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Browsing ENG: Bioinformatics: Scholarly Papers by Issue Date

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Browsing ENG: Bioinformatics: Scholarly Papers by Issue Date

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  • Rachlin, John; Ding, Chunming; Cantor, Charles; Kasif, Simon (BioMed Central, 2005-7-25)
    BACKGROUND: Multiplex PCR is a key technology for detecting infectious microorganisms, whole-genome sequencing, forensic analysis, and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR ...
  • Iyer, Lakshminarayan M; Burroughs, A Maxwell; Aravind, L (BioMed Central, 2006-07-19)
    A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history. BACKGROUND. Ubiquitin (Ub)-mediated signaling is one of the hallmarks of ...
  • Ryan, Joseph F; Burton, Patrick M; Mazza, Maureen E; Kwong, Grace K; Mullikin, James C; Finnerty, John R (BioMed Central, 2006-07-24)
    The first near-complete set of homeodomains from a non-bilaterian animal is described. BACKGROUND. Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass ...
  • Gustafson, Adam M; Snitkin, Evan S; Parker, Stephen CJ; DeLisi, Charles; Kasif, Simon (BioMed Central, 2006-10-19)
    BACKGROUND: The identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in the identification of potential ...
  • Mintseris, Julian; Eisen, Michael B (BioMed Central, 2006-10-3)
    BACKGROUND. Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding ...
  • Holloway, Dustin T.; Kon, Mark; DeLisi, Charles (Kluwer Academic Publishers, 2006-10-31)
    High throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps-the identity and location of regulatory binding sites within genomes. Still, ...
  • Guo, Yuchun; Eichler, Gabriel S.; Feng, Ying; Ingber, Donald E.; Huang, Sui (Hindawi Publishing Corporation, 2006-11-2)
    Genome-wide gene expression profile studies encompass increasingly large number of samples, posing a challenge to their presentation and interpretation without losing the notion that each transcriptome constitutes a complex ...
  • Liu, Donglin; Brockman, J. Michael; Dass, Brinda; Hutchins, Lucie N.; Singh, Priyam; McCarrey, John R.; MacDonald, Clinton C.; Graber, Joel H. (Oxford University Press, 2006-12-08)
    Gene expression and processing during mouse male germ cell maturation (spermatogenesis) is highly specialized. Previous reports have suggested that there is a high incidence of alternative 3′-processing in male germ cell ...
  • Wu, Jie; Hu, Zhenjun; DeLisi, Charles (BioMed Central, 2006-2-17)
    BACKGROUND. Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functionally related genes. The effectiveness ...
  • Mellor, Joe; DeLisi, Charles (BioMed Central, 2006-6-8)
    A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the topological structure of ...
  • Millien, Guetchyn; Spira, Avrum; Hinds, Anne; Wang, Junling; Williams, Mary C; Ramirez, Maria I (BioMed Central, 2006-7-25)
    BACKGROUND. Development of lung alveolar sacs of normal structure and size at late gestation is necessary for the gas exchange process that sustains respiration at birth. Mice lacking the lung differentiation gene T1α ...
  • Li, Jian-Liang; Hayden, Michael R.; Warby, Simon C.; Durr, Alexandra; Morrison, Patrick J.; Nance, Martha; Ross, Christopher A.; Margolis, Russell L.; Rosenblatt, Adam; Squitieri, Ferdinando; Frati, Luigi; Gómez-Tortosa, Estrella; García, Carmen Ayuso; Suchowersky, Oksana; Klimek, Mary Lou; Trent, Ronald J.A.; McCusker, Elizabeth; Novelletto, Andrea; Frontali, Marina; Paulsen, Jane S; Jones, Randi; Ashizawa, Tetsuo; Lazzarini, Alice; Wheeler, Vanessa C.; Prakash, Ranjana; Xu, Gang; Djoussé, Luc; Mysore, Jayalakshmi Srinidhi; Gillis, Tammy; Hakky, Michael; Cupples, L Adrienne; Saint-Hilaire, Marie H.; Cha, Jang-Ho J.; Hersch, Steven M.; Penney, John B.; Harrison, Madaline B.; Perlman, Susan L.; Zanko, Andrea; Abramson, Ruth K.; Lechich, Anthony J.; Duckett, Ayana; Marder, Karen; Conneally, P. Michael; Gusella, James F.; MacDonald, Marcy E.; Myers, Richard H. (BioMed Central, 2006-8-17)
    BACKGROUND: Age at onset of Huntington's disease (HD) is correlated with the size of the abnormal CAG repeat expansion in the HD gene; however, several studies have indicated that other genetic factors also contribute to ...
  • Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D (BioMed Central, 2006-9-26)
    BACKGROUND. Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed ...
  • Snitkin, Evan S; Gustafson, Adam M; Mellor, Joseph; Wu, Jie; DeLisi, Charles (BioMed Central, 2006-9-27)
    BACKGROUND. The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced ...
  • Reddy, Timothy E.; Shakhnovich, Boris E.; Roberts, Daniel S.; Russek, Shelley J.; DeLisi, Charles (Oxford University Press, 2007-01-03)
    Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity ...
  • Hayete, Boris; Gardner, Timothy S; Collins, James J (2007-02-13)
  • Lehár, Joseph; Zimmermann, Grant R; Krueger, Andrew S; Molnar, Raymond A; Ledell, Jebediah T; Heilbut, Adrian M; Short, Glenn F; Giusti, Leanne C; Nolan, Garry P; Magid, Omar A; Lee, Margaret S; Borisy, Alexis A; Stockwell, Brent R; Keith, Curtis T (2007-02-27)
    Efforts to construct therapeutically useful models of biological systems require large and diverse sets of data on functional connections between their components. Here we show that cellular responses to combinations of ...
  • Dwyer, Daniel J; Kohanski, Michael A; Hayete, Boris; Collins, James J (2007-03-13)
    Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase ...
  • Eichler, Gabriel S; Reimers, Mark; Kane, David; Weinstein, John N (BioMed Central, 2007-09-10)
    The LeFE algorithm has been developed to address the complex, non-linear regulation of gene expression. Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear ...
  • Beane, Jennifer; Sebastiani, Paola; Liu, Gang; Brody, Jerome S; Lenburg, Marc E; Spira, Avrum (BioMed Central, 2007-09-25)
    Oligonucleotide microarray analysis revealed 175 genes that are differentially expressed in large airway epithelial cells of people who currently smoke compared with those who never smoked, with 28 classified as irreversible, ...

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