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  1. The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBM...

    Authors: Yunlong Liu, Matthew P Vincenti and Hiroki Yokota
    Citation: BMC Bioinformatics 2005 6:276
    Content type: Methodology article Published on:

  2. In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the...

    Authors: Mehrnoush Khojasteh, Wan L Lam, Rabab K Ward and Calum MacAulay
    Citation: BMC Bioinformatics 2005 6:274
    Content type: Methodology article Published on:

  3. Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algor...

    Authors: Alexander K Hudek and Daniel G Brown
    Citation: BMC Bioinformatics 2005 6:273
    Content type: Research article Published on:

  6. In a genetic interaction, the phenotype of a double mutant differs from the combined phenotypes of the underlying single mutants. When the single mutants have no growth defect, but the double mutant is lethal ...

    Authors: Ping Ye, Brian D Peyser, Forrest A Spencer and Joel S Bader
    Citation: BMC Bioinformatics 2005 6:270
    Content type: Research article Published on:

  7. It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis...

    Authors: Homin K Lee, William Braynen, Kiran Keshav and Paul Pavlidis
    Citation: BMC Bioinformatics 2005 6:269
    Content type: Software Published on:

  8. The generation of large amounts of microarray data presents challenges for data collection, annotation, exchange and analysis. Although there are now widely accepted formats, minimum standards for data content...

    Authors: Mahendra Navarange, Laurence Game, Derek Fowler, Vihar Wadekar, Helen Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick and Helen C Causton
    Citation: BMC Bioinformatics 2005 6:268
    Content type: Database Published on:

  9. MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds of them have been identified in...

    Authors: Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J Brownstein, Thomas Tuschl, Erik van Nimwegen and Mihaela Zavolan
    Citation: BMC Bioinformatics 2005 6:267
    Content type: Research article Published on:

  10. Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whethe...

    Authors: AD Neverov, II Artamonova, RN Nurtdinov, D Frishman, MS Gelfand and AA Mironov
    Citation: BMC Bioinformatics 2005 6:266
    Content type: Research article Published on:

  11. The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies. Although similar questions for t...

    Authors: Patrick Warnat, Roland Eils and Benedikt Brors
    Citation: BMC Bioinformatics 2005 6:265
    Content type: Methodology article Published on:

  12. maxdLoad2 is a relational database schema and Java® application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification...

    Authors: David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A Joseph Wood, Karim Nashar, Douglas B Kell and Andy Brass
    Citation: BMC Bioinformatics 2005 6:264
    Content type: Software Published on:

  14. Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upst...

    Authors: Bob Y Chan and Dennis Kibler
    Citation: BMC Bioinformatics 2005 6:262
    Content type: Methodology article Published on:

  15. Accurate and automatic gene finding and structural prediction is a common problem in bioinformatics, and applications need to be capable of handling non-canonical splice sites, micro-exons and partial gene str...

    Authors: Alexander Churbanov, Mark Pauley, Daniel Quest and Hesham Ali
    Citation: BMC Bioinformatics 2005 6:261
    Content type: Methodology article Published on:

  17. The purpose of this study is to determine whether or not there exists nonrandom grouping of cis-regulatory elements within gene promoters that can be perceived independent of gene expression data and whether o...

    Authors: Markey C McNutt, Ron Tongbai, Wenwu Cui, Irene Collins, Wendy J Freebern, Idalia Montano, Cynthia M Haggerty, GVR Chandramouli and Kevin Gardner
    Citation: BMC Bioinformatics 2005 6:259
    Content type: Research article Published on:

  18. Gene expression programs depend on recognition of cis elements in promoter region of target genes by transcription factors (TFs), but how TFs regulate gene expression via recognition of cis elements is still not ...

    Authors: Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li and Bor-Sen Chen
    Citation: BMC Bioinformatics 2005 6:258
    Content type: Methodology article Published on:

  20. Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six softw...

    Authors: Eric W Klee and Lynda BM Ellis
    Citation: BMC Bioinformatics 2005 6:256
    Content type: Research article Published on:

  21. The Flaviviridae virus family includes major human and animal pathogens. The RNA dependent RNA polymerase (RdRp) plays a central role in the replication process, and thus is a validated target for antiviral drugs...

    Authors: François Ferron, Cécile Bussetta, Hélène Dutartre and Bruno Canard
    Citation: BMC Bioinformatics 2005 6:255
    Content type: Research article Published on:

  23. Profile-profile methods have been used for some years now to detect and align homologous proteins. The best such methods use information from the background distribution of amino acids and substitution tables ...

    Authors: Tomas Ohlson and Arne Elofsson
    Citation: BMC Bioinformatics 2005 6:253
    Content type: Research article Published on:

  24. Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data s...

    Authors: Thomas Mailund, Mikkel H Schierup, Christian NS Pedersen, Peter JM Mechlenborg, Jesper N Madsen and Leif Schauser
    Citation: BMC Bioinformatics 2005 6:252
    Content type: Software Published on:

  26. cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to...

    Authors: Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Michael Sjöström, Stefan Jansson, Henrik Antti and Johan Trygg
    Citation: BMC Bioinformatics 2005 6:250
    Content type: Methodology article Published on:

  27. The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an ...

    Authors: Khar Heng Choo, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Bioinformatics 2005 6:249
    Content type: Database Published on:

  30. Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficu...

    Authors: Stéphanie Monnier, David G Cox, Tim Albion and Federico Canzian
    Citation: BMC Bioinformatics 2005 6:246
    Content type: Software Published on:

  32. Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationall...

    Authors: Paola Bonizzoni, Raffaella Rizzi and Graziano Pesole
    Citation: BMC Bioinformatics 2005 6:244
    Content type: Software Published on:

  34. The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. While a majority of the approximately 30000 known and predicted...

    Authors: Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D Szustakowski and NR Nirmala
    Citation: BMC Bioinformatics 2005 6:242
    Content type: Methodology article Published on:

  35. In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investig...

    Authors: Eva Freyhult, Paul P Gardner and Vincent Moulton
    Citation: BMC Bioinformatics 2005 6:241
    Content type: Research article Published on:

  36. The recent explosion in the availability of complete genome sequences has led to the cataloging of tens of thousands of new proteins and putative proteins. Many of these proteins can be structurally or functio...

    Authors: Thomas J Magliery and Lynne Regan
    Citation: BMC Bioinformatics 2005 6:240
    Content type: Research article Published on:

  37. A recent publication described a supervised classification method for microarray data: Between Group Analysis (BGA). This method which is based on performing multivariate ordination of groups proved to be very...

    Authors: Florent Baty, Michel P Bihl, Guy Perrière, Aedín C Culhane and Martin H Brutsche
    Citation: BMC Bioinformatics 2005 6:239
    Content type: Methodology article Published on:

  38. Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome seq...

    Authors: Bart Pieterse, Elisabeth J Quirijns, Frank HJ Schuren and Mariët J van der Werf
    Citation: BMC Bioinformatics 2005 6:238
    Content type: Methodology article Published on:

  39. Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of tra...

    Authors: Szymon M Kielbasa, Didier Gonze and Hanspeter Herzel
    Citation: BMC Bioinformatics 2005 6:237
    Content type: Software Published on:

  40. General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificia...

    Authors: Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier
    Citation: BMC Bioinformatics 2005 6:236
    Content type: Software Published on:

  41. Several data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types....

    Authors: Andrew R Jones and Norman W Paton
    Citation: BMC Bioinformatics 2005 6:235
    Content type: Methodology article Published on:

  42. A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots a...

    Authors: Brian DM Tom, Walter R Gilks, Elizabeth T Brooke-Powell and James W Ajioka
    Citation: BMC Bioinformatics 2005 6:234
    Content type: Methodology article Published on:

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