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  3. Proteins are the primary regulatory agents of transcription even though mRNA expression data alone, from systems like DNA microarrays, are widely used. In addition, the regulation process in genetic systems is...

    Authors: Reuben Thomas, Carlos J Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis and Eleftherios T Papoutsakis
    Citation: BMC Bioinformatics 2007 8:228
    Content type: Methodology article Published on:

  4. In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such inde...

    Authors: Simon K Chan, Michael Hsing, Fereydoun Hormozdiari and Artem Cherkasov
    Citation: BMC Bioinformatics 2007 8:227
    Content type: Research article Published on:

  6. Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completely sequenced to date, it is tempting to ask...

    Authors: Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki and Minoru Kanehisa
    Citation: BMC Bioinformatics 2007 8:225
    Content type: Research article Published on:

  7. Analyzing differential-gene-expression data in the context of protein-interaction networks (PINs) yields information on the functional cellular status. PINs can be formally represented as graphs, and approxima...

    Authors: Alexander Platzer, Paul Perco, Arno Lukas and Bernd Mayer
    Citation: BMC Bioinformatics 2007 8:224
    Content type: Research article Published on:

  11. The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to exp...

    Authors: Johanna Hardin, Aya Mitani, Leanne Hicks and Brian VanKoten
    Citation: BMC Bioinformatics 2007 8:220
    Content type: Methodology article Published on:

  12. Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing ...

    Authors: Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda and Peter J Park
    Citation: BMC Bioinformatics 2007 8:219
    Content type: Research article Published on:

  13. With microarray technology, variability in experimental environments such as RNA sources, microarray production, or the use of different platforms, can cause bias. Such systematic differences present a substan...

    Authors: Ki-Yeol Kim, Dong Hyuk Ki, Ha Jin Jeong, Hei-Cheul Jeung, Hyun Cheol Chung and Sun Young Rha
    Citation: BMC Bioinformatics 2007 8:218
    Content type: Research article Published on:

  14. Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displa...

    Authors: Nathan Salomonis, Kristina Hanspers, Alexander C Zambon, Karen Vranizan, Steven C Lawlor, Kam D Dahlquist, Scott W Doniger, Josh Stuart, Bruce R Conklin and Alexander R Pico
    Citation: BMC Bioinformatics 2007 8:217
    Content type: Software Published on:

  15. In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Gol...

    Authors: Jan Hummel, Michaela Niemann, Stefanie Wienkoop, Waltraud Schulze, Dirk Steinhauser, Joachim Selbig, Dirk Walther and Wolfram Weckwerth
    Citation: BMC Bioinformatics 2007 8:216
    Content type: Database Published on:

  17. Mass spectrometry based quantification of peptides can be performed using the iTRAQ™ reagent in conjunction with mass spectrometry. This technology yields information about the relative abundance of single pep...

    Authors: Andreas M Boehm, Stephanie Pütz, Daniela Altenhöfer, Albert Sickmann and Michael Falk
    Citation: BMC Bioinformatics 2007 8:214
    Content type: Software Published on:

  18. Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful a...

    Authors: Namshin Kim and Christopher Lee
    Citation: BMC Bioinformatics 2007 8:213
    Content type: Software Published on:

  19. Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these re...

    Authors: Vinay Satish Kumar, Madhukar S Dasika and Costas D Maranas
    Citation: BMC Bioinformatics 2007 8:212
    Content type: Methodology article Published on:

  21. Fluorescence microscopy is widely used to determine the subcellular location of proteins. Efforts to determine location on a proteome-wide basis create a need for automated methods to analyze the resulting ima...

    Authors: Amina Chebira, Yann Barbotin, Charles Jackson, Thomas Merryman, Gowri Srinivasa, Robert F Murphy and Jelena Kovačević
    Citation: BMC Bioinformatics 2007 8:210
    Content type: Research article Published on:

  22. Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their propos...

    Authors: Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides and Philip Hugenholtz
    Citation: BMC Bioinformatics 2007 8:209
    Content type: Software Published on:

  24. During generation of microarray data, various forms of systematic biases are frequently introduced which limits accuracy and precision of the results. In order to properly estimate biological effects, these bi...

    Authors: Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Stefan Jansson, Thomas Moritz and Johan Trygg
    Citation: BMC Bioinformatics 2007 8:207
    Content type: Methodology article Published on:

  25. Gene expression microarray is a powerful technology for genetic profiling diseases and their associated treatments. Such a process involves a key step of biomarker identification, which are expected to be clos...

    Authors: Zhipeng Cai, Randy Goebel, Mohammad R Salavatipour and Guohui Lin
    Citation: BMC Bioinformatics 2007 8:206
    Content type: Research article Published on:

  26. We have developed a new haplotyping program based on the combination of an iterative multiallelic EM algorithm (IEM), bootstrap resampling and a pseudo Gibbs sampler. The use of the IEM-bootstrap procedure con...

    Authors: Olivier Delaneau, Cédric Coulonges, Pierre-Yves Boelle, George Nelson, Jean-Louis Spadoni and Jean-François Zagury
    Citation: BMC Bioinformatics 2007 8:205
    Content type: Research article Published on:

  27. The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a softwar...

    Authors: Jason D Gans and Murray Wolinsky
    Citation: BMC Bioinformatics 2007 8:204
    Content type: Software Published on:

  28. The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hyb...

    Authors: Dmitriy Skvortsov, Diana Abdueva, Michael E Stitzer, Steven E Finkel and Simon Tavaré
    Citation: BMC Bioinformatics 2007 8:203
    Content type: Methodology article Published on:

  29. The ability to obtain profiles of gene expressions, proteins and metabolites with the advent of high throughput technologies has advanced the study of pathway and network reconstruction. Genome-wide network re...

    Authors: Zheng Li, Shireesh Srivastava, Sheenu Mittal, Xuerui Yang, Lufang Sheng and Christina Chan
    Citation: BMC Bioinformatics 2007 8:202
    Content type: Methodology article Published on:

  30. Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to k...

    Authors: Gianluca Pollastri, Alberto JM Martin, Catherine Mooney and Alessandro Vullo
    Citation: BMC Bioinformatics 2007 8:201
    Content type: Methodology article Published on:

  31. Genome-wide maps of linkage disequilibrium (LD) and haplotypes have been created for different populations. Substantial sharing of the boundaries and haplotypes among populations was observed, but haplotype va...

    Authors: Dai Osabe, Toshihito Tanahashi, Kyoko Nomura, Shuichi Shinohara, Naoto Nakamura, Toshikazu Yoshikawa, Hiroshi Shiota, Parvaneh Keshavarz, Yuka Yamaguchi, Kiyoshi Kunika, Maki Moritani, Hiroshi Inoue and Mitsuo Itakura
    Citation: BMC Bioinformatics 2007 8:200
    Content type: Research article Published on:

  33. Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an ard...

    Authors: Elena Taycher, Andreas Rolfs, Yanhui Hu, Dongmei Zuo, Stephanie E Mohr, Janice Williamson and Joshua LaBaer
    Citation: BMC Bioinformatics 2007 8:198
    Content type: Software Published on:

  34. The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires t...

    Authors: Jürgen Hartler, Gerhard G Thallinger, Gernot Stocker, Alexander Sturn, Thomas R Burkard, Erik Körner, Robert Rader, Andreas Schmidt, Karl Mechtler and Zlatko Trajanoski
    Citation: BMC Bioinformatics 2007 8:197
    Content type: Software Published on:

  35. Quantifying cell division and death is central to many studies in the biological sciences. The fluorescent dye CFSE allows the tracking of cell division in vitro and in vivo and provides a rich source of informat...

    Authors: Andrew Yates, Cliburn Chan, Jessica Strid, Simon Moon, Robin Callard, Andrew JT George and Jaroslav Stark
    Citation: BMC Bioinformatics 2007 8:196
    Content type: Research article Published on:

  37. The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset i...

    Authors: Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li and Yi-Xue Li
    Citation: BMC Bioinformatics 2007 8:194
    Content type: Research article Published on:

  38. An important step in annotation of sequenced genomes is the identification of transcription factor binding sites. More than a hundred different computational methods have been proposed, and it is difficult to ...

    Authors: Geir Kjetil Sandve, Osman Abul, Vegard Walseng and Finn Drabløs
    Citation: BMC Bioinformatics 2007 8:193
    Content type: Research article Published on:

  39. Microarray techniques survey gene expressions on a global scale. Extensive biomedical studies have been designed to discover subsets of genes that are associated with survival risks for diseases such as lympho...

    Authors: Shuangge Ma and Jian Huang
    Citation: BMC Bioinformatics 2007 8:192
    Content type: Methodology article Published on:

  40. Evolutionary analysis provides a formal framework for comparative analysis of genomic and other data. In evolutionary analysis, observed data are treated as the terminal states of characters that have evolved ...

    Authors: Thomas Hladish, Vivek Gopalan, Chengzhi Liang, Weigang Qiu, Peter Yang and Arlin Stoltzfus
    Citation: BMC Bioinformatics 2007 8:191
    Content type: Software Published on:

  41. In ribonucleic acid (RNA) molecules whose function depends on their final, folded three-dimensional shape (such as those in ribosomes or spliceosome complexes), the secondary structure, defined by the set of i...

    Authors: Amelia B Bellamy-Royds and Marcel Turcotte
    Citation: BMC Bioinformatics 2007 8:190
    Content type: Research article Published on:

  42. Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the ...

    Authors: Matti Kankainen and Ari Löytynoja
    Citation: BMC Bioinformatics 2007 8:189
    Content type: Software Published on:

  44. Detection of adaptive amino acid changes in proteins under recent short-term selection is of great interest for researchers studying microevolutionary processes in microbial pathogens or any other biological s...

    Authors: Sujay Chattopadhyay, Daniel E Dykhuizen and Evgeni V Sokurenko
    Citation: BMC Bioinformatics 2007 8:187
    Content type: Software Published on:

  45. Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding s...

    Authors: Thomas E Royce, Nicholas J Carriero and Mark B Gerstein
    Citation: BMC Bioinformatics 2007 8:186
    Content type: Methodology article Published on:

  48. Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make compari...

    Authors: R Brent Calder, Rudolf B Beems, Harry van Steeg, I Saira Mian, Paul HM Lohman and Jan Vijg
    Citation: BMC Bioinformatics 2007 8:183
    Content type: Software Published on:

  50. Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expressio...

    Authors: Katrijn Van Deun, Kathleen Marchal, Willem J Heiser, Kristof Engelen and Iven Van Mechelen
    Citation: BMC Bioinformatics 2007 8:181
    Content type: Methodology article Published on:

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