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  1. Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of ci...

    Authors: Maksim V Plikus, Zina Zhang and Cheng-Ming Chuong
    Citation: BMC Bioinformatics 2006 7:424
    Content type: Software Published on:

  2. In bacteria, sigma factors and other transcriptional regulatory proteins recognize DNA patterns upstream of their target genes and interact with RNA polymerase to control transcription. As a consequence of evo...

    Authors: Pierre-Étienne Jacques, Sébastien Rodrigue, Luc Gaudreau, Jean Goulet and Ryszard Brzezinski
    Citation: BMC Bioinformatics 2006 7:423
    Content type: Research article Published on:

  3. Evaluating the importance of the different sources of variations is essential in microarray data experiments. Complex experimental designs generally include various factors structuring the data which should be...

    Authors: Florent Baty, Michaël Facompré, Jan Wiegand, Joseph Schwager and Martin H Brutsche
    Citation: BMC Bioinformatics 2006 7:422
    Content type: Methodology article Published on:

  5. The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced eukar...

    Authors: Evan S Snitkin, Adam M Gustafson, Joseph Mellor, Jie Wu and Charles DeLisi
    Citation: BMC Bioinformatics 2006 7:420
    Content type: Research article Published on:

  7. Gene Ontology (GO) characterizes and categorizes the functions of genes and their products according to biological processes, molecular functions and cellular components, facilitating interpretation of data fr...

    Authors: Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins and Weida Tong
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S23
    Content type: Proceedings Published on:

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

  8. 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

  9. 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

  10. 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

  11. Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families...

    Authors: Ronald L Frank, Ajay Mane and Fikret Ercal
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S19
    Content type: Proceedings Published on:

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

  12. 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

  13. DNA microarrays, which have been increasingly used to monitor mRNA transcripts at a global level, can provide detailed insight into cellular processes involved in response to drugs and toxins. This is leading ...

    Authors: Tao Han, Cathy D Melvin, Leming Shi, William S Branham, Carrie L Moland, P Scott Pine, Karol L Thompson and James C Fuscoe
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S17
    Content type: Proceedings Published on:

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

  14. 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

  15. We present a novel strategy for classification of DNA molecules using measurements from an alpha-Hemolysin channel detector. The proposed approach provides excellent classification performance for five differe...

    Authors: Raja Tanveer Iqbal, Matthew Landry and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S15
    Content type: Proceedings Published on:

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

  17. Massive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the r...

    Authors: Alexdander Kel, Nico Voss, Ruy Jauregui, Olga Kel-Margoulis and Edgar Wingender
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S13
    Content type: Proceedings Published on:

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

  18. Recursive Feature Elimination is a common and well-studied method for reducing the number of attributes used for further analysis or development of prediction models. The effectiveness of the RFE algorithm is ...

    Authors: Yuanyuan Ding and Dawn Wilkins
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S12
    Content type: Proceedings Published on:

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

  19. In studies that use DNA arrays to assess changes in gene expression, our goal is to evaluate the statistical significance of treatments on sets of genes. Genes can be grouped by a molecular function, a biologi...

    Authors: Robert Delongchamp, Taewon Lee and Cruz Velasco
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S11
    Content type: Proceedings Published on:

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

  20. Periodic processes, such as the circadian rhythm, are important factors modulating and coordinating transcription of genes governing key metabolic pathways. Theoretically, even small fluctuations in the orches...

    Authors: Andrey A Ptitsyn, Sanjin Zvonic and Jeffrey M Gimble
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S10
    Content type: Proceedings Published on:

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

  21. 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

  22. Independent Component Analysis (ICA) proves to be useful in the analysis of neural activity, as it allows for identification of distinct sources of activity. Applied to measurements registered in a controlled ...

    Authors: Tomasz G Smolinski, Roger Buchanan, Grzegorz M Boratyn, Mariofanna Milanova and Astrid A Prinz
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S8
    Content type: Proceedings Published on:

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

  23. Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed E

    Authors: Laila A Nahum, Matthew T Reynolds, Zhengyuan O Wang, Jeremiah J Faith, Rahul Jonna, Zhi J Jiang, Thomas J Meyer and David D Pollock
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S7
    Content type: Proceedings Published on:

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

  24. Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selec...

    Authors: Venkata Thodima, Mehdi Pirooznia and Youping Deng
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S6
    Content type: Proceedings Published on:

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

  25. 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

  26. We describe Support Vector Machine (SVM) applications to classification and clustering of channel current data. SVMs are variational-calculus based methods that are constrained to have structural risk minimiza...

    Authors: Stephen Winters-Hilt, Anil Yelundur, Charlie McChesney and Matthew Landry
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S4
    Content type: Proceedings Published on:

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

  27. 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

  28. Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is p...

    Authors: Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O Elasri and Youping Deng
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S2
    Content type: Proceedings Published on:

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

  32. 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:

  34. 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:

  35. 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:

  36. 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:

  39. 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:

  40. 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:

  42. 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

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  49. 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:

  50. 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:

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