Skip to main content

Articles

Page 224 of 248

  1. Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires sp...

    Authors: Oleksiy Kohany, Andrew J Gentles, Lukasz Hankus and Jerzy Jurka
    Citation: BMC Bioinformatics 2006 7:474
    Content type: Software Published on:

  2. The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources r...

    Authors: Coral del Val, Vladimir Yurjevich Kuryshev, Karl-Heinz Glatting, Peter Ernst, Agnes Hotz-Wagenblatt, Annemarie Poustka, Sandor Suhai and Stefan Wiemann
    Citation: BMC Bioinformatics 2006 7:473
    Content type: Software Published on:

  3. The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculatio...

    Authors: Ikuo Uchiyama, Toshio Higuchi and Ichizo Kobayashi
    Citation: BMC Bioinformatics 2006 7:472
    Content type: Software Published on:

  5. Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for t...

    Authors: Vidar Beisvag, Frode KR Jünge, Hallgeir Bergum, Lars Jølsum, Stian Lydersen, Clara-Cecilie Günther, Heri Ramampiaro, Mette Langaas, Arne K Sandvik and Astrid Lægreid
    Citation: BMC Bioinformatics 2006 7:470
    Content type: Software Published on:

  6. With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of ...

    Authors: André Fujita, João Ricardo Sato, Leonardo de Oliveira Rodrigues, Carlos Eduardo Ferreira and Mari Cleide Sogayar
    Citation: BMC Bioinformatics 2006 7:469
    Content type: Methodology article Published on:

  7. Single nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the ava...

    Authors: Lakshmi K Matukumalli, John J Grefenstette, David L Hyten, Ik-Young Choi, Perry B Cregan and Curtis P Van Tassell
    Citation: BMC Bioinformatics 2006 7:468
    Content type: Software Published on:

  8. Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packag...

    Authors: Sophie Lemoine, Florence Combes, Nicolas Servant and Stéphane Le Crom
    Citation: BMC Bioinformatics 2006 7:467
    Content type: Software Published on:

  10. Many attempts are being made to understand biological subjects at a systems level. A major resource for these approaches are biological databases, storing manifold information about DNA, RNA and protein sequen...

    Authors: Stephan Weise, Ivo Grosse, Christian Klukas, Dirk Koschützki, Uwe Scholz, Falk Schreiber and Björn H Junker
    Citation: BMC Bioinformatics 2006 7:465
    Content type: Software Published on:

  11. Many of the most popular pre-processing methods for Affymetrix expression arrays, such as RMA, gcRMA, and PLIER, simultaneously analyze data across a set of predetermined arrays to improve precision of the fin...

    Authors: Simon Katz, Rafael A Irizarry, Xue Lin, Mark Tripputi and Mark W Porter
    Citation: BMC Bioinformatics 2006 7:464
    Content type: Methodology article Published on:

  12. The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope scr...

    Authors: Ji Wan, Wen Liu, Qiqi Xu, Yongliang Ren, Darren R Flower and Tongbin Li
    Citation: BMC Bioinformatics 2006 7:463
    Content type: Software Published on:

  16. MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or prote...

    Authors: Carol L Ecale Zhou, Marisa W Lam, Jason R Smith, Adam T Zemla, Matthew D Dyer, Thomas A Kuczmarski, Elizabeth A Vitalis and Thomas R Slezak
    Citation: BMC Bioinformatics 2006 7:459
    Content type: Database Published on:

  22. In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes open...

    Authors: Alessandro Coppe, Gian Antonio Danieli and Stefania Bortoluzzi
    Citation: BMC Bioinformatics 2006 7:453
    Content type: Software Published on:

  23. Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from table...

    Authors: Min Wu, Cheng Thao, Xiangming Mu and Ethan V Munson
    Citation: BMC Bioinformatics 2006 7:452
    Content type: Software Published on:

  24. Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. I...

    Authors: Jian Huang, Alex Gutteridge, Wataru Honda and Minoru Kanehisa
    Citation: BMC Bioinformatics 2006 7:451
    Content type: Software Published on:

  25. Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be execu...

    Authors: Stéphane Descorps-Declère, Danielle Ziébelin, François Rechenmann and Alain Viari
    Citation: BMC Bioinformatics 2006 7:450
    Content type: Software Published on:

  26. Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with hig...

    Authors: Jianjun Hu, Haifeng Li, Michael S Waterman and Xianghong Jasmine Zhou
    Citation: BMC Bioinformatics 2006 7:449
    Content type: Research article Published on:

  28. The identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homolog...

    Authors: Xiyin Wang, Xiaoli Shi, Zhe Li, Qihui Zhu, Lei Kong, Wen Tang, Song Ge and Jingchu Luo
    Citation: BMC Bioinformatics 2006 7:447
    Content type: Methodology article Published on:

  29. Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current a...

    Authors: Michael Hackenberg, Christopher Previti, Pedro Luis Luque-Escamilla, Pedro Carpena, José Martínez-Aroza and José L Oliver
    Citation: BMC Bioinformatics 2006 7:446
    Content type: Research article Published on:

  31. In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a databa...

    Authors: Tim Hulsen, Jacob de Vlieg, Jack AM Leunissen and Peter MA Groenen
    Citation: BMC Bioinformatics 2006 7:444
    Content type: Research article Published on:

  32. The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been devel...

    Authors: Rachel SG Sealfon, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers and Olga G Troyanskaya
    Citation: BMC Bioinformatics 2006 7:443
    Content type: Software Published on:

  33. In spite of the recognized diagnostic potential of biomarkers, the quest for squelching noise and wringing in information from a given set of biomarkers continues. Here, we suggest a statistical algorithm that...

    Authors: Manju R Mamtani, Tushar P Thakre, Mrunal Y Kalkonde, Manik A Amin, Yogeshwar V Kalkonde, Amit P Amin and Hemant Kulkarni
    Citation: BMC Bioinformatics 2006 7:442
    Content type: Methodology article Published on:

  34. Compositionally biased (CB) regions are stretches in protein sequences made from mainly a distinct subset of amino acid residues; such regions are frequently associated with a structural role in the cell, or w...

    Authors: Paul M Harrison
    Citation: BMC Bioinformatics 2006 7:441
    Content type: Research article Published on:

  36. Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools ...

    Authors: François Chevenet, Christine Brun, Anne-Laure Bañuls, Bernard Jacq and Richard Christen
    Citation: BMC Bioinformatics 2006 7:439
    Content type: Software Published on:

  37. Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present ...

    Authors: Jifeng Tang, Ben Vosman, Roeland E Voorrips, C Gerard van der Linden and Jack AM Leunissen
    Citation: BMC Bioinformatics 2006 7:438
    Content type: Software Published on:

  38. Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired p...

    Authors: Denis C Bauer, Mikael Bodén, Ricarda Thier and Elizabeth M Gillam
    Citation: BMC Bioinformatics 2006 7:437
    Content type: Software Published on:

  39. Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union o...

    Authors: Olivier Lespinet and Bernard Labedan
    Citation: BMC Bioinformatics 2006 7:436
    Content type: Database Published on:

  40. Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis can be extended to model any stable protein-DNA co...

    Authors: Isabel K Darcy, Jeff Chang, Nathan Druivenga, Colin McKinney, Ram K Medikonduri, Stacy Mills, Junalyn Navarra-Madsen, Arun Ponnusamy, Jesse Sweet and Travis Thompson
    Citation: BMC Bioinformatics 2006 7:435
    Content type: Methodology article Published on:

  41. High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ...

    Authors: Srinka Ghosh, Heather A Hirsch, Edward Sekinger, Kevin Struhl and Thomas R Gingeras
    Citation: BMC Bioinformatics 2006 7:434
    Content type: Methodology article Published on:

  42. Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic se...

    Authors: Todd J Treangen and Xavier Messeguer
    Citation: BMC Bioinformatics 2006 7:433
    Content type: Software Published on:

  43. Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of the...

    Authors: Prabakaran Subramani, Rajendra Sahu and Shekhar Verma
    Citation: BMC Bioinformatics 2006 7:432
    Content type: Research article Published on:

  44. A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genom...

    Authors: Tamás Arányi, András Váradi, István Simon and Gábor E Tusnády
    Citation: BMC Bioinformatics 2006 7:431
    Content type: Software Published on:

  45. In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable ...

    Authors: Hiraku Morisawa, Mikako Hirota and Tosifusa Toda
    Citation: BMC Bioinformatics 2006 7:430
    Content type: Software Published on:

  47. Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have...

    Authors: Peter S Klosterman, Andrew V Uzilov, Yuri R Bendaña, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman and Ian Holmes
    Citation: BMC Bioinformatics 2006 7:428
    Content type: Software Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

    2023 Usage
    5,987,678 downloads
    4,858 Altmetric mentions 

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us