MSCL Publications
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- Berezhkovskii AM, Murphy RD, Buchete NV "Network random walk model of two-state protein folding: Test of the theory" J. Chem. Phys. 138(3):036101, 2pp.
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM, Bezrukov SM "Particle lifetime in cylindrical cavity with absorbing spot on the wall: Going beyond the narrow escape problem" J. Chem. Phys. 137(23), 234108, 6 pp.
[Abstract] [Full Article] - Berezhkovskii AM "Aris-Taylor dispersion from single-particle point of view" J. Chem. Phys. 137(6) 066101, 2 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Sample C, Shvartsman SY "Formation of morphogen gradients: Local accumulation time" Phys. Rev. E 83(5) 051906, 7 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV "Extended narrow escape problem. Boundary homogenization based analysis" Phys. Rev. E 82(1) 011114, 5 pp.
[Abstract] [Full Article] - Nestorovich EM, Karginov VA, Berezhkovskii AM, Parsegian VA, Bezrukov SM "Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative" Proc. Natl. Acad. Sci. USA 109(45):18453-58
[Abstract] [Full Article] - Banerjee A, Berezhkovskii A, Nossal R "Distribution of lifetime and maximum size of abortive clathrin-coated pits." Phys. Rev. E 86, 031907, 8 pp.
[Abstract] [Full Article] - Berezhkovskii AM "Aris-Taylor dispersion from single-particle point of veiw." J. Chem. Phys. 137(6), 066101, 2 pp.
[Abstract] [Full Article] - Banerjee A, Berezhkovskii A, Nossal R "Stochastic Model of Clathrin-Coated Pit Assembly." Biophys. J. 102(12):2725-30
[Abstract] [Full Article] [Supplementary] - Dagdug L, Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu, Bezrukov SM "Force-dependent mobility and entropic rectification in tubes of periodically varying geometry" J. Chem. Phys. 136(21) 214110, 6 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Lizunov VA, Zimmerberg J, Bezrukov SM "Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles" J. Chem. Phys. 136(21) 211102, 4 pp.
[Abstract] [Full Article] - Dagdug L, Vazquez M-V, Berezhkovskii AM, Zitserman VY, Bezrukov SM "Diffusion in the presence of cylindrical obstacles arranged in a square lattice analyzed with generalized Fick-Jacobs equation." J. Chem.Phys. 136(20): 204106, 5 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L "Effect of binding on escape from cavity through narrow tunnel" J. Chem. Phys. 136(12) 124110
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV "Search for a small hole in a cavity wall by intermittent bulk and surface diffusion." J. Chem. Phys. 136(5): 054115, 6 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Surface area of the domain visited by a spherical Brownian particle" Chaos 21(4) 047519, 3 pp.
[Abstract] [Full Article] - Pineda I, Vazquez M-V, Berezhkovskii AM, Dagdug L "Diffusion in periodic two-dimensional channels formed by overlapping circles: Comparison of analytical and numerical results." J. Chem. Phys. 135(22):224101, 5 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Shvartsman SY "Physical interpretation of mean local accumulation time of morphogen gradient formation" J. Chem. Phys. 135(15): 154115, 6 pp.
[Abstract] [Full Article] - Zitserman VYu, Berezhkovskii AM, Antipov AE, Makhnovskii YuA "Drift velocity of Brownian particle in a periodically tapered tube induced by a time-periodic force with zero mean: Dependence on the force period" J. Chem. Phys. 135(12):121102-1-4
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Effective drift and diffusion of a particle jumping between mobile and immobile states." J. Electroanal. Chem. 660:352-355
[Abstract] [Full Article] - Berezhkovskii AM, Szabo A, Zhou H-X "Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels." J. Chem. Phys. 135(7):075103-1-5
[Abstract] [Full Article] - Berezhkovakii AM, Szabo A "Time scale separation leads to position-dependent diffusion along the slow coordinate." J. Chem. Phys. 135(7):074108-1-5
[Abstract] [Full Article] - Berezhkovskii AM "Ordinary differential equation for local accumulation time." J. Chem. Phys. 135(7):074112-1-5
[Abstract] [Full Article] - Berezhkovskii AM, Lizunov VA, Zimmerberg J, Bezrukov SM "Functional Role for Transporter Isoforms in Optimizing Membrane Transport" Biophys. J.101(2):L14-L16
[Abstract] [Full Article] - Berezhkovskii AM, Sample C, Shvartsman SY "Formation of morphogen gradients: Local accumulation time." Phys. Rev. E 83(5):051906, 7pp.
[Abstract] [Full Article] - Gordon PV,Sample C, Berezhkovskii AM, Muratov CB, Svartsman SY "Local kinetics of morphogen gradients." PNAS 108(15):6157-62
[Abstract] [Full Article] [Supplementary] - Berezhkovskii AM, Dagdug L "Analytical treatment of biased diffusion in tubes with periodic dead ends." J. Chem. Phys. 134(12):124109, 8 pp.
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu, Bezrukov SM "Turnover behavior of effective mobility in a tube with periodic entropy potential." J. Chem. Phys. 134(10): 101102-1-3
[Abstract] [Full Article] - Berezhkovskii AM "Renewal theory for single-molecule systems with multiple reaction channels." J. Chem. Phys. 134(7), 8 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Sample C, Shvartsman SY "How long does it take to establish a morphogen gradient" Biophys. J. 99(8):L59-61
[Abstract] [Full Article] - Berezhkovskii AM, Pustovoit MA, Bezrukov SM "Fluxes of non-interacting and strongly repelling particles through a single conical channel: Analytical results and their numerical tests." Chem. Phys. 375(2-3): 523-28
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L "Bised diffusion in tubes formed by spherical compartments." J. Chem. Phys. 133(13):134102 (6 pp.)
[Abstract] [Full Article] - Berezhkovskii AM, Pustovoit MA, Bezrukov SM "Entropic effects in channel-facilitated transport: Inter-particle interactions break the flux symmetry." Phys. Rev. E 80(2): 020904(R), 4 pp.
[Abstract] [Full Article] - Dagdug L, Vazquez M-V, Berezhkovskii AM, Bezrukov SM "Unbiased diffusion in tubes with corrugated walls" J. Chem. Phys. 133(3): 034707, 3 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV "Extended narrow escape problem: Boundary homogenization-based analysis." Phys. Rev. E82(1): 011114, 5pp.
[Abstract] [Full Article] - Nestorovich EM, Karginov VA, Berezhkovskii AM, Bezrukov SM "Blockage of Anthrax PA63 Pore by a Multicharged High-Affinity Toxin Inhibitor" Biophys. J. 99(1):134-143
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Makhnovskii YuA, Zitserman VYu "Communications: Drift and diffusion in a tube of periodically varying diameter. Driving force induced intermittency." J. Chem. Phys. 132(22): 221104-1-4
[Abstract] [Full Article] - Makhnovskii YuA, Berezhkovskii AM, Zitserman VYu, "Diffusion in a tube of alternating diameter." Chem. Phys. 370(1-3):238-43
[Abstract] [Full Article] - Berezhkovskii AM "Variance of residence time spent by diffusing particle in a sub-domain: Path integral based approach" Chem. Phys. 370(1-3):253-57
[Abstract] [Full Article] - Makhnovskii YuA, Berezhkovskii AM, Zitserman VYu "Diffusion in a tube of alternating diameter." Chem. Phys. 367(1):110-14
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV, Zitserman VYu "One-dimensional description of diffusion in a tube of abruptly changing diameter: Boundary homogenization based approach." J. Chem. Phys. 131(22): 224110-1-8
[Abstract] [Full Article] - Makhnovskii YuA, Berezhkovskii AM, Zitserman VYu "Time-dependent diffusion in tubes with periodic partitions." J. Che. Phys. 131(10): 104705-1-5
[Abstract] [Full Article] - Shvartsman SY, Coppey M, Berezhkovskii AM "MAPK signaling in equations and embryos." Fly 3(1):62-67
[Abstract] [PubMed] - Bailey MJ, Coon SL, Carter DA, Humphries A, Kim JS, Shi Q, Gaildrat P, Morin F, Ganguly S, Hogenesch JB, Weller JL, Rath MF, Mller M, Baler R, Sugden D, Rangel ZG, Munson PJ, Klein DC. Night/Day Changes in Pineal Expression of >600 Genes: CENTRAL ROLE OF ADRENERGIC/cAMP SIGNALING." J Biol Chem. 2009 Mar 20;284(12):7606-22. Epub 2008 Dec 22.
[Abstract] [PubMed] - Dagdug L, Berezhkovskii AM, Makhnovskii YA, Zitserman VY "Transient diffusion in a tube with dead ends" J Chem. Phys. 127(22): 224712-1 - 224712-9
[Abstract] [Full Article] - Coppey M, Berezhkovskii AM, Kin Y, Boettiger AN, Shvartsma SY "Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein." Dev. Biol. 312: 623-30
[Abstract] [Full Article] - Coppey M, Boettiger AN, Berezhkovskii AM, Shvartsman SY "Nuclear Trapping Shapes the Terminal Gradient in the Drosophila Ebryo." Current Biology 18(12): 915-19
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Fluctuation theorem for channel-facilitated membrane transport of interacting and non-interacting solutes" J Phys. Chem. B 112(19): 6228-32
[Abstract] [Full Article] - Berezhkovskii AM, Weiss GH "Propagators and related descriptors for non-Markovian asymmetric random walks with and without boundaries" J Chem. Phys. 128(4) 044914, 5 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Counting translocations of strongly repelling particles through single channels: Fluctuation theorem for membrane transport" Phys. Rev. Lett. 100(3): 038104, 4pp.
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Counting Translocations of Strongly Repelling Particles through Single Channels: Fluctuation Theorem for Membrane Transport." Phys. Rev. Lett. 100(3): 038104, 4pp.
[Abstract] [Full Article] - Berezhkovskii AM, Weiss GH "Propagators and related descriptors for non-Markovian asymmetric random walks with and without boundaries." J. Chem. Phys. 128(1): 044914, 5 pp.
[Abstract] [Full Article] - Coppey M, Berezhkovskii AM, Kin Y, Boettinger AN, Shvartsman SY "Modeling the Bicoid gradient: Diffusion and reversible nuclear trapping of stable protein" Developmental Biology 312(2):623-30
[Abstract] [Full Article] - Coppey M, Berezhkovskii AM, Kim Y, Boettiger AN, Shvartsman SY "Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein" Dev. Biol.
[Abstract] [Full Article] - Nishizuka1,S., Washburn,N.R., and Munson, P.J. "Evaluation method of ordinary flatbed scanners for quantitative density analysis" BioTechniques. 40:442-448 (2006)
[Abstract] [Full Article] - Wang,S., Zhang, J., Theel,S., Barb, J.J, Munson, P.J. and Danner,R.L. "Nitric oxide activation of Erk1/2 regulates thestability and translation of mRNA transcriptscontaining CU-rich elements" Nucleic Acids Research, Vol. 34, No. 10 30443056 (2006)
[Abstract] [Full Article] - Talwar,S.,Munson,P.J., Barb,J.,Fiuza, C., Cintron,A.P., Logun,C., Tropea,M., Khan,S., Reda,D., Shelhamer,J.H., Danner,R.L. and Suffredini,A.F. "Gene expression profiles of peripheral blood leukocytes after endotoxin challenge in humans" Physiol Genomics 25:203-215, (2006)
[Abstract] [Full Article] - Sam,V., Tai,C.H., Garnier1,J., Gibrat,J.F., Lee,B. and Munson, P.J. "ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification" BMC Bioinformatics. 7:206 (2006)
[Abstract] [Full Article] - HUYNH,T.T., PACAK,K., WONG,D.L., LINEHAN,W.M., GOLDSTEIN,D.S., ELKAHLOUN,A.G., MUNSON,P.J. and Eisenhofer,G."Transcriptional Regulation ofPhenylethanolamineN-Methyltransferase in Pheochromocytomas from Patients with von HippelLindau Syndrome and Multiple Endocrine Neoplasia Type 2" Ann. N.Y. Acad. Sci. 1073: 241252 (2006)
[Abstract] [Full Article] - Hoover,S.E., Cohrs,R.J., Rangel,Z.G., Gilden,D.H., Munson, P. and Cohen, J.I. "Downregulation of Varicella-Zoster Virus (VZV) Immediate-EarlyORF62 Transcription by VZV ORF63 Correlates withVirus Replication In Vitro and with Latency" JOURNAL OF VIROLOGY. 80.7.34593468 (2006)
[Abstract] [Full Article] - Torre,C., Ying,S., Munson, P.J.,Meduri,G.U., and Suffredini, A.F."Proteomic analysis of inflammatory biomarkers inbronchoalveolar lavage" Proteomics 6: 39493957 (2006)
[Abstract] [Full Article] - Cassiani-Ingoni,R.,Cabral, E.S.,Lunemann,J.D,Garza,Z.,Magnus,T.,Gelderblom,H.,Munson,P.J.,Marques,M. and Roland Martin, "Borrelia burgdorferi Induces TLR1 and TLR2 in Human Microgliaand Peripheral Blood Monocytes but Differentially RegulatesHLA-Class II Expression" J Neuropathol Exp Neurol Volume 65, Number 6, (2006)
[Abstract] [Full Article] - Cabral,E.S.,Gelderblom,H.,Hornung,R.L.,Munson,P.J.,Martin,R.and Marques,A.R "Borrelia burgdorferi LipoproteinMediated TLR2Stimulation Causes the Down-Regulation of TLR5in Human Monocytes" The Journal of Infectious Diseases: 193:84959 (2006)
[Abstract] [Full Article] - BROUWERS,F.M.,ELKAHLOUN,A.G.,Munson,P.J.,EISENHOFER, G.,BARB,J.LINEHAN,W.M.,LENDERS,J.W.M,KRIJGER,R.D., MANNELLI,M.,UDELSMAN,R., OCAL,I.T.,SHULKIN,B.L.,BORNSTEIN,S.R.,BREZA,J., KSINANTOVA,L.AND PACAK,K. "Gene Expression Profiling of Benignand Malignant Pheochromocytoma" Ann. N.Y. Acad. Sci. 1073: 541556 (2006)
[Abstract] [Full Article] - Dudko O.K., Weiss G.H. and Chernomordik V. "Mean-time-of flight of photons in transillumination measurements of optically anisotropic tissue with an inclusion", Phys. Med. Biol. 51: 4719-4733 (2006)
[Abstract] [Full Article] - McQueen PG, McKenzie FE "Competition for red blood cells can enhance Plasmodium vivax parasitemia in mixed-speces malaria infections," American Journal of Tropical Medicine and Hygiene, Vol. 75, pp. 112-125 (2006).
[PubMed] - Williams R., Azuara V., Perry P., Sauer S., Dvorkina M., Jorgensen H., Jeffery Roix, McQueen P., Misteli T., Merkenschlager M. and Fisher A.
"Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus" Journal of Cell Science 119, 132-140 (2006) [PubMed] - Dudko O.K., Hummer G., and Szabo A., "Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments", Phys. Rev. Lett. 96 (10), 108101 (2006)
- Dudko OK, Szabo A, Ketter J, and R.M.Wightman.Analytic theory of the current at inlaid planar ultramicroelectrodes: Comparison with experiments on elliptic disks"J ELECTROANAL CHEM 586 (1): 18-22
- Gupta V., Parisi M., Sturgill D., Nuttall R., Doctolero M., Dudko O.K., Malley J.D., Eastman P.S., and Oliver B.
"Global analysis of X-chromosome dosage compensation", Journal of Biology 5:3 - Kovanen, P.E.,Young, L., Al-Shami1, A., Rovella,V., Pise-Masison,C.A, Radonovich, M.F., Powell, J., Fu, J., Brady, J.N., Munson, P.J., and Leonard,W.J. "Global analysis of IL-2 target genes: identificationof chromosomal clusters of expressed genes" International Immunology, Vol. 17, No. 8, pp. 10091021
[Abstract] [Full Article] - Cui,X., Zhang,J., Ma,P.,Myers, D.E, Goldberg,I.G., Sittler, K.J.,Barb,J.J., Munson,P.J.,Cintron,A.P.,McCoy,J.P.,Wang, S. and Danner, R.L. "cGMP-independent nitric oxide signaling and regulation of the cell cycle" BMC Genomics.6:151 doi:10.1186/1471-2164-6-151 (2005)
[Abstract] [Full Article] - Dudko OK, Berezhkovskii AM, Weiss GH
"Time-dependent diffusion coefficients in periodic porous materials" J PHYS CHEM B 109 (45): 21296-21299 - Olga K. Dudko and Attila Szabo
"Time-dependent rate coefficients for diffusion-influenced reactions with centrosymmetric potentials" J PHYS CHEM B 109 (12): 5891-5894 - Olga K. Dudko and George H. Weiss
"Estimation of Anisotropic Optical Parameters of Tissue in a Slab Geometry" Biophysical Journal 88: 3205-3211
[PubMed] - Boguna, M., Basser, P. J., Pajevic, S., Weiss, G. H."A model for noise effects on fibre tract trajectories in diffusion tensor imaging: theory and simulations", New Journal of Physics, 7, 24, 2005
- Dudko OK, Filippov AE, Klafter J, et al.
"Following single molecules by force spectroscopy" ISRAEL J CHEM 44 (4): 363-372 - Dudko OK, Berezhkovskii AM, and Weiss GH
"Diffusion in the presence of periodically spaced permeable membranes." J Chem Phys 121: 11283-11288
[PubMed] - O'Hanlon TP, Koneru B, Bayat E, Love L, Targoff IN, Malley JD, Malley KG, Miller FW
"Immunogenetic Differences between Women who Develop Myositis with and without Silicone Implants." Arthritis Rheum 50(11):3646-50
[PubMed] - Parisi M, Nuttall R, Edwards P, Minor J, Naiman D, Lu J, Doctolero M, Vainer M, Chan C, Malley J, Eastman S, Oliver B
"A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults." Genome Biol. 5(6):R40
[PubMed] - Dudko O, Weiss GH, Chernomordik V, Gandjbakhche A
"Photon Migration in Turbid media with Anisotropic Optical Properties." Phys Med Biol. 49:3979-3989
[PubMed] - Dagdug L, Berezhkovskii AM, Weiss GH
"The kinetics of ligand equilibration between tubular and vesicular parts of the endosome." Phys Rev E. 69:012902
[PubMed] - Dudko O, Berezhkovskii AM, Weiss GH
"Rate constant for diffusion-influenced ligand binding to receptors of arbitrary shape on a cell surface." J Chem Phys. 121:1562-1565
[PubMed] - Wu S, Baxendale V, Chen Y, Pang AL, Stitely T, Munson PJ, Leung M, Ravindranath N, Dym M, Rennert O, Chan W
"Analysis of Mouse Germ Cell Transcriptome at Different Stages of Spermatogenesis by SAGE: Biological Significance." Genomics 84(6):971-81
[PubMed] - Pawliczak R, Woszczek G, Logun C, Barb J, Suffredini AF, Munson PJ, Danner RL, Shelhamer JH
"The influence of interferon gamma on gene expression in human normal bronchial epithelial cells." Am J Respir Crit Care Med. 2004:A675 - Jison ML, Munson PJ, Barb JJ, Suffredini AF, Talwar S, Logun C, Raghavachari N, Beigel JH, Shelhamer JH, Danner RL, Gladwin MT
"Blood mononuclear cell gene expression profiles characterize the oxidant, hemolytic, and inflammatory stress of sickle cell disease." Blood 104(1):270-80
[PubMed] - Gius D, Cui H, Bradbury M, Cook J, Smart DK, Zhao S, Young L, Brandenburg SA, Hu Y, Bisht KS, Ho aS, Mattson D, Sun L, Munson PJ, Chuang EY, Mitchel JB, Feinberg AP
"Distinct Effects on Gene Expression of Chemical and Genetic Manipulation of the Cancer Epigenome Revealed by a Multimodality Approach." Cancer Cell. 6(4):361-71
[PubMed] - Eisenhofer G, Huynh T, Pacak K, Brouwers FM, Walther M, Linehan WM, Munson PJ, Mannelli M, Goldstein DS, Elkahloun AG
"Distinct gene expression profiles in norepinephrine and epinephrine producing hereditary and sporadic pheochromocytomas: Activation of hypoxia-driven angiogenic pathways in von Hippel-Lindau syndrome." Endocrine-Related Cancer 11(4):897-911
[PubMed] - Boissinot S, Entezam A, Young L, Munson PJ, Furano AV
"The insertional history of an active family of L1 retrotransposons in humans." Genome Res. 14(7):1221-31
[PubMed] - Kim SH, McQueen PG, Litchman MK, Shevach EM, Parada LA, Misteli T
"Spatial genome organization during T-cell differentiation" Cytogenetic and Genome Research 105:292-301
[PubMed] - Parada LA, McQueen PG, and Misteli T
"Tissue-specific spatial organization of genomes" Genome Biology vol. 5 [PubMed] - McQueen PG and McKenzie EF
"Age-structured red blood cell susceptibility and the dynamics of malaria infections" Proceedings of the National Academy of Sciences 101: 1961-1966
[PubMed] - Dagdug, L. and G. H. Weiss
"Suggested Parameter to Estimate the Region Probed by Photons in Laser-Based." Journal of Modern Optics 51(4): 469-478 - Berezhkovskii AM, Batsilas L, Shvartsman SY
"Ligand Trapping in Epithelial Layers and Cell Cultures." Biophys. Chem. 107(3): 221-7
[PubMed] - Berezhkovskii, A. M. and A. V. Barzykin
"Diffusive Escape and Reentry through a Channel in the Cavity Wall." Chem. Phys. Lett. 383(1-2): 6-10 - Parada LA, McQueen P, Munson P, Misteli T
"Cell type specific spatial organization of genomes," Fourth European Cytogenetics Conference published in Annales de Genetique, 46:208 - Grigor'ev IV, Makhnovskii YA, Berezhkovskii AM, Zitserman V
"Kinetics of geminate recombination in a cavity." Russ J Phys Chem. 77:1277-1281 - Grigor'ev IV, Makhnovskii YA, Berezhkovskii AM, Zitserman V
"Kinetics of diffusion-controlled ligand binding to a site hidden in a cavity." Chem Phys Rep. 22:49-54 - Miller M, Jerebko AK, Malley JD, Summers RM
"Comparison of stochastic vs. heuristic feature subset selection methods for improving classification algorithms in computer-aided detection." SPIE Medical Imaging 2003: Physiology and Function from Multidimensional Images 5031:102-110 - Larralde H, Weiss GH
"Expected number of sites visited by N random walks in the presence of an absorbing boundary." J. Phys. A. 36:8367-8372 - Dagdug L, Berezhkovskii AM, Weiss GH
"Smoluchowski-like theory for trapping kinetics in a slab." Physica A. 318:341-346 - Berezhkovskii AM, Hummer G
"Unsolved problems in noise and fluctuations. In Random walk model for single-file transport of water molecules through carbon nanotubes." AIP (New York, NY) 267-272 - Talwar S, Munson PJ, Fiuza C, Barb J, Danner RL, Suffredini A
"Gene expression profiling of lung lavage and peripheral blood cells in humans after local pulmonary endotoxin challenge." Am J Respir Crit Care Med. 167:A428 - Nishizuka S, Chen ST, Gwadry FG, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee JK, Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF 3rd, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN
"Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling." Cancer Res. 63(17):5243-50.
[PubMed] - Daoud SS, Munson PJ, Reinhold W, Young L, Prabhu VV, Yu Q, LaRose J, Kohn KW, Weinstein JN, Pommier Y
"Impact of p53 knockout and topotecan treatment on gene expression profiles in human colon carcinoma cells: a pharmacogenomic study." Cancer Res. 63(11):2782-93
[PubMed] - Pajevic S and Basser PJ "Parametric and non-parametric statistical analysis of DT-MRI data" J Magn Reson 161:1-14
[PubMed] - Basser PJ and Pajevic S
"A Normal Distribution for Tensor-valued Random Variables: Applications to Diffusion Tensor MRI" IEEE Trans Med Imag Vol 22, No 7, 785-794 [PubMed] - Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B
"Paucity of Genes on the Drosophilia X Crhomosome Showing Male-Based Expression." Science 299(5607):697-700
[PubMed] - Nishizuka, S., Charboneau, L., Young, L., Kauor, S., Reinhold, W. C., Waltham, M., Kouros-Mehr, H., Bussey, K. J., Lee, J. K., Espina, V., Munson, P. J.,
"Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays." PNAS 100(24): 14229-14234 - Miller, M. T., Jerebko, A. K., Malley, J. D., Summers, R. M.
"Feature Selection for Computer-Aided Detection using Genetic Algorithms." SPIE 2003, Section on Medical Imaging 2003. - Liotta, L. A., Espina, V., Mehta, A. I., Calvert, V., Rosenblatt, K., Geho, D., Munson, P. J., Young, L., Wulfkuhle, J., Petricoin, E. F.,
"Protein microarrays: Meeting Analytical challenges for clinical applications." Cancer Cell 3: 317-324
[PubMed] - Klein AP, Kovac I, Sorant AJ, Baffoe-Bonnie A, Doan BQ, Ibay G, Lockwood E, Mandal D, Santhosh L, Weissbecker K, Woo J, Zambelli-Weiner A, Zhang J, Naiman DQ, Malley J, Bailey-Wilson JE
"Importance Sampling Method of Correction for Multiple Testing in Affectd Sib-pair Linkage Analysis." BMC Genet. 4 Suppl 1:S73 - Jerebko AK, Summers RM, Malley JD, Franaszek M, Johnson CD
"Computer-assisted detection of colonic polyps with CT colongraphy using neural networks and binary classification trees." Medical Physics 30(1):52-60
[PubMed] - Elvevag B, Kerbs M, Malley JD, Seeley E, Goldberg TE
"Autobiographical memory in schizophrenia: an examination of the distribution of memories." Neuropsychology 17(3):402-9
[PubMed] - Earl, P. L., Wyatt, L. S., Montefiori, D. C., Woodward, R., Markham, P. D., Malley, J. D., Vogel, T. U., Allen, T. M., Watkins, D. I., Miller, N., Moss, B.
"Prime Versus Prime-Boost Vaccinations with a Recombinant Replication-Defective Vaccinia Virus (MVA) Expressing SHIV-89.6 Env-Gag-Pol followed by Soluble Oligometric Env Protein." Virology - Dishon M, Taitelbaum H, Weiss GH
"Effects of the scattering Coefficient on width Estimates in a Two Layer Tissue." Journal of Modern Optics 50:2727-40 - Young, L., P. E. Kovanen, et al.
"Scanning the Human Genome Sequence for Clusters of Expressed Genes." Presented at the TGIR conference in Savannah Georgia in September 2003 - Stojilkovic KS, Berezhkovskii AM, Zitserman VY, Bezrukov SM
"Conductivity and Microviscosity of Electrolyte Solutions Containing Polyethylene Glycols." J. Chem. Phys. 119: 6973-78 - Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T
"Spatial proximity of translocation-prone gene loci in human lymphomas." Nature Genetics 34(3):287-91
[PubMed] - Pajevic, S., G. H. Weiss, et al.
"Applications of Adaptive Line Enhancer (ALE) to NMR signals." ISMRM proceedings - Malley, J. D., A. K. Jerebko, et al.
"Variance Reduction for Error Estimation When Classifying Colon Polyps from CT Colongraphy." SPIE 2003 Proceedings - Malley JD, Redner RA, Severini TA, Badner JA, Pajevic S and Bailey-Wilson JE
"Estimation of linkage and association from allele transmission data." Biometrical Journal 45(3): 349-366 - Malley, J. D., D. Q. Naiman, et al.
"A Comprehensive Method for Multiple Testing, with Application to Genome Scans." Presented at Int'l Genetic Epi. Soc meeting, September 2001 - Malley JD, Jerebko AK, Summers RM
"A committee of support vector machines for detection of colonic polyps." SPIE Medical Imaging 2003: Physiology and Function from Multidimensional Images San Diego, CA, 5031:570-578 - Larralde H, Berezhkovskii AM, Weiss GH
"Effect of the Absorbing Boundary on the Average Volume Visited by N Spherical Browian Particles." Physica A. 330:167-176 - Jerebko AK, Malley JD, Franaszek M, Summers RM
"Multiple Neural Network Classification Scheme for Detection of Colonic Polyps in CT Colonography Data Sets." Acad Radiol. 10(2):154-160
[PubMed] - Jerebko AK, Malley JD, Franaszek M, Summers RM
"Computer aided poly detection in CT colongraphy using an Ensemble of Support Vector Machines." Computer Assisted Radiology and Surgery. Proceedings of the 17th International Congress and Exhibition. 1256:1019-1024 - Dagdug L, Berezhkovskii AM, Shvartsman S, Weiss GH
"Equilibration in two chambers connected by a capillary." Journal of Chemical Physics 119:12473-12478 - Dagdug L, Weiss GH, Gandjbakhche AH
"Effects of anisotropic optical properties on photon migration in structured tissues." Physics in Medicine and Biology 48: 1361-1370
[PubMed] - Dagdug, L., A. M. Berezhkovskii, et al.
"Diffusion-controlled reactions with a trapping site hidden in a channel." Journal of Chemical Physics 118: 2367-73 - Dagdug L, Weiss GH
"Absorptive Effects on a Parameter used to Characterize the Region of Tissue Visited by Photons in Continous Wave." Optics Communications 226:149-154 - Berezhkovskii, A. M. and I. V. Gopich
"Translocation of rod-like polymers through membrane channels." Biophysical Journal 84: 787-793
[PubMed] - Berezhkovskii, A. M. and A. V. Barzykin
"Escape and Reentry of a Brownian Particle through a Hole in a Cavity." J. Chem. Phys. 118: 6700-01 - Berezhkovskii, A. M., V. Y. Zitserman, et al.
"Effective Diffusivity in Periodic Porous Materials." J. Chem. Phys. 119: 6991-93 - Berezhkovskii AM, Zitserman VY, Shvartsman SY
"Diffusivity in Periodic Arrays of Spherical Cavities." J. Chem. Phys. 118: 7146-47 - Berezhkovskii, A. M. and V. Y. Zitserman
"Diffusion in Potential Field in the Presence of Gaussian Sink. Analytical Solution of the Problem." Russ. J. Electrochemistry 39: 53-60 - Berezhkovskii AM, Pustovoit MA, Bezrukov SM
"Channel-Facilitated Membrane Transport: Average Lifetimes in the Channel." J. Chem. Phys 119: 3943-51 - Batsilas L, Berezhkovskii AM, Shvartsman SY
"Stochastic Model of Autocrine and Paracrine Signals in Cell Culture Assays." Biophys J. 85(6):3659-65
[PubMed] - Bailey JJ, Hodges M, Church TR
"Risk Stratification in Diabetic Patients with a Previous Myocardial Infarction." Journal of Electrtocardiol 36 Suppl:121-5
[PubMed] - Basser PJ, Pajevic S, Pierpaoli C and Aldroubi A
"Fiber tract following in the human brain using DT-MRI data" IEICE Trans Inf Sys E85D:15-21 - Pajevic S, Aldroubi A and Basser PJ
"A continuous tensor field approximation of discrete DT-MRI data for extracting microstructural and architectural features of tissue" J Magn Reson 154:85-100
[PubMed] - Catani M, Howard RJ, Pajevic S and Jones DK
"Virtual in vivo interactive dissection of white matter fasciculi in the human brain" Neuroimage 17:77-94
[PubMed] - Weickert TN, Terrazas A, Bigelow LB, Malley JD, Egan MF, Weinberger DR, Goldberg TE
"Habit and skill learning in schzophrenia: evidence of normal striatal processing with abnormal cortical loading." Learning and Memory 9(6):430-42 - Church TR, Hodges M, Bailey JJ, Mongin SJ
"Risk Stratification Applied to CAST Registry Data: Combining 9 Predictors." Journal of Electrocardiology 35: 117-122
[PubMed] - Suzuki, T., Shen, H., Akagi, K., Morse, H. C., Malley, J. D., et al
"New genes involved in cancer identified by retroviral tagging." Nature Genetics 32: 166-174
[PubMed] - Summers RM, Jerebko AK, Franaszek M, Malley JD, Johnson CD
"Colonic polyps: complementary role of computer-aided detection in CT colonog." Radiology 225(2):391-9
[PubMed] - Makhnovskii, Y. A., Grigor'ev, I. V., Berezhkovskii, A. M.
"Kinetics of Annihilation of Brownian Particles on Traps with Distributed Radii." JETPh 94: 403-10 - Kloczkowski, A., Ting, K. L., Jernigan, R. L., Garnier, J.
"Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information." Polymer 43: 441-449 - Hecht D, Jung D, Prabhu VV, Munson PJ, Hoffman MP, Kleinman HK
"Metallothionein Promotes Laminin-1-induced Acinar Differentiation in Vitro and Reduces Tumor Growth in Vivo." Cancer Research 65: 5370-5374
[PubMed] - Grove, A. D., Prabhu, V., Young, B. L., Lee, F. C., Kulpa, V., Munson, P. J., Kohn, E. C.
"Both Protein Activation and Gene Expression Are Involved in Early Vascular Tub Formation in Vitro." Clinical Cancer Research 2002 8: 3019-3026
[PubMed] - Earl, P. L., Wyatt, L. S., Montefiori, D. C., Bilska, M., Woodward, R., Markham, P. D., Malley, J. D., Vogel, T. U., Allen, T. M., Watkins, D. I., Miller, N., Moss, B.
"Comparison of vaccine strategies using recombinant env-gag-pol MVA with or without an oligomeric Env protein boost in the SHIV rhesus macaque model." Virology 294(2): 270-281
[PubMed] - Weiss, G. H.
"Some applications of persistent random walks and the telegrapher's equation." Physica A 311: 381-410 - Shrager, R., D. K. Jones, et al.
"When is a Gaussian displacement distribution adequate to describe water diffusion in tissues." Abstracts of the International Society of Magnetic Resonance in Medicine - Parada LA, McQueen PG, Munson PJ, Misteli T
"Conservation of Relative Chromosome Positioning in Normal and Cancer Cells." Current Biology 12: 1692-1697
[PubMed] - Malley, J. D., A. K. Jerebko, et al.
"Significant reductions in sample variance for estimating sensitivity of a CAD algorithm for CTC detection of colon polyps." presented at the Radiological Society of North America Meeting December 1, 2002 in Chicago, IL - Malley JD, Naiman DQ, Bailey-Wilson JE
"A comprehensive method for genome scans." Human Heredity 54(4):174-85
[PubMed] - Moak JP, Bailey JJ, Makhlouf FT
"Simultaneous Heart Rate and Blood Pressure Vriability Analysis: Insight Into Mechanisms Underlying Neuraly Mediated Cardiac Syncope in Children." Journal of the American College of Cardiology 40(8): 1466-1474
[PubMed] - Gopich, I. V., A. M. Berezhkovskii, et al.
"Concentration Dependence of the Diffusion Controlled Steady-State Rate Constant." J. Chem. Phys 117: 2987-88 - Dagdug, L. and L. Young
"A Theoretical framework for the study of the melting transition of DNA using the stochastic matrix method." Physical Review E. - Dagdug, L., A. M. Berezhkovskii, et al.
"Smoluchowski-like theory for trapping kinetics in a slab." Physica A. - Dagdug L, Berezhkovskii AM, Weiss GH
"The Number of Distinct Sites Visited by a Random Walker Trapped by an Absorbing Boundary." Physical Review E. 66(012901): 1-4
[PubMed] - Berezhkovskii, A. M. and G. Sutman
"Time and Length Scales for Diffusion in Liquids." Phys. Rev. E 65: 060201
[PubMed] - Berezhkovskii, A. M. and G. Hummer
"Single-File Transport of Water Molecules Through a Carbon Nanotube." Phys. Rev. Lett 9: 064503-1-1-064503-4
[PubMed] - Berezhkovskii, A. M., M. A. Pustovoit, et al.
"Effect of Binding on Particle Number Fluctuations in a Membrane Channel." J. Chem. Phys. 116: 6216-20 - Berezhkovskii, A. M. and G. H. Weiss
"Detailed description of a two-state non-Markov system." Physica A 303: 1-12 - Berezhkovskii, A. M., M. Pustovoit, et al.
"Channel Facilitated Membrane Transport: Transit Probability and Interaction with the Channel." J. Chem. Phys 116: 9952-56 - Bailey, J. J., T. R. Church, et al.
"Risk Stratification Applied to CAST Registry Data: Extended Criteria for Prophylactic Use of ICDs after Myocardial Infarction." The International Society for Computerized Electrocardiology 27th Annual Conference Doorwerth, The Netherlands - Pierpaoli C, Barnett A, Pajevic S, et al.
"Water Diffusion Changes in Wallerian Degeneration and Their Dependence on White Matter Architecture" NeuroImage 13:1174-1185
[PubMed] - McCray AT, Bodenreider O, Malley JD, Browne AC
"Evaluating UMLS strings for natural language processing" Proc AMIA Symp 2001 448-52
[PubMed] - Summers, R. M., Jerebko, A. K., Franaszek, M., Malley, J. D.
"An Integrated System for Computer-Aided Diagnosis in CT Colonography: Work-In Progress." Proceedings of the 15th International Congress of Computer Assisted Radiology and Surgery - Summers, R. M., Johnson, C. D., Pusanik, L. M., Malley, J. D., Youssef, A., Reed, J. E.
"Automated Polyp Detection at CTColongraphy: Feasibility Assessment in a Human Population." Radiology 219: 51-59
[PubMed] - Liu, K., Li, Y., Prabhu, V. V., Young, B. L., Becker, K. G., Munson, P. J., Weng, N.
"Augmentation in Expression of Activation-Induced Genes Differentiates Memory from Naive CD4+ T Cells and Is a Molecular Mechanism for Enhanced Cellular Response of Memory CD4+ T Cells." The American Association of Immunologists 7335-7344
[PubMed] - Knezevic, V., Leethanakul, C., Bichesel, V., Worth, J. M., Prabhu, V., Gutkind, J., Liotta, L. A., Munson, P.
"Proteomic profiling of the cancer microenvironment by antibody arrays." Proteomics 1: 1271-1278
[PubMed] - Jerebko, A. K., Summers, R. M., Malley, J. D., Franaszek, M., Johnson, C. D.
"Computer-Assisted Detection of Colonic Polyps in Noisy CT Colonography Data Sets Using Neural Networks and Binary Classification Trees." IEEE Transactrions on Medical Imaging - Blank, P. S., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"A Kinetic Analysis of Calcium-Triggered Exocytosis." J. Gen. Phys. 118(2):145-56
[PubMed] - Bailey-Wilson JE, Sorant AJ, Malley JD, Presciuttini S, Redner RA, Severini TA, Badner JA, Pajevic S, et al.
"Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data." Genetic Epidemiology 21 Suppl 1:S378-83
[PubMed] - Weiss, G. H. and J. Masoliver
"Statistics of Dwell Time in a Reaction with Randomy Fluctuating Rates." Physica A 296: 75-82 - Shrager, R. I. and R. W. Hendler
"Supporting information for "Theory and procedures for finding a correct kinetic model for the bacteriorphdopsim photocycle." Journal of Physical Chemistry 105: 3319 - Makhnovskii, Y. A. and A. M. Berezhkovskii
"Effect of a group of Traps on Fluctuation Assisted Inhibition of Browian Particle Decay." Chem. Phys. Rep. 19: 853-59 - Hendler, R. W., R. I. Shrager, et al.
"Theory and procedures for finding a correct kinetic model for the bacteriorbadopsim photocycle." Journal of Physical Chemistry B 105: 3319-3328 - Bogu¿a, M., A. M. Berezhkovskii, et al.
"Single-Molecule Fluorescence Spectroscopy: Rate Constants for Slow Conformational Transitions and their Sampling Errors." Journal of Physical Chemistry A 105: 4898-4901 - Berezhkovskii, A. M., Y. A. Makhnovskii, et al.
"Trapping of Brownian particles by random spheres of different radii." Journal of Chemical Physics 115: 5376-80 - Berezhkovskii, A. M., H. Larralde, et al.
"Region visited by a pherical Brownian particle in the presence of an abosrbing boundary." Physical Review E 64: 062104-1 - 062104-3 - Berezhkovskii, A. M., M. Bogu¿a, et al.
"Evaluation of Rate Constants for Conformational Transitions using Single-Molecule Fluroescence Spectroscopy." Chemical Physics Letter 336: 321-324 - Bailey, J. J.
"Utility of current risk stratification tests for predicting major arrhythmic events after myocardial infarction." J. Am. Coll Cardiol 1902-1911
[PubMed] - Bailey, J. J.
"Technical Information Report: TIR 24: Acquisition and use of physiological waveform databases for testing of medical devices." Association for the Advancement of Medical Instrumentation monograph - Bailey, J. J.
"Standard Communications Protocol - Computer Assisted Electrocardiography." AAMI EC71: monograph - Bailey, J.J. and M. Hodges
"Ambulatory Electrocardiography: Use in Arrhythmia Risk Assessment."¿ In Risk of Arrhythmia and Sudden Death BMJ Publishing, Ltd: 194-201.
[Abstract] - Pajevic S, Aldroubi A, Basser P
"Continuous Tensor Field Approximation of Diffusion Tensor MRI data. In Visualization and Image Processing of Tensor Fields." Springer-Verlag - Summers, R. M., Pusanik, L. M., Malley, J. D., Reed, J. E., Johnson, C. D.
"Method of Labeling Colonic Polys at CT Colonography using Computer-assisted Detection." Proceedings of the 14th International Congress of Computer Assisted Radiology and Surgery (CARS) - Summers, R. M., Beaulieu, C. F., Pusanik, L. M., Malley, J. D., Jeffrey, R. B., Jr., Glazer, D. I., Napel, S.
"An Automated Polyp Detector for CT Colonography - Feasibility Study." Canadian Mathematical Society Conference Proceedings 216: 284-290
[PubMed] - Smith, T. D., Kuczenski, R., George-Friedman, K., Malley, J. D., Foote, S. L.
"In Vivo Microdialysis Assessment of Extracellular Serotonin and Dopamine Levels in Awake Monekys During Sustained Fluoxetine Administration." Synapse 38: 460-470 - Peng, A., Koffman, B. M., Malley, J. D., Dalakas, M. D.
"Disease progression and functional muscle decline in sporadic inclusion body myositis (s-IBM): observations in 78 patients." Neurology 55: 296-298
[PubMed] - Nees, M., Geoghegan, J. M., Munson, P., Prabhu, V., Liu, Y., Androphy, E., Woodworth, C. D.
"Human papillomavirus type 16 E6 and E7 proteins inhibit differentiation-dependent expression of transforming growth factor-beta2 in cervical keratinocytes." Cancer Res 60: 4289-98
[PubMed] - Laks, M. M., Arzbaecher, R., Geselowitz, D. B., Bailey, J. J., Berson, A. S.
"Revisiting the question: Will relaxing safe current limits for electromedical equipment increase hazards to patients?" Circulation 103: 823-5
[PubMed] - Kim HJ, Tisdale JF, Wu T, Takatoku M, Sellers SE, Zickler P, Metzger ME, Agricola BA, Malley JD, Kato I, Donahue RE, Brown KE, Dunbar CE
"Many multi-potential gene-marked progenitor or stem cell clones contribute to hematopoiesis in non-human primates." Blood 96(1):1-8
[PubMed] - Grove, A.D., Lee, F.C., Prabhu, V.V., Young, B.L., Munson, P.J., Kohn, E.C.
"In Validation and application of nylon cDNA microarrays in the analysis of endothelial cell gene expression during tubulogenesis (abstract)" AACR - Boguna, M., Kullman, L., Bezrukov, S. M., Berezhkovskii, A. M., Weiss, G. H."Rate Constants from Uncorrelated Single-Molecule Data." J. Phys. Chem.B 105: 6246-6250
- Bogachev, L. V., Molchanov, S. A., Makhnovskii, Y. A., Berezhkovskii, A. M.
"Correlation Effects in the Trapping Problem: General Approach and Rigorous Results." Canadian Mathematical Society Conference Proceedings 2000 29: 29-42 - Smith RD, Malley JD, Schechter AN
"Quantitative analysis of globin gene expression in single human erythroleukemic cells." Nucleic Acids Research 28(24): 4998-5004
[PubMed] - Selbie, W. S., J. D. Malley, et al.
"Method for segmenting medical images and detecting surface anomalies in anatomical structures" U.S. Patent Application No. 09/136,136 filed August 18, 1998. Accepted: 2000 - Pajevic, S. and P. J. Basser
"Parametric and Non-Parametric Statistical Approaches in Diffusion Tensor Magnetic Resonance Imaging" Journal of Magnetic Resonance - Makhnovskii, Y. A., A. M. Berezhkovskii, et al.
"Trapping by Clusters of traps." Phys. Rev. E 61: 6302-07
[PubMed] - Bezrukov, S. M., A. M. Berezhkovskii, et al.
"Particle Number Fluctuations in a Membrane Channel." J. Chem. Phys. 113(8206-11) - Basser PJ, Pajevic S
"Statistical artifacts in diffusion tensor MRI (DT-MRI) caused by background noise." Magn. Reson. Med. 44(1): 41-50
[PubMed] - Basser PJ, Pajevic S, Pierpaoli C, Duda J, Aldroubi A
"In vivo fiber tractography using DT-MRI data." Magn. Reson. Med. 44(4): 625-632
[PubMed] - Basser, P. J., S. Pajevic, et al.
"Fiber-Tractography in Human Brain Using Diffusion Tensor MRI (DT-MRI)" International Society for Magnetic Resonance in Medicine Annual Meeting Proceedings 784 - Bailey, J. J.
"Signal averaging electrocardiography." Association for the Advancement of Medical Instrumentation Technical Information Report 23: monograph. - Berezhkovskii, A.M., A. Szabo and G.H. Weiss
"Theory of Fluorescence of Single Molecules Undergoing Multistate Conformational Dyanmics." J. Phys. Chem. B104(16): 3776-80
[Abstract] - Wong, M.-L., M.A. Kling, P.J. Munson, S. Listak, et al.
"Pronounced and Sustained Central Hypernoradrenergic Function in Major Depression with Melancholic features: Relation to Hypercortisolism and Corticotropin-releasing Harmone." PNAS 97(1): 325-330 Full Article - Weiss, G.H., M. Boguna and A.M. Berezhkovskii "Occupancy of a Single Site by Many Random Walkers."ý Physical Review E ý62(3): 3250-3256
[Abstract] [PubMed] - Vieira, N.E., R.E. Goans, G.H. Weiss, J.C. Marini, et al.
"Calcium Kinetics in Children with Osteogenesis Imperfecta Type III and IV: Pre- and Post- Growth Harmone Therapy."
[Abstract] - Hendler, R., R. Shrager and S. Bose
"Results from a Search for the Correct Kinetic Model for the Bacteriorhodospin Photocycle."
[Abstract] - Grouse, L.H., P.J. Munson and P.S. Nelson
"Sequence Database and Microarrays as Tools for Identifying Prostate Cancer Biomarkers."
[Abstract] [PubMed] - Gandjbakhche, A.H. and G. H. Weiss
"A Descriptive Parameter for Photon Trajectories in a Turbid Medium."¿ Physical Review E ¿61(6): 6958-6962 [PubMed] - Emmert-Buck, M.R., R.L. Strausberg, D.B. Krizman, M.F. Bonaldo, ..., P.J. Munson, et al.
"Molecular Profiling of Clinical Tissue Specimens Feasibility and Applications." American Journal of Pathology 156(4): 1109-1115 [PubMed] - Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB
"Development of a Prostate cDNA Microarray and Statistical Gene Expression Analysis Package." Molecular Carcinogenesis 28(1):12-22
[Abstract] [PubMed] - Boguna, M., M. Masoliver and G.H. Weiss"The Asympototic Form of the Probability Density of Sojourn Times in Randomly Changing Multistate Systems."
[Abstract] - Boguna, M., A.M. Berezhkovskii and G.H. Weiss"Residence time densities for non-Markovian systems 1. The two-state system." Physica A 282: 475-485
[Abstract] - Bailey, J.J., A.S. Berson, H. Handelsman
"Metanalysis by ROC: ECG Diagnostic Methods Compared."
[Abstract] - Bailey JJ, Berson AS, Handelsman H
"Dysrhythmia hazard after hospitalization for myocardial infarction: two ECG prognostic methods compared." J Electrocardiol 33:151-4
[Abstract] [PubMed] - Summers, R. M., Pusanik, L. M., Malley, J. D., Hoeg, J. M.
"Fractal analysis of virtual endoscopy reconstructions." Proceedings of SPIE 1999 3660: 258-269. - Ioannidis JP, Goedert JJ, McQueen PG, Enger C, Kaslow RA
"Comparison of Viral Load and HLA Statistical and Neural Network Predictive Models for the Rate of Human Immunodeficiency Virus Disease Progression." Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 20: 129-136
[PubMed] - Hecht, D., Jung, D., Munson, P. J., Prabhu, V. V., Kleinman, H. K.
"In Laminin-1 Dependent Gene Expression During Acinar Differentiation of Human Salivary Gland Cells: Analysis Using cDNA Arrays" Pan-pacific connective tissue societies, 4th symposium Queenstown, New Zealand, November 15-19 - Blank, P. S., Coorssen, J. R., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"Calcium-triggered exocytosis: Unifying biophysical, biochemical, and physiological studies." J. Gen. Physiol. - Shrager, R. I.
"On a three term variant of the Lomb periodogram." Astrophysics and Space Science - Pajevic, S. and P. J. Basser
"Parametric Description of Noise in Diffusion Tensor MRI." 7th ISMRM Proceedings 1787 - Pajevic, S. and P. J. Basser
"Non-parametric Statistical Analysis of Diffusion Tensor MRI Data Using the Bootstrap Method." 7th ISMRM Proceedings 1790 - McQueen, PG
"Monte Carlo Methods in Statistical Physics (book review)" Journal of Statistical Physics 97: 1029-1030 - Makhnovskii, Y. A., A. M. Berezhkovskii, et al.
"Role of Trap Clustering in the Trapping Kinetics." J. Chem. Phys 111: 711-20 - Bicout, D. J., A. M. Berezhkovskii, et al.
"First Passage Times in Phase Space for the Strong Collision Model." Physical Review E 59: 3702-3705 - Berezhkovskii, A. M., A. Szabo, et al.
"Reaction dynamics on a thermally fluctuating potential." J. Chem. Phys 111: 9952-9957 - Berezhkovskii, A. M., S. M. Bezrukov, et al.
"The influence of polymer on the diffusion of a spherical tracer." J. Chem. Phys. 111: 5641-5644 - Basser, P. J., S. Pajevic, et al.
"Quantitative Statistical Tests for Assessing Changes in the Trace of the Diffusion Tensor: Clinical and Biological Implications." 7th ISMRM Proceedings 1789 - Basser, P. J., S. Pajevic, et al.
"Methods to reduce Eigenvalue Sorting Bias in DT-MRI." 7th ISMRM Proceedings 1788 - Bailey, J. J.
"Testing and reporting performance results of cardiac rhythm and ST measurement algorithms." Association for the Advancement of Medical Instrumentation American National Standard 2nd ed(EC57): monograph. - Bailey, J.J.
"Ambulatory electrocardiographs" Association for the Advancement of Medical Instrumentation American National Standard 2nd ed(EC38): monograph - Whitney LW, Becker KG, Tresser NJ, Caballero-Ramos CI, Munson PJ, et al.
"Analysis of gene expression in multiple sclerosis lesions using cDNA microarrays." Annals of Neurology 46(3): 425
[Abstract] [PubMed] - Taitelbaum, H., Z. Koza, T. Yhanir and G.H. Weiss
"Tiger and Rabbits: a single trap and many walkers." Physica A 266: 280-290
[Abstract] - Pajevic S, Pierpaoli C.
"Color Schemes to Represent the Orientation of Anisotropic Tissues from diffusion Tensor Data: Application to White Matter Fiber Tract Mapping in the Human Brain." Magnetic Resonance in Medicine 42: 526-540 [PubMed] - Holbrook, P.G., V. Geetha, M.A. Beaven and P.J. Munson
"Recognizing the Pleckstrin homology doman fold in mammalian phospholipase D using Markov models." FEBS Letters 448: 269-272
[Abstract] Full Article - Geetha, V., V.D. Francesco, J. Garnier and P.J. Munson
"Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologs." Protein Engineering 12(7): 101-108 [PubMed] - DiFrancesco, V., P.J. Munson and J. Garnier
"Foresst: fold recognition from secondary structure predictions of proteins." Bioinformatics 15(2): 131-140 [PubMed] - Burklow, T.R., J.P. Moak, J.J. Bailey and F.T. Makhlouf
"Neurally Mediated Cardiac Syncope: Autonomic Modulation After Normal Saline Infusion." Journal of the American College of Cardiology 33(7): 2059-2066
[Abstract] [PubMed] - Bogu¿a, M., J. Masoliver and G.H. Weiss
"A discrete formulation of the theory of sojourm times in a two-state system."¿¿
[Abstract] - Berezhkovskii, A. M., D. J. Bicout, G. H. Weiss
"Collision Model for Activated Rate Processes: Turnover Behavior of the Rate Constant." J. Chem. Phys 111: 11050-11059
[Abstract] - Berezhkovskii, A.M., A. Szabo and G.H. Weiss
"Theory of single-molecule flourescence spectroscopy of two-state systems." Chemical Physics 110(18): 9145-9150
[Abstract] - Berezhkovskii, A.M., D.J. Bicout and G.H. Weiss
"Target and Trapping Problems: From the Ballistic to the Diffusive Regime." Chemical Physics 110(2): 1112-1122
[Abstract] - Summers, R. M., Selbie, W. S., Malley, J. D., et al
"Polypoid lesions of airways: early experience with computer-assisted detection by using virtual bronchoscopy and surface curvature." Radiology 208: 331-337
[PubMed] - Summers, R. M., Brune, A. M., Choyke, P. L., Chow, C. K., Patronas, N. J., Miller, F. W., White, P. H., Malley, J. D., Rider, L. G.
"Juvenile Idiopathic inflammatory mypoathy: exercise-induced changes in muscle at short inversion time inversion-recovery MR imaging." Radiology 191-196
[PubMed] - Summers, R. M., Pusanik, L. M., Malley, J. D.
"Automatic detection of endobronchial lesions with virtual bronchoscopy: comparison of two methods." Medical Imaging, Proceedings of SPIE 1998 3338: 327-335 - Radko, S. P., Chrambach, A., Weiss, G. H.
"The asymmetry of protein peaks in capillary zone electrophoresis. Effect of starting zone length and presence of polymer." J. Chromatography A 817: 253-262
[PubMed] - Hecht, D., Jung, D., Munson, P. J., Prabhu, V. V., Kleinman, H. K.
"In Initial array analysis of gene expression during laminin dependent acinar differentiation of a human submandibular gland cell line (Abstract)" Toward a molecular understanding of craniofacial morphogenesis, NIH, Bethesda, MD, November 22-24 - Geetha, V., Di Francesco, V., Garnier, J., Munson, P. J.
"In Comparison of methods for identification of remote homologs in proteins ( Abstract and Poster)" Intelligent Systems in Molecular Biology 98 Montreal, Canada, June 28-July 02 - Geetha, V., Di Francesco, V., Garnier, J., Munson, P. J.
"In Assessment of methods for fold assignment in proteins (abstract)" The Protein Society San Diego, CA, 1998, 159-T. - Blank, P. S., Cho, M. S., Vogel, S. S., Kaplan, D., Kang, A., Malley, J. D., Zimmerberg, J.
"Submaximal responses in calcium-triggered exocytosis are explained by differences in the calcium sensitivity of individual secretory vesicles." J. Gen. Physiol. 112: 559-567
[PubMed] - Blank, P. S., Vogel, S. S., Cho, M. S., Kaplan, D., Bhuva, D., Malley, J. D., Zimmerberg, J.
"The calcium sensitivity of individual secretory vesicles is invariant with the rate of calcium delivery." J. Gen. Physiol. 112: 569-576
[PubMed] - Weiss, G. H., J. M. Porrâ, et al.
"Statistics of the depth probed by cw measurements of photons in a turbid medium." Physical Review E 58(51): 6431-6439 - Weiss, G. H.
"Statistical properties of the penetration depth of photons into a semi-infinite turbid medium: A random walk analysis." Applied Optics 37: 3558-3563 - Weiss, G. H. and J. E. Kiefer
"A numerical study of the statistics of penetration depth of photons re-emitted from irradiated media." J. Mod. Optics 45: 2315-2325 - Weiss, G. H., J. M. Porrâ, et al.
"The continuous-time random walk description of photon motion in an isotropic medium." Optics Comm. 146: 268-276 - Shrager, R. I., G. H. Weiss, et al.
"Selection of optimal measurements for monoexponential T2 determinations in NMR spectroscopy and imaging experiments." NMR in Biomed. 11: 297-305 - Shrager, R. I., G. H. Weiss, et al.
"Optimal time spacings for T2 measurements: monoexpoenential and biexponential systems." NMR in Biomed. 11: 297-305
[PubMed] - Pajevic, S., R. E. Carson, et al.
"Noise Characteristics of 3-D and 2-D Pet Images." IEEE Trans. Med. Imaging 17(1): 9-23
[PubMed] - Pajevic, S. and C. Pierpaoli
"Improved Representation of the Directional Information Contained in the Diffusion Tensor." 6th ISMRM Proceedings 1233 - Norman, J. E., J. J. Bailey, et al.
"NHLBI workshop on the utilization of ECG databases: Preservation and use of existing ECG databases and development of future resources." J. Electrocardiol 31(2): 83-89
[PubMed] - Ioannidis JPA, McQueen PG, Goedert JJ, Kaslow RA
"Use of Neural Networks to Model Complex Immunogenetic Associations of Disease: Human Leukocyte Antigen Impact on the Progression of Human Immunodeficiency Virus Infections." American Journal of Epidemiology 147: 464-471
[PubMed] - Goldstein SR, McQueen PG, Bonner RF.
"Thermal modeling of Laser Capture Microdissection." Applied Optics 37: 7378-7391
[Abstract] - Bicout, D. J., A. M. Berezhkovskii, et al.
"Where do Brownian particles spend their time?" Physica A 258: 352-364 - Bicout, D. J., A. M. Berezhkovskii, et al.
"Turnover in the mean survival time for a particle moving between two traps." Physica A 256: 342-350 - Yarmola, E., Calabrese, P. O., Chrambach, A., Weiss, G. H."Interaction with the matrix: The dominant factor in macromolecular band spreading in gel electrophoresis." J. Phys. Chem. 101: 2381-2387
- Summers, R. M., Selbie, W. S., Malley, J. D., et al
"Computer-Assisted Detection of Endobronchial Lesions Using Virtual Bronchoscopy: Application of Concepts from Different Geometry." International Conference on Mathematical Models in Medical and Health Sciences Nashville, TN May 28-31 - Porr¿, J. M., Masoliver, J., Weiss, G. H.
"When the telegrapher's equation furnishes a better approximation to transport equation than the diffusion approximation." Phys. Rev. E 55: 7771-7774 - Laks, M. M., Arzbaecher, R., Bailey, J. J., Geselowitz, D. B., Berson, A. S.
"Special report: Recommendations for safe current limits for electrocardiographs - Response." Circulation 95(1): 277-278. - Blank, P. S., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"Kinetic models for calcium-triggered exocytosis." J. Gen. Phys. 110(1) - Blank, P. S., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"Heterogeneity in calcium-triggered exocytosis." Mol. Biol. Cell 297a - Weiss, G. H. and J. E. Kiefer
"Some properties of a measure of resolution in gel electrophoresis and CZE." Electrophoresis 18: 2008-2011 - Weiss, G. H. and A. H. Gandjbakhche
"Effects of nonlocalized target shape in the random walk description of transillumination experiments for optical imaging." Phys. Rev. E 55: 3451-3459 - Schubert, S. F., S. Pajevic, et al.
"While Body PET Using Overlapped 3D Acquision and Weighted Image Summation." IEEE 1(97): 1284-1289 - Radko SP, Weiss GH, Chrambach A
"Protein band spreading in CZE: Effects of sample zone length and presence of polymer." J. Chromatog. A 781: 277-286
[PubMed] - Munson, P. J. and R. K. Singh
"Multi-body Interactions within the Graph of Protein Structure" ISMB 5: 198-201
[PubMed] - McQueen, PG
"Physics and Fractal Structures (book review)" Journal of Statistical Physics 86: 1397-1398 - Gitterman, M., R. I. Shrager, et al.
"Stochastic resonance and symmetry breaking in a one-dimensional system." Phys. Rev. E 56: 3713-3716 - Di Francesco V, McQueen PG, Garnier J, Munson PJ
"Incorporating global information into secondary structure prediction with hidden Markov models of protein folds." Proc Int Conf Intell Syst Mol Biol. 5:100-3
[PubMed] - Bailey, J. J. and J. P. Moak
"Simultaneous Heart Rate and Blood Pressure Variability Analysis: Insight into Possible Mechanisms Underlying Vasodepressor Synscope." J. Electrocardiol 30: 54 - Gitterman M, Weiss GH
"An overall view of stochastic resonance."¿ Chaos & Bifurcation ¿7: 911-916 - Gandjbakhche AH, Bonner RF, Nossal RJ, Weiss GH
"Effects of multiple passage probability on fluorescent signals from biological media."¿ Applied Optics 36: 4613-4619 - Bose S, Hendler RW, Shrager RI, Smith PD
"Multichannel analysis of single turnover kinetics of cytochrome aa3 reduction of O2." Biochemistry 36: 2439-2449
[PubMed] - Pajevic S, Bacharach SL, Carson RE, Weiss GH
"Effects of time delay in cardiac blood flow measurements by bolus H2(15)O." IEEE Trans. on Medical Imaging 16:294-300
[Abstract] [PubMed] - McQueen PG, Jin AJ, Pierpaoli C, Basser PJ,
"A Finite Element Model of Molecular Diffusion in Brain Incorporating in vivo Diffusion Tensor MRI Data" Proceedings of the International Society for Magnetic Resonance in Medicine, Fourth Scientific Meeting and Exhibition. 1:193 - Rosenstein, D. L., Kalogeras, K. T., Kalafut, M., Malley, J. D., Rubinow, D. R.
"Peripheral measures of arginine vasopressin, artial natriuretic peptide, and adrenocorticotropic hormone in premenstrual syndrome." Psychoneuroendocrinology 21: 347-359 - Nunez, S. B., Blye, R. P., Thomas, P. M., Reel, J. R., Barnes, K. M., Malley, J. D., Cutler, G. B.
"Recovery of reproductive function in rats treated with the aromatase inhibitor fadrozole." Reproductive Toxicology 10(5): 373-377
[PubMed] - Magiakou, M. A., Mastorakos, G., Rabin, D., Margioris, A. N., Dubbert, B., Calogero, A. E., Tsigos, C., Munson, P. J., Chrousos, G. P.
"The Maternal Hypothalamic-Pituitary-Adrenal Axis in Third Trimester Human Pregnancy." Clin. Endocrinol. 44: 419-428
[PubMed] - Laks, M. M., Arzbaecher, R., Bailey, J. J., Geselowitz, D. B., Berson, A. S.
"Recommendations for safe current limits for electrocardiographs." Circulation 93: 837-9, A statement for healthcare professionals from the Committee on Electrocardiography, American Heart Association. - Vasudevan, G. and P. J. Munson
"Simplified Representation of Proteins." J. Biomol. Struct. and Dynamics 13(5): 781-793 - McQueen PG, Jin AJ, Pierpaoli C, and Basser PJ
"Development of a Finite Element Model of Molecular Diffusion in Living Brain from in vivo Magnetic Resonance." IEEE Service Center - Proceedings of the 1996 Fifteenth Southern Biomedical Engineering Conference: 289-292. - Weiss GH, Calabrese P
"Occupation times of a CTRW on a lattice."¿ Physica A 234: 443-454 - Weiss GH "Onsager′s contribution to reaction-rate theory." Physica A 234: 443-454
- Spouge J, Szabo A, Weiss GH
"Single particle survival in gated trapping." Phys Rev E 54: 2248-2255
[PubMed] - Spouge JL, Shrager RI, Dimitrov DS"HIV-1 infection kinetics in tissue cultures." Mathematical Biosciences 138: 1-22
[PubMed] - Masoliver J, Weiss GH
"Finite-velocity diffusion." Eur J Physics 17: 190-196 - Katki H, Weiss GH, Kiefer JE
"Optimization of magnetization transfer experiments to measure first-order rate constants and spin-lattice relaxation times." NMR in Biomed 9(3):135-9.
[PubMed] - Havlin S, Yen A, Kopelman R, Taitelbaum H, Weiss GH
"Effects of bias on the kinetics of A+B C with initially separated reactants."¿ Phys Rev E 54: 5942-5947¿
[PubMed] - Goans RE, Weiss GH, Vieira NE, Sidbury JB, Abrams SA, Yergey AL
"Calcium kinetics in glycogen storage disease type 1a."¿ Calcified Tissue Intl ¿59: 449-453
[PubMed] - Gandjbakhche, A. H., Chernomordik, V., Bonner, R. F., Nossal, R. J., Weiss, G. H., Hebden, J.
"Optical detection of abnormally absorbing regions in tissue." OSA Trends in Optics and Photonics on Advances in Optical Imaging and Photon Migration , Editors: Alfano, RR, and Fujimoto, JG, (OSA, Washington DC) 2, 183-189 - Bryngelson JD, Weiss GH "Polymers with internal length and displacement constraints: Bounds and exact expressions for free energies." Macromolecules 29: 7995-7999
- Weiss GH, Sokoloff H, Zakharov SF, Chrambach A
"Interpretation of electrophoretic band shapes by a partition chromatographic model." Electrophoresis 17:1325-32 - Rovati GE, Shrager RI, Nicosia S, Munson PJ
"KINFIT II: A nonlinear least squares program for analysis of kinetic binding data." Molecular Pharmacology 50:86-95
[PubMed] - Masoliver J, Weiss GH
"Resolution in time of two electrophoretic peaks." Sep Sci & Tech 31:319-26 - Gandjbakhche AH, Bonner RF, Nossal R, Weiss GH, Hebden J
"Optical detection of abnormally absorbing regions in tissue." Advances in Optical Imaging and Photon Migration 1996, Orlando - Gandjbakhche AH, Bonner RF, Nossal RJ, Weiss GH
"Absorptivity contrast in transillumination imaging of tissue abnormalities." Appl Opt 1996 35:1767-74 - Gandjbakhche AH, Bonner RF, Gannot I, Knutson J, Navai R, Nossal R, Weiss GH
"Fluorescent photon migration for turbid biological media." Proceedings of Advances in Laser and Light Spectroscopy to Diagnose Cancer and Other Diseases III: Optical Biopsy SPIE 1996, 2679:8-15 - Carson RE, Yan Y, Shrager RI
"Absolute cerebral blood flow with [150]-water and PET." Quantification of Brain Function Using PET. Myers, Cunningham, Bailey, and Jones (eds.). Academic Press 1996, 185-90. - Burklow TR, Moak JP, Bailey JJ
"Prevention of vasodepressor syncope following normal saline infusion."¿ PACE ¿19:640 - Boguna M, Porrý J, Masoliver J, Weiss GH"Isotropization time for non-Markovian CTRW?s."Physica A 230:149-55
- Berkolaiko G, Havlin S, Larralde H, Weiss GH
"The expected number of distinct sites visited by N discrete L_vy flights on a one-dimensional lattice."¿Phys Rev E¿53:5774-78 - Berezhkovskii AM, Weiss GH
"Average volume of the domain visited by randomly injected spherical particles in d dimensions."¿Phys Rev E¿54:92-9
[PubMed] - Weiss GH, Garner M, Yarmola E, Bocek P, Chrambach A
"A comparison of resolution of DNA fragments between agarose gel and capillary zone electrophoresis in agarose solutions." Electrophoresis 16:1345-53
[PubMed] - Weiss GH, Gandjbakhche AH, Masoliver J
"Isotropization length of random walk models of photon migration in turbid media." J of Mod Optics 42:1567-74 - Porr JM, Weiss GH, Masoliver J"A diffusion model incorporating anisotropic properties." Physica A 218:229-36
- Larralde H, Weiss GH
"Expected number of sites visited by a constrained n-step random walk." Phys Rev E 52:1313-17
[PubMed] - Larralde H, Weiss GH
"A generating function for the second moment of the distinct number of sites visited by an n-step lattice random Walk." J Physics A 28:5217-25 - Goans RE, Weiss GH, Abrams SA, Perez MD, Yergey AL
"Calcium tracer kinetics show decreased irreversible flow to bone in glucocorticoid treated patients." Calcified Tissue Intl 56:533-35
[PubMed] - Gitterman M, Weiss GH
"Coherent stochastic resonance in the presence of a field." Phys Rev E 52:5708-11
[PubMed] - Bansil R, Pajevic S, Konak C
"Dynamic light scattering study of linear polyelectrolyte diffusion in gel." Macromolecules 28:7536 - Bailey JJ, Moak JP
"Heart rate variability in patients with neurally medicated syncope: Table- tilt and pharmacological testing." J Electrocardiology 28:89 - Berger, M.P. and Munson, P.J. "A novel randomized iterative strategy for aligning multiple protein sequences" CABIOS Vol. 7 no. 4 478-484 (1991)
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