- Inference of population structure using multilocus genotype data
J K Pritchard
Department of Statistics, University of Oxford, United Kingdom
Genetics 155:945-59. 2000
..g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html...
- Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Burnham Institute for Medical Research La Jolla, CA 92037, USA
Bioinformatics 22:1658-9. 2006
..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
- MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Robert C Edgar
Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
BMC Bioinformatics 5:113. 2004
..We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles...
- Open source clustering software
M J L de Hoon
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639 Japan
Bioinformatics 20:1453-4. 2004
..In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C...
- CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
Bioinformatics 23:1801-6. 2007
- Clustal W and Clustal X version 2.0
M A Larkin
The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
Bioinformatics 23:2947-8. 2007
..ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/..
- Bacterial community variation in human body habitats across space and time
Elizabeth K Costello
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
Science 326:1694-7. 2009
..These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease...
- Gene expression profiling predicts clinical outcome of breast cancer
Laura J van 't Veer
Division of Diagnostic Oncology, The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
Nature 415:530-6. 2002
..This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy...
- Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
Bioinformatics 22:1600-7. 2006
..g. based on Gene Ontology (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance...
- Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Susan M Huse
Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
Environ Microbiol 12:1889-98. 2010
..This new clustering method can reduce the OTU richness in environmental samples by as much as 30-60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere...
- Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Environ Microbiol 12:118-23. 2010
..We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere...
- TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
The Institute for Genomic Research, Rockville, MD 20850, USA
Bioinformatics 19:651-2. 2003
..The system can run on multi-CPU architectures including SMP and PVM...
- CONSORT statement: extension to cluster randomised trials
Marion K Campbell
Health Services Research Unit, University of Aberdeen, Aberdeen, AB25 2ZD
BMJ 328:702-8. 2004
- Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Department of Computer Science, University of Colorado, Boulder, CO, USA
ISME J 4:17-27. 2010
..Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac...
- Tandem repeats finder: a program to analyze DNA sequences
Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029 6574, USA
Nucleic Acids Res 27:573-80. 1999
..These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program...
- Functional profiling of the Saccharomyces cerevisiae genome
Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
Nature 418:387-91. 2002
..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
- CD-HIT Suite: a web server for clustering and comparing biological sequences
California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
Bioinformatics 26:680-2. 2010
..Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels...
- De novo characterization of a whitefly transcriptome and analysis of its gene expression during development
Xiao Wei Wang
Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China
BMC Genomics 11:400. 2010
..Yet little is understood about its genes involved in development, insecticide resistance, host range plasticity and virus transmission...
- Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
J Clin Microbiol 44:4498-510. 2006
..This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies...
- Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
BMC Genomics 10:219. 2009
..We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora...
- Neighbor-net: an agglomerative method for the construction of phylogenetic networks
McGill Centre for Bioinformatics, Montreal, Quebec, Canada
Mol Biol Evol 21:255-65. 2004
..and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package...
- Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
Syst Biol 56:564-77. 2007
..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
- Pvclust: an R package for assessing the uncertainty in hierarchical clustering
Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2 12 1 Ookayama, Meguro ku, Tokyo 152 8552, Japan
Bioinformatics 22:1540-2. 2006
Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap ..
- Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans
Coleen T Murphy
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
Nature 424:277-83. 2003
- Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
DNA Res 14:169-81. 2007
..In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes...
- Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds
Cheng Ying Shi
Key Laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei, 230036, PR China
BMC Genomics 12:131. 2011
- Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
Nucleic Acids Res 33:e175. 2005
..It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions...
- Community genomics among stratified microbial assemblages in the ocean's interior
Edward F DeLong
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 311:496-503. 2006
..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
- Effect of community-based newborn-care intervention package implemented through two service-delivery strategies in Sylhet district, Bangladesh: a cluster-randomised controlled trial
Abdullah H Baqui
Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
Lancet 371:1936-44. 2008
..Therefore the project for advancing the health of newborns and mothers (Projahnmo) implemented a community-based intervention package through government and non-government organisation infrastructures to reduce neonatal mortality...
- UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
BMC Bioinformatics 7:371. 2006
..Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses...
- Combinatorial patterns of histone acetylations and methylations in the human genome
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 40:897-903. 2008
..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
- Clustering by passing messages between data points
Brendan J Frey
Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
Science 315:972-6. 2007
..Affinity propagation found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time...
- Detecting overlapping protein complexes in protein-protein interaction networks
Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK
Nat Methods 9:471-2. 2012
..The results also showed a high extent of functional homogeneity...
- The humoral immune system has a key prognostic impact in node-negative breast cancer
Department of Obstetrics and Gynecology, Medical School, Johannes Gutenberg University, Mainz, Germany
Cancer Res 68:5405-13. 2008
..After performing hierarchical cluster analysis, we identified coregulated genes related to the biological process of proliferation, steroid hormone receptor ..
- Small-world networks and functional connectivity in Alzheimer's disease
C J Stam
Department of Clinical Neurophysiology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
Cereb Cortex 17:92-9. 2007
..Graph theoretical analysis may be a useful approach to study the complexity of patterns of interrelations between EEG channels...
- Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet
Efrain M Ribot
Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
Foodborne Pathog Dis 3:59-67. 2006
- Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
Jason I Herschkowitz
Lineberger Comprehensive Cancer Center
Genome Biol 8:R76. 2007
..To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors...
- Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
Christopher A Francis
Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 102:14683-8. 2005
..Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle...
- Design and analysis of stepped wedge cluster randomized trials
Michael A Hussey
Fred Hutchinson Cancer Research Center, Seattle, WA, United States
Contemp Clin Trials 28:182-91. 2007
..In this article we discuss the design and analysis of a particular type of crossover CRT - the stepped wedge - and provide an example of its use...
- An automated method for finding molecular complexes in large protein interaction networks
Gary D Bader
Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
BMC Bioinformatics 4:2. 2003
..As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery...
- Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
Hon Nian Chua
Graduate School for Integrated Sciences and Engineering, National University of Singapore, Singapore
Bioinformatics 22:1623-30. 2006
..We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction...
- Search and clustering orders of magnitude faster than BLAST
Robert C Edgar
Tiburon, CA 94920, USA
Bioinformatics 26:2460-1. 2010
..Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification...
- Neurophysiological architecture of functional magnetic resonance images of human brain
Brain Mapping Unit and Wolfson Brain Imaging Centre, University of Cambridge, Addenbrooke s Hospital, Cambridge CB2 2QQ, UK
Cereb Cortex 15:1332-42. 2005
- Characterization of microRNA expression levels and their biological correlates in human cancer cell lines
Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire 03755, USA
Cancer Res 67:2456-68. 2007
..These findings call attention to the potential of microRNAs to provide etiologic insights as well as to serve as both diagnostic markers and therapeutic targets for many different tumor types...
- 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)...
- Geometric interpretation of gene coexpression network analysis
Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
PLoS Comput Biol 4:e1000117. 2008
..The unification of coexpression network methods with traditional data mining methods can inform the application and development of systems biologic methods...
- Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
Department of Mathematics, Fänriksgatan 3B, Abo Akademi University, Abo, Finland
BMC Bioinformatics 9:539. 2008
..However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions...
- Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
Catherine A Lozupone
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
Appl Environ Microbiol 73:1576-85. 2007
..We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny...
- Genesis: cluster analysis of microarray data
Institute of Biomedical Engineering, Graz University of Technology, Krenngasse 37, 8010 Graz, Austria
Bioinformatics 18:207-8. 2002
..Additionally, mapping of gene expression data onto chromosomal sequences was implemented to enhance promoter analysis and investigation of transcriptional control mechanisms...
- Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
Department of Human Genetics, University of California at Los Angeles, CA 90095 7088, USA
Bioinformatics 24:719-20. 2008
..We illustrate the use of these methods by applying them to protein-protein interaction network data and to a simulated gene expression data set...
- MetaboAnalyst: a web server for metabolomic data analysis and interpretation
Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E8, Canada
Nucleic Acids Res 37:W652-60. 2009
..MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses. MetaboAnalyst is accessible at http://www.metaboanalyst.ca...
- Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures
Swiss Institute of Bioinformatics, Batiment Genopode, University of Lausanne, 1015 Lausanne, Switzerland
Breast Cancer Res 10:R65. 2008
- ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
Interdisciplinary Center for Biotechnology Research University of Florida, Gainesville, FL 32610, USA
Nucleic Acids Res 39:e95. 2011
..The new algorithm exhibits a quasilinear time and space complexity comparable to greedy heuristic clustering algorithms, while achieving a similar accuracy to the standard hierarchical clustering algorithm...
- Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)
Noelle A Barkley
Department of Botany and Plant Sciences and Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA 92521, USA
Theor Appl Genet 112:1519-31. 2006
- The molecular portraits of breast tumors are conserved across microarray platforms
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
BMC Genomics 7:96. 2006
..To overcome this problem we used publicly available breast cancer gene expression data sets and a novel approach to data fusion, in order to validate a new breast tumor intrinsic list...
- Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms
M C Maiden
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
Proc Natl Acad Sci U S A 95:3140-5. 1998
..numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus ..
- Effect of community-based behaviour change management on neonatal mortality in Shivgarh, Uttar Pradesh, India: a cluster-randomised controlled trial
International Center for Advancing Neonatal Health, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
Lancet 372:1151-62. 2008
..We developed an intervention of behaviour change management, with a focus on prevention of hypothermia, aimed at modifying practices and reducing neonatal mortality...
- Patterns of intra-cluster correlation from primary care research to inform study design and analysis
Department of Public Health Sciences, King s College London, Capital House, 42 Weston Street, London SE1 3QD, UK
J Clin Epidemiol 57:785-94. 2004
..To provide information concerning the magnitude of the intraclass correlation coefficient (ICC) for cluster-based studies set in primary care...
- The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access
RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
Plant J 55:526-42. 2008
..Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to ..
- Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis
Patrick D Schloss
Department of Microbiology and Immunology University of Michigan, Ann Arbor, MI 48109, USA
Appl Environ Microbiol 77:3219-26. 2011
..The ability to quickly and accurately assign sequences to OTUs and then obtain taxonomic information for those OTUs will greatly improve OTU-based analyses and overcome many of the challenges encountered with phylotype-based methods...
- Contemporary cryptic sexuality in Trypanosoma cruzi
Juan David Ramírez
Centro de Investigaciones en Microbiologia y Parasitologia Tropical, Universidad de Los Andes, Bogota, Colombia
Mol Ecol 21:4216-26. 2012
- A global test for groups of genes: testing association with a clinical outcome
Jelle J Goeman
Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
Bioinformatics 20:93-9. 2004
..Groups of genes may be any size from a single gene to all genes on the chip (e.g. known pathways, specific areas of the genome or clusters from a cluster analysis).
- Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
Laurent G Deluc
Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557 0014, USA
BMC Genomics 8:429. 2007
- A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610 3622, USA
Brief Bioinform 13:107-21. 2012
- Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008
Sheng Wen Huang
Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, One University Road, Tainan, 701, Taiwan
J Clin Microbiol 47:3653-62. 2009
..Therefore, continuous surveillance of EV71 including the monitoring of genetic evolution and antigenic changes is recommended and may contribute to the development of a vaccine for EV71...
- Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes
Benjamin P Tu
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, L3 124, Dallas, TX 75390, USA
Science 310:1152-8. 2005
..Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time...
- Genetic structure of human populations
Noah A Rosenberg
Molecular and Computational Biology, 1042 West 36th Place DRB 289, University of Southern California, Los Angeles, CA 90089, USA
Science 298:2381-5. 2002
..General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies...
- Complex discovery from weighted PPI networks
School of Computing, National University of Singapore, Singapore and Institute for Infocomm Research, Singapore
Bioinformatics 25:1891-7. 2009
..However, protein interaction data produced by high-throughput experiments are often associated with high false positive and false negative rates, which makes it difficult to predict complexes accurately...
- Inference of bacterial microevolution using multilocus sequence data
Department of Statistics, University of Oxford, Oxford OX1 3SY, United Kingdom
Genetics 175:1251-66. 2007
..The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/...
- ClustalW-MPI: ClustalW analysis using distributed and parallel computing
Kuo Bin Li
Bioinformatics Institute, 30 Medical Drive, Singapore 117609, Republic of Singapore
Bioinformatics 19:1585-6. 2003
..The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers...
- Brain anatomical network and intelligence
LIAMA Center for Computational Medicine, National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
PLoS Comput Biol 5:e1000395. 2009
..Our findings suggest that the efficiency of brain structural organization may be an important biological basis for intelligence...
- A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genetics 176:1635-51. 2007
- Network visualization and analysis of gene expression data using BioLayout Express(3D)
The Roslin Institute, R D SVS, University of Edinburgh, Roslin Biocentre, Midlothian, Scotland, UK
Nat Protoc 4:1535-50. 2009
- Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast
Matthew J Brauer
Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Mol Biol Cell 19:352-67. 2008
..This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle...
- Gene expression analyses reveal molecular relationships among 20 regions of the human CNS
Richard B Roth
Department of Molecular Medicine, Neurocrine Biosciences, Incorporated, 12790 El Camino Real, San Diego, CA 92130, USA
Neurogenetics 7:67-80. 2006
..In summary, we have generated a database of gene expression that can be used to gain valuable insight into the molecular characterization of functions carried out by different sites of the human CNS...
- The evolutionary genetics and emergence of avian influenza viruses in wild birds
Vivien G Dugan
Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
PLoS Pathog 4:e1000076. 2008
- Subtypes of breast cancer show preferential site of relapse
Department of Medical Oncology, Erasmus MC, Josephine Nefkens Institute, Rotterdam, The Netherlands
Cancer Res 68:3108-14. 2008
..The five major molecular subtypes in breast cancer are evidently different with regard to their ability to metastasize to distant organ(s), and share biological features and pathways with their preferred distant metastatic site...
- 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
- Empirically derived eating patterns using factor or cluster analysis: a review
P K Newby
Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
Nutr Rev 62:177-203. 2004
..Although the research considered herein has created a meaningful body of literature, refining both the factor and cluster analysis methods will help to further establish eating patterns as a sound dietary assessment method.
- A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells
Ju Seog Lee
Lab of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 4146, Bethesda, Maryland 20892, USA
Nat Med 12:410-6. 2006
..Analyses of gene networks showed that activation of AP-1 transcription factors in this newly identified HCC subtype might have key roles in tumor development...
- 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...
- Micro-RNA profiling in kidney and bladder cancers
Department of Urology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
Urol Oncol 25:387-92. 2007
..To study the role of the micro-RNAs in human kidney and bladder cancer, we analyzed the expression profile of 245 micro-RNAs in kidney and bladder primary tumors...
- MicroRNA expression profiles for the NCI-60 cancer cell panel
Paul E Blower
Program of Pharmacogenomics, Department of Pharmacology and the Comprehensive Cancer Center, College of Medicine, The Ohio State University, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, USA
Mol Cancer Ther 6:1483-91. 2007
..Combined with gene expression and other biological data using multivariate analysis, microRNA expression profiles may provide a critical link for understanding mechanisms involved in chemosensitivity and chemoresistance...
- Effectiveness of the diabetes education and self management for ongoing and newly diagnosed (DESMOND) programme for people with newly diagnosed type 2 diabetes: cluster randomised controlled trial
M J Davies
Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 5WW
BMJ 336:491-5. 2008
..To evaluate the effectiveness of a structured group education programme on biomedical, psychosocial, and lifestyle measures in people with newly diagnosed type 2 diabetes...
- Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers
Jen Tsan Chi
Department of Biochemistry, Stanford University School of Medicine, Palo Alto, California, United States of America
PLoS Med 3:e47. 2006
- Finding statistically significant communities in networks
Complex Networks and Systems Lagrange Laboratory, Institute for Scientific Interchange, Torino, Italy
PLoS ONE 6:e18961. 2011
..Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks...
- A note on robust variance estimation for cluster-correlated data
R L Williams
Research Triangle Institute, Research Triangle Park, North Carolina 27709 2194, USA
Biometrics 56:645-6. 2000
..The result is not new, but a simple and general reference is not readily available. The use of the method will benefit from a general explanation of its wide applicability...
- Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua
Nathan L Yozwiak
Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
J Virol 84:9047-58. 2010
..Further experimentation is required to more fully characterize the pathogenic role, disease associations, and global distribution of EV109...
- Arabidopsis gene co-expression network and its functional modules
Virtual Reality Applications Center, Iowa State University, Ames, IA 50010, USA
BMC Bioinformatics 10:346. 2009
..The organization of gene functional modules was also investigated...
- A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses
Ryan T Jones
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
ISME J 3:442-53. 2009
- An information-intensive approach to the molecular pharmacology of cancer
J N Weinstein
Laboratory of Molecular Pharmacology LMP, Division of Basic Science, National Cancer Institute NCI, National Institutes of Health, Bethesda, MD 20892, USA
Science 275:343-9. 1997
..It remains to be seen how effective this information-intensive strategy will be at generating new clinically active agents...
- A microarray-based DNA methylation study of glioblastoma multiforme
Department of Neurosurgery, University of Goettingen, Goettingen WT 084071, Germany
Epigenetics 4:255-64. 2009
..Furthermore, we identified that promoter hypermethylation of the transcription factor gene GATA6 (occurring in 30% of GBM) was significantly associated with unfavorable patient survival...
- Two hybridization events define the population structure of Trypanosoma cruzi
Scott J Westenberger
Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
Genetics 171:527-43. 2005
..The second hybridization between DTU IIb and IIc strains that generated DTUs IId and IIe resulted in extensive heterozygosity with subsequent recombination of parental genotypes...
- Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response
The Broad Institute, Cambridge, MA, USA
Blood 105:1851-61. 2005
..These studies identify tumor microenvironment and host inflammatory response as defining features in DLBCL and suggest rational treatment targets in specific DLBCL subsets...
- A unique H3K4me2 profile marks tissue-specific gene regulation
Centre d immunologie de Marseille Luminy, Universite Aix Marseille, Marseille 13009, France
Genome Res 20:1493-502. 2010
..We propose that this epigenetic feature reflects the activity of an as yet unrecognized, intragenic cis-regulatory platform dedicated to refining tissue-specificity in gene expression...
- Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung
Molecular Diagnostics, Veridex LLC a Johnson and Johnson Company, 3210 Merryfriend Row, San Diego, CA 92121, USA
Cancer Res 66:7466-72. 2006
..0002; HR, 3.54; 95% CI, 1.74-7.19). This prognostic signature could be used to identify patients with early-stage high-risk NSCLC who might benefit from adjuvant therapy following surgery...
- Coexpression analysis of human genes across many microarray data sets
Homin K Lee
Columbia Genome Center, Columbia University, New York, New York 10032, USA
Genome Res 14:1085-94. 2004
..confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes...
- TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
Naryttza N Diaz
Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
BMC Bioinformatics 10:56. 2009
..We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning...
- Reverse engineering of regulatory networks in human B cells
Institute for Cancer Genetics, 1300 St Nicholas Avenue, Room 912, New York, New York 10032, USA
Nat Genet 37:382-90. 2005
..The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells...
- Network-based prediction of protein function
School of Computer Science, Tel Aviv University, Tel Aviv, Israel
Mol Syst Biol 3:88. 2007
..Although a broad variety of interesting approaches has been developed, further progress in the field will depend on systematic evaluation of the methods and their dissemination in the biological community...
- Human epicardial adipose tissue is a source of inflammatory mediators
Department of Surgery, Thomas Jefferson University, Suite 623, 1025 Walnut St, Philadelphia, PA 19107, USA
Circulation 108:2460-6. 2003
..In this study, we sought to compare expression of inflammatory mediators in epicardial and subcutaneous adipose stores in patients with critical CAD...