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Genomes and Genes | mathematical computingSummarySummary: Computer-assisted interpretation and analysis of various mathematical functions related to a particular problem. Top Publications
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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculationsTodd J Dolinsky
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S. Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA
Nucleic Acids Res 32:W665-7. 2004....
Biological evaluation of d2, an algorithm for high-performance sequence comparisonW Hide
Department of Biochemical and Biophysical Sciences, University of Houston, TX 77204 5934, USA
J Comput Biol 1:199-215. 1994..This work demonstrates that d2 is a unique, sensitive, and selective method of rapid sequence comparison that can detect novel sequence relationships which remain undetected by alternate methodologies...- Resolving fiber crossing using advanced fast marching tractography based on diffusion tensor imagingP Staempfli
Institute for Biomedical Engineering, ETH and University Zurich, Gloriastrasse 35, CH 8092 Zurich, Switzerland
Neuroimage 30:110-20. 2006..The in vivo results illustrate that the elucidated major white matter pathways are consistent with known anatomy and that multiple crossings and tract branching are handled correctly... - Dynamic discrimination analysis: a spatial-temporal SVMJanaina Mourao-Miranda
Brain Image Analysis Unit, Biostatics Department, Centre for Neuroimaging Sciences PO 89, Institute of Psychiatry, KCL, De Crespigny Park, London SE5 8AF, UK
Neuroimage 36:88-99. 2007..This produces a discriminating weight vector encompassing both voxels and time. The resulting vector furnishes discriminating responses, at each voxel without imposing any constraints on their temporal form... - Distributional regimes for the number of k-word matches between two random sequencesRoss A Lippert
Informatics Research, Celera Genomics, Rockville, MD 20878, USA
Proc Natl Acad Sci U S A 99:13980-9. 2002..In this situation the uniform distribution provides the exception to other letter distributions. Therefore a naive, one distribution fits all, approach to D(2) statistics could easily create serious errors in estimating significance... - PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostaticsCyril Azuara
, URA 2185 du C.N.R.S, Institut Pasteur, 75015 Paris, France
Nucleic Acids Res 34:W38-42. 2006.... - 76-space analysis of grey matter diffusivity: methods and applicationsTianming Liu
Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, MA 02478, USA
Neuroimage 31:51-65. 2006..We evaluate and validate this computational framework for 76-space GM diffusivity analysis using data from normal volunteers and from patients with Creutzfeldt-Jakob disease... - Gender difference analysis of cortical thickness in healthy young adults with surface-based methodsKiho Im
Department of Biomedical Engineering, Hanyang University, Sungdong P.O. Box 55, Seoul 133-605, South Korea
Neuroimage 31:31-8. 2006..These findings suggest statistically significant cortical thickening in women in localized anatomical regions, which is consistent with several previous studies and may support a hypothesis of sexual dimorphism... - Common MRI acquisition non-idealities significantly impact the output of the boundary shift integral method of measuring brain atrophy on serial MRIGregory M Preboske
Mayo Clinic and Foundation, Department of Radiology, 200 First Street SW, Rochester, MN 55905, USA
Neuroimage 30:1196-202. 2006..Methods to maximize consistency of image quality over time are an essential component of any quantitative serial MRI study... - User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliabilityPaul A Yushkevich
Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, PA 19104 6274, USA
Neuroimage 31:1116-28. 2006..Analogous results for lateral ventricle segmentation are provided... - Bayesian model averaging in EEG/MEG imagingNelson J Trujillo-Barreto
Cuban Neuroscience Center, Havana, Cuba
Neuroimage 21:1300-19. 2004.... - Mapping anatomical correlations across cerebral cortex (MACACC) using cortical thickness from MRIJason P Lerch
McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, QC, Canada H3A 2B4
Neuroimage 31:993-1003. 2006..Lastly, IQ-dependent MACACC differences were investigated, revealing steeper correlations between BA 44 and multiple frontal and parietal regions for the higher IQ group, most significantly (t = 4.0) in the anterior cingulate... - A knowledge-driven algorithm for a rapid and automatic extraction of the human cerebral ventricular system from MR neuroimagesYan Xia
Biomedical Imaging Laboratory, Institute for Infocomm Research, 119613, Singapore, Singapore
Neuroimage 21:269-82. 2004..0 GHz PC. The best overlap metric between the results of a radiology expert and the algorithm is 0.9879 and the worst 0.9527; the mean and standard deviation of the overlap metric are 0.9723 and 0.01087, respectively... - Fibertract segmentation in position orientation space from high angular resolution diffusion MRIPatric Hagmann
Department of Radiology, Lausanne University Hospital CHUV, Switzerland
Neuroimage 32:665-75. 2006..Potential advantages and drawbacks as compared to classical tractography are discussed; for example, it appears that our formulation handles naturally crossing tracts and is not biased by human intervention... - Functional MRI of memory in the hippocampus: Laterality indices may be more meaningful if calculated from whole voxel distributionsDaniel M Branco
Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
Neuroimage 32:592-602. 2006..Our results suggest that using weighted distributions can be a useful strategy for assessing memory lateralization by fMRI in the MTL... - Interindividual functional mapping: a nonlinear local approachI Corouge
Projet Vista, IRISA INRIA CNRS, Campus de Beaulieu, 35042 Rennes Cedex, France
Neuroimage 19:1337-48. 2003..In this paper, we present results on MEG somatosensory data acquired on 18 subjects. We show that the nonlinear local fusion scheme significantly reduces the observed functional variability... - BOLD correlates of EMG spectral density in cortical myoclonus: description of method and case reportMark P Richardson
Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
Neuroimage 32:558-65. 2006.... - Voxel-based morphometry in patients with idiopathic generalized epilepsiesLuiz Eduardo Betting
Department of Neurology, Brazil
Neuroimage 32:498-502. 2006..Our results support subtle GMC abnormalities in patients with JME and AE when compared to controls. These findings suggest the existence of different patterns of cortical abnormalities in IGE subsyndromes... - Hippocampal volume in chronic posttraumatic stress disorder (PTSD): MRI study using two different evaluation methodsA Jatzko
Central Institute of Mental Health, Faculty for Clinical Medicine Mannheim, University of Heidelberg, Germany
J Affect Disord 94:121-6. 2006..This supports the hypothesis that previously described hippocampal volume reduction is not necessarily due to PTSD or at least that, after 15 years, volume changes have been restored or have not yet developed... - [MRI morphometry, an insight into brain function]A Curie
Institut des Sciences Cognitives, CNRS UMR 5015, 67, boulevard Pinel, 69675 Bron, France
Arch Pediatr 13:674-7. 2006 - Optimization of diffusion-tensor MR imaging data acquisition parameters for brain fiber tracking using parallel imaging at 3 TShinji Naganawa
Department of Radiology, Nagoya University School of Medicine, 65 Tsurumai Cho, Shouwa ku, 466 8550 Nagoya, Japan
Eur Radiol 14:234-8. 2004..The DT MRI data sufficient for brain fiber tracking in healthy subjects can be obtained in <2 min with a 2-mm slice thickness, 700-s/mm2 b-factor, 6 MPG directions, and no averaging (number of averages=1)... - Decrements in volume of anterior ventromedial temporal lobe and olfactory dysfunction in schizophreniaBruce I Turetsky
Schizophrenia Research Center, Department of Psychiatry, University of Pennsylvania, Philadelphia 19104, USA
Arch Gen Psychiatry 60:1193-200. 2003..Patients with schizophrenia exhibit olfactory deficits, but it is unclear whether these represent a specific abnormality. The link between olfactory impairments and regional brain abnormalities has yet to be established... - Analysis and validation of automated skull stripping tools: a validation study based on 296 MR images from the Honolulu Asia aging studyS W Hartley
Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
Neuroimage 30:1179-86. 2006..Although method accuracy was statistically associated with some subject characteristics, the extent of the misclassification (in terms of percent of brain volume) was small... - [Multisegmental image fusion of the spine]J Kaminsky
Abteilungen Neurochirurgie, Medizinische Hochschule Hannover
Biomed Tech (Berl) 49:49-55. 2004.... - Comparing gray matter loss profiles between dementia with Lewy bodies and Alzheimer's disease using cortical pattern matching: diagnosis and gender effectsMartina Ballmaier
Laboratory of Neuroimaging, Department of Neurology, David Geffen UCLA School of Medicine, Los Angeles, CA 90095-1769, USA
Neuroimage 23:325-35. 2004..Further investigation of the influence of gender might provide a more comprehensive understanding of the pathophysiological differences underlying the two forms of dementia... - How reliable are fMRI-EEG studies of epilepsy? A nonparametric approach to analysis validation and optimizationAnthony B Waites
Brain Research Institute, Austin Health, Heidelberg West, Australia
Neuroimage 24:192-9. 2005..This is an important step beyond standard analysis. It informs clinical interpretation because it permits assessment of the reliability of the connection between interictal EEG events and the BOLD response to those events... - Integrated wavelet processing and spatial statistical testing of fMRI dataDimitri van de Ville
Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne EPFL, CH 1015 Lausanne, Switzerland
Neuroimage 23:1472-85. 2004..We show by experimental results that our method is able to detect activation patterns; the results are comparable to those obtained by SPM even though statistical assumptions are more conservative... - The neuroanatomy of general intelligence: sex mattersRichard J Haier
Department of Pediatrics, University of California, Med Sci I, B140, Irvine, CA 92697 5000, USA
Neuroimage 25:320-7. 2005.... - Assessment of shape variation of the levator ani with optimal scan planning and statistical shape modelingSu-Lin Lee
Royal Society/Wolfson Foundation Medical Image Computing Laboratory, Imperial College of Science, Technology and Medicine, London, United Kingdom
J Comput Assist Tomogr 29:154-62. 2005..The proposed technique offers a new way forward for studying dynamic shape changes of 3D structures where complete volumetric imaging is prohibited by the inherent temporal resolution of the scanning technique... - Valid conjunction inference with the minimum statisticThomas Nichols
Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Neuroimage 25:653-60. 2005..This result holds even if the comparisons are not independent. We suggest that the revised test proposed here is the appropriate means for conjunction inference in neuroimaging... - Neuromagnetic localization of rhythmic activity in the human brain: a comparison of three methodsM Liljestrom
Brain Research Unit, Low Temperature Laboratory, Helsinki University of Technology, P O BOX 2200, FIN 02015 HUT, Espoo, Finland
Neuroimage 25:734-45. 2005..MCE(FD) provides simultaneous localization of sources and was found to give a good overview of the data. With DICS, it was possible to separate close-by sources that were not retrieved by the other two methods... - Identification of large-scale networks in the brain using fMRIPierre Bellec
Unité 678, Inserm UPMC, 91 Boulevard de l Hopital, 75634 Paris Cedex 13, France
Neuroimage 29:1231-43. 2006..The LSNI method we propose allows to detect in an exploratory and systematic way all the regions and large-scale networks activated in the working brain... - A rotation-invariant spherical harmonic decomposition method for mapping intravoxel multiple fiber structuresWang Zhan
Neuroimaging Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Nathan Shock Dr. Room 383, Baltimore, MD 21224, USA
Neuroimage 29:1212-23. 2006..Compared with the regular SHD methods used in HARD imaging, the proposed RI-SHD method is superior in characterizing the diffusion patterns of multiple fiber structures between different brain regions or across subjects... - ROC-based assessments of 3D cortical surface-matching algorithmsRavi Bansal
New York State Psychiatric Institute, New York, NY 10032, USA
Neuroimage 24:150-62. 2005..The GD and NN algorithms, moreover, are both vulnerable to detecting false-positive activations at points of high curvature, particularly along large fissures, cisterns, and cortical sulci... - Cerebral atrophy in myotonic dystrophy: a voxel based morphometric studyG Antonini
Neurological Clinic, S, II Faculty of Medicine, University of Rome La Sapienza, Italy
J Neurol Neurosurg Psychiatry 75:1611-3. 2004..Grey matter atrophy was located mainly in the bilateral frontal and parietal lobes, in the bilateral middle temporal gyrus, and in the left superior temporal and occipital gyrus... - Voxel-based morphometry in adolescents with bipolar disorder: first resultsMarko Wilke
Imaging Research Center and Department of Psychiatry, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
Psychiatry Res 131:57-69. 2004..VBM confirmed bilaterally larger basal ganglia. Localized gray matter deficits in bipolar subjects were found in the medial temporal lobe, orbito-frontal cortex, and the anterior cingulate, confirming and extending earlier studies... - Deformable registration of cortical structures via hybrid volumetric and surface warpingTianming Liu
Section of Biomedical Image Analysis, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
Neuroimage 22:1790-801. 2004..Experimental results on both synthesized and real brain data demonstrate the performance of the proposed method in the registration of cortical structures across individuals... - Fast and robust parameter estimation for statistical partial volume models in brain MRIJussi Tohka
Digital Media Institute Signal Processing, Tampere University of Technology, FIN 33101, Finland
Neuroimage 23:84-97. 2004.... - Less white matter concentration in autism: 2D voxel-based morphometryMoo K Chung
Department of Statistics, University of Wisconsin Madison, Madison, WI 53706, USA
Neuroimage 23:242-51. 2004..Further, it is shown that the less white matter concentration in the corpus callosum in autism is due to hypoplasia rather than atrophy... - Superior temporal sulcus anatomical abnormalities in childhood autism: a voxel-based morphometry MRI studyN Boddaert
ERM 0205 INSERM CEA, Service Hospitalier Frederic Joliot, CEA, 91406, Orsay, France
Neuroimage 23:364-9. 2004..Therefore, the convergent anatomical and functional temporal abnormalities observed in autism may be important in the understanding of brain behavior relationships in this severe developmental disorder... - Cross-relaxation imaging reveals detailed anatomy of white matter fiber tracts in the human brainVasily L Yarnykh
Department of Radiology, University of Washington, Seattle, WA 98195, USA
Neuroimage 23:409-24. 2004..Cross-relaxation imaging can be used in various clinical studies focused on brain development and white matter diseases... - Structural brain variation and general intelligenceRichard J Haier
Department of Pediatrics, University of California, Irvine, CA 92697 5000, USA
Neuroimage 23:425-33. 2004..These results underscore the distributed neural basis of intelligence and suggest a developmental course for volume--IQ relationships in adulthood... - Creating a statistical atlas of the craniumSascha Däuber
University of Karlsruhe TH, Institute for Process Control and Robotics, Kaiserstrasse 12, 76128 Karlsruhe, Germany
Stud Health Technol Inform 85:116-20. 2002..e. it manages averaging without landmarks and it provides a complete description of the shape. In addition the shape space can be used to classify shapes to identify different types of an anatomy... - (1)H MR spectroscopy of the brain in multiple sclerosis subtypes with analysis of the metabolite concentrations in gray and white matter: initial findingsPaul E Sijens
Department of Radiology, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, The Netherlands
Eur Radiol 16:489-95. 2006..In conclusion, the concentrations of Cho, Cr and NAA are reduced in PPMS/SPMS patients, especially in GM and in WML. Despite contrary observations in previous studies, increases in the concentrations of Cr and/or Cho were not observed... - A new point-based warping method for enhanced and simplified analysis of functional brain image dataRainer Pielot
Leibniz Institute for Neurobiology, Brenneckestrasse 6, D 39118 Magdeburg, Germany
Neuroimage 19:1716-29. 2003..Therefore, the new method is a powerful tool, which enhances the comparison of complex biological structures and the quantitative evaluation of functional imaging data... - The quantitative evaluation of functional neuroimaging experiments: mutual information learning curvesU Kjems
Department of Mathematical Modelling, Technical University of Denmark, DK 2800 Lyngby, Denmark
Neuroimage 15:772-86. 2002.... - The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis frameworkStephen C Strother
Department of Radiology, University of Minnesota, Minneapolis, Minnesota 55455, USA
Neuroimage 15:747-71. 2002..We propose the NPAIRS framework as a validation tool for testing and optimizing methodological choices and tools in functional neuroimaging... - Cortical layer-dependent BOLD and CBV responses measured by spin-echo and gradient-echo fMRI: insights into hemodynamic regulationFuqiang Zhao
Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15203, USA
Neuroimage 30:1149-60. 2006..Our data supports the notion of laminar-dependent CBV regulation at a sub-millimeter scale... - Akaike causality in state space. Instantaneous causality between visual cortex in fMRI time seriesKin Foon Kevin Wong
Institute of Statistical Mathematics, Minami Azabu 4 6 7, Tokyo 106 8569, Japan
Biol Cybern 97:151-7. 2007..By assuming that noises are independent, a causality map is drawn using Akaike noise contribution ratio theory. The method is illustrated by an application to fMRI data recorded under visual stimulation... - Automated hippocampal segmentation by regional fluid registration of serial MRI: validation and application in Alzheimer's diseaseW R Crum
Dementia Research Group, Institute of Neurology, 8-11 Queen Square, London, WC1N 3BG, United Kingdom
Neuroimage 13:847-55. 2001..7%. Fluid registration has potential importance for tracking longitudinal structural changes in brain particularly in the context of the clinical trial where large numbers of subjects may have multiple MR scans... - Voxel-based morphometry using the RAVENS maps: methods and validation using simulated longitudinal atrophyC Davatzikos
Center for Biomedical Image Computing, Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
Neuroimage 14:1361-9. 2001..Improved sensitivity was achieved at the expense of human effort involved in defining a number of sulcal curves that serve as constraints on the 3D elastic warping... - 3D-gradient coil structures for MRI designed using fuzzy membership functionsH Sanchez
School of Information Technology and Electrical Engineering, University of Queensland, Australia
Conf Proc IEEE Eng Med Biol Soc 2007:2042-5. 2007..The resulting dome-shape coil has superior gradient performance compared to a standard fingerprint coil. New quadrupolar gradient coil designs for breast imaging are also obtained with the proposed method... - Magnetic resonance image tissue classification using a partial volume modelD W Shattuck
Signal and Image Processing Institute, University of Southern California, Los Angeles, California 90089, USA
Neuroimage 13:856-76. 2001..Our method achieved average kappa indices kappa = 0.893 +/- 0.041 for GM and kappa = 0.928 +/- 0.039 for WM compared to the ground truth labeling on 12 volumes from the Montreal Neurological Institute's BrainWeb phantom... - Landmark-based morphometrics of the normal adult brain using MRIS L Free
Epilepsy Research Group, National Society for Epilepsy MRI unit, Institute of Neurology, Queen Square, London
Neuroimage 13:801-13. 2001..001) between left and right hemispheres. This finding was significant for right- but not left-handed subjects alone. No other significant age, gender, handedness, or brain-size correlations with shape differences were found... - Detecting deception from neuroimaging signals--a data-driven perspectiveJohn-Dylan Haynes
Trends Cogn Sci 12:126-7; author reply 127-8. 2008 - Thresholding of statistical maps in functional neuroimaging using the false discovery rateChristopher R Genovese
Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
Neuroimage 15:870-8. 2002..We demonstrate this approach using both simulations and functional magnetic resonance imaging data from two simple experiments... - Two- and three dimensional measures of vestibular schwannomas and posterior fossa--implications for the treatmentP H Roche
Service de Neurochirurgie, Centre Hospitalier et Universitaire Sainte Marguerite, Assistance Publique des Hopitaux de Marseille, Marseille, France
Acta Neurochir (Wien) 149:267-73; discussion 273. 2007..To help the treatment decision we investigated the VS and PF morphometry using a computerized method... - Hippocampal atrophy confounds template-based functional MR imaging measures of hippocampal activation in patients with mild cognitive impairmentC K Sandstrom
Department of Radiology, Brain Imaging and Analysis Center, Duke University Medical Center, Durham, NC, USA
AJNR Am J Neuroradiol 27:1622-7. 2006..Template-based measures of hippocampal activation that do not adequately account for hippocampal atrophy should be used with caution in patients with MCI... - MR imaging anatomy in neurodegeneration: a robust volumetric parcellation method of the frontal lobe gyri with quantitative validation in patients with dementiaB Iordanova
Department of Radiology, Magnetic Resonance Unit, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
AJNR Am J Neuroradiol 27:1747-54. 2006.... - Creutzfeldt-jakob disease involvement of rolandic cortex: a quantitative apparent diffusion coefficient evaluationY-R Lin
Department of Radiology, Brigham and Women's Hospital--Harvard Medical School, Boston, MA, USA
AJNR Am J Neuroradiol 27:1755-9. 2006.... - Neocortical temporal FDG-PET hypometabolism correlates with temporal lobe atrophy in hippocampal sclerosis associated with microscopic cortical dysplasiaBeate Diehl
Department of Neurology, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
Epilepsia 44:559-64. 2003..We investigate the relation between FDG-PET metabolism and temporal lobe (TL) and hippocampal atrophy in patients with histologically proven isolated HS and HS associated with CD... - Performance evaluation of a multi-slice CT system with 16-slice detector and increased gantry rotation speed for isotropic submillimeter imaging of the heartThomas Flohr
Siemens Medical Solutions, Computed Tomography, Forchheim, Germany
Herz 28:7-19. 2003..We evaluate advances in ECG-gated scanning of the heart and the coronary arteries with recently introduced 16-slice CT equipment (SOMATOM Sensation 16, Siemens, Forchheim, Germany)... - Impaired thalamocortical connectivity in humans during general-anesthetic-induced unconsciousnessNathan S White
Department of Anesthesiology, University of California at Irvine, Irvine, CA 92868, USA
Neuroimage 19:402-11. 2003..These findings support the hypothesis that a mechanistic component underlying general-anesthetic-induced unconsciousness involves disruption of functional interactions within thalamocortical neural networks... - The bootstrap and cross-validation in neuroimaging applications: estimation of the distribution of extrema of random fields for single volume tests, with an application to ADC mapsRoberto Viviani
Department of Psychiatry III, University of Ulm, Germany
Hum Brain Mapp 28:1075-88. 2007..As case studies, we present parametric maps of lesions in patients suffering from stroke and glioblastoma at different stages of evolution... - Measurement of amygdala T2 relaxation time in temporal lobe epilepsyP A Bartlett
MRI Unit, National Society for Epilepsy, Chalfont St Peter, Buckinghamshire, UK
J Neurol Neurosurg Psychiatry 73:753-5. 2002..Two of five patients with bilateral HS had unilateral abnormal AT2. CONCLUSION: Reliable T2 measurements can be obtained in the amygdala, and may be useful in the detection of amygdala abnormality... - Optimized EPI for fMRI studies of the orbitofrontal cortexR Deichmann
Wellcome Department of Imaging Neuroscience, Institute of Neurology, London WC1N 3BG, UK
Neuroimage 19:430-41. 2003..In contrast to several other techniques proposed in the literature for reducing susceptibility effects, this method does not compromise the temporal resolution and is therefore applicable to event-related studies... 
Alphabetic bias in the selection of reviewers for the American Journal of RoentgenologyMichael L Richardson
Department of Radiology, University of Washington School of Medicine, Roosevelt Clinic, 4245 Roosevelt Way NE, Seattle, WA 98105, USA
AJR Am J Roentgenol 191:W213-6. 2008..This study was performed to determine whether the number of invitations extended to American Journal of Roentgenology (AJR) reviewers is biased toward reviewers with last names that start with early letters of the alphabet...- Interpolation of animal tracking data in a fluid environmentYann Tremblay
University of California, Santa Cruz, Long Marine Laboratory, Center for Ocean Health, 100 Shaffer Road, Santa Cruz, CA 95060, USA
J Exp Biol 209:128-40. 2006..Given their popularity in mathematical computing, we chose Bézier, hermite and cubic splines, in addition to a commonly used linear algorithm to .. - Evaluation of normalization methods for cDNA microarray data by k-NN classificationWei Wu
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
BMC Bioinformatics 6:191. 2005..However, to date there have been few published systematic evaluations of these techniques for removing variations arising from dye biases in the context of downstream, higher-order analytical tasks such as classification... - Cost-effective use of breast biopsy techniques in a Veterans health care systemAllison R Hatmaker
Department of General Surgery, VA Tennessee Valley Healthcare System, CCC 4312 Medical Center North, Nashville, TN 37232 2730, USA
Am J Surg 192:e37-41. 2006..We examined the costs and trends in the use of surgical versus percutaneous image-guided biopsy procedures in this diagnostic algorithm... - periodR - an R package to calculate long-term cancer survival estimates using period analysisBernd Holleczek
Saarland Cancer Registry, Präsident Baltz Strasse 5, 66119 Saarbrücken, Germany
Methods Inf Med 48:123-8. 2009.... - A methodology for monitoring globular milk protein changes induced by ultrafiltration: a dual structural and functional approachM van Audenhaege
INRA, UMR1253 Science et Technologie du Lait et de l Oeuf, 35042 Rennes, France
J Dairy Sci 93:3910-24. 2010..Such a hypothesis corroborates results previously mentioned in the literature... - Multiple imputation using an iterative hot-deck with distance-based donor selectionJuned Siddique
Department of Health Studies, University of Chicago, Chicago, IL 60637, U S A
Stat Med 27:83-102. 2008..The choice of starting value did not have an impact on inferences but the order in which the variables were chosen for imputation was significant even after iteration... - Global analysis of Förster resonance energy transfer in live cells measured by fluorescence lifetime imaging microscopy exploiting the rise time of acceptor fluorescenceSergey P Laptenok
Laboratory of Biophysics, Wageningen University, Dreijenlaan 3 6703 HA Wageningen, The Netherlands
Phys Chem Chem Phys 12:7593-602. 2010..Software to reproduce the presented results is provided in an open-source and freely available package called "TIMP" for "The R project for Statistical Computing"... - Statins might reduce risk of renal cell carcinoma in humans: case-control study of 500,000 veteransVikas Khurana
Gastroenterology Service, Overton Brooks Veterans Affairs Medical Center, Shreveport, Louisiana 71101, USA
Urology 71:118-22. 2008..Statins are commonly used cholesterol-lowering agents noted to suppress tumor cell growth in several in vitro and animal models... - Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methodsSubhash R Lele
Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB T6G2G1, Canada
Ecol Lett 10:551-63. 2007..We illustrate the method by fitting two nonlinear population dynamics models to data in the presence of process and observation noise... - Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selectionMichael C Wu
Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
Bioinformatics 25:1145-51. 2009..For a significantly differentially expressed pathway, it is also of substantial interest to select important genes that drive the differential expression of the pathway... - Bias in random forest variable importance measures: illustrations, sources and a solutionCarolin Strobl
Institut für Statistik, Ludwig Maximilians Universitat Munchen, Ludwigstr, 33, 80539 Munchen, Germany
BMC Bioinformatics 8:25. 2007.... - Detection of errors of interpretation in experiments in enzyme kineticsA Cornish-Bowden
Institut Fédératif Biologie Structurale et Microbiologie, Bioenergetique et Ingenierie des Proteines, Centre National de la Recherche Scientifique, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France
Methods 24:181-90. 2001..Finally, the Scatchard plot (together with the Eadie-Hofstee plot) is used as an example to discuss the dangers of publishing derived information unaccompanied by any primary data... - An overview of randomization techniques: An unbiased assessment of outcome in clinical researchKp Suresh
Department of Biostatics, National Institute of Animal Nutrition and Physiology NIANP, Adugodi, Bangalore, India
J Hum Reprod Sci 4:8-11. 2011..graphpad.com/quickcalcs or www.randomization.com) to generate the randomization schedule. Issues related to randomization are also discussed in this paper... - Potential for bias in case-crossover studies with shared exposures analyzed using SASShirley V Wang
Center for Environmental Health and Technology, Brown University, Providence, Rhode Island, USA
Am J Epidemiol 174:118-24. 2011..0. This potential bias does not arise in R (R Foundation for Statistical Computing, Vienna, Austria) or Stata (Stata Corporation, College Station, Texas)... - Statins reduce the risk of pancreatic cancer in humans: a case-control study of half a million veteransVikas Khurana
Division of Gastroenterology and Hepatology, Overton Brooks Veterans Affairs Medical Center, Shreveport, LA 71101 4295, USA
Pancreas 34:260-5. 2007..Statins are commonly used cholesterol-lowering agents that are noted to suppress tumor cell growth in several in vitro and animal models... - [The impact of incorrectly-measured variables when mixed with precisely measured variables on the study of validity in epidemiological research]Mei Xia Yang
Xuhui District Center for Disease Control and Prevention, Shanghai 200031, China
Zhonghua Liu Xing Bing Xue Za Zhi 28:810-3. 2007..To explore the impact of measurement error on the associated effects under the incorrectly-measured variables when mixed with precisely measured variables... - A time series analysis performed on a 25-year period of kidney transplantation activity in a single centerG Santori
Department of Transplantation, San Martino University Hospital, Genoa, Italy
Transplant Proc 42:1080-3. 2010..The time series approach may be helpful to establish a minimum volume/y at a single-center level... - The Cataract National Dataset electronic multicentre audit of 55,567 operations: when should IOLMaster biometric measurements be rechecked?N E Knox Cartwright
Department of Ophthalmology, Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, Avon, UK
Eye (Lond) 24:894-900. 2010.... - A 20-year period of orthotopic liver transplantation activity in a single center: a time series analysis performed using the R Statistical SoftwareG Santori
Department of Transplantation, San Martino University Hospital, Genoa, Italy
Transplant Proc 41:1286-9. 2009..The time series approach may be helpful to establish a minimum volume/y at a single-center level... - [''R"--project for statistical computing]Ram Benny Dessau
Naestved Sygehus, Klinisk mikrobiologisk afdeling, Naestved
Ugeskr Laeger 170:328-30. 2008..R is seen as a tool for teaching statistics and implementing complex modelling of medical data among medical professionals... - An R package for analysis of whole-genome association studiesDavid Clayton
Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
Hum Hered 64:45-51. 2007..To provide data classes and methods to facilitate the analysis of whole genome association studies in the R language for statistical computing... - Survival analysis in public health researchE T Lee
College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City 73190, USA
Annu Rev Public Health 18:105-34. 1997..Examples from published literature are given to illustrate the various methods. The paper is intended for public health professionals who are interested in survival data analysis... - Image analysis and statistical inference in neuroimaging with RK Tabelow
Weierstrass Institute, Berlin, Germany
Neuroimage 55:1686-93. 2011..We review their methodology and give an overview of their capabilities for neuroimaging. In addition we summarize some of the current activities in the area of neuroimaging software development in R... - Differential diagnosis of thyroid nodules with US elastography using carotid artery pulsationManjiri Dighe
Department of Radiology, University of Washington Medical Center, Seattle, WA 98195, USA
Radiology 248:662-9. 2008..To explore the sensitivity and specificity of ultrasonographic (US) elastography using carotid arterial pulsation as the compression source for differential diagnosis of thyroid nodules... - Statins reduce the risk of lung cancer in humans: a large case-control study of US veteransVikas Khurana
Department of Medicine, Overton Brooks VAMC, East Stoner Avenue 151 Research, Shreveport, LA 71101, USA
Chest 131:1282-8. 2007..Statins are commonly used cholesterol-lowering agents that are noted to suppress tumor cell growth in several in vitro and animal models... - A less field-intensive robust design for estimating demographic parameters with mark-resight dataBrett T McClintock
Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado 80523, USA
Ecology 90:313-20. 2009..We found this method to be a viable alternative to traditional mark-recapture when cost or disturbance to species is of particular concern in long-term population monitoring programs... - snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting packageAugustin Luna
GCAP CBDB, NIMH NIH, 10 Center Drive, Room 4s 235, Bethesda, MD 20814, USA
Bioinformatics 23:774-6. 2007..AVAILABILITY: Downloadable R package and example datasets are available at http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html and http://www.r-project.org... - Generalized linear mixed models: a review and some extensionsC B Dean
Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Lifetime Data Anal 13:497-512. 2007..To provide the reader with a flavor of the utility and wide applicability of this fundamental methodology we consider a few extensions including additive models, models for zero-heavy data, and models accommodating latent clusters... - Estimating abundance using mark-resight when sampling is with replacement or the number of marked individuals is unknownBrett T McClintock
Department of Fish, Wildlife, and Conservation Biology, Department of Statistics, Colorado State University, Fort Collins, Colorado 80523, USA
Biometrics 65:237-46. 2009.... - Catmap: case-control and TDT meta-analysis packageKristin K Nicodemus
Genes, Cognition and Psychosis Program, Clinical Brain Disorders Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
BMC Bioinformatics 9:130. 2008.... - StatFingerprints: a friendly graphical interface program for processing and analysis of microbial fingerprint profilesR J Michelland
INRA, UMR 1289 TANDEM, Tissus Animaux, Nutrition, Digestion, Ecosystème et Métabolisme, Universite de Toulouse, F 31326 Castanet Tolosan Cedex, France, INPT ENSAT, UMR 1289 TANDEM, Universite de Toulouse, F 31326 Castanet Tolosan Cedex, France, ENVT, UMR 1289 TANDEM, F 31076 Toulouse cedex, France, Institut de Mathématiques, Universite Paul Sabatier, 31062 Toulouse Cedex 9, France
Mol Ecol Resour 9:1359-63. 2009.... - PHAST and RPHAST: phylogenetic analysis with space/time modelsMelissa J Hubisz
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
Brief Bioinform 12:41-51. 2011..0 are available for download at http://compgen.bscb.cornell.edu/phast, under the terms of an unrestrictive BSD-style license. RPHAST can also be obtained from the Comprehensive R Archive Network (CRAN; http://cran.r-project.org)... - How to use the computing environment R to analyze ATP-induced ribonucleotide reductase R1 hexamerization dataT Radivoyevitch
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
Nucleosides Nucleotides Nucleic Acids 29:427-32. 2010..This example involves ATP-induced R1 hexamerization dynamic light scattering data that suggests that R1 hexamers have two types of a-sites, one that binds ATP and another that does not (here, R1 is the large subunit of RNR)... - HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in RHeidi Dvinge
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
Bioinformatics 25:3325-6. 2009..This is problematic when an experiment involves more than a simple comparison between a control and treatment sample, or when many qPCR datasets are to be analyzed in a high-throughput facility...
Research Grants
- San Antonio STI TM CRCJoel Baseman; Fiscal Year: 2004..These projects are supported by Statistical/Computing and Administrative Cores. ..
- KU Medical Center Clinical Research Curriculum ProgramEdward Ellerbeck; Fiscal Year: 2007..Overall, the program is designed to increase the number of program Scholars who apply for and receive extramural funding for clinical research at both the novice and transitional investigator levels. ..
- POSTDOCTORAL TRAINING IN THE STUDY OF AGINGJULIE ZISSIMOPOULOS; Fiscal Year: 2007..Fellows are also encouraged to develop a research proposal for submission to a funding agency, as a step towards continuing their progress after the training program ends. ..
- NCRR - High end instrumentation (HEI)J Landis; Fiscal Year: 2004..This specialized computing equipment request meets the NCRR goals of providing shared resources across multiple grants that are cost-prohibitive and difficult to justify for individual projects. ..
- Training Program in Biostatistics for Cancer ResearchGary Rosner; Fiscal Year: 2005..D. Anderson Cancer Center with practical experience will enable trainees upon completion to make fundamental contributions to cancer research working alongside biomedical investigators. ..
- Boston University Summer Institute in BiostatisticsLisa Sullivan; Fiscal Year: 2007..Our goal is to create a model program that is both effective in motivating students towards careers in biostatistics and easily replicated by other institutions. ..
- CSHL Integrated Data Analysis for High Throughput BiologyDavid Stewart; Fiscal Year: 2007....
- EDUCATION IN PATIENT ORIENTED RESEARCHCharles McCall; Fiscal Year: 2004..The PEPOR of WFUSM will meet the challenge of training talented clinical investigators. ..