- Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Genet 38:904-9. 2006
..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
- Population structure and eigenanalysis
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
PLoS Genet 2:e190. 2006
..This means that we can predict the dataset size needed to detect structure...
- Reconstructing Indian population history
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 461:489-94. 2009
..We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically...
- Genes mirror geography within Europe
Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
Nature 456:98-101. 2008
..In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres...
- The genetic structure and history of Africans and African Americans
Sarah A Tishkoff
Department of Biology, University of Maryland, College Park, MD 20742, USA
Science 324:1035-44. 2009
..This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies...
- A genealogical interpretation of principal components analysis
Department of Statistics, University of Oxford, Oxford, United Kingdom
PLoS Genet 5:e1000686. 2009
..Using examples from human genetics, I discuss the application of these results to empirical data and the implications for inference...
- Genesis: cluster analysis of microarray data
Institute of Biomedical Engineering, Graz University of Technology, Krenngasse 37, 8010 Graz, Austria
Bioinformatics 18:207-8. 2002
..well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines...
- Interpreting principal component analyses of spatial population genetic variation
Department of Human Genetics, University of Chicago, 920 E 58th Street, CLSC 5th floor, Chicago, Illinois 60637, USA
Nat Genet 40:646-9. 2008
Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions...
- What is principal component analysis?
Markus Ringnér is in the Division of Oncology, Department of Clinical Sciences, Barngatan 2, Lund University, 221 85, Lund, Sweden
Nat Biotechnol 26:303-4. 2008
- Defining the healthy "core microbiome" of oral microbial communities
Department of Cariology, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and Free University Amsterdam, The Netherlands
BMC Microbiol 9:259. 2009
..The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing)...
- Relationships between circulating metabolic intermediates and insulin action in overweight to obese, inactive men and women
Kim M Huffman
Physical Medicine and Rehabilitation, Veterans Affairs Medical Center, Durham, North Carolina, USA
Diabetes Care 32:1678-83. 2009
..To determine whether circulating metabolic intermediates are related to insulin resistance and beta-cell dysfunction in individuals at risk for type 2 diabetes...
- Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA
Nat Methods 7:813-9. 2010
..These results also provide a basis for understanding tradeoffs between number of samples and depth of coverage, tradeoffs that are important to consider when designing studies to characterize microbial communities...
- Genetic structure of Europeans: a view from the North-East
Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
PLoS ONE 4:e5472. 2009
..Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS)...
- A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
Daniela M Witten
Department of Statistics, Stanford University, Stanford, CA 94305, USA
Biostatistics 10:515-34. 2009
..We also establish connections between the SCoTLASS method for sparse principal component analysis and the method of Zou and others (2006)...
- Estimating the number of independent components for functional magnetic resonance imaging data
Yi Ou Li
Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
Hum Brain Mapp 28:1251-66. 2007
- Fisher discriminative analysis of resting-state brain function for attention-deficit/hyperactivity disorder
Chao Zhe Zhu
State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, PR China
Neuroimage 40:110-20. 2008
..We conclude that the classifier, using resting-state brain function as classification feature, has potential ability to improve current diagnosis and treatment evaluation of ADHD...
- A principal components regression approach to multilocus genetic association studies
Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, IA 52242, USA
Genet Epidemiol 32:108-18. 2008
..An application to CHI3L2 gene expression data confirms a significant association between CHI3L2 gene expression level and SNPs from this gene that has been previously reported by others...
- A quantitative comparison of the similarity between genes and geography in worldwide human populations
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
PLoS Genet 8:e1002886. 2012
..Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure...
- Adjustment of systematic microarray data biases
Department of Statistics and Econometrics, University of Carlos III, Madrid, Spain
Bioinformatics 20:105-14. 2004
..These systematic effects present a substantial hurdle to the analysis of microarray data...
- Interrogating local population structure for fine mapping in genome-wide association studies
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
Bioinformatics 26:2961-8. 2010
..Current association methods for correcting population stratification usually involve adjustment of global ancestry between study subjects...
- Tensorial extensions of independent component analysis for multisubject FMRI analysis
C F Beckmann
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
Neuroimage 25:294-311. 2005
- Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets
Dipti W Pitta
Texas AgriLife Research, Vernon, TX, USA
Microb Ecol 59:511-22. 2010
..Overall, bermudagrass hay diets clustered more clearly than wheat diets.These data are the first to explore bacterial diversity dynamics in a common population of animals in response to contrasting grass forage diets...
- Testing association between disease and multiple SNPs in a candidate gene
W James Gauderman
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
Genet Epidemiol 31:383-95. 2007
..We observe stronger evidence of an association using the PC approach (p = 0.044) than using either a genotype-based (p = 0.13) or haplotype-based (p = 0.052) approach...
- Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
Proc Natl Acad Sci U S A 107:8954-61. 2010
..Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, ..
- Gene expression profiling--Clusters of possibilities
MultiD Analyses AB, Gothenburg, Sweden
Methods 50:323-35. 2010
..Techniques include hierarchical clustering, heatmap, principal component analysis and self-organizing maps...
- A high-performance computing toolset for relatedness and principal component analysis of SNP data
Department of Biostatistics, University of Washington, Seattle, WA 98195 7232, USA
Bioinformatics 28:3326-8. 2012
..symmetric multiprocessing computer architectures) to accelerate two key computations on SNP data: principal component analysis (PCA) and relatedness analysis using identity-by-descent measures...
- MPCA: Multilinear Principal Component Analysis of Tensor Objects
Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada
IEEE Trans Neural Netw 19:18-39. 2008
This paper introduces a multilinear principal component analysis (MPCA) framework for tensor object feature extraction...
- Comparison of mixed-model approaches for association mapping
Institute for Plant Breeding, Seed Science, and Poulation Genetics, University of Hohenheim, Stuttgart, Germany
Genetics 178:1745-54. 2008
- Independent component analysis of fMRI group studies by self-organizing clustering
Second Division of Neurology, Second University of Naples, Italy
Neuroimage 25:193-205. 2005
..This property is particularly of interest for a blind group and subgroup pattern extraction and selection...
- Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
Delphine Van Inghelandt
Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany
Theor Appl Genet 120:1289-99. 2010
- Software news and updates. Carma: a molecular dynamics analysis program
Nicholas M Glykos
Department of Molecular Biology and Genetics, Democritus University of Thrace, Dimitras 19, 68100 Alexandroupoli, Greece
J Comput Chem 27:1765-8. 2006
..standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors...
- Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development
Abteilung Willmitzer, Max Planck Institut fur Molekulare Pflanzenphysiologie, Potsdam Golm, Germany
Plant Physiol 148:730-50. 2008
..The data are discussed within the context of current models both of the interaction of primary and secondary metabolism and of the metabolic interaction between the different plant organs...
- Revealing cryptic spatial patterns in genetic variability by a new multivariate method
Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, Universite de Lyon, Universite Lyon 1, Villeurbanne Cedex, France
Heredity (Edinb) 101:92-103. 2008
..In this paper we propose a new spatially explicit multivariate method, spatial principal component analysis (sPCA), to investigate the spatial pattern of genetic variability using allelic frequency data of ..
- The influence of natural barriers in shaping the genetic structure of Maharashtra populations
Centre for Cellular and Molecular Biology, Hyderabad, India
PLoS ONE 5:e15283. 2010
..The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level...
- The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
Zentrum für Molekularbiologie der Pflanzen, Pflanzenphysiologie, Universitat Tubingen, Auf der Morgenstelle 1, 72076 Tubingen, Germany
Plant J 50:347-63. 2007
..In summary, the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress...
- Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
De Shuang Huang
Intelligent Computing Lab, Institute of Intelligent Machines, Chinese Academy of Sciences PO Box 1130, Hefei, Anhui 230031, China
Bioinformatics 22:1855-62. 2006
..So, modification of existing statistical methodologies or development of new methodologies is needed for the analysis of microarray data...
- African pastoralism: genetic imprints of origins and migrations
International Livestock Research Institute, Post Office Box 30709, Nairobi, Kenya
Science 296:336-9. 2002
..The B. indicus genetic influence shows a major entry point through the Horn and the East Coast of Africa and two modes of introgression into the continent...
- Population genetic structure of the people of Qatar
Program in Computational Biology and Medicine, Cornell University, Ithaca, NY 14850, USA
Am J Hum Genet 87:17-25. 2010
- pcaMethods--a bioconductor package providing PCA methods for incomplete data
CAS MPG Partner Institute for Comp Biology, Shanghai, China
Bioinformatics 23:1164-7. 2007
pcaMethods is a Bioconductor compliant library for computing principal component analysis (PCA) on incomplete data sets...
- Automatic independent component labeling for artifact removal in fMRI
Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
Neuroimage 39:1227-45. 2008
..We conclude that automatic ICA-based denoising offers a potentially useful approach to improve the quality of fMRI data and consequently increase the accuracy of the statistical analysis of these data...
- Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics
Lee Wei Yang
University of Tokyo, Institute of Molecular and Cellular Bioscience, Tokyo, Japan
Bioinformatics 25:606-14. 2009
- Global transcriptome and deletome profiles of yeast exposed to transition metals
Yong Hwan Jin
Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina, United States of America
PLoS Genet 4:e1000053. 2008
- Neuronal assembly detection and cell membership specification by principal component analysis
Brain Institute, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
PLoS ONE 6:e20996. 2011
..The results indicate that the PCA method presented here is able to properly detect, track and specify neuronal assemblies, irrespective of overlapping membership...
- European population genetic substructure: further definition of ancestry informative markers for distinguishing among diverse European ethnic groups
Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California 95616, USA
Mol Med 15:371-83. 2009
- Principal component analysis of dietary and lifestyle patterns in relation to risk of subtypes of esophageal and gastric cancer
Stephanie A Navarro Silvera
Montclair State University, Department of Health and Nutrition Sciences, Montclair, NJ 07043, USA
Ann Epidemiol 21:543-50. 2011
..To carry out pattern analyses of dietary and lifestyle factors in relation to risk of esophageal and gastric cancers...
- Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana: evidence for modular genetic architecture
Section of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin C0930, Austin, TX 78712, USA
Evol Dev 7:259-71. 2005
..Only two genomic locations affected both flower and leaf growth. These results are discussed in the context of the evolution of modules, pleiotropy, and the putative homologous relationship between leaves and flowers...
- Metabonomic study of Chinese medicine Shuanglong formula as an effective treatment for myocardial infarction in rats
School of Pharmaceutics, East China University of Science and Technology, PR China
J Proteome Res 10:790-9. 2011
..The shifts in urinary TCA cycle as well as pentose phosphate pathway suggested that SLF may diminish cardiac injury of MI with its potential pharmacological effect in the regulation of myocardial energy metabolism...
- Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation
Dipartimento di Genetica e Microbiologia, Universita di Pavia, Pavia, Italy
BMC Evol Biol 9:154. 2009
..Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures...
- Quantitative morphological study of microglial cells in the ischemic rat brain using principal component analysis
Department of Neuroanatomy, Institute of Zoology, Jagiellonian University, 6 Ingardena St, 30 060 Cracow, Poland
J Neurosci Methods 146:50-60. 2005
..Then the resultant data were processed using principal component analysis (PCA)...
- Dihedral angle principal component analysis of molecular dynamics simulations
Institute of Physical and Theoretical Chemistry, J W Goethe University, Max von Laue Strasse 7, D 60438 Frankfurt, Germany
J Chem Phys 126:244111. 2007
..Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations...
- A geometric morphometric analysis of heterochrony in the cranium of chimpanzees and bonobos
Daniel E Lieberman
Peabody Museum, Harvard University, Cambridge, MA 02138, USA
J Hum Evol 52:647-62. 2007
- Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case
Department of Biotechnology and Bioscience, University of Milano Bicocca, 20126 Milan, Italy
J Mol Graph Model 27:889-99. 2009
- Population structure and genome-wide patterns of variation in Ireland and Britain
Colm T O'Dushlaine
Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College, Dublin, Ireland
Eur J Hum Genet 18:1248-54. 2010
..These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants...
- Pathway-based analysis for genome-wide association studies using supervised principal components
Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
Genet Epidemiol 34:716-24. 2010
..We propose a new pathway-based analysis method for GWAS, the supervised principal component analysis (SPCA) model...
- Discovering genetic ancestry using spectral graph theory
Ann B Lee
Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
Genet Epidemiol 34:51-9. 2010
..Ancestry is commonly estimated using the eigenvectors derived from principal component analysis (PCA)...
- Multivariate analysis of heavy metal contamination in urban dusts of Xi'an, Central China
Department of Earth Sciences and Land Resources, Chang an University, Xi an 710054, China
Sci Total Environ 355:176-86. 2006
..These concentration levels are comparable to those in other studies. Correlation coefficient analysis, principal component analysis (PCA) and cluster analysis (CA) were performed and three main sources with corresponding cluster ..
- Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies
Eva Maria Willing
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen D72076, Germany
Mol Ecol 19:968-84. 2010
..Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and ..
- Genetic markers in the playground of multivariate analysis
Universite de Lyon, Lyon, France
Heredity (Edinb) 102:330-41. 2009
Multivariate analyses such as principal component analysis were among the first statistical methods employed to extract information from genetic markers...
- Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development
INRA UMR 619 Biologie du Fruit, Centre de Bordeaux, F 33140 Villenave d Ornon, France
Plant Physiol 149:1505-28. 2009
- Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs
David López Herráez
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
PLoS ONE 4:e7888. 2009
..Moreover, genome-wide data can be used to search for signals of recent positive selection, thereby providing new insights into the genetic adaptations that occurred as modern humans spread out of Africa and around the world...
- Investigating the behavioral and self-report constructs of impulsivity domains using principal component analysis
Shashwath A Meda
Olin Neuropsychiatry Research Center, Institute of Living at Hartford Hospital, Hartford, Connecticut 06106, USA
Behav Pharmacol 20:390-9. 2009
..In addition, our supplemental analysis also suggested that the impulsivity constructs were largely, but not entirely the same within the healthy and ARA groups...
- A sliding time-window ICA reveals spatial variability of the default mode network in time
Department of Diagnostic Radiology, Oulu University Hospital, Finland
Brain Connect 1:339-47. 2011
..In conclusion, SliTICA shows marked spatial variance of DMN activity in time, which may offer a more comprehensive measurement of the overall functional activity of a network...
- An overview of the genetic structure within the Italian population from genome-wide data
Cornelia Di Gaetano
Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy
PLoS ONE 7:e43759. 2012
..We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly ..
- Patterns of covariation in the masticatory apparatus of hystricognathous rodents: implications for evolution and diversification
Museum of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
J Morphol 273:1319-37. 2012
- Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM
Department of Mathematics, Xidian University, Xi an, P R China
J Biomol Struct Dyn 29:634-42. 2012
..Comparison of our results with other methods shows that the proposed method by us is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity data-sets...
- Convergence and remarkably consistent constraint in the evolution of carnivore skull shape
School of Biological, Earth, and Environmental Sciences, The University of New South Wales, Sydney, Australia
Evolution 61:1251-60. 2007
- Shoe midsole hardness, sex and age effects on lower extremity kinematics during running
Benno M Nigg
Human Performance Laboratory HPL, Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
J Biomech 45:1692-7. 2012
..Participants ran at 3.33±0.15 m/s on a 30 m-long runway with soft, medium and hard midsoles. A principal component analysis combined with a support vector machine showed that running kinematics based on shoe midsole hardness, ..
- Responses of calves to acute stress: individual consistency and relations between behavioral and physiological measures
Cornelis G van Reenen
Animal Sciences Group of Wageningen University and Research Centre WUR, P O Box 65, 8200 AB, Lelystad, The Netherlands
Physiol Behav 85:557-70. 2005
..b>Principal component analysis (PCA) was used to condense correlated measures within ages into principal components reflecting ..
- Gene- or region-based association study via kernel principal component analysis
Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan 250012, China
BMC Genet 12:75. 2011
..Kernel principal component analysis combined with logistic regression test (KPCA-LRT) has been successfully used in classifying gene ..
- Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms
Department of Plant and Soil Sciences, Oklahoma State University, OK, USA
Genet Mol Res 10:2976-86. 2011
..The trnL marker confirmed that TN104 was a lowland genotype, but the trnL marker identification of upland and lowland genotypes was not consistent with the AFLP analysis in two germplasms (Miami and AR4)...
- Discrimination of gender-, speed-, and shoe-dependent movement patterns in runners using full-body kinematics
Human Performance Laboratory, Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
Gait Posture 36:40-5. 2012
Changes in gait kinematics have often been analyzed using pattern recognition methods such as principal component analysis (PCA)...
- Application of principal component analysis to pharmacogenomic studies in Canada
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
Pharmacogenomics J 9:362-72. 2009
..We evaluated the application of principal component analysis (PCA) in a pharmacogenomic study in Canada to detect and correct for genetic ancestry differences using ..
- Metabonomics study of brain-specific human S100B transgenic mice by using high-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry
Jia Lin Liu
Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory of Human Disease Animal Model, State Administration of Traditional Chinese Medicine, Beijing, P R China
Biol Pharm Bull 34:871-6. 2011
..Acquired data were subjected to principal component analysis (PCA) to investigate the effects of S100B protein on mice mesencephalon metabolite profiles...
- Feature constrained compressed sensing CT image reconstruction from incomplete data via robust principal component analysis of the database
Department of Engineering Physics, Tsinghua University, Beijing, 100084, People s Republic of China
Phys Med Biol 58:4047-70. 2013
..Robust principal component analysis is employed to retrieve features of the training images to sparsify the target image...
- Shape, variance and integration during craniogenesis: contrasting marsupial and placental mammals
Department of Genetics, Evolution and Environment, University College London, London, UK
J Evol Biol 25:862-72. 2012
..Our results suggest that high integration of the oral region combined with functional constraints for suckling during early postnatal ontogeny may drive the stagnant variance observed in Monodelphis and potentially other marsupials...
- Fully automated reduction of ocular artifacts in high-dimensional neural data
John W Kelly
Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
IEEE Trans Biomed Eng 58:598-606. 2011
..Through this evaluation, the novel adaptation of wavelet thresholding is shown to produce superior reduction of ocular artifacts when compared to regression, principal component analysis, and ICA.
- Principal component analysis, hierarchical clustering, and decision tree assessment of plasma mRNA and hormone levels as an early detection strategy for small intestinal neuroendocrine (carcinoid) tumors
Irvin M Modlin
Department of Gastroenterological Surgery, Yale University School of Medicine, New Haven, CT 06520 8062, USA
Ann Surg Oncol 16:487-98. 2009
..Including NET-related circulating hormones and growth factors in the algorithm increased the sensitivity of detection of SI-NETs from 58 to 82%...
- Metabolic signatures of lung cancer in biofluids: NMR-based metabonomics of urine
CICECO, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810 193 Aveiro, Portugal
J Proteome Res 10:221-30. 2011
..resolution ¹H NMR (500 MHz), and their spectral profiles subjected to multivariate statistics, namely, Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Orthogonal Projections to Latent ..
- Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic
R J King
Department of Psychiatry and Behavioral Sciences, Stanford University, 401 Quarry Road, Stanford, CA 94305 5722, USA
Ann Hum Genet 72:205-14. 2008
- Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions
Matthew C Dulik
Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
PLoS ONE 6:e17548. 2011
..In addition, all of them showed evidence of genetic influence by the 13(th) century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation...
- Identification of distinct characteristics of postural sway in Parkinson's disease: a feature selection procedure based on principal component analysis
Department of Electronics, Computer Science and Systems, University of Bologna, Italy
Neurosci Lett 394:140-5. 2006
..of the centre of pressure (CoP) displacement in quiet standing, by means of a procedure based on principal component analysis, in two groups particularly different in terms of postural behaviours, such as subjects with Parkinson'..
- Dietary patterns and ethnicity are associated with distinct plasma proteomic groups
Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Canada
Am J Clin Nutr 95:352-61. 2012
..However, little is known about how concentrations of many plasma proteins vary between individuals from different ethnocultural groups with different dietary habits...
- Artifact due to differential error when cases and controls are imputed from different platforms
Jennifer A Sinnott
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
Hum Genet 131:111-9. 2012
..Every SNP found with genome-wide significance should be validated on another platform to verify that its significance is not an artifact of study design...
- Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data
Nicholas F Marko
Department of Neurosurgery and Brain Tumor and Neuro Oncology Center, Cleveland Clinic, Cleveland, Ohio, United States of America
PLoS ONE 6:e20826. 2011
..We seek to clarify the nature and relative contributions of these factors, to focus additional investigations, and to improve the accuracy and consistency of translational glioblastoma analyses...
- A cross-modal system linking primary auditory and visual cortices: evidence from intrinsic fMRI connectivity analysis
Mark A Eckert
Department of Otolaryngology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
Hum Brain Mapp 29:848-57. 2008
..Our study provides novel, fcMRI-based, support for a neural system involving low-level auditory and visual cortices...
- Comparative analysis of the volatile fraction of fruit juice from different Citrus species
M Carmen González-Mas
Centro de Citricultura, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
PLoS ONE 6:e22016. 2011
..This volatile profiling platform for Citrus juice by HS-SPME-GC-MS and the interrelationship detected among the volatiles can be used as a roadmap for future breeding or biotechnological applications...
- Structural comparison of F1-ATPase: interplay among enzyme structures, catalysis, and rotations
Kei Ichi Okazaki
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Structure 19:588-98. 2011
..Finally, calculating the helix 6 angle of β, we identified the recently observed partially closed conformation being consistent with β(HC)...
- Two-dimensional PCA: a new approach to appearance-based face representation and recognition
Department of Computing, Hong Kong Polytechnic University, Kowloon, Hong Kong
IEEE Trans Pattern Anal Mach Intell 26:131-7. 2004
In this paper, a new technique coined two-dimensional principal component analysis (2DPCA) is developed for image representation...
- Applications of mass spectrometry to metabolomics and metabonomics: detection of biomarkers of aging and of age-related diseases
Robert J Mishur
Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA
Mass Spectrom Rev 31:70-95. 2012
- Principal component analysis based methods in bioinformatics studies
60 College St, LEPH 209, School of Public Health, Yale University, New Haven, CT 06520, USA
Brief Bioinform 12:714-22. 2011
..b>Principal component analysis (PCA) is a classic dimension reduction approach...
- A principal component analysis of 39 scientific impact measures
Digital Library Research and Prototyping Team, Research Library, Los Alamos National Laboratory, Los Alamos, NM, USA
PLoS ONE 4:e6022. 2009
..Here we investigate how these new measures relate to each other, and how accurately and completely they express scientific impact...
- Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N 5009 Bergen, Norway
Proteins 79:232-43. 2011
b>Principal component analysis (PCA) and normal mode analysis (NMA) have emerged as two invaluable tools for studying conformational changes in proteins...
- Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry
Brian P McEvoy
Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia
Am J Hum Genet 87:297-305. 2010
- Genome-wide insights into the patterns and determinants of fine-scale population structure in humans
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
Am J Hum Genet 84:641-50. 2009
- Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis
Institute of Clinical Molecular Biology, Christian Albrechts University Kiel, Kiel, Germany
Gastroenterology 141:227-36. 2011
..We analyzed the interaction between gastrointestinal mucosal microbiota and host genes in twin pairs discordant for ulcerative colitis (UC) to study the functional interaction between microbiota and mucosal epithelium...
- A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
Am J Phys Anthropol 143:555-69. 2010
- In situ proteomics with imaging mass spectrometry and principal component analysis in the Scrapper-knockout mouse brain
Mitsubishi Kagaku Institute of Life Sciences MITILS, Machida, Tokyo, Japan
Proteomics 8:3692-701. 2008
..By imaging MS analysis based on principal component analysis (PCA), we could find numerous alterations in the KO mouse brain...
- Ancestry informative markers for fine-scale individual assignment to worldwide populations
Department of Molecular Biology and Genetics, Democritus University of Thrace, Panepistimioupoli, Dragana, Ktirio 8, Alexandroupoli 68100, Greece
J Med Genet 47:835-47. 2010
- Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study
Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA
Proteins 79:99-114. 2011
..and targeted molecular dynamics simulations on the active and inactive states of EGFR, followed by principal component analysis on the simulated trajectories, to identify correlated motions in the EGFR kinase domain upon ..
- Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms
International Maize and Wheat Improvement Center CIMMYT, km 45, Carretera, Mexico Veracruz, El Batan, Texcoco, Mexico
Theor Appl Genet 120:93-115. 2009
..These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs...
- Tri-dimensional and triphasic muscle organization of whole-body pointing movements
Italian Institute of Technology, Via Morego 30, 16163 Genoa, Italy
Neuroscience 170:1223-38. 2010
..The present findings link together, in a hierarchical view of motor control, the joint coordination characterizing whole-body pointing movements with a basic muscle synergistic organization, namely a triphasic pattern...