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  2. Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to ass...

    Authors: James J Chen, Huey-Miin Hsueh, Robert R Delongchamp, Chien-Ju Lin and Chen-An Tsai
    Citation: BMC Bioinformatics 2007 8:412
    Content type: Correspondence Published on:

  3. Answers to several fundamental questions in statistical genetics would ideally require knowledge of the ancestral pedigree and of the gene flow therein. A few examples of such questions are haplotype estimatio...

    Authors: Dario Gasbarra, Matti Pirinen, Mikko J Sillanpää and Elja Arjas
    Citation: BMC Bioinformatics 2007 8:411
    Content type: Methodology article Published on:

  4. Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and int...

    Authors: Rezarta Islamaj Dogan, Lise Getoor, W John Wilbur and Stephen M Mount
    Citation: BMC Bioinformatics 2007 8:410
    Content type: Research article Published on:

  5. Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to ...

    Authors: Marjo V Smith, Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
    Citation: BMC Bioinformatics 2007 8:409
    Content type: Methodology article Published on:

  6. Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interaction (PPI) networks. A key concept in the organization of PPI networks is the existen...

    Authors: Ioannis A Maraziotis, Konstantina Dimitrakopoulou and Anastasios Bezerianos
    Citation: BMC Bioinformatics 2007 8:408
    Content type: Research article Published on:

  7. Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is d...

    Authors: Charles G Danko, Vera A McIlvain, Maochun Qin, Barry E Knox and Arkady M Pertsov
    Citation: BMC Bioinformatics 2007 8:407
    Content type: Research article Published on:

  8. Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenome...

    Authors: Thierry Lombardot, Renzo Kottmann, Gregory Giuliani, Andrea de Bono, Nans Addor and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2007 8:406
    Content type: Software Published on:

  9. Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented ...

    Authors: Alexandros Stamatakis, Alexander F Auch, Jan Meier-Kolthoff and Markus Göker
    Citation: BMC Bioinformatics 2007 8:405
    Content type: Software Published on:

  12. Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence dat...

    Authors: Daniel Dalevi, Todd Z DeSantis, Jakob Fredslund, Gary L Andersen, Victor M Markowitz and Philip Hugenholtz
    Citation: BMC Bioinformatics 2007 8:402
    Content type: Software Published on:

  13. Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is ...

    Authors: Richard G Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler and Henning Hermjakob
    Citation: BMC Bioinformatics 2007 8:401
    Content type: Software Published on:

  14. The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research co...

    Authors: Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin TR Kuiper and Pierre Hilson
    Citation: BMC Bioinformatics 2007 8:400
    Content type: Research article Published on:

  15. The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher t...

    Authors: Randy Z Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li and Shoudan Liang
    Citation: BMC Bioinformatics 2007 8:399
    Content type: Methodology article Published on:

  17. Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent tech...

    Authors: Dennis R Livesay, Patrick D Kidd, Sepehr Eskandari and Usman Roshan
    Citation: BMC Bioinformatics 2007 8:397
    Content type: Research article Published on:

  18. Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different st...

    Authors: Tobias Wittkop, Jan Baumbach, Francisco P Lobo and Sven Rahmann
    Citation: BMC Bioinformatics 2007 8:396
    Content type: Research article Published on:

  20. Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nuc...

    Authors: Oscar M Rueda and Ramon Diaz-Uriarte
    Citation: BMC Bioinformatics 2007 8:394
    Content type: Correspondence Published on:

  21. In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Rényi ent...

    Authors: Susana Vinga and Jonas S Almeida
    Citation: BMC Bioinformatics 2007 8:393
    Content type: Research article Published on:

  23. Domains are the basic functional units of proteins. It is believed that protein-protein interactions are realized through domain interactions. Revealing multi-domain cooperation can provide deep insights into ...

    Authors: Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen
    Citation: BMC Bioinformatics 2007 8:391
    Content type: Research article Published on:

  24. Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinati...

    Authors: William A McLaughlin, Ken Chen, Tingjun Hou and Wei Wang
    Citation: BMC Bioinformatics 2007 8:390
    Content type: Research article Published on:

  25. Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that i...

    Authors: Eider B Moore, Andrew V Poliakov, Peter Lincoln and James F Brinkley
    Citation: BMC Bioinformatics 2007 8:389
    Content type: Software Published on:

  26. Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein s...

    Authors: Joe Dundas, TA Binkowski, Bhaskar DasGupta and Jie Liang
    Citation: BMC Bioinformatics 2007 8:388
    Content type: Research article Published on:

  27. In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be inval...

    Authors: Anders Sjögren, Erik Kristiansson, Mats Rudemo and Olle Nerman
    Citation: BMC Bioinformatics 2007 8:387
    Content type: Methodology article Published on:

  28. The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain i...

    Authors: Holger Froehlich, Mark Fellmann, Holger Sueltmann, Annemarie Poustka and Tim Beissbarth
    Citation: BMC Bioinformatics 2007 8:386
    Content type: Research article Published on:

  30. A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes. For instance, connectivity, clustering c...

    Authors: Yung-Keun Kwon, Sun Shim Choi and Kwang-Hyun Cho
    Citation: BMC Bioinformatics 2007 8:384
    Content type: Research article Published on:

  33. By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. T...

    Authors: Daniel R Caffrey, Paul H Dana, Vidhya Mathur, Marco Ocano, Eun-Jong Hong, Yaoyu E Wang, Shyamal Somaroo, Brian E Caffrey, Shobha Potluri and Enoch S Huang
    Citation: BMC Bioinformatics 2007 8:381
    Content type: Software Published on:

  35. Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is e...

    Authors: Dianhui Zhu, George E Fox and Sugoto Chakravarty
    Citation: BMC Bioinformatics 2007 8:379
    Content type: Software Published on:

  36. Deficiencies in microarray technology cause unwanted variation in the hybridization signal, obscuring the true measurements of intracellular transcript levels. Here we describe a general method that can improv...

    Authors: William O Ward, Carol D Swartz, Steffen Porwollik, Sarah H Warren, Nancy M Hanley, Geremy W Knapp, Michael McClelland and David M DeMarini
    Citation: BMC Bioinformatics 2007 8:378
    Content type: Research article Published on:

  37. Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will co...

    Authors: Robert Hoehndorf, Frank Loebe, Janet Kelso and Heinrich Herre
    Citation: BMC Bioinformatics 2007 8:377
    Content type: Methodology article Published on:

  39. Safety assessment of genetically modified (GM) food, with regard to allergenic potential of transgene-encoded xenoproteins, typically involves several different methods, evaluation by digestibility being one t...

    Authors: Bingjun Jiang, Hong Qu, Yuanlei Hu, Ting Ni and Zhongping Lin
    Citation: BMC Bioinformatics 2007 8:375
    Content type: Research article Published on:

  41. The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computationa...

    Authors: Razif R Gabdoulline, Matthias Stein and Rebecca C Wade
    Citation: BMC Bioinformatics 2007 8:373
    Content type: Research article Published on:

  46. Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in unaffected individuals as polymorphi...

    Authors: Ágnes Baross, Allen D Delaney, H Irene Li, Tarun Nayar, Stephane Flibotte, Hong Qian, Susanna Y Chan, Jennifer Asano, Adrian Ally, Manqiu Cao, Patricia Birch, Mabel Brown-John, Nicole Fernandes, Anne Go, Giulia Kennedy, Sylvie Langlois…
    Citation: BMC Bioinformatics 2007 8:368
    Content type: Research article Published on:

  47. Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been estab...

    Authors: Jan Küntzer, Christina Backes, Torsten Blum, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher and Hans-Peter Lenhof
    Citation: BMC Bioinformatics 2007 8:367
    Content type: Database Published on:

  48. In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important compu...

    Authors: Yair Horesh, Tirza Doniger, Shulamit Michaeli and Ron Unger
    Citation: BMC Bioinformatics 2007 8:366
    Content type: Methodology article Published on:

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