Skip to main content

Articles

Page 208 of 247

  1. As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (...

    Authors: Ana C Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal and Nicolas Pollet
    Citation: BMC Bioinformatics 2008 9:1
  2. The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types...

    Authors: Egon L Willighagen, Noel M O'Boyle, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck and David J Wild
    Citation: BMC Bioinformatics 2007 8:487
  3. Much recent work in bioinformatics has focused on the inference of various types of biological networks, representing gene regulation, metabolic processes, protein-protein interactions, etc. A common setting i...

    Authors: Jean-Philippe Vert, Jian Qiu and William S Noble
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S8

    This article is part of a Supplement: Volume 8 Supplement 10

  4. For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to...

    Authors: Sören Sonnenburg, Gabriele Schweikert, Petra Philips, Jonas Behr and Gunnar Rätsch
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S7

    This article is part of a Supplement: Volume 8 Supplement 10

  5. High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researche...

    Authors: Yanjun Qi, Judith Klein-Seetharaman and Ziv Bar-Joseph
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S6

    This article is part of a Supplement: Volume 8 Supplement 10

  6. Many important high throughput projects use in situ hybridization and may require the analysis of images of spatial cross sections of organisms taken with cellular level resolution. Projects creating gene express...

    Authors: Manjunatha Jagalur, Chris Pal, Erik Learned-Miller, R Thomas Zoeller and David Kulp
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S5

    This article is part of a Supplement: Volume 8 Supplement 10

  7. Quantitative analysis of differential protein expressions requires to align temporal elution measurements from liquid chromatography coupled to mass spectrometry (LC/MS). We propose multiple Canonical Correlation...

    Authors: Bernd Fischer, Volker Roth and Joachim M Buhmann
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S4

    This article is part of a Supplement: Volume 8 Supplement 10

  8. Gene expression measurements during the development of the fly Drosophila melanogaster are routinely used to find functional modules of temporally co-expressed genes. Complimentary large data sets of in situ RNA ...

    Authors: Ivan G Costa, Roland Krause, Lennart Opitz and Alexander Schliep
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S3

    This article is part of a Supplement: Volume 8 Supplement 10

  9. In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression.

    Authors: Xiaoyu Chen and Mathieu Blanchette
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S2

    This article is part of a Supplement: Volume 8 Supplement 10

  10. An ever increasing number of techniques are being used to find genes with similar profiles from microarray studies. Visualization of gene expression profiles can aid this process, potentially contributing to t...

    Authors: Yvonne E Pittelkow and Susan R Wilson
    Citation: BMC Bioinformatics 2007 8:486
  11. The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been sugge...

    Authors: Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong Sung Lee, Young Seek Lee and Jin Hyuk Kim
    Citation: BMC Bioinformatics 2007 8:485
  12. In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results i...

    Authors: Arnaud Droit, Joanna M Hunter, Michèle Rouleau, Chantal Ethier, Aude Picard-Cloutier, David Bourgais and Guy G Poirier
    Citation: BMC Bioinformatics 2007 8:483
  13. Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rel...

    Authors: Wasinee Rungsarityotin, Roland Krause, Arno Schödl and Alexander Schliep
    Citation: BMC Bioinformatics 2007 8:482
  14. Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the...

    Authors: Victor G Levitsky, Elena V Ignatieva, Elena A Ananko, Igor I Turnaev, Tatyana I Merkulova, Nikolay A Kolchanov and TC Hodgman
    Citation: BMC Bioinformatics 2007 8:481
  15. Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequen...

    Authors: Scott A Givan, Christopher M Sullivan and James C Carrington
    Citation: BMC Bioinformatics 2007 8:479
  16. Novel molecular and statistical methods are in rising demand for disease diagnosis and prognosis with the help of recent advanced biotechnology. High-resolution mass spectrometry (MS) is one of those biotechno...

    Authors: Jingjing Ye, Hao Liu, Crystal Kirmiz, Carlito B Lebrilla and David M Rocke
    Citation: BMC Bioinformatics 2007 8:477
  17. The joint analysis of several categorical variables is a common task in many areas of biology, and is becoming central to systems biology investigations whose goal is to identify potentially complex interactio...

    Authors: Corinne Dahinden, Giovanni Parmigiani, Mark C Emerick and Peter Bühlmann
    Citation: BMC Bioinformatics 2007 8:476
  18. The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated f...

    Authors: Michael C Schatz, Cole Trapnell, Arthur L Delcher and Amitabh Varshney
    Citation: BMC Bioinformatics 2007 8:474
  19. Eukaryotic cells have developed mechanisms to respond to external environmental or physiological changes (stresses). In order to increase the activities of stress-protection functions in response to an environ...

    Authors: Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li and Bor-Sen Chen
    Citation: BMC Bioinformatics 2007 8:473
  20. Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis,...

    Authors: Srinath Sridhar, Fumei Lam, Guy E Blelloch, R Ravi and Russell Schwartz
    Citation: BMC Bioinformatics 2007 8:472
  21. Ribozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (...

    Authors: Yu Shao, Susan Wu, Chi Yu Chan, Jessie R Klapper, Erasmus Schneider and Ye Ding
    Citation: BMC Bioinformatics 2007 8:469
  22. High-throughput peptide and protein identification technologies have benefited tremendously from strategies based on tandem mass spectrometry (MS/MS) in combination with database searching algorithms. A major ...

    Authors: Nico Pfeifer, Andreas Leinenbach, Christian G Huber and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2007 8:468
  23. In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network ma...

    Authors: Thomas Thorne and Michael PH Stumpf
    Citation: BMC Bioinformatics 2007 8:467
  24. Subcellular location prediction of proteins is an important and well-studied problem in bioinformatics. This is a problem of predicting which part in a cell a given protein is transported to, where an amino ac...

    Authors: Takeyuki Tamura and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2007 8:466
  25. Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched f...

    Authors: Alexis Dereeper, Xavier Argout, Claire Billot, Jean-François Rami and Manuel Ruiz
    Citation: BMC Bioinformatics 2007 8:465
  26. The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical l...

    Authors: Hyunsoo Kim, Haesun Park and Barry L Drake
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S6

    This article is part of a Supplement: Volume 8 Supplement 9

  27. With more and more research dedicated to literature mining in the biomedical domain, more and more systems are available for people to choose from when building literature mining applications. In this study, w...

    Authors: Manabu Torii, Zhang-zhi Hu, Min Song, Cathy H Wu and Hongfang Liu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S5

    This article is part of a Supplement: Volume 8 Supplement 9

  28. A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summariz...

    Authors: Illhoi Yoo, Xiaohua Hu and Il-Yeol Song
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S4

    This article is part of a Supplement: Volume 8 Supplement 9

  29. Annotating genes and their products with Gene Ontology codes is an important area of research. One approach is to use the information available about these genes in the biomedical literature. The goal in this ...

    Authors: Padmini Srinivasan and Xin Ying Qiu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S3

    This article is part of a Supplement: Volume 8 Supplement 9

  30. As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far...

    Authors: Doheon Lee, Sangwoo Kim and Younghoon Kim
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S2

    This article is part of a Supplement: Volume 8 Supplement 9

  31. Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. A number of ontologies describe properties that can be a...

    Authors: Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith and Cathy H Wu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S1

    This article is part of a Supplement: Volume 8 Supplement 9

  32. The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of t...

    Authors: Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios and Luis Mendoza
    Citation: BMC Bioinformatics 2007 8:462
  33. Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desi...

    Authors: Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp
    Citation: BMC Bioinformatics 2007 8:460
  34. Peptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an im...

    Authors: Menaka Rajapakse, Bertil Schmidt, Lin Feng and Vladimir Brusic
    Citation: BMC Bioinformatics 2007 8:459

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