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  1. In real-time quantitative PCR studies using absolute plasmid DNA standards, a calibration curve is developed to estimate an unknown DNA concentration. However, potential differences in the amplification perfor...

    Authors: Mano Sivaganesan, Shawn Seifring, Manju Varma, Richard A Haugland and Orin C Shanks
    Citation: BMC Bioinformatics 2008 9:120
    Content type: Methodology article Published on:

  2. Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge about protein function. The resul...

    Authors: Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia and Charles DeLisi
    Citation: BMC Bioinformatics 2008 9:119
    Content type: Research article Published on:

  3. Choosing the appropriate sample size is an important step in the design of a microarray experiment, and recently methods have been proposed that estimate sample sizes for control of the False Discovery Rate (F...

    Authors: Tommy S Jørstad, Herman Midelfart and Atle M Bones
    Citation: BMC Bioinformatics 2008 9:117
    Content type: Methodology article Published on:

  5. Promoter region plays an important role in determining where the transcription of a particular gene should be initiated. Computational prediction of eukaryotic Pol II promoter sequences is one of the most sign...

    Authors: Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh and Li-Qian Zhou
    Citation: BMC Bioinformatics 2008 9:113
    Content type: Methodology article Published on:

  6. Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can n...

    Authors: Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao and Toshihiko Ishida
    Citation: BMC Bioinformatics 2008 9:112
    Content type: Software Published on:

  8. Biological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The...

    Authors: Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh and Ron Shamir
    Citation: BMC Bioinformatics 2008 9:110
    Content type: Software Published on:

  9. As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the ques...

    Authors: Wolfram Gronwald, Tim Hohm and Daniel Hoffmann
    Citation: BMC Bioinformatics 2008 9:109
    Content type: Research article Published on:

  10. Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate informat...

    Authors: Graham L Poulter, Daniel L Rubin, Russ B Altman and Cathal Seoighe
    Citation: BMC Bioinformatics 2008 9:108
    Content type: Research article Published on:

  11. Last years' mapping of diverse genomes has generated huge amounts of biological data which are currently dispersed through many databases. Integration of the information available in the various databases is r...

    Authors: Francisco J Lopez, Armando Blanco, Fernando Garcia, Carlos Cano and Antonio Marin
    Citation: BMC Bioinformatics 2008 9:107
    Content type: Research article Published on:

  12. Kernel-based classification and regression methods have been successfully applied to modelling a wide variety of biological data. The Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method of...

    Authors: Max Bylesjö, Mattias Rantalainen, Jeremy K Nicholson, Elaine Holmes and Johan Trygg
    Citation: BMC Bioinformatics 2008 9:106
    Content type: Software Published on:

  13. Modelling the time-related behaviour of biological systems is essential for understanding their dynamic responses to perturbations. In metabolic profiling studies, the sampling rate and number of sampling poin...

    Authors: Mattias Rantalainen, Olivier Cloarec, Timothy MD Ebbels, Torbjörn Lundstedt, Jeremy K Nicholson, Elaine Holmes and Johan Trygg
    Citation: BMC Bioinformatics 2008 9:105
    Content type: Methodology article Published on:

  14. Target identification is important for modern drug discovery. With the advances in the development of molecular docking, potential binding proteins may be discovered by docking a small molecule to a repository...

    Authors: Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang and Hualiang Jiang
    Citation: BMC Bioinformatics 2008 9:104
    Content type: Database Published on:

  15. The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant...

    Authors: Indra Neil Sarkar, Mary G Egan, Gloria Coruzzi, Ernest K Lee and Rob DeSalle
    Citation: BMC Bioinformatics 2008 9:103
    Content type: Software Published on:

  17. As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequ...

    Authors: Yong-Zi Chen, Yu-Rong Tang, Zhi-Ya Sheng and Ziding Zhang
    Citation: BMC Bioinformatics 2008 9:101
    Content type: Research article Published on:

  18. The analysis of high-throughput gene expression data sets derived from microarray experiments still is a field of extensive investigation. Although new approaches and algorithms are published continuously, mos...

    Authors: Dominik Lutter, Peter Ugocsai, Margot Grandl, Evelyn Orso, Fabian Theis, Elmar W Lang and Gerd Schmitz
    Citation: BMC Bioinformatics 2008 9:100
    Content type: Research article Published on:

  19. The integration of biomedical information is essential for tackling medical problems. We describe a data model in the domain of flow cytometry (FC) allowing for massive management, analysis and integration wit...

    Authors: John Drakos, Marina Karakantza, Nicholas C Zoumbos, John Lakoumentas, George C Nikiforidis and George C Sakellaropoulos
    Citation: BMC Bioinformatics 2008 9:99
    Content type: Research article Published on:

  20. In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-spec...

    Authors: Tristan Mary-Huard, Julie Aubert, Nadera Mansouri-Attia, Olivier Sandra and Jean-Jacques Daudin
    Citation: BMC Bioinformatics 2008 9:98
    Content type: Methodology article Published on:

  21. Preparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any...

    Authors: Dadabhai T Singh, Rahul Trehan, Bertil Schmidt and Timo Bretschneider
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  22. The Potato type II (Pot II) family of proteinase inhibitors plays critical roles in the defense system of plants from Solanaceae family against pests. To better understand the evolution of this family, we investi...

    Authors: Lesheng Kong and Shoba Ranganathan
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  23. Network Component Analysis (NCA) has shown its effectiveness in discovering regulators and inferring transcription factor activities (TFAs) when both microarray data and ChIP-on-chip data are available. Howeve...

    Authors: Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke and Eric Hoffman
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  24. Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, ...

    Authors: Woo-Yeon Kim, Sungsoo Kang, Byoung-Chul Kim, Jeehyun Oh, Seongwoong Cho, Jong Bhak and Jong-Soon Choi
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  25. T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large p...

    Authors: Guang Lan Zhang, Asif M Khan, Kellathur N Srinivasan, AT Heiny, KX Lee, Chee Keong Kwoh, J Thomas August and Vladimir Brusic
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  26. The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying a...

    Authors: Olivo Miotto, AT Heiny, Tin Wee Tan, J Thomas August and Vladimir Brusic
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  27. The tumour suppressor protein p53 protein has a core domain that binds DNA and is the site for most oncogenic mutations. This domain is quite unstable compared to its homologs p63 and p73. Two key residues in ...

    Authors: Arumugam Madhumalar, Derek John Smith and Chandra Verma
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  28. Metabotropic glutamate receptors (mGluRs) are G protein coupled receptors that play important roles in synaptic plasticity and other neuro-physiological and pathological processes. Allosteric mGluR ligands are...

    Authors: Naveena Yanamala, Kalyan C Tirupula and Judith Klein-Seetharaman
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  29. Type I signal peptidases (SPases) are essential membrane-bound serine proteases responsible for the cleavage of signal peptides from proteins that are translocated across biological membranes. The crystal stru...

    Authors: Khar Heng Choo, Joo Chuan Tong and Shoba Ranganathan
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  30. G protein-coupled receptors (GPCRs) are abundant, activate complex signalling and represent the targets for up to ~60% of pharmaceuticals but there is a paucity of structural data. Bovine rhodopsin is the firs...

    Authors: Siavoush Dastmalchi, W Bret Church and Michael B Morris
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  31. The prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to ...

    Authors: Vijayalakshmi Chelliah and William R Taylor
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  32. Protein domains present some of the most useful information that can be used to understand protein structure and functions. Recent research on protein domain boundary prediction has been mainly based on widely...

    Authors: Paul D Yoo, Abdur R Sikder, Bing Bing Zhou and Albert Y Zomaya
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  33. The fast growing Protein Data Bank contains the three-dimensional description of more than 45000 protein- and nucleic-acid structures today. The large majority of the data in the PDB are measured by X-ray crys...

    Authors: Rafael Ördög, Zoltán Szabadka and Vince Grolmusz
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  34. The analysis of expressed sequence tags (EST) offers a rapid and cost effective approach to elucidate the transcriptome of an organism, but requires several computational methods for assembly and annotation. R...

    Authors: Shivashankar H Nagaraj, Robin B Gasser, Alasdair J Nisbet and Shoba Ranganathan
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  35. Identification of differentially expressed genes is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular to solve this type of proble...

    Authors: Hongya Zhao, Kwok-Leung Chan, Lee-Ming Cheng and Hong Yan
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  36. Nucleic acid hybridization, a fundamental technique in molecular biology, can be modified into very effective and sensitive methods for detecting particular targets mixed with millions of non-target sequences....

    Authors: Shu-Hwa Chen, Chen-Zen Lo, Ming-Chi Tsai, Chao A Hsiung and Chung-Yen Lin
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  37. The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such stud...

    Authors: Olivo Miotto, Tin Wee Tan and Vladimir Brusic
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  38. The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework...

    Authors: Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo and Yixue Li
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  39. The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challe...

    Authors: Christopher JO Baker, Rajaraman Kanagasabai, Wee Tiong Ang, Anitha Veeramani, Hong-Sang Low and Markus R Wenk
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  40. Prediction of transmembrane (TM) helices by statistical methods suffers from lack of sufficient training data. Current best methods use hundreds or even thousands of free parameters in their models which are t...

    Authors: Madhavi Ganapathiraju, N Balakrishnan, Raj Reddy and Judith Klein-Seetharaman
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  41. Experimentally verified protein-protein interactions (PPI) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be made faster by ranking newly-...

    Authors: Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  42. Analysis of single nucleotide polymorphism (SNP) is becoming a key research in genomics fields. Many functional analyses of SNPs have been carried out for coding regions and splicing sites that can alter prote...

    Authors: Byoung-Chul Kim, Woo-Yeon Kim, Daeui Park, Won-Hyong Chung, Kwang-sik Shin and Jong Bhak
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  43. We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNe...

    Authors: Shoba Ranganathan, Michael Gribskov and Tin Wee Tan
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  44. A logical model of the known metabolic processes in S. cerevisiae was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. ...

    Authors: KE Whelan and RD King
    Citation: BMC Bioinformatics 2008 9:97
    Content type: Research article Published on:

  45. Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through t...

    Authors: Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot and Roeland CHJ van Ham
    Citation: BMC Bioinformatics 2008 9:96
    Content type: Software Published on:

  46. In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve ...

    Authors: Anke Batsch, Andrea Noetel, Christian Fork, Anita Urban, Daliborka Lazic, Tina Lucas, Julia Pietsch, Andreas Lazar, Edgar Schömig and Dirk Gründemann
    Citation: BMC Bioinformatics 2008 9:95
    Content type: Methodology article Published on:

  48. Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome sequences than eukaryotes, se...

    Authors: Sacha AFT van Hijum, Richard JS Baerends, Aldert L Zomer, Harma A Karsens, Victoria Martin-Requena, Oswaldo Trelles, Jan Kok and Oscar P Kuipers
    Citation: BMC Bioinformatics 2008 9:93
    Content type: Research article Published on:

  49. Clustering is a popular data exploration technique widely used in microarray data analysis. Most conventional clustering algorithms, however, generate only one set of clusters independent of the biological con...

    Authors: Pankaj Chopra, Jaewoo Kang, Jiong Yang, HyungJun Cho, Heenam Stanley Kim and Min-Goo Lee
    Citation: BMC Bioinformatics 2008 9:92
    Content type: Methodology article Published on:

  50. Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network...

    Authors: Cédric Auliac, Vincent Frouin, Xavier Gidrol and Florence d'Alché-Buc
    Citation: BMC Bioinformatics 2008 9:91
    Content type: Methodology article Published on:

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