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  1. Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data...

    Authors: Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota and Yusu Wang
    Citation: BMC Bioinformatics 2008 9:344
    Content type: Methodology article Published on:

  2. Tiling arrays are an important tool for the study of transcriptional activity, protein-DNA interactions and chromatin structure on a genome-wide scale at high resolution. Although hidden Markov models have bee...

    Authors: Peter Humburg, David Bulger and Glenn Stone
    Citation: BMC Bioinformatics 2008 9:343
    Content type: Methodology article Published on:

  4. Slow-fast analysis is a simple and effective method to reduce the influence of substitution saturation, one of the causes of phylogenetic noise and long branch attraction (LBA) artifacts. In several steps of i...

    Authors: Martin Kostka, Magdalena Uzlikova, Ivan Cepicka and Jaroslav Flegr
    Citation: BMC Bioinformatics 2008 9:341
    Content type: Software Published on:

  6. Innumerable biological investigations require comparing collections of molecules, cells or organisms to one another with respect to one or more of their properties. Almost all of these comparisons are performe...

    Authors: Arnab Bhattacharya, Sasha Levy, Adria LeBoeuf, Michelle Gaylord, Leslie Wilson, Ambuj K Singh and Stuart C Feinstein
    Citation: BMC Bioinformatics 2008 9:339
    Content type: Research article Published on:

  8. In studies that use DNA arrays to assess changes in gene expression, it is preferable to measure the significance of treatment effects on a group of genes from a pathway or functional category such as gene ont...

    Authors: Taewon Lee, Varsha G Desai, Cruz Velasco, Robert J S Reis and Robert R Delongchamp
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  9. Biological systems can be modeled as complex network systems with many interactions between the components. These interactions give rise to the function and behavior of that system. For example, the protein-pr...

    Authors: Mutlu Mete, Fusheng Tang, Xiaowei Xu and Nurcan Yuruk
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  10. Circadian rhythm is a crucial factor in orchestration of plant physiology, keeping it in synchrony with the daylight cycle. Previous studies have reported that up to 16% of plant transcriptome are circadially ...

    Authors: Andrey Ptitsyn
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  11. Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with phenotypic traits such as diseas...

    Authors: Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, Roger Perkins, Hong Fang, Joshua Xu, James J Chen, Tao Han, Jim Kaput, James C Fuscoe and Weida Tong
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  12. Biological chemistry is very stereospecific. Nonetheless, the diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distingui...

    Authors: Christopher A Bottoms and Dong Xu
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  13. Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector ...

    Authors: Minho Chae, Robert J Shmookler Reis and John J Thaden
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  14. Over the past decade, many investigators have used sophisticated time series tools for the analysis of genomic sequences. Specifically, the correlation of the nucleotide chain has been studied by examining the...

    Authors: Jerzy S Zielinski, Nidhal Bouaynaya, Dan Schonfeld and William O'Neill
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  15. Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties with potential implications for DNA sequencing. The α-Hemolysin transmembr...

    Authors: Alexander Churbanov and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  16. In this paper we present preliminary results stemming from a novel application of Markov Models and Support Vector Machines to splice site classification of Intron-Exon and Exon-Intron (5' and 3') splice sites...

    Authors: Brian Roux and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  17. Relationships between entities such as genes, chemicals, metabolites, phenotypes and diseases in MEDLINE are often directional. That is, one may affect the other in a positive or negative manner. Detection of ...

    Authors: Cory B Giles and Jonathan D Wren
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  18. Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not repr...

    Authors: Leming Shi, Wendell D Jones, Roderick V Jensen, Stephen C Harris, Roger G Perkins, Federico M Goodsaid, Lei Guo, Lisa J Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Catalin C Barbacioru, Vincent Bertholet, Xiaoxi Megan Cao…
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  19. Advances in DNA microarray technology portend that molecular signatures from which microarray will eventually be used in clinical environments and personalized medicine. Derivation of biomarkers is a large ste...

    Authors: Zhenqiang Su, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins and Weida Tong
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  20. Metastases are responsible for the majority of cancer fatalities. The molecular mechanisms governing metastasis are poorly understood, hindering early diagnosis and treatment. Previous studies of gene expressi...

    Authors: Andrey A Ptitsyn, Michael M Weil and Douglas H Thamm
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  21. Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (sim...

    Authors: Arun Rawat, Georg J Seifert and Youping Deng
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  22. In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences....

    Authors: Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola and Hesham Ali
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  23. New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many soft...

    Authors: Tianxiao Huan, Andrey Y Sivachenko, Scott H Harrison and Jake Y Chen
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  24. A statistically robust and biologically-based approach for analysis of microarray data is described that integrates independent biological knowledge and data with a global F-test for finding genes of interest ...

    Authors: Mikhail G Dozmorov, Kimberly D Kyker, Paul J Hauser, Ricardo Saban, David D Buethe, Igor Dozmorov, Michael B Centola, Daniel J Culkin and Robert E Hurst
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  25. Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selec...

    Authors: Vinayak Kulkarni, Mounir Errami, Robert Barber and Harold R Garner
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  26. Gene family identification from ESTs can be a valuable resource for analysis of genome evolution but presents unique challenges in organisms for which the entire genome is not yet sequenced. We have developed ...

    Authors: Ronald L Frank, Cyriac Kandoth and Fikret Ercal
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 9

  28. Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylat...

    Authors: Wei Dai, Jens M Teodoridis, Janet Graham, Constanze Zeller, Tim HM Huang, Pearlly Yan, J Keith Vass, Robert Brown and Jim Paul
    Citation: BMC Bioinformatics 2008 9:337
    Content type: Methodology article Published on:

  30. Both microarrays and quantitative real-time PCR are convenient tools for studying the transcriptional levels of genes. The former is preferable for large scale studies while the latter is a more targeted techn...

    Authors: Andreas W Schreiber, Neil J Shirley, Rachel A Burton and Geoffrey B Fincher
    Citation: BMC Bioinformatics 2008 9:335
    Content type: Methodology article Published on:

  31. There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a numb...

    Authors: Peter Li, Juan I Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R Pocock, Carole A Goble, Stephen G Oliver and Douglas B Kell
    Citation: BMC Bioinformatics 2008 9:334
    Content type: Software Published on:

  32. Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visua...

    Authors: Hamilton Ganesan, Anna S Rakitianskaia, Colin F Davenport, Burkhard Tümmler and Oleg N Reva
    Citation: BMC Bioinformatics 2008 9:333
    Content type: Software Published on:

  33. Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been prop...

    Authors: Olivier Bastien and Eric Maréchal
    Citation: BMC Bioinformatics 2008 9:332
    Content type: Research article Published on:

  35. Laboratory techniques used to determine haplotypes are often too expensive for large-scale studies and lack of phase information is commonly overcome using likelihood-based calculations. Whereas a number of pr...

    Authors: Robert M Nowak and Rafał Płoski
    Citation: BMC Bioinformatics 2008 9:330
    Content type: Software Published on:

  37. Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed mi...

    Authors: Da Meng, Shira L Broschat and Douglas R Call
    Citation: BMC Bioinformatics 2008 9:328
    Content type: Software Published on:

  39. Real-time PCR analysis is a sensitive DNA quantification technique that has recently gained considerable attention in biotechnology, microbiology and molecular diagnostics. Although, the cycle-threshold (Ct) meth...

    Authors: Michele Guescini, Davide Sisti, Marco BL Rocchi, Laura Stocchi and Vilberto Stocchi
    Citation: BMC Bioinformatics 2008 9:326
    Content type: Methodology article Published on:

  40. A better understanding of the mechanisms involved in gas-phase fragmentation of peptides is essential for the development of more reliable algorithms for high-throughput protein identification using mass spect...

    Authors: Cong Zhou, Lucas D Bowler and Jianfeng Feng
    Citation: BMC Bioinformatics 2008 9:325
    Content type: Research article Published on:

  42. Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone ...

    Authors: Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira and Gordon Luikart
    Citation: BMC Bioinformatics 2008 9:323
    Content type: Software Published on:

  44. GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is...

    Authors: Tae-Ho Lee, Yeon-Ki Kim and Baek Hie Nahm
    Citation: BMC Bioinformatics 2008 9:321
    Content type: Software Published on:

  46. Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deplo...

    Authors: Alexander Statnikov, Lily Wang and Constantin F Aliferis
    Citation: BMC Bioinformatics 2008 9:319
    Content type: Research article Published on:

  47. Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines,...

    Authors: Kengo Sato, Toutai Mituyama, Kiyoshi Asai and Yasubumi Sakakibara
    Citation: BMC Bioinformatics 2008 9:318
    Content type: Methodology article Published on:

  48. The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability a...

    Authors: Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R Macías, Gabrielle A Reeves and Andreas Prlić
    Citation: BMC Bioinformatics 2008 9(Suppl 8):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 8

  49. Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Au...

    Authors: Samira Jaeger, Sylvain Gaudan, Ulf Leser and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2008 9(Suppl 8):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 8

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