Genomes and Genes
Experts and Doctors on genetic databases in United States
Locale: United States
Topic: genetic databases
Publications121 found, 100 shown here
- Sucheston L, Chanda P, Zhang A, Tritchler D, Ramanathan M. Comparison of information-theoretic to statistical methods for gene-gene interactions in the presence of genetic heterogeneity. BMC Genomics. 2010;11:487 pubmed publisher..KWII performed similar to logistic regression. Information theoretic models are flexible and have excellent power to detect GGI under a variety of conditions that characterize complex diseases. ..
- Smith A, Vollrath A, Bradfield C, Craven M. Clustered alignments of gene-expression time series data. Bioinformatics. 2009;25:i119-27 pubmed publisher..Additionally, we apply our clustered alignment approach to characterize the effects of a conditional Mop3 knockout in mouse liver. Source code is available at http://www.biostat.wisc.edu/ approximately aasmith/catcode. ..
- Knudsen B, Miyamoto M. Incorporating experimental design and error into coalescent/mutation models of population history. Genetics. 2007;176:2335-42 pubmed..It is currently implemented as a maximum-likelihood method, but this model may also serve as the basis for the development of Bayesian approaches that incorporate experimental design and error. ..
- Yilmaz A, Nishiyama M, Fuentes B, Souza G, Janies D, Gray J, et al. GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol. 2009;149:171-80 pubmed publisher..The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org. ..
- Han M, Zmasek C. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics. 2009;10:356 pubmed publisher..More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org. ..
- Zhu Y, Li H, Miller D, Wang Z, Xuan J, Clarke R, et al. caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data. BMC Bioinformatics. 2008;9:383 pubmed publisher..VISDA also captured the pathological relationships among different phenotypes revealed at the molecular level, through phenotype clustering on muscular dystrophy data and multi-category cancer data. ..
- Pace J, Gilbert C, Clark M, FESCHOTTE C. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci U S A. 2008;105:17023-8 pubmed publisher..In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species. ..
- Li J, Spletter M, Johnson J. Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays. Physiol Genomics. 2005;21:43-58 pubmed..Integration of the gene expression profiles from different array platforms may not only help for cross-validation but also provide a more complete view of the transcriptional scenario. ..
- Yoneyama N, Crabbe J, Ford M, Murillo A, Finn D. Voluntary ethanol consumption in 22 inbred mouse strains. Alcohol. 2008;42:149-60 pubmed publisher..37-0.45). These results add new strains to the strain mean database that will facilitate the identification of genetic relationships between voluntary ethanol consumption, saccharin preference, and other phenotypes. ..
- Miclaus K, Chierici M, Lambert C, Zhang L, Vega S, Hong H, et al. Variability in GWAS analysis: the impact of genotype calling algorithm inconsistencies. Pharmacogenomics J. 2010;10:324-35 pubmed publisher..Further work using HapMap samples shows that inconsistencies between Affymetrix arrays and calling algorithms can lead to genotyping errors that influence downstream analysis. ..
- Blair J, Shah P, Hedges S. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics. 2005;6:53 pubmed..They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes. ..
- Matuszek G, Talebizadeh Z. Autism Genetic Database (AGD): a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites. BMC Med Genet. 2009;10:102 pubmed publisher..AGD provides a genome browser and a web based query client for conveniently selecting features of interest. Access to AGD is freely available at http://wren.bcf.ku.edu/. ..
- Higgs B, Elashoff M, Richman S, Barci B. An online database for brain disease research. BMC Genomics. 2006;7:70 pubmed
- Nakamoto K, Kidd J, Jenison R, Klaassen C, Wan Y, Kidd K, et al. Genotyping and haplotyping of CYP2C19 functional alleles on thin-film biosensor chips. Pharmacogenet Genomics. 2007;17:103-14 pubmed..This assay can be applied in pharmacogenomic studies in both basic research and clinical laboratories. It is also an ideal technology for pharmacogenomic tests in both developed and developing countries. ..
- Xu H, Freitas M. A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data. BMC Bioinformatics. 2007;8:133 pubmed..High mass accuracy will not only reduce false positives, but also improves the scores of true positive matches. The algorithm is incorporated in an automated database search program MassMatrix. ..
- Settles A, Holding D, Tan B, Latshaw S, Liu J, Suzuki M, et al. Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics. 2007;8:116 pubmed..We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics. ..
- Huang L, Zhu W, Saunders C, MacLeod J, Zhou M, Stromberg A, et al. A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data. BMC Bioinformatics. 2008;9:300 pubmed publisher..Then we performed linear quantile regression to identify genes with a cartilage-restricted pattern of expression. ..
- McCormick S, Alexander N, Harris L. CLM1 of Fusarium graminearum encodes a longiborneol synthase required for culmorin production. Appl Environ Microbiol. 2010;76:136-41 pubmed publisher..Longiborneol accumulated transiently in culmorin-producing strains. The results indicate that CLM1 encodes a longiborneol synthase and is required for culmorin biosynthesis in F. graminearum. ..
- Friedman R, Hughes A. Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse. Mol Biol Evol. 2004;21:1008-13 pubmed
- Wu X, Kan D, Cooper R, Zhu X. Identifying genetic variation affecting a complex trait in simulated data: a comparison of meta-analysis with pooled data analysis. BMC Genet. 2005;6 Suppl 1:S97 pubmed..Thus, meta-analysis can provide an overall evaluation of linkage and association when the original raw data is not available for combining. ..
- Blalock E, Grondin R, Chen K, Thibault O, Thibault V, Pandya J, et al. Aging-related gene expression in hippocampus proper compared with dentate gyrus is selectively associated with metabolic syndrome variables in rhesus monkeys. J Neurosci. 2010;30:6058-71 pubmed publisher..In turn, these MSI-associated neuroenergetic changes may promote inflammation, neuronal vulnerability, and risk of cognitive impairment/AD. ..
- Rouchka E, Khalyfa A, Cooper N. MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. BMC Bioinformatics. 2005;6:175 pubmed..In addition, sequence similarity for a set of oligonucleotides constructed for the same set of genes indicates high specificity in oligo design. ..
- Smith A, Vollrath A, Bradfield C, Craven M. Similarity queries for temporal toxicogenomic expression profiles. PLoS Comput Biol. 2008;4:e1000116 pubmed publisher..More significantly, they show that our time warping method provides more accurate alignments and classifications than previous standard alignment methods for time series. ..
- Wu Y, Bhat P, Close T, Lonardi S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 2008;4:e1000212 pubmed publisher..The software implementing our algorithm is available in the public domain as a web tool under the name MSTmap. ..
- Greenblatt M, Brody L, Foulkes W, Genuardi M, Hofstra R, Olivier M, et al. Locus-specific databases and recommendations to strengthen their contribution to the classification of variants in cancer susceptibility genes. Hum Mutat. 2008;29:1273-81 pubmed publisher..4) Variants should only be classified as pathogenic if more than one type of evidence has been considered. 5) All instances of all variants should be recorded. ..
- Hall B, Ma C, Liang P, Singh K. Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis. Bioinformatics. 2009;25:1564-5 pubmed publisher..The FALCOR rate calculator is currently accessible at http://www.mitochondria.org/protocols/FALCOR.html. This program is written as a Java Applet, requiring a web browser enabled with Sun MicroSystems' Java Virtual Machine. ..
- Fu L, Fu Liu C. Evaluation of gene importance in microarray data based upon probability of selection. BMC Bioinformatics. 2005;6:67 pubmed
- Kachouri R, Stribinskis V, Zhu Y, Ramos K, Westhof E, Li Y. A surprisingly large RNase P RNA in Candida glabrata. RNA. 2005;11:1064-72 pubmed..RNase P RNA, therefore, represents one of the most diversified noncoding RNAs in terms of size variation and structural diversity. ..
- Shaw J, Colbourne J, Davey J, Glaholt S, Hampton T, Chen C, et al. Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins. BMC Genomics. 2007;8:477 pubmed..Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences. ..
- Tang Z, Choi J, Hemmerich C, Sarangi A, Colbourne J, Dong Q. ESTPiper--a web-based analysis pipeline for expressed sequence tags. BMC Genomics. 2009;10:174 pubmed publisher..A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local installations. ..
- Lichtenberg J, Jacox E, Welch J, Kurz K, Liang X, Yang M, et al. Word-based characterization of promoters involved in human DNA repair pathways. BMC Genomics. 2009;10 Suppl 1:S18 pubmed publisher..In addition to providing an effective characterization method for related DNA sequences, the signatures elucidate putative regulatory aspects of DNA repair pathways, which are notably under-characterized. ..
- Bhasi A, Senalik D, Simon P, Kumar B, Manikandan V, Philip P, et al. RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. BMC Plant Biol. 2010;10:161 pubmed publisher..RoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables. ..
- Wang C, Lefkowitz E. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters. BMC Bioinformatics. 2004;5:171 pubmed..Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. ..
- McKillen D, Chen Y, Chen C, Jenny M, Trent H, Robalino J, et al. Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics. 2005;6:34 pubmed..This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment. ..
- Burgler C, Macdonald P. Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. BMC Genomics. 2005;6:88 pubmed
- Korb M, Rust A, Thorsson V, Battail C, Li B, Hwang D, et al. The Innate Immune Database (IIDB). BMC Immunol. 2008;9:7 pubmed publisher..The database website can be freely accessed at http://db.systemsbiology.net/IIDB. ..
- Sun S, Yan P, Huang T, Lin S. Identifying differentially methylated genes using mixed effect and generalized least square models. BMC Bioinformatics. 2009;10:404 pubmed publisher..We also assess the false discovery rate of different models using CGIs associated with housekeeping genes. ..
- Jani S, Argraves G, Barth J, Argraves W. GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. BMC Bioinformatics. 2010;11:166 pubmed publisher..GeneMesh is freely available online at http://proteogenomics.musc.edu/genemesh/. ..
- Lee Y, Lee C. Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics. 2003;19:1132-9 pubmed..2001). Comparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods. http://www.stat.ohio-state.edu/~yklee/msvm.htm ..
- Namciu S, Friedman R, Marsden M, Sarausad L, Jasoni C, Fournier R. Sequence organization and matrix attachment regions of the human serine protease inhibitor gene cluster at 14q32.1. Mamm Genome. 2004;15:162-78 pubmed..Several differences between the MAR-Wiz predictions and the results of biochemical tests were observed. The genomic organization of the serpin gene cluster is discussed. ..
- Reneker J, Shyu C. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. BMC Bioinformatics. 2005;6:111 pubmed..Our experiments show that subsequently searching the annotation data can refine and focus the results for the user. Our algorithms are also space-efficient in terms of main memory requirements. Source code is available upon request. ..
- Casola C, Hucks D, FESCHOTTE C. Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol. 2008;25:29-41 pubmed..quot; These findings highlight the propensity of transposases to give rise to new host proteins and the potential of transposons as sources of genetic innovation. ..
- Hu M, Choi K, Su W, Kim S, Yang J. A gene pattern mining algorithm using interchangeable gene sets for prokaryotes. BMC Bioinformatics. 2008;9:124 pubmed publisher..The discovered gene patterns can be used for the detecting of ortholog and genes that collaborate for a common biological function. ..
- Zhu Q, Miecznikowski J, Halfon M. Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. BMC Bioinformatics. 2010;11:285 pubmed publisher..We present updated best-route methods for Affymetrix GeneChip analysis and demonstrate that the degree of "imbalance" in gene expression has a significant effect on the performance of these methods. ..
- Ge X, Wu Q, Wang S. SAGE detects microRNA precursors. BMC Genomics. 2006;7:285 pubmed..The observation that some orphan longSAGE tags uniquely match miRNA precursors provides information about the expression of some known and predicted miRNAs. ..
- Liang C, Wang G, Liu L, Ji G, Fang L, Liu Y, et al. ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics. 2007;8:134 pubmed..While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation due to their inherent deficiencies, particularly for species without genome sequences...
- Hyatt D, Chen G, Locascio P, Land M, Larimer F, Hauser L. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119 pubmed publisher..Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals...
- Zhang H, Ramanathan Y, Soteropoulos P, Recce M, Tolias P. EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites. Nucleic Acids Res. 2002;30:e121 pubmed..A major application of EZ-Retrieve is the analysis of co-expressed genes that are highlighted as expression clusters in DNA microarray experiments. ..
- Sawyer S, Emerman M, Malik H. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2004;2:E275 pubmed..Despite being only recently discovered, editing of RNA and DNA may thus represent an ancient form of host defense in primate genomes. ..
- Liu J, Wang J, Hu J, Tian B. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics. 2005;6:89 pubmed..This tool shall be useful to researchers interested in comparing RNA structures obtained from wet lab experiments or RNA folding programs, particularly when the size of the structure dataset is large. ..
- Lorenzen M, Doyungan Z, Savard J, Snow K, Crumly L, Shippy T, et al. Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags. Genetics. 2005;170:741-7 pubmed..The map and corresponding sequences can be accessed through BeetleBase (http://www.bioinformatics.ksu.edu/BeetleBase/). ..
- Li H, Jiang T. A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs. J Comput Biol. 2005;12:702-18 pubmed
- Klees R, Salasznyk R, Vandenberg S, Bennett K, Plopper G. Laminin-5 activates extracellular matrix production and osteogenic gene focusing in human mesenchymal stem cells. Matrix Biol. 2007;26:106-14 pubmed
- Stitham J, Arehart E, Gleim S, Douville K, MacKenzie T, Hwa J. Arginine (CGC) codon targeting in the human prostacyclin receptor gene (PTGIR) and G-protein coupled receptors (GPCR). Gene. 2007;396:180-7 pubmed..In the case of the human prostacyclin receptor, such alterations may reduce the cardio-, vasculo-, and cytoprotective effects of prostacyclin. ..
- Ostrov D, Hernandez Prada J, Corsino P, Finton K, Le N, Rowe T. Discovery of novel DNA gyrase inhibitors by high-throughput virtual screening. Antimicrob Agents Chemother. 2007;51:3688-98 pubmed..coli DNA gyrase. These compounds are structurally unrelated to previously identified gyrase inhibitors and represent potential scaffolds for the optimization of novel antibacterial agents that act on fluoroquinolone-resistant strains. ..
- Kaplarevic M, Murray A, Cary S, Gao G. EnGenIUS -- Environmental Genome Informational Utility System. J Bioinform Comput Biol. 2008;6:1193-211 pubmed..A fully browsable EnGenIUS portal is available at (http://ocean.dbi.udel.edu/) (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset. ..
- Tu Z, Argmann C, Wong K, Mitnaul L, Edwards S, Sach I, et al. Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network. Genome Res. 2009;19:1057-67 pubmed publisher..We experimentally validated one of the predictions, S1pr2, as a novel candidate gene for T2D. ..
- Wang X, Cooper N. Characterization of the transcripts and protein isoforms for cytoplasmic polyadenylation element binding protein-3 (CPEB3) in the mouse retina. BMC Mol Biol. 2009;10:109 pubmed publisher..The level of CPEB3 was up-regulated in the retina during development. The presence of multiple CPEB3 isoforms indicates remarkable complexity in the regulation and function of CPEB3. ..
- Feng W, Leach S, Tipney H, Phang T, Geraci M, Spritz R, et al. Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences. PLoS ONE. 2009;4:e8066 pubmed publisher..Overall, our studies provide a valuable resource for probing orofacial development and a robust dataset for bioinformatic analysis of spatial and temporal gene expression changes during embryogenesis. ..
- Hemmerich C, Buechlein A, Podicheti R, Revanna K, Dong Q. An Ergatis-based prokaryotic genome annotation web server. Bioinformatics. 2010;26:1122-4 pubmed publisher..ISGA is designed to be installed at genomics core facilities and be used directly by biologists...
- Wu L, Hughes T, Davierwala A, Robinson M, Stoughton R, Altschuler S. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002;31:255-65 pubmed..We present experimental validation confirming the involvement of several of these proteins in ribosomal RNA processing. Our methodology can be applied to a variety of genomics data types and organisms. ..
- Kaeberlein M, Kirkland K, Fields S, Kennedy B. Sir2-independent life span extension by calorie restriction in yeast. PLoS Biol. 2004;2:E296 pubmed..These findings indicate that Sir2 and calorie restriction act in parallel pathways to promote longevity in yeast and, perhaps, higher eukaryotes. ..
- Hong J, Wu L. Structural characterization of the gene encoding the large zinc finger protein ZAS3: implication to the origin of multiple promoters in eukaryotic genes. Biochim Biophys Acta. 2005;1681:74-87 pubmed
- Agah R, Ellis S, Chase S, Henderson M, Mlady L, Murugesan G, et al. Creation of a large-scale genetic data bank for cardiovascular association studies. Am Heart J. 2005;150:500-6 pubmed..Lastly, as a "proof of concept" for the utility of this resource to discern gene variants associated with disease, we validated apoE4 polymorphism as an independent risk factor for CAD. ..
- Materna S, Berney K, Cameron R. The S. purpuratus genome: a comparative perspective. Dev Biol. 2006;300:485-95 pubmed..However, several striking expansions shed light on how the sea urchin lives and develops. ..
- Gowda M, Venu R, Jia Y, Stahlberg E, Pampanwar V, Soderlund C, et al. Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions. Methods Mol Biol. 2007;354:131-44 pubmed..Bioinformatic tools and databases for analyzing the RL-SAGE data were developed. Our results demonstrate that RL-SAGE is an effective approach for large-scale identification of expressed genes in fungal and plant genomes. ..
- Lee I, Lehner B, Crombie C, Wong W, Fraser A, Marcotte E. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet. 2008;40:181-8 pubmed publisher..We conclude that an analogous network for human genes might be similarly predictive and thus facilitate identification of disease genes and rational therapeutic targets. ..
- Hu Y, Li L, Seidelmann S, Timur A, Shen P, Driscoll D, et al. Identification of association of common AGGF1 variants with susceptibility for Klippel-Trenaunay syndrome using the structure association program. Ann Hum Genet. 2008;72:636-43 pubmed publisher..These results suggest that common AGGF1 variants confer risk of KTS. ..
- Meinke D, Muralla R, Sweeney C, Dickerman A. Identifying essential genes in Arabidopsis thaliana. Trends Plant Sci. 2008;13:483-91 pubmed publisher..The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms. ..
- Catchen J, Conery J, Postlethwait J. Automated identification of conserved synteny after whole-genome duplication. Genome Res. 2009;19:1497-505 pubmed publisher..To demonstrate the utility of the system, we present a case study of gene family evolution, investigating the ARNTL gene family in the genomes of Ciona intestinalis, amphioxus, zebrafish, and human. ..
- Briegel A, Ortega D, Tocheva E, Wuichet K, Li Z, Chen S, et al. Universal architecture of bacterial chemoreceptor arrays. Proc Natl Acad Sci U S A. 2009;106:17181-6 pubmed publisher..Our results suggest that the basic mechanism and function of receptor clustering is universal among bacterial species and was thus conserved during evolution. ..
- Ponomarev I, Schafer G, Blednov Y, Williams R, Iyer V, Harris R. Convergent analysis of cDNA and short oligomer microarrays, mouse null mutants and bioinformatics resources to study complex traits. Genes Brain Behav. 2004;3:360-8 pubmed..Our results point to the increasing potential of the convergent approach and biological databases to investigate genetic mechanisms of complex traits. ..
- Burnside J, Neiman P, Tang J, Basom R, Talbot R, Aronszajn M, et al. Development of a cDNA array for chicken gene expression analysis. BMC Genomics. 2005;6:13 pubmed..Targeted users include researchers in comparative and developmental biology, immunology, vaccine and agricultural technology. These arrays will be an important resource for the entire research community using the chicken as a model. ..
- Zhao Y, Marotta M, Eichler E, Eng C, Tanaka H. Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes. PLoS Genet. 2009;5:e1000472 pubmed publisher..These results show a complex genomic organization and unexpected biological functions of CNVs within segmental duplications and emphasize the importance of detailed structural characterization for disease association studies. ..
- Li B, Ruotti V, Stewart R, Thomson J, Dewey C. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2010;26:493-500 pubmed publisher..Simulations with our method indicate that a read length of 20-25 bases is optimal for gene-level expression estimation from mouse and maize RNA-Seq data when sequencing throughput is fixed. ..
- Fan Y, Linardopoulou E, Friedman C, Williams E, Trask B. Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes. Genome Res. 2002;12:1651-62 pubmed..Several of these duplicated blocks may be associated with breakpoints of inversions that occurred during primate evolution and of recurrent chromosome rearrangements in humans...
- Iwanaga Y, Davey M, Martin T, Planck S, DePriest M, Baugh M, et al. Cloning, sequencing and expression analysis of the mouse NOD2/CARD15 gene. Inflamm Res. 2003;52:272-6 pubmed..Common structural and functional features between human and mouse NOD2 were identified. This should allow for development of relevant animal models to evaluate the role of NOD2 in chronic inflammatory disorders. ..
- Murphy J, Barrantes Reynolds R, Kocherlakota R, Bond J, Greenblatt M. The CDKN2A database: Integrating allelic variants with evolution, structure, function, and disease association. Hum Mutat. 2004;24:296-304 pubmed..We describe the database structure, content, current uses, and potential implications (http://biodesktop.uvm.edu/perl/p16). ..
- Michaud E, Culiat C, Klebig M, Barker P, Cain K, Carpenter D, et al. Efficient gene-driven germ-line point mutagenesis of C57BL/6J mice. BMC Genomics. 2005;6:164 pubmed..The ability of ENU to induce mutations that cause various types of changes in proteins will provide additional insights into the functions of mammalian proteins that may not be detectable by knockout mutations. ..
- Grumbling G, Strelets V. FlyBase: anatomical data, images and queries. Nucleic Acids Res. 2006;34:D484-8 pubmed
- Wei T, Geiser A, Qian H, Su C, Helvering L, Kulkarini N, et al. DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids. BMC Womens Health. 2007;7:5 pubmed..This work provides new avenues of study which could influence the future direction of therapeutic intervention for the disease. ..
- Cameron R, Samanta M, Yuan A, He D, Davidson E. SpBase: the sea urchin genome database and web site. Nucleic Acids Res. 2009;37:D750-4 pubmed publisher..Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided...
- Wu C, Kim Y, Smith K, Li W, Hood H, Staben C, et al. Characterization of chromosome ends in the filamentous fungus Neurospora crassa. Genetics. 2009;181:1129-45 pubmed publisher..Finally, despite the absence of many features typically found in the telomere regions of other organisms, the Neurospora chromosome termini still retain the dynamic nature that is characteristic of chromosome ends. ..
- Pulliam J, Dushoff J. Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses. J Infect Dis. 2009;199:565-8 pubmed publisher..This finding highlights nuclear entry as a barrier to transmission and suggests that the ability to complete replication in the cytoplasm may prove to be a useful indicator of the threat of cross-species transmission. ..
- Ye Y, Tang H. An ORFome assembly approach to metagenomics sequences analysis. J Bioinform Comput Biol. 2009;7:455-71 pubmed..This improvement is especially useful for metagenomic projects when the genome assembly does not work because of the low sequence coverage. ..