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  2. PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been descr...

    Authors: Yann Karlen, Alan McNair, Sébastien Perseguers, Christian Mazza and Nicolas Mermod
    Citation: BMC Bioinformatics 2007 8:131
    Content type: Methodology article Published on:

  3. Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ cons...

    Authors: Arif Ozgun Harmanci, Gaurav Sharma and David H Mathews
    Citation: BMC Bioinformatics 2007 8:130
    Content type: Methodology article Published on:

  4. Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by po...

    Authors: Xianfeng Chen, Thomas W Laudeman, Paul J Rushton, Thomas A Spraggins and Michael P Timko
    Citation: BMC Bioinformatics 2007 8:129
    Content type: Database Published on:

  5. A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames) of the yeast Saccharomyces cerevisiae has been systematically constructed. Tag microarrays are widely used to measure t...

    Authors: Chulyun Kim, Sangkyum Kim, Russell Dorer, Dan Xie, Jiawei Han and Sheng Zhong
    Citation: BMC Bioinformatics 2007 8:128
    Content type: Software Published on:

  7. Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesi...

    Authors: Alexander L Chernorudskiy, Alejandro Garcia, Eugene V Eremin, Anastasia S Shorina, Ekaterina V Kondratieva and Murat R Gainullin
    Citation: BMC Bioinformatics 2007 8:126
    Content type: Database Published on:

  10. Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are ti...

    Authors: Nathan C Rockwell and J Clark Lagarias
    Citation: BMC Bioinformatics 2007 8:123
    Content type: Software Published on:

  12. A metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while ot...

    Authors: Wei-chung Liu, Wen-hsien Lin, Andrew J Davis, Ferenc Jordán, Hsih-te Yang and Ming-jing Hwang
    Citation: BMC Bioinformatics 2007 8:121
    Content type: Research article Published on:

  16. Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniq...

    Authors: Negar Memarian, Matthew Jessulat, Javad Alirezaie, Nadereh Mir-Rashed, Jianhua Xu, Mehri Zareie, Myron Smith and Ashkan Golshani
    Citation: BMC Bioinformatics 2007 8:117
    Content type: Research article Published on:

  18. We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution o...

    Authors: Thomas L York, Rick Durrett and Rasmus Nielsen
    Citation: BMC Bioinformatics 2007 8:115
    Content type: Research article Published on:

  19. With the popularisation of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biolo...

    Authors: Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo, Jaime Huerta-Cepas, Pablo Mínguez, David Montaner and Joaquín Dopazo
    Citation: BMC Bioinformatics 2007 8:114
    Content type: Software Published on:

  23. The genomic revolution has led to rapid growth in sequencing of genes and proteins, and attention is now turning to the function of the encoded proteins. In this respect, microscope imaging of a protein's sub-...

    Authors: Nicholas A Hamilton, Radosav S Pantelic, Kelly Hanson and Rohan D Teasdale
    Citation: BMC Bioinformatics 2007 8:110
    Content type: Methodology article Published on:

  24. DNA microarray experiments are conducted in logical sets, such as time course profiling after a treatment is applied to the samples, or comparisons of the samples under two or more conditions. Due to cost and ...

    Authors: Rebecka Jörnsten, Ming Ouyang and Hui-Yu Wang
    Citation: BMC Bioinformatics 2007 8:109
    Content type: Research article Published on:

  25. Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotati...

    Authors: Jun Lu, Joseph C Lee, Marc L Salit and Margaret C Cam
    Citation: BMC Bioinformatics 2007 8:108
    Content type: Methodology article Published on:

  26. DNA melting curve analysis using double-stranded DNA-specific dyes such as SYTO9 produce complex and reproducible melting profiles, resulting in the detection of multiple melting peaks from a single amplicon a...

    Authors: John P Rasmussen, Christopher P Saint and Paul T Monis
    Citation: BMC Bioinformatics 2007 8:107
    Content type: Research article Published on:

  29. Profile Hidden Markov Models (HMM) are statistical representations of protein families derived from patterns of sequence conservation in multiple alignments and have been used in identifying remote homologues ...

    Authors: Prashant K Srivastava, Dhwani K Desai, Soumyadeep Nandi and Andrew M Lynn
    Citation: BMC Bioinformatics 2007 8:104
    Content type: Methodology article Published on:

  31. Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to s...

    Authors: Hans-Michael Kaltenbach, Andreas Wilke and Sebastian Böcker
    Citation: BMC Bioinformatics 2007 8:102
    Content type: Research article Published on:

  32. Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is requi...

    Authors: Dante Mantini, Francesca Petrucci, Damiana Pieragostino, Piero Del Boccio, Marta Di Nicola, Carmine Di Ilio, Giorgio Federici, Paolo Sacchetta, Silvia Comani and Andrea Urbani
    Citation: BMC Bioinformatics 2007 8:101
    Content type: Methodology article Published on:

  34. The gene encoding the envelope of lentiviruses exhibits a considerable plasticity, particularly the region which encodes the surface (SU) glycoprotein. Interestingly, mutations do not appear uniformly along th...

    Authors: Aurélia Boissin-Quillon, Didier Piau and Caroline Leroux
    Citation: BMC Bioinformatics 2007 8:99
    Content type: Research article Published on:

  37. The pyridine nucleotide disulfide reductase (PNDR) is a large and heterogeneous protein family divided into two classes (I and II), which reflect the divergent evolution of its characteristic disulfide redox a...

    Authors: César L Avila, Viviana A Rapisarda, Ricardo N Farías, Javier De Las Rivas and Rosana Chehín
    Citation: BMC Bioinformatics 2007 8:96
    Content type: Research article Published on:

  38. The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic res...

    Authors: Robert P Hanzlik, Yakov M Koen, Bhargav Theertham, Yinghua Dong and Jianwen Fang
    Citation: BMC Bioinformatics 2007 8:95
    Content type: Database Published on:

  40. Success of metabolomics as the phenotyping platform largely depends on its ability to detect various sources of biological variability. Removal of platform-specific sources of variability such as systematic er...

    Authors: Marko Sysi-Aho, Mikko Katajamaa, Laxman Yetukuri and Matej Orešič
    Citation: BMC Bioinformatics 2007 8:93
    Content type: Methodology article Published on:

  41. During gene expression analysis by Serial Analysis of Gene Expression (SAGE), duplicate ditags are routinely removed from the data analysis, because they are suspected to stem from artifacts during SAGE librar...

    Authors: Jeppe Emmersen, Anna M Heidenblut, Annabeth Laursen Høgh, Stephan A Hahn, Karen G Welinder and Kåre L Nielsen
    Citation: BMC Bioinformatics 2007 8:92
    Content type: Research article Published on:

  43. With the advance of microarray technology, several methods for gene classification and prognosis have been already designed. However, under various denominations, some of these methods have similar approaches....

    Authors: Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier and Pascal Roy
    Citation: BMC Bioinformatics 2007 8:90
    Content type: Research article Published on:

  44. Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise dista...

    Authors: Isaac Elias and Jens Lagergren
    Citation: BMC Bioinformatics 2007 8:89
    Content type: Research article Published on:

  45. The ability to regulate metabolism is a fundamental process in living systems. We present an analysis of one of the mechanisms by which metabolic regulation occurs: enzyme inhibition and activation by small mo...

    Authors: Alex Gutteridge, Minoru Kanehisa and Susumu Goto
    Citation: BMC Bioinformatics 2007 8:88
    Content type: Research article Published on:

  48. Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation...

    Authors: Mariano J Alvarez, Guillermo J Vila-Ortiz, Mariano C Salibe, Osvaldo L Podhajcer and Fernando J Pitossi
    Citation: BMC Bioinformatics 2007 8:85
    Content type: Methodology article Published on:

  49. Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2–5% of the genes encode for peptidases, irrespectively of the organism source. The basic p...

    Authors: Lisa Bartoli, Remo Calabrese, Piero Fariselli, Damiano G Mita and Rita Casadio
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

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