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  1. In spite of the recognized diagnostic potential of biomarkers, the quest for squelching noise and wringing in information from a given set of biomarkers continues. Here, we suggest a statistical algorithm that...

    Authors: Manju R Mamtani, Tushar P Thakre, Mrunal Y Kalkonde, Manik A Amin, Yogeshwar V Kalkonde, Amit P Amin and Hemant Kulkarni
    Citation: BMC Bioinformatics 2006 7:442
    Content type: Methodology article Published on:

  2. Compositionally biased (CB) regions are stretches in protein sequences made from mainly a distinct subset of amino acid residues; such regions are frequently associated with a structural role in the cell, or w...

    Authors: Paul M Harrison
    Citation: BMC Bioinformatics 2006 7:441
    Content type: Research article Published on:

  4. Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present ...

    Authors: Jifeng Tang, Ben Vosman, Roeland E Voorrips, C Gerard van der Linden and Jack AM Leunissen
    Citation: BMC Bioinformatics 2006 7:438
    Content type: Software Published on:

  5. Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired p...

    Authors: Denis C Bauer, Mikael Bodén, Ricarda Thier and Elizabeth M Gillam
    Citation: BMC Bioinformatics 2006 7:437
    Content type: Software Published on:

  6. Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union o...

    Authors: Olivier Lespinet and Bernard Labedan
    Citation: BMC Bioinformatics 2006 7:436
    Content type: Database Published on:

  7. Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis can be extended to model any stable protein-DNA co...

    Authors: Isabel K Darcy, Jeff Chang, Nathan Druivenga, Colin McKinney, Ram K Medikonduri, Stacy Mills, Junalyn Navarra-Madsen, Arun Ponnusamy, Jesse Sweet and Travis Thompson
    Citation: BMC Bioinformatics 2006 7:435
    Content type: Methodology article Published on:

  8. High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ...

    Authors: Srinka Ghosh, Heather A Hirsch, Edward Sekinger, Kevin Struhl and Thomas R Gingeras
    Citation: BMC Bioinformatics 2006 7:434
    Content type: Methodology article Published on:

  9. Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic se...

    Authors: Todd J Treangen and Xavier Messeguer
    Citation: BMC Bioinformatics 2006 7:433
    Content type: Software Published on:

  10. Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of the...

    Authors: Prabakaran Subramani, Rajendra Sahu and Shekhar Verma
    Citation: BMC Bioinformatics 2006 7:432
    Content type: Research article Published on:

  11. A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genom...

    Authors: Tamás Arányi, András Váradi, István Simon and Gábor E Tusnády
    Citation: BMC Bioinformatics 2006 7:431
    Content type: Software Published on:

  12. In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable ...

    Authors: Hiraku Morisawa, Mikako Hirota and Tosifusa Toda
    Citation: BMC Bioinformatics 2006 7:430
    Content type: Software Published on:

  14. Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have...

    Authors: Peter S Klosterman, Andrew V Uzilov, Yuri R Bendaña, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman and Ian Holmes
    Citation: BMC Bioinformatics 2006 7:428
    Content type: Software Published on:

  18. 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:

  19. 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:

  20. 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:

  22. 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:

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  49. 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:

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