harmonic Generation. Appl. Phys. Lett. 85, (15) 3095-3097 (2004).
L. Tsetseris, X. J. Zhou, D. M. Fleetwood, R. D. Schrimpf, and S. T. Pantelides
Dual Role of Fluorine at the Si-SiO2 Interface. Appl. Phys. Lett. 85, (21) 4950-4952 (2004).
B. Jun, H. D. Xiong, A. L. Sternberg, C. R. Cirba, D. Chen, R. D. Schrimpf, D. M. Fleetwood, J. R. Schwank, and S. Cristoloveanu
Total Dose Effects on Double Gate Fully Depleted SOI MOSFETs. IEEE Trans. Nucl. Sci. 51, 3767-3772 (2004).
S. Ducret, F. Saigne, J. Boch, R. D. Schrimpf, D. M. Fleetwood, J. R. Vaille, L. Dusseau, J. P. David, and R. Ecoffet
Effect of Thermal Annealing on Radiation-induced Degradation of Bipolar Technologies when the Dose Rate is Switched from High to Low. IEEE Trans. Nucl. Sci. 51, 3219-3224 (2004).
J. Boch, F. Saigne, S. Ducret, R. D. Schrimpf, D. M. Fleetwood, P. Iacconi, and L. Dusseau
Total Dose Effects on Bipolar Integrated Circuits: Characterization of the Saturation Region. IEEE Trans. Nucl. Sci. 51, 3225-3230 (2004).
A. P. Karmarkar, B. Jun, D. M. Fleetwood, R. D. Schrimpf, R. A. Weller, B. D. White, L. J. Brillson, and U. K. Mishra
Proton Irradiation Effects on GaN-based High Electron Mobility Transistors with Si-doped AlxGa1-xN and Thick GaN Cap Layers. IEEE Trans. Nucl. Sci. 51, 3801-3806 (2004).
B. Jun, R. D. Schrimpf, D. M. Fleetwood, Y. V. White, R. Pasternak, S. N. Rashkeev, F. Brunier, N. Bresson, M. Fouillat, S. Cristoloveanu, and N. H. Tolk
Charge Trapping in Irradiated SOI Wafers Measured by Second Harmonic Generation. IEEE Trans. Nucl. Sci. 51, 3231-3237 (2004).
M. R. Shaneyfelt, J. R. Schwank, D. M. Fleetwood, R. L. Pease, J. A. Felix, P. E. Dodd, and M. C. Maher
Annealing Behavior of Linear Bipolar Devices with Enhanced Low-dose-rate Sensitivity. IEEE Trans. Nucl. Sci. 51, 3172-3177 (2004).
J. W. Stacey, R. D. Schrimpf, D. M. Fleetwood, and K. C. Holmes
Using Surface Charge Analysis to Characterize the Radiation Response of Si/SiO2 Structures. IEEE Trans. Nucl. Sci. 51, 3686-3691 (2004).
R. A. Weller, M. H. Mendenhall, and D. M. Fleetwood
A Screened Coulomb Scattering Module for Displacement Damage Computations in Geant4. IEEE Trans. Nucl. Sci. 51, 3669-3678 (2004).
J. A. Felix, M. R. Shaneyfelt, D. M. Fleetwood, J. R. Schwank, P. E. Dodd, E. P. Gusev, R. M. Fleming, and C. D'Emic
Charge Trapping and Annealing in High-rate Dielectrics. IEEE Trans. Nucl. Sci. 51, 3143-3149 (2004).
H. D. Xiong, B. Jun, D. M. Fleetwood, R. D. Schrimpf, and J. R. Schwank
Charge Trapping and Low Frequency Noise in SOI Buried Oxides. IEEE Trans. Nucl. Sci. 51, 3238-3242 (2004).
S. N. Rashkeev, D. M. Fleetwood, R. D. Schrimpf, and S. T. Pantelides
Effects of Hydrogen Motion on Interface Trap Formation and Annealing. IEEE Trans. Nucl. Sci. 51, 3158-3165 (2004).
Kobayashi, A.S.; Sternberg, A.L.; Massengill, L.W.; Schrimpf, R.D.; Weller, R.A.
Spatial and Temporal Characteristics of Energy Deposition by Protons and Alpha Particles in Silicon. IEEE Trans. Nucl. Sci. 51, 3312-3317 (2004).
Boulghassoul, Y.; Adell, P.C.; Rowe, J.D.; Massengill, L.W.; Schrimpf, R.D.; Sternberg, A.L.
System-level Design Hardening Based on Worst-case ASET Simulations. IEEE Trans. Nucl. Sci. 51, 2787-2793 (2004).
Mikyas Y, Makabi M, Raval-Fernandes S, Harrington L, Kickhoefer VA, Rome LH, Stewart PL.
Cryoelectron Microscopy Imaging of Recombinant and Tissue Derived Vaults: Localization of the MVP N Termini and VPARP. J. Mol. Biol., 344:91-105 (2004). (Cover article)
Williams SM, MD Ritchie, JA Phillips, E Dawson, M Prince, E Dzhura, A Willis, A Semenya, M Summar, BC White, JH Addy, J Kpodonu, L-J Wong, RA Felder, PA Jose, and JH Moore
Multilocus Analysis of Hypertension: a Hierarchical Approach. Human Heredity 57(1):28-38 (2004).
Harikumar HG, Pinion DI, Wessels WS, Dawson ES, Lybrand TP, Prendergast FG, and Miller LJ
Measurement of Intermolecular Distances for the Natural Agonist Peptide Docked at the Cholecystokinin Receptor Expressed in situ Using Fluorescence Resonance Energy Transfer. Molecular Pharmacology 65(1):28-35 (2004).
Cho, Y.M., Ritchie, M.D., Moore, J.H., Moon, M.K., Lee, Y.Y, Yoon, K.H., Sung, Y.A., Lang, H.C., Park, J.Y., Lee, K.U., Shin, H.D., Kim, S.Y., Lee, H.K., Park, K.S.
Multifactor Dimensionality Reduction Reveals a Two-Locus Interaction Associated with Type 2 Diabetes Mellitus. Diabetologia 47(3):549-554 (2004).
Tsai, C.T., Lai, L.P., Chiang, F.T., Fallin, D., Hwang, J.J., Ritchie, M.D., Moore, J.H., Hsu, K.L., Tseng, C.D., Liau, C.S., Lin, J.L., Tseng, Y.Z.
Renin-Angiotensin System Gene Polymorphisms and Atrial Fibrillation. Circulation 109:1640-1646 (2004).
Coffey, C.S., Hebert, P.R., Ritchie, M.D., Krumholz, H.M., Morgan, T.M., Gaziano, J.M., Ridker, P.M., and Moore, J.H.
An Application of Conditional Logistic Regression and Multifactor Dimensionality Reduction for Detecting Gene-gene Interactions on Risk of Myocardial Infarction: The Importance of Model Validation. BMC Bioinformatics, 5:49 (2004).
Ritchie, M.D., Coffey, C.S., and Moore J.H.
Genetic Programming Neural Networks: A Bioinformatics Tool for Human Genetics. Lecture Notes in Computer Science, 3102: 438-448 (2004).
Moore, J.H., Hahn, L.W., Ritchie, M.D., Thornton, T.A., White, B.
Routine Discovery of High-Order Epistasis Models for Computational Studies in Human Genetics. Applied Soft Computing 4:79-86 (2004).
A. Statnikov, C.F. Aliferis, and I. Tsamardinos
Methods for Multi-category Cancer Diagnosis from Gene Expression Data: A Comprehensive Evaluation to Inform Decision Support System Development. Medinfo, 2004.
Moore, J.H., Hahn, L.W.
Evaluation of a Discrete Dynamic Systems Approach for Modeling the Hierarchical Relationship Between Genes, Biochemistry, and Disease Susceptibility. Discrete and Continuous Dynamical Systems: Series B 4(1):275-287 (2004).
Reif, D.M., White, B.C., Moore, J.H.
Integrated Analysis of Genetic, Genomic, and Proteomic data. Expert Review of Proteomics 1(1):67-75 (2004).
Aune, T.M., Parker, J.S., Maas, K., Olsen, N., Moore, J.H.
Co-localization of Differentially Expressed Genes and Shared Susceptibility Loci in Human Autoimmunity. Genetic Epidemiology 27(2):162-172 (2004).
Moore, J.H., Hahn, L.W.
An Improved Grammatical Evolution Strategy for Petri Net Modeling of Complex Genetic Systems. In Raidl, G.R., Cagnoni, S., Branke, J., Corne, D.W., Rolf, D., Jin, Y., Johnson, C., Machado, P., Marchiori, E., Rothlauf, F., Smith, G.D., Squillero, G. (eds), Lecture Notes in Computer Science 3005, 62-71, Springer-Verlag, Berlin (2004).
Moore, J.H., Hahn, L.W.
Systems Biology Modeling in Human Genetics Using Petri Nets and Grammatical Evolution. In Deb, K., Poli, R., Banzhaf, W., Beyer, H.-G., Burke, E., Darwen, P., Dasgupta, D., Floreano, D., Foster, J., Harman, M., Holland, O., Lanzi, P.L., Spector, L., Tettamanzi, A., Thierens, D., Tyrrell, A. (eds), Lecture Notes in Computer Science 3102, 392-401, Springer, New York (2004).
White, B.C., Moore, J.H.
Systems Biology Thought Experiments in Human Genetics Using Artificial Life and Grammatical Evolution. In Pollack, J., Bedau, M., Husbands, P., Ikegami, T., Watson, R.A. (eds), Artificial Life IX. The MIT Press, Cambridge, pp 581-86 (2004).
E687 Collaboration
On the Narrow Dip Structure at 1.9~GeV/$c^2$ in Diffractive Photoproduction. Phys. Lett. B 578:290-296 (2004).
FOCUS Collaboration
Study of Hadronic Five-Body Decays of Charmed Mesons Involving \KSH. Phys. Lett. B 586:191-197 (2004).
FOCUS Collaboration
Charm - Anticharm Baryon Production Asymmetries in Photon Nucleon Interactions. Phys. Lett. B 581:39-48 (2004).
FOCUS Collaboration
Dalitz Plot Analysis of \DsP\ and \DP\ Decay to \PIP\PIM\PIP\ Using the K-Matrix Formalism. Phys. Lett. B 585:200-212 (2004).
FOCUS Collaboration
Measurement of Masses and Widths of Excited Charm Mesons $D_2^*$ and Evidence for Broad States. Phys. Lett. B 586:11-20 (2004).
FOCUS Collaboration
New Measurements of the $\DsP \to \phi\MP\N$ Form Factor Ratios. Phys. Lett. B 586:183-190 (2004).
FOCUS Collaboration
Measurements of Six-Body Hadronic Decays of the \DZ\ Charmed Meson. Phys. Lett. B 586:21-26 (2004).
FOCUS Collaboration
Measurement of the Ratio of the Vector to Pseudoscalar Charm Semileptonic Decay Rate $\Gamma(\DP \to \overline{K}{}^{*{\tiny0}} \MP \NM)/\Gamma(\DP \to \KZB \MP \NM)$. Phys. Lett. B 598:33-41 (2004).
FOCUS Collaboration
Study of the Doubly and Singly Cabibbo Suppressed Decays $\DP \to \KP\PIP\PIM$ and $\DsP \to \KP\PIP\PIM$. Phys. Lett. B 601:10-19 (2004).
Schwartz SA, Weil RJ, Johnson MD, Toms SA, Caprioli RM.
Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression, Clin Cancer Res, 10(3):981-7 (2004)
D.G. Walker and R.A. Weller
Phonon Production and Nonequilibrium Transport from Ion Strikes, IEEE Transactions on Nuclear Science 51(6):3318-3323 (2004).
D.G. Walker and T.S. Fisher
Simulation of field-emitted electron trajectories and transport from carbon nanotubes, Journal of Vacuum Science and Technology B, 22(3):1101-1107 (2004) (Also published in Virtual Journal of Nanoscale Science and Technology Vol. 9, No. 21, 2004).
C.T. Harris, D.G. Walker, T.S. Fisher and W.H. Hofmeister
Experimental Characterization of Anode Heating due to Electron Field Emission, Microscale Thermophysical Engineering , 8(2):101-110 (2004).
P.C. Adell, R.D. Schrimpf, W.T. Holman, J. Boch, J. Stacey, P. Ribero, A.L. Sternberg, K.F. Galloway
Total-dose and Single-event Effects in DC/DC Converter Control Circuitry. IEEE Trans. Nucl. Sci. 50, 1867-1872 (2003).
J. Boch, D. M. Fleetwood, R. D. Schrimpf, R. R. Cizmarik, and F. Saigne
Impact of Mechanical Stress on Total-dose Effects in Bipolar ICs. IEEE Trans. Nucl. Sci. 50, 2335-2340 (2003).
Chakravarthy B, Pietenpol JA.
Combined modality management of breast cancer: development of predictive markers through proteomics, Semin Oncol, 30(4 Suppl 9):23-36, review article (2003)
Dooley, P.A., Zhang, M., Korbel, G.A., Nechev, L.V., Harris, C.M., Stone, M.P., & Harris, T.M.
NMR Determination of the Conformation of a Trimethylene Interstrand Crosslink in an Oligodeoxynucleotide Duplex Containing a 5'-d(GpC) Motif. " J. Am. Chem. Soc. 125:62-72 (2003).
J. A. Felix, M. R. Shaneyfelt, D. M. Fleetwood, T. L. Meisenheimer, J. R. Schwank, R. D. Schrimpf, P. E. Dodd, E. P. Gusev, and C. D'Emic
Radiation-induced Charge Trapping in Thin Al2O3/SiOxNy/Si(100) Gate Dielectric Stacks. IEEE Trans. Nucl. Sci. 50, 1910-1918 (2003).
D. M. Fleetwood and H. A. Eisen
Total-Dose Radiation Hardness Assurance. IEEE Trans. Nucl. Sci. 50, 552-564 (2003).
FOCUS Collaboration
Observation of a 1750-MeV/c$^2$ Enhancement in the Diffractive Photoproduction of \KM \KP. Phys. Lett. B 545:50-56 (2003).
FOCUS Collaboration
A Study of the Cabbibo-Suppressed Decays $\DZ\to\PIP\PIM$ and $\DZ\to\KP\KM$. Phys. Lett. B 555:167-173 (2003).
FOCUS Collaboration
Charm System Tests of CPT and Lorentz Invariance with FOCUS. Phys. Lett. B 556:7-13 (2003).
FOCUS Collaboration
A Measurement of the $\Omega_c^0$ Lifetime. Phys. Lett. B 561:41-48 (2003).
FOCUS Collaboration
The Target Silicon Detector for the FOCUS Spectrometer. Nucl. Instrum. Meth. A 516:364-376 (2003).
FOCUS Collaboration
Study of Hadronic Five-Body Decays of Charmed Mesons. Phys. Lett. B 561:225-232 (2003).
FOCUS Collaboration
Studies of Correlations Between $D$ and $\DB$ Mesons in High Energy Photoproduction. Phys. Lett. B 566:51-60 (2003).
FOCUS Collaboration
Measurements of $\Xi_c^+$ Branching Ratios. Phys. Lett. B 571:139-147 (2003).
FOCUS Collaboration
Search for Rare and Forbidden 3-body Di-muon Decays of the Charmed Mesons \DP\ and \DsP. Phys. Lett. B 572:21-31 (2003).
FOCUS Collaboration
Study of the Decay Mode $\DZ\to\KM\KM\KP\PIP$. Phys. Lett. B 575:190-197 (2003).
Giri, I., & Stone, M.P.
Wobble dCdA Pairing 5' to the Cationic Guanine N7 8,9-Dihydro-8-(N7-guanyl)-9-Hydroxy-Aflatoxin B1 Adduct: Implications for Non-targeted AFB1 Mutagenesis. Biochemistry 42:7023-7034 (2003)
Hahn, L.W., Ritchie, M.D., and Moore, J.H.
Multifactor Dimensionality Reduction Software for Detecting Gene-gene and Gene-environment Interactions. Bioinformatics 19:376-382 (2003).
X. Hu, A. P. Karmarkar, B. Jun, D. M. Fleetwood, R. D. Schrimpf, R. D. Geil, R. A. Weller, B. D. White, M. Bataiev, L. J. Brillson, and U. K. Mishra
Proton Irradiation Effects on AlGaN/AlN/GaN High Electron Mobility Transistors. IEEE Trans. Nucl. Sci. 50, 1791-1796 (2003).
Y. Jiang, R. Pasternak, Z. Marka, Y. V. Shirovkaya, J. K. Miller, S. N. Rashkeev, Yu. D. Glinka, I. E. Perakis, P. K. Roy, J. Kozub, B. K. Choi, D. M. Fleetwood, R. D. Schrimpf, X. Liu, Y. Sasaki, J. K. Furdyna, and N. H. Tolk
Spin/Carrier Dynamics at Semiconductor Interfaces Using Intense, Tunable Ultra-Fast Lasers. Phys. Stat. Sol. (b) 240(3):490-499 (2003).
B. Jun, D. M. Fleetwood, R. D. Schrimpf, X. J. Zhou, E. J. Montes, and S. Cristoloveanu
Charge Separation Techniques for Irradiated Pseudo-MOS SOI Transistors. IEEE Trans. Nucl. Sci. 50, 1891-1895 (2003).
Kalavagunta, A.; Bo Choi; Neifeld, M.A.; Schrimpf, R.
Effects of 2 MeV Proton Irradiation on Operating Wavelength and Leakage Current of Vertical Cavity Surface Emitting Lasers. IEEE Trans. Nucl. Sci. 50, 1982-1990 (2003).
Kim, H-.Y., Wilkinson, A.S., Harris, C.M., Harris, T.M., & Stone, M.P.
Minor Groove Orientation for the (1S,2R,3S,4R)-N2-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxy-benz[a]anthracenyl)]-2¢-deoxyguanosyl Adduct in the N-ras Codon 12 Sequence. Biochemistry 42:2328-2338 (2003)
R. A. Knop et al. including R. A. Gibbons
New Constraints on Ω_Μ, Ω_Λ, and w From an Independent Set of 11 High-Redshift Supernovae Observed with the Hubble Space Telescope. Astrophysical Journal 598(1):102-137 (2003).
Kozekov, I.D., Nechev, L.V., Moseley, M.S., Harris, C.M., Rizzo, C.J., Stone, M.P., & Harris, T.M.
DNA Interchain Crosslinks Formed by Acrolein and Crotonaldehyde. J. Am. Chem. Soc. 125:50-61 (2003).
Krstic, P. S.; Dean, D. J.; Zha