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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  8. 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:

  9. 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:

  13. 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:

  16. 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:

  17. Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison...

    Authors: Christian V Forst, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
    Citation: BMC Bioinformatics 2006 7:67
    Content type: Research article Published on:

  20. Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large dataset...

    Authors: Christoph Gille and Peter N Robinson
    Citation: BMC Bioinformatics 2006 7:64
    Content type: Methodology article Published on:

  22. In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, suc...

    Authors: Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern and Stephan Waack
    Citation: BMC Bioinformatics 2006 7:62
    Content type: Research article Published on:

  23. Finding the genetic causes of quantitative traits is a complex and difficult task. Classical methods for mapping quantitative trail loci (QTL) in miceuse an F2 cross between two strains with substantially diff...

    Authors: Phillip McClurg, Mathew T Pletcher, Tim Wiltshire and Andrew I Su
    Citation: BMC Bioinformatics 2006 7:61
    Content type: Research article Published on:

  24. A great deal of effort and expense are being expended internationally in attempts to detect genetic polymorphisms contributing to susceptibility to complex human disease. Techniques such as Linkage Disequilibr...

    Authors: Kim W Carter, Pamela A McCaskie and Lyle J Palmer
    Citation: BMC Bioinformatics 2006 7:60
    Content type: Software Published on:

  28. Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional capabilities. While the structural analy...

    Authors: Steffen Klamt, Julio Saez-Rodriguez, Jonathan A Lindquist, Luca Simeoni and Ernst D Gilles
    Citation: BMC Bioinformatics 2006 7:56
    Content type: Methodology article Published on:

  29. The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data manag...

    Authors: Michael Baitaluk, Xufei Qian, Shubhada Godbole, Alpan Raval, Animesh Ray and Amarnath Gupta
    Citation: BMC Bioinformatics 2006 7:55
    Content type: Methodology article Published on:

  30. Microarray technology is generating huge amounts of data about the expression level of thousands of genes, or even whole genomes, across different experimental conditions. To extract biological knowledge, and ...

    Authors: Pedro Carmona-Saez, Monica Chagoyen, Andres Rodriguez, Oswaldo Trelles, Jose M Carazo and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2006 7:54
    Content type: Methodology article Published on:

  31. The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence simi...

    Authors: Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski and Eugene I Shakhnovich
    Citation: BMC Bioinformatics 2006 7:53
    Content type: Database Published on:

  33. A key problem of drug development is to decide which compounds to evaluate further in expensive clinical trials (Phase I- III). This decision is primarily based on the primary targets and mechanisms of action ...

    Authors: Kristofer Hallén, Johan Björkegren and Jesper Tegnér
    Citation: BMC Bioinformatics 2006 7:51
    Content type: Research article Published on:

  34. The number of genes declared differentially expressed is a random variable and its variability can be assessed by resampling techniques. Another important stability indicator is the frequency with which a give...

    Authors: Xing Qiu, Yuanhui Xiao, Alexander Gordon and Andrei Yakovlev
    Citation: BMC Bioinformatics 2006 7:50
    Content type: Methodology article Published on:

  37. Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphor...

    Authors: Ross I Brinkworth, Alan L Munn and Boštjan Kobe
    Citation: BMC Bioinformatics 2006 7:47
    Content type: Research article Published on:

  38. While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most du...

    Authors: Wen-Yu Chung, Reka Albert, Istvan Albert, Anton Nekrutenko and Kateryna D Makova
    Citation: BMC Bioinformatics 2006 7:46
    Content type: Research article Published on:

  41. The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark d...

    Authors: Tim Van den Bulcke, Koenraad Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor and Kathleen Marchal
    Citation: BMC Bioinformatics 2006 7:43
    Content type: Methodology article Published on:

  42. Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many sm...

    Authors: Harald Barsnes, Svein-Ole Mikalsen and Ingvar Eidhammer
    Citation: BMC Bioinformatics 2006 7:42
    Content type: Software Published on:

  43. Experimental techniques such as DNA microarray, serial analysis of gene expression (SAGE) and mass spectrometry proteomics, among others, are generating large amounts of data related to genes and proteins at d...

    Authors: Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, Jose M Carazo and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2006 7:41
    Content type: Methodology article Published on:

  45. The identification and characterization of genes that influence the risk of common, complex multifactorial disease primarily through interactions with other genes and environmental factors remains a statistica...

    Authors: Alison A Motsinger, Stephen L Lee, George Mellick and Marylyn D Ritchie
    Citation: BMC Bioinformatics 2006 7:39
    Content type: Research article Published on:

  46. Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with hig...

    Authors: Hao-Teng Chang, Tun-Wen Pai, Tan-chi Fan, Bo-Han Su, Pei-Chih Wu, Chuan-Yi Tang, Chun-Tien Chang, Shi-Hwei Liu and Margaret Dah-Tsyr Chang
    Citation: BMC Bioinformatics 2006 7:38
    Content type: Methodology article Published on:

  47. With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a re...

    Authors: Xiao I Liu, Neeraj Korde, Ursula Jakob and Lars I Leichert
    Citation: BMC Bioinformatics 2006 7:37
    Content type: Database Published on:

  48. Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being...

    Authors: Domenico Catalano, Flavio Licciulli, Antonio Turi, Giorgio Grillo, Cecilia Saccone and Domenica D'Elia
    Citation: BMC Bioinformatics 2006 7:36
    Content type: Database Published on:

  49. High-density microarray technology is increasingly applied to study gene expression levels on a large scale. Microarray experiments rely on several critical steps that may introduce error and uncertainty in an...

    Authors: Kyoungmi Kim, Grier P Page, T Mark Beasley, Stephen Barnes, Katherine E Scheirer and David B Allison
    Citation: BMC Bioinformatics 2006 7:35
    Content type: Research article Published on:

  50. There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sourc...

    Authors: Erdahl T Teber, Edward Crawford, Kent B Bolton, Derek Van Dyk, Peter R Schofield, Vimal Kapoor and W Bret Church
    Citation: BMC Bioinformatics 2006 7:33
    Content type: Software Published on:

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