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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  24. 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:

  25. 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:

  26. 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:

  28. Knowledge of the subcellular location of a protein is critical to understanding how that protein works in a cell. This location is frequently determined by the interpretation of fluorescence microscope images....

    Authors: Shann-Ching Chen and Robert F Murphy
    Citation: BMC Bioinformatics 2006 7:90
    Content type: Methodology article Published on:

  29. When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to ne...

    Authors: Michael E Bradley and Steven A Benner
    Citation: BMC Bioinformatics 2006 7:89
    Content type: Research article Published on:

  31. Recent circadian clock studies using gene expression microarray in two different tissues of mouse have revealed not all circadian-related genes are synchronized in phase or peak expression times across tissues in...

    Authors: Delong Liu, Shyamal D Peddada, Leping Li and Clarice R Weinberg
    Citation: BMC Bioinformatics 2006 7:87
    Content type: Methodology article Published on:

  32. The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tr...

    Authors: Ricardo ZN Vêncio, Tie Koide, Suely L Gomes and Carlos A de B Pereira
    Citation: BMC Bioinformatics 2006 7:86
    Content type: Software Published on:

  33. Even though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate ...

    Authors: Joshua S Yuan, Ann Reed, Feng Chen and C Neal Stewart Jr
    Citation: BMC Bioinformatics 2006 7:85
    Content type: Methodology article Published on:

  34. Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size requ...

    Authors: Grier P Page, Jode W Edwards, Gary L Gadbury, Prashanth Yelisetti, Jelai Wang, Prinal Trivedi and David B Allison
    Citation: BMC Bioinformatics 2006 7:84
    Content type: Software Published on:

  35. DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogene...

    Authors: Jing Huang, Wen Wei, Joyce Chen, Jane Zhang, Guoying Liu, Xiaojun Di, Rui Mei, Shumpei Ishikawa, Hiroyuki Aburatani, Keith W Jones and Michael H Shapero
    Citation: BMC Bioinformatics 2006 7:83
    Content type: Methodology article Published on:

  36. Protein kinases and protein phosphatases are the fundamental components of phosphorylation dependent protein regulatory systems. We have created a database for the protein kinase-like and phosphatase-like loci...

    Authors: Alistair RR Forrest, Darrin F Taylor, J Lynn Fink, M Milena Gongora, Cameron Flegg, Rohan D Teasdale, Harukazu Suzuki, Mutsumi Kanamori, Chikatoshi Kai, Yoshihide Hayashizaki and Sean M Grimmond
    Citation: BMC Bioinformatics 2006 7:82
    Content type: Research article Published on:

  37. Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map ...

    Authors: GW Patton, R Stephens, IA Sidorov, X Xiao, RA Lempicki, DS Dimitrov, RH Shoemaker and G Tudor
    Citation: BMC Bioinformatics 2006 7:81
    Content type: Methodology article Published on:

  38. Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functionally related genes. The effectiveness wi...

    Authors: Jie Wu, Zhenjun Hu and Charles DeLisi
    Citation: BMC Bioinformatics 2006 7:80
    Content type: Methodology article Published on:

  39. Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of th...

    Authors: Gareth Palidwor, Emmanuel G Reynaud and Miguel A Andrade-Navarro
    Citation: BMC Bioinformatics 2006 7:79
    Content type: Software Published on:

  40. The extended use of microarray technologies has enabled the generation and accumulation of gene expression datasets that contain expression levels of thousands of genes across tens or hundreds of different exp...

    Authors: Pedro Carmona-Saez, Roberto D Pascual-Marqui, F Tirado, Jose M Carazo and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2006 7:78
    Content type: Methodology article Published on:

  42. Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site sequences separated by intervening distances that vary a...

    Authors: Chengpeng Bi and Peter K Rogan
    Citation: BMC Bioinformatics 2006 7:76
    Content type: Software Published on:

  43. Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which...

    Authors: Andrew E Firth and Chris M Brown
    Citation: BMC Bioinformatics 2006 7:75
    Content type: Software Published on:

  47. Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually so...

    Authors: Paul Shafer, Timothy Isganitis and Golan Yona
    Citation: BMC Bioinformatics 2006 7:71
    Content type: Methodology article Published on:

  50. The structure of proteins may change as a result of the inherent flexibility of some protein regions. We develop and explore probabilistic machine learning methods for predicting a continuum secondary structur...

    Authors: Mikael Bodén, Zheng Yuan and Timothy L Bailey
    Citation: BMC Bioinformatics 2006 7:68
    Content type: Methodology article Published on:

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