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  3. Short oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operati...

    Authors: Frank F Millenaar, John Okyere, Sean T May, Martijn van Zanten, Laurentius ACJ Voesenek and Anton JM Peeters
    Citation: BMC Bioinformatics 2006 7:137
    Content type: Research article Published on:

  4. Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult...

    Authors: Feng-Chi Chen, Chuang-Jong Chen, Jar-Yi Ho and Trees-Juen Chuang
    Citation: BMC Bioinformatics 2006 7:136
    Content type: Research article Published on:

  5. With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and th...

    Authors: Peisen Zhang, Jinghui Zhang, Huitao Sheng, James J Russo, Brian Osborne and Kenneth Buetow
    Citation: BMC Bioinformatics 2006 7:135
    Content type: Methodology article Published on:

  8. Extreme pathways (ExPas) have been shown to be valuable for studying the functions and capabilities of metabolic networks through characterization of the null space of the stoichiometric matrix (S). Singular valu...

    Authors: Christian L Barrett, Nathan D Price and Bernhard O Palsson
    Citation: BMC Bioinformatics 2006 7:132
    Content type: Research article Published on:

  9. The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endo...

    Authors: Irini A Doytchinova, Pingping Guan and Darren R Flower
    Citation: BMC Bioinformatics 2006 7:131
    Content type: Research article Published on:

  13. Supervised learning for classification of cancer employs a set of design examples to learn how to discriminate between tumors. In practice it is crucial to confirm that the classifier is robust with good gener...

    Authors: Ulrika Wickenberg-Bolin, Hanna Göransson, Mårten Fryknäs, Mats G Gustafsson and Anders Isaksson
    Citation: BMC Bioinformatics 2006 7:127
    Content type: Research article Published on:

  14. Determining whether a gene is differentially expressed in two different samples remains an important statistical problem. Prior work in this area has featured the use of t-tests with pooled estimates of the sampl...

    Authors: Richard J Fox and Matthew W Dimmic
    Citation: BMC Bioinformatics 2006 7:126
    Content type: Research article Published on:

  15. Particle Swarm Optimization (PSO) is an established method for parameter optimization. It represents a population-based adaptive optimization technique that is influenced by several "strategy parameters". Choo...

    Authors: Michael Meissner, Michael Schmuker and Gisbert Schneider
    Citation: BMC Bioinformatics 2006 7:125
    Content type: Methodology article Published on:

  16. The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomeri...

    Authors: Jiangning Song, Kevin Burrage, Zheng Yuan and Thomas Huber
    Citation: BMC Bioinformatics 2006 7:124
    Content type: Research article Published on:

  17. Nonlinear regression, like linear regression, assumes that the scatter of data around the ideal curve follows a Gaussian or normal distribution. This assumption leads to the familiar goal of regression: to min...

    Authors: Harvey J Motulsky and Ronald E Brown
    Citation: BMC Bioinformatics 2006 7:123
    Content type: Methodology article Published on:

  18. Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties ...

    Authors: Xiaochen Bo, Shaoke Lou, Daochun Sun, Wenjie Shu, Jing Yang and Shengqi Wang
    Citation: BMC Bioinformatics 2006 7:122
    Content type: Methodology article Published on:

  20. In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation ...

    Authors: Sebastiaan Horsman, Michael J Moorhouse, Victor CL de Jager, Peter van der Spek, Frank Grosveld, John Strouboulis and Eleni Z Katsantoni
    Citation: BMC Bioinformatics 2006 7:120
    Content type: Software Published on:

  21. Microarray technology produces gene expression data on a genomic scale for an endless variety of organisms and conditions. However, this vast amount of information needs to be extracted in a reasonable way and...

    Authors: Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt and Roland Eils
    Citation: BMC Bioinformatics 2006 7:119
    Content type: Methodology article Published on:

  22. Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the org...

    Authors: Areejit Samal, Shalini Singh, Varun Giri, Sandeep Krishna, Nandula Raghuram and Sanjay Jain
    Citation: BMC Bioinformatics 2006 7:118
    Content type: Research article Published on:

  23. The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usu...

    Authors: Zhengdong Zhang, George W Jackson, George E Fox and Richard C Willson
    Citation: BMC Bioinformatics 2006 7:117
    Content type: Research article Published on:

  24. Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor c...

    Authors: Haiying Wang, Huiru Zheng, David Simpson and Francisco Azuaje
    Citation: BMC Bioinformatics 2006 7:116
    Content type: Research article Published on:

  25. Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in wi...

    Authors: Chun Liang, Feng Sun, Haiming Wang, Junfeng Qu, Robert M Freeman Jr, Lee H Pratt and Marie-Michèle Cordonnier-Pratt
    Citation: BMC Bioinformatics 2006 7:115
    Content type: Software Published on:

  26. The canonical core promoter elements consist of the TATA box, initiator (Inr), downstream core promoter element (DPE), TFIIB recognition element (BRE) and the newly-discovered motif 10 element (MTE). The motif...

    Authors: Victor X Jin, Gregory AC Singer, Francisco J Agosto-Pérez, Sandya Liyanarachchi and Ramana V Davuluri
    Citation: BMC Bioinformatics 2006 7:114
    Content type: Research article Published on:

  27. The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was recently published using six motif disco...

    Authors: Kenzie D MacIsaac, Ting Wang, D Benjamin Gordon, David K Gifford, Gary D Stormo and Ernest Fraenkel
    Citation: BMC Bioinformatics 2006 7:113
    Content type: Research article Published on:

  28. MicroRNAs (miRNAs) are recently discovered short non-protein-coding RNA molecules. miRNAs are increasingly implicated in tissue-specific transcriptional control and particularly in development. Because there i...

    Authors: Hidenori Inaoka, Yutaka Fukuoka and Isaac S Kohane
    Citation: BMC Bioinformatics 2006 7:112
    Content type: Research article Published on:

  29. Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been man...

    Authors: Scott A Becker, Nathan D Price and Bernhard Ø Palsson
    Citation: BMC Bioinformatics 2006 7:111
    Content type: Research article Published on:

  30. Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to...

    Authors: Michael Spitzer, Stefan Lorkowski, Paul Cullen, Alexander Sczyrba and Georg Fuellen
    Citation: BMC Bioinformatics 2006 7:110
    Content type: Research article Published on:

  35. Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set ...

    Authors: Roel GW Verhaak, Frank JT Staal, Peter JM Valk, Bob Lowenberg, Marcel JT Reinders and Dick de Ridder
    Citation: BMC Bioinformatics 2006 7:105
    Content type: Research article Published on:

  36. Currently there is a strong need for methods that help to obtain an accurate description of protein interfaces in order to be able to understand the principles that govern molecular recognition and protein fun...

    Authors: Joan Teyra, Andreas Doms, Michael Schroeder and M Teresa Pisabarro
    Citation: BMC Bioinformatics 2006 7:104
    Content type: Database Published on:

  37. Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence...

    Authors: Arthur Chun-Chieh Shih, DT Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao and Mu-Fen Hsieh
    Citation: BMC Bioinformatics 2006 7:103
    Content type: Software Published on:

  38. Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, effici...

    Authors: Richard P Auburn, Roslin R Russell, Bettina Fischer, Lisa A Meadows, Santiago Sevillano Matilla and Steven Russell
    Citation: BMC Bioinformatics 2006 7:102
    Content type: Software Published on:

  39. Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of potential cross-hybridization. This i...

    Authors: Yian A Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H Slate, Konan Peck, Wenying Xu, Eberhard O Voit and Jonas S Almeida
    Citation: BMC Bioinformatics 2006 7:101
    Content type: Research article Published on:

  40. Low-level processing and normalization of microarray data are most important steps in microarray analysis, which have profound impact on downstream analysis. Multiple methods have been suggested to date, but i...

    Authors: Henrik Bengtsson and Ola Hössjer
    Citation: BMC Bioinformatics 2006 7:100
    Content type: Methodology article Published on:

  41. As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease develop...

    Authors: Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie and Michael F Ochs
    Citation: BMC Bioinformatics 2006 7:99
    Content type: Methodology article Published on:

  42. Restriction enzymes are one of the everyday tools used in molecular biology. The continuously expanding panel of known restriction enzymes (several thousands) renders their optimal use virtually impossible wit...

    Authors: Patrick Martin, Kim E Boulukos and Philippe Pognonec
    Citation: BMC Bioinformatics 2006 7:98
    Content type: Software Published on:

  43. With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for eas...

    Authors: Richard G Côté, Philip Jones, Rolf Apweiler and Henning Hermjakob
    Citation: BMC Bioinformatics 2006 7:97
    Content type: Software Published on:

  46. Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable "balls in a bag", as may be appropriate for transcripts in mi...

    Authors: Stefan M Stanley, Timothy L Bailey and John S Mattick
    Citation: BMC Bioinformatics 2006 7:94
    Content type: Methodology article Published on:

  47. Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations pr...

    Authors: Howard Salis, Vassilios Sotiropoulos and Yiannis N Kaznessis
    Citation: BMC Bioinformatics 2006 7:93
    Content type: Software Published on:

  48. Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated corpora, GENIA and GENETAG, are most...

    Authors: Richard Tzong-Han Tsai, Shih-Hung Wu, Wen-Chi Chou, Yu-Chun Lin, Ding He, Jieh Hsiang, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2006 7:92
    Content type: Research article Published on:

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