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  1. Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in...

    Authors: Stephen Winters-Hilt, Matthew Landry, Mark Akeson, Maria Tanase, Iftekhar Amin, Amy Coombs, Eric Morales, John Millet, Carl Baribault and Srikanth Sendamangalam
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  2. A Nanopore Detector provides a means to transduce single molecule events into observable channel current changes. Nanopore-based detection can report directly, or indirectly, on single molecule kinetics. The n...

    Authors: Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  3. Aristolochic acid (AA) is the active component of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. AA, however, induced nephropathy and urothelial cancer ...

    Authors: Tao Chen, Lei Guo, Lu Zhang, Leming Shi, Hong Fang, Yongming Sun, James C Fuscoe and Nan Mei
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  4. Fibrates are a unique hypolipidemic drugs that lower plasma triglyceride and cholesterol levels through their action as peroxisome proliferator-activated receptor alpha (PPARα) agonists. The activation of PPAR...

    Authors: Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey Dial, Alex Wong, Kshama Mehta, Ernice Blann, Leming Shi, Weida Tong and Yvonne P Dragan
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  5. Comfrey is consumed by humans as a vegetable and a tea, and has been used as an herbal medicine for more than 2000 years. Comfrey, however, is hepatotoxic in livestock and humans and carcinogenic in experiment...

    Authors: Nan Mei, Lei Guo, Lu Zhang, Leming Shi, Yongming Andrew Sun, Chris Fung, Carrie L Moland, Stacey L Dial, James C Fuscoe and Tao Chen
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  7. The Thymidine kinase (Tk) mutants generated from the widely used L5178Y mouse lymphoma assay fall into two categories, small colony and large colony. Cells from the large colonies grow at a normal rate while cell...

    Authors: Tao Han, Jianyong Wang, Weida Tong, Martha M Moore, James C Fuscoe and Tao Chen
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  8. The recent advancement of microarray technology with lower noise and better affordability makes it possible to determine expression of several thousand genes simultaneously. The differentially expressed genes ...

    Authors: Raja Loganantharaj, Satish Cheepala and John Clifford
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  9. The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names w...

    Authors: Jonathan D Wren
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 2

  12. Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simp...

    Authors: Mary E Dolan, Constance C Holden, M Kate Beard and Carol J Bult
    Citation: BMC Bioinformatics 2006 7:416
    Content type: Methodology article Published on:

  14. Various statistical scores have been proposed for evaluating the significance of genes that may exhibit differential expression between two or more controlled conditions. However, in many clinical studies to d...

    Authors: Shigeyuki Oba and Shin lshii
    Citation: BMC Bioinformatics 2006 7:414
    Content type: Methodology article Published on:

  15. Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that commo...

    Authors: Angela Re, Davide Cora, Alda Maria Puliti, Michele Caselle and Isabella Sbrana
    Citation: BMC Bioinformatics 2006 7:413
    Content type: Research article Published on:

  16. Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions, which consequently compl...

    Authors: Cheong Xin Chan, Robert G Beiko and Mark A Ragan
    Citation: BMC Bioinformatics 2006 7:412
    Content type: Research article Published on:

  19. DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The re...

    Authors: Stephan Hutter, Albert J Vilella and Julio Rozas
    Citation: BMC Bioinformatics 2006 7:409
    Content type: Software Published on:

  20. Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such a...

    Authors: Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey L Sheetlin, David Landsman and John L Spouge
    Citation: BMC Bioinformatics 2006 7:408
    Content type: Software Published on:

  22. After the publication of [1], we were alerted to an error in our data. The error was an one-off miscalculation in the extraction of position information for our set of true negatives. Our data set should have use...

    Authors: James Thompson and Shuba Gopal
    Citation: BMC Bioinformatics 2006 7:406
    Content type: Erratum Published on:

    The original article was published in BMC Bioinformatics 2006 7:145

  23. A number of methods that use both protein structural and evolutionary information are available to predict the functional consequences of missense mutations. However, many of these methods break down if either...

    Authors: Chris J Needham, James R Bradford, Andrew J Bulpitt, Matthew A Care and David R Westhead
    Citation: BMC Bioinformatics 2006 7:405
    Content type: Research article Published on:

  24. The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted...

    Authors: Wenjie Shu, Xiaochen Bo, Rujia Liu, Dongsheng Zhao, Zhiqiang Zheng and Shengqi Wang
    Citation: BMC Bioinformatics 2006 7:404
    Content type: Software Published on:

  25. Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and sta...

    Authors: Mark K Titulaer, Ivar Siccama, Lennard J Dekker, Angelique LCT van Rijswijk, Ron MA Heeren, Peter A Sillevis Smitt and Theo M Luider
    Citation: BMC Bioinformatics 2006 7:403
    Content type: Software Published on:

  26. We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps...

    Authors: Davide Baú, Alberto JM Martin, Catherine Mooney, Alessandro Vullo, Ian Walsh and Gianluca Pollastri
    Citation: BMC Bioinformatics 2006 7:402
    Content type: Software Published on:

  29. Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis and selection of treatm...

    Authors: Hiro Takahashi, Takeshi Nemoto, Teruhiko Yoshida, Hiroyuki Honda and Tadashi Hasegawa
    Citation: BMC Bioinformatics 2006 7:399
    Content type: Research article Published on:

  30. Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of species. They can also be used to determine sets of genes or proteins that occur only in certain evolutionary branche...

    Authors: Tim Hulsen, Jacob de Vlieg and Peter MA Groenen
    Citation: BMC Bioinformatics 2006 7:398
    Content type: Database Published on:

  33. Affymetrix microarrays have become a standard experimental platform for studies of mRNA expression profiling. Their success is due, in part, to the multiple oligonucleotide features (probes) against each trans...

    Authors: Jinwook Seo and Eric P Hoffman
    Citation: BMC Bioinformatics 2006 7:395
    Content type: Commentary Published on:

  35. Olfactory receptors (ORs), the largest mammalian gene superfamily (900–1400 genes), has >50% pseudogenes in humans. While most of these inactive genes are identified via coding frame (nonsense) disruptions, se...

    Authors: Idan Menashe, Ronny Aloni and Doron Lancet
    Citation: BMC Bioinformatics 2006 7:393
    Content type: Methodology article Published on:

  38. We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments ra...

    Authors: Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Ken Sung and Yijun Ruan
    Citation: BMC Bioinformatics 2006 7:390
    Content type: Software Published on:

  39. In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes ...

    Authors: Michael Beckstette, Robert Homann, Robert Giegerich and Stefan Kurtz
    Citation: BMC Bioinformatics 2006 7:389
    Content type: Methodology article Published on:

  40. Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normaliz...

    Authors: Jochen Jaeger and Rainer Spang
    Citation: BMC Bioinformatics 2006 7:388
    Content type: Methodology article Published on:

  41. In this paper we present a method for the statistical assessment of cancer predictors which make use of gene expression profiles. The methodology is applied to a new data set of microarray gene expression data...

    Authors: N Ancona, R Maglietta, A Piepoli, A D'Addabbo, R Cotugno, M Savino, S Liuni, M Carella, G Pesole and F Perri
    Citation: BMC Bioinformatics 2006 7:387
    Content type: Research article Published on:

  42. The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metab...

    Authors: Jing Zhao, Hong Yu, Jian-Hua Luo, Zhi-Wei Cao and Yi-Xue Li
    Citation: BMC Bioinformatics 2006 7:386
    Content type: Research article Published on:

  45. With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of gen...

    Authors: B Jayashree, Praveen T Reddy, Y Leeladevi, Jonathan H Crouch, V Mahalakshmi, Hutokshi K Buhariwalla, KE Eshwar, Emma Mace, Rolf Folksterma, S Senthilvel, Rajeev K Varshney, K Seetha, R Rajalakshmi, VP Prasanth, Subhash Chandra, L Swarupa…
    Citation: BMC Bioinformatics 2006 7:383
    Content type: Software Published on:

  47. Reverse-engineering regulatory networks is one of the central challenges for computational biology. Many techniques have been developed to accomplish this by utilizing transcription factor binding data in conj...

    Authors: Shawn Cokus, Sherri Rose, David Haynor, Niels Grønbech-Jensen and Matteo Pellegrini
    Citation: BMC Bioinformatics 2006 7:381
    Content type: Research article Published on:

  49. Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in ...

    Authors: Li-Yeh Chuang, Cheng-Hong Yang, Yu-Huei Cheng, De-Leung Gu, Phei-Lang Chang, Ke-Hung Tsui and Hsueh-Wei Chang
    Citation: BMC Bioinformatics 2006 7:379
    Content type: Database Published on:

  50. The highly dimensional data produced by functional genomic (FG) studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays). Although dimensionality r...

    Authors: Derrick K Rollins, Dongmei Zhai, Alrica L Joe, Jack W Guidarelli, Abhishek Murarka and Ramon Gonzalez
    Citation: BMC Bioinformatics 2006 7:377
    Content type: Methodology article Published on:

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