Skip to main content

Articles

Page 214 of 247

  1. Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate f...

    Authors: Paolo Ferragina, Raffaele Giancarlo, Valentina Greco, Giovanni Manzini and Gabriel Valiente
    Citation: BMC Bioinformatics 2007 8:252
  2. The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrat...

    Authors: Curtis Huttenhower, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya and Hilary A Coller
    Citation: BMC Bioinformatics 2007 8:250
  3. Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorit...

    Authors: Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani and Robert H Gross
    Citation: BMC Bioinformatics 2007 8:249
  4. Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or vot...

    Authors: Ricardo ZN Vêncio, Leonardo Varuzza, Carlos A de B Pereira, Helena Brentani and Ilya Shmulevich
    Citation: BMC Bioinformatics 2007 8:246
  5. Oral delivery is a highly desirable property for candidate drugs under development. Computational modeling could provide a quick and inexpensive way to assess the intestinal permeability of a molecule. Althoug...

    Authors: Eunkyoung Jung, Junhyoung Kim, Minkyoung Kim, Dong Hyun Jung, Hokyoung Rhee, Jae-Min Shin, Kihang Choi, Sang-Kee Kang, Min-Kook Kim, Cheol-Heui Yun, Yun-Jaie Choi and Seung-Hoon Choi
    Citation: BMC Bioinformatics 2007 8:245
  6. Using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an Enzyme Commission number. Here we p...

    Authors: Yannick Pouliot and Peter D Karp
    Citation: BMC Bioinformatics 2007 8:244
  7. Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein funct...

    Authors: Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Ilya Mazo and Iaroslav Ispolatov
    Citation: BMC Bioinformatics 2007 8:243
  8. Gene-set analysis evaluates the expression of biological pathways, or a priori defined gene sets, rather than that of individual genes, in association with a binary phenotype, and is of great biologic interest in...

    Authors: Irina Dinu, John D Potter, Thomas Mueller, Qi Liu, Adeniyi J Adewale, Gian S Jhangri, Gunilla Einecke, Konrad S Famulski, Philip Halloran and Yutaka Yasui
    Citation: BMC Bioinformatics 2007 8:242
  9. Researchers using RNA expression microarrays in experimental designs with more than two treatment groups often identify statistically significant genes with ANOVA approaches. However, the ANOVA test does not d...

    Authors: Randall Hulshizer and Eric M Blalock
    Citation: BMC Bioinformatics 2007 8:240
  10. Classifying nuclear magnetic resonance (NMR) spectra is a crucial step in many metabolomics experiments. Since several multivariate classification techniques depend upon the variance of the data, it is importa...

    Authors: Helen M Parsons, Christian Ludwig, Ulrich L Günther and Mark R Viant
    Citation: BMC Bioinformatics 2007 8:234
  11. In practice many biological time series measurements, including gene microarrays, are conducted at time points that seem to be interesting in the biologist's opinion and not necessarily at fixed time intervals...

    Authors: Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, llya Shmulevich and Olli Yli-Harja
    Citation: BMC Bioinformatics 2007 8:233
  12. Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, the regulation process in genetic systems is...

    Authors: Reuben Thomas, Carlos J Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis and Eleftherios T Papoutsakis
    Citation: BMC Bioinformatics 2007 8:228
  13. In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such inde...

    Authors: Simon K Chan, Michael Hsing, Fereydoun Hormozdiari and Artem Cherkasov
    Citation: BMC Bioinformatics 2007 8:227
  14. Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completely sequenced to date, it is tempting to ask...

    Authors: Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki and Minoru Kanehisa
    Citation: BMC Bioinformatics 2007 8:225
  15. Analyzing differential-gene-expression data in the context of protein-interaction networks (PINs) yields information on the functional cellular status. PINs can be formally represented as graphs, and approxima...

    Authors: Alexander Platzer, Paul Perco, Arno Lukas and Bernd Mayer
    Citation: BMC Bioinformatics 2007 8:224
  16. The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to exp...

    Authors: Johanna Hardin, Aya Mitani, Leanne Hicks and Brian VanKoten
    Citation: BMC Bioinformatics 2007 8:220
  17. Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing ...

    Authors: Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda and Peter J Park
    Citation: BMC Bioinformatics 2007 8:219
  18. With microarray technology, variability in experimental environments such as RNA sources, microarray production, or the use of different platforms, can cause bias. Such systematic differences present a substan...

    Authors: Ki-Yeol Kim, Dong Hyuk Ki, Ha Jin Jeong, Hei-Cheul Jeung, Hyun Cheol Chung and Sun Young Rha
    Citation: BMC Bioinformatics 2007 8:218
  19. Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displa...

    Authors: Nathan Salomonis, Kristina Hanspers, Alexander C Zambon, Karen Vranizan, Steven C Lawlor, Kam D Dahlquist, Scott W Doniger, Josh Stuart, Bruce R Conklin and Alexander R Pico
    Citation: BMC Bioinformatics 2007 8:217
  20. In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Gol...

    Authors: Jan Hummel, Michaela Niemann, Stefanie Wienkoop, Waltraud Schulze, Dirk Steinhauser, Joachim Selbig, Dirk Walther and Wolfram Weckwerth
    Citation: BMC Bioinformatics 2007 8:216
  21. Mass spectrometry based quantification of peptides can be performed using the iTRAQ™ reagent in conjunction with mass spectrometry. This technology yields information about the relative abundance of single pep...

    Authors: Andreas M Boehm, Stephanie Pütz, Daniela Altenhöfer, Albert Sickmann and Michael Falk
    Citation: BMC Bioinformatics 2007 8:214
  22. Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful a...

    Authors: Namshin Kim and Christopher Lee
    Citation: BMC Bioinformatics 2007 8:213
  23. Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these re...

    Authors: Vinay Satish Kumar, Madhukar S Dasika and Costas D Maranas
    Citation: BMC Bioinformatics 2007 8:212
  24. Fluorescence microscopy is widely used to determine the subcellular location of proteins. Efforts to determine location on a proteome-wide basis create a need for automated methods to analyze the resulting ima...

    Authors: Amina Chebira, Yann Barbotin, Charles Jackson, Thomas Merryman, Gowri Srinivasa, Robert F Murphy and Jelena Kovačević
    Citation: BMC Bioinformatics 2007 8:210
  25. Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their propos...

    Authors: Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides and Philip Hugenholtz
    Citation: BMC Bioinformatics 2007 8:209
  26. During generation of microarray data, various forms of systematic biases are frequently introduced which limits accuracy and precision of the results. In order to properly estimate biological effects, these bi...

    Authors: Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Stefan Jansson, Thomas Moritz and Johan Trygg
    Citation: BMC Bioinformatics 2007 8:207
  27. Gene expression microarray is a powerful technology for genetic profiling diseases and their associated treatments. Such a process involves a key step of biomarker identification, which are expected to be clos...

    Authors: Zhipeng Cai, Randy Goebel, Mohammad R Salavatipour and Guohui Lin
    Citation: BMC Bioinformatics 2007 8:206
  28. We have developed a new haplotyping program based on the combination of an iterative multiallelic EM algorithm (IEM), bootstrap resampling and a pseudo Gibbs sampler. The use of the IEM-bootstrap procedure con...

    Authors: Olivier Delaneau, Cédric Coulonges, Pierre-Yves Boelle, George Nelson, Jean-Louis Spadoni and Jean-François Zagury
    Citation: BMC Bioinformatics 2007 8:205
  29. The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a softwar...

    Authors: Jason D Gans and Murray Wolinsky
    Citation: BMC Bioinformatics 2007 8:204
  30. Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to k...

    Authors: Gianluca Pollastri, Alberto JM Martin, Catherine Mooney and Alessandro Vullo
    Citation: BMC Bioinformatics 2007 8:201

Featured videos

View featured videos from across the BMC-series journals

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 

Sign up for article alerts and news from this journal