Skip to main content

Articles

Page 225 of 249

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  9. 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:

  10. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  28. 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:

  32. Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of ci...

    Authors: Maksim V Plikus, Zina Zhang and Cheng-Ming Chuong
    Citation: BMC Bioinformatics 2006 7:424
    Content type: Software Published on:

  33. In bacteria, sigma factors and other transcriptional regulatory proteins recognize DNA patterns upstream of their target genes and interact with RNA polymerase to control transcription. As a consequence of evo...

    Authors: Pierre-Étienne Jacques, Sébastien Rodrigue, Luc Gaudreau, Jean Goulet and Ryszard Brzezinski
    Citation: BMC Bioinformatics 2006 7:423
    Content type: Research article Published on:

  34. Evaluating the importance of the different sources of variations is essential in microarray data experiments. Complex experimental designs generally include various factors structuring the data which should be...

    Authors: Florent Baty, Michaël Facompré, Jan Wiegand, Joseph Schwager and Martin H Brutsche
    Citation: BMC Bioinformatics 2006 7:422
    Content type: Methodology article Published on:

  36. 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 eukar...

    Authors: Evan S Snitkin, Adam M Gustafson, Joseph Mellor, Jie Wu and Charles DeLisi
    Citation: BMC Bioinformatics 2006 7:420
    Content type: Research article Published on:

  38. Gene Ontology (GO) characterizes and categorizes the functions of genes and their products according to biological processes, molecular functions and cellular components, facilitating interpretation of data fr...

    Authors: Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins and Weida Tong
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  39. Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families...

    Authors: Ronald L Frank, Ajay Mane and Fikret Ercal
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  40. We present a novel strategy for classification of DNA molecules using measurements from an alpha-Hemolysin channel detector. The proposed approach provides excellent classification performance for five differe...

    Authors: Raja Tanveer Iqbal, Matthew Landry and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  41. Massive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the r...

    Authors: Alexdander Kel, Nico Voss, Ruy Jauregui, Olga Kel-Margoulis and Edgar Wingender
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  42. Recursive Feature Elimination is a common and well-studied method for reducing the number of attributes used for further analysis or development of prediction models. The effectiveness of the RFE algorithm is ...

    Authors: Yuanyuan Ding and Dawn Wilkins
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  43. In studies that use DNA arrays to assess changes in gene expression, our goal is to evaluate the statistical significance of treatments on sets of genes. Genes can be grouped by a molecular function, a biologi...

    Authors: Robert Delongchamp, Taewon Lee and Cruz Velasco
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  44. Periodic processes, such as the circadian rhythm, are important factors modulating and coordinating transcription of genes governing key metabolic pathways. Theoretically, even small fluctuations in the orches...

    Authors: Andrey A Ptitsyn, Sanjin Zvonic and Jeffrey M Gimble
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  45. Independent Component Analysis (ICA) proves to be useful in the analysis of neural activity, as it allows for identification of distinct sources of activity. Applied to measurements registered in a controlled ...

    Authors: Tomasz G Smolinski, Roger Buchanan, Grzegorz M Boratyn, Mariofanna Milanova and Astrid A Prinz
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  46. 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 E

    Authors: Laila A Nahum, Matthew T Reynolds, Zhengyuan O Wang, Jeremiah J Faith, Rahul Jonna, Zhi J Jiang, Thomas J Meyer and David D Pollock
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  47. Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selec...

    Authors: Venkata Thodima, Mehdi Pirooznia and Youping Deng
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  48. We describe Support Vector Machine (SVM) applications to classification and clustering of channel current data. SVMs are variational-calculus based methods that are constrained to have structural risk minimiza...

    Authors: Stephen Winters-Hilt, Anil Yelundur, Charlie McChesney and Matthew Landry
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  49. Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is p...

    Authors: Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O Elasri and Youping Deng
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

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