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  1. Propositional representations of biomedical knowledge are a critical component of most aspects of semantic mining in biomedicine. However, the proper set of propositions has yet to be determined. Recently, the...

    Authors: K Bretonnel Cohen and Lawrence Hunter
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S5

    This article is part of a Supplement: Volume 7 Supplement 3

  2. Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics...

    Authors: Mariano Latorre, Herman Silva, Juan Saba, Carito Guziolowski, Paula Vizoso, Veronica Martinez, Jonathan Maldonado, Andrea Morales, Rodrigo Caroca, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana, Julio Retamales and Lee A Meisel
    Citation: BMC Bioinformatics 2006 7:513
  3. Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for t...

    Authors: Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell and Gordon K Smyth
    Citation: BMC Bioinformatics 2006 7:511
  4. Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore th...

    Authors: Bjoern Kolbeck, Patrick May, Tobias Schmidt-Goenner, Thomas Steinke and Ernst-Walter Knapp
    Citation: BMC Bioinformatics 2006 7:510
  5. Circular Dichroism (CD) spectroscopy is a widely used method for studying protein structures in solution. Modern synchrotron radiation CD (SRCD) instruments have considerably higher photon fluxes than do conve...

    Authors: Jonathan G Lees, Andrew J Miles, Robert W Janes and B A Wallace
    Citation: BMC Bioinformatics 2006 7:507
  6. The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networ...

    Authors: Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles and Martin Ginkel
    Citation: BMC Bioinformatics 2006 7:506
  7. We present an approach designed to identify gene regulation patterns using sequence and expression data collected for Saccharomyces cerevisae. Our main goal is to relate the combinations of transcription factor b...

    Authors: Bartek Wilczyński, Torgeir R Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski and Krzysztof Fidelis
    Citation: BMC Bioinformatics 2006 7:505
  8. Serial Analysis of Gene Expression (SAGE) is a powerful tool to determine gene expression profiles. Two types of SAGE libraries, ShortSAGE and LongSAGE, are classified based on the length of the SAGE tag (10 v...

    Authors: Yi-Ju Li, Puting Xu, Xuejun Qin, Donald E Schmechel, Christine M Hulette, Jonathan L Haines, Margaret A Pericak-Vance and John R Gilbert
    Citation: BMC Bioinformatics 2006 7:504
  9. An important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments to find these binding motifs are often laborious and expens...

    Authors: Soon-Heng Tan, Willy Hugo, Wing-Kin Sung and See-Kiong Ng
    Citation: BMC Bioinformatics 2006 7:502
  10. Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific olig...

    Authors: Sreedevi Thiyagarajan, Miloslav Karhanek, Michael Akhras, Ronald W Davis and Nader Pourmand
    Citation: BMC Bioinformatics 2006 7:500
  11. Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resultin...

    Authors: Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen and Stephen H Bryant
    Citation: BMC Bioinformatics 2006 7:499
  12. In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong prediction...

    Authors: Philipp N Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz and Matthias Wolf
    Citation: BMC Bioinformatics 2006 7:498
  13. DNA methylation plays an important role in development and tumorigenesis by epigenetic modification and silencing of critical genes. The development of PCR-based methylation assays on bisulphite modified DNA h...

    Authors: Filip Pattyn, Jasmien Hoebeeck, Piet Robbrecht, Evi Michels, Anne De Paepe, Guy Bottu, David Coornaert, Robert Herzog, Frank Speleman and Jo Vandesompele
    Citation: BMC Bioinformatics 2006 7:496
  14. The progress through the eukaryotic cell division cycle is driven by an underlying molecular regulatory network. Cell cycle progression can be considered as a series of irreversible transitions from one steady...

    Authors: Anna Lovrics, Attila Csikász-Nagy, István Gy Zsély, Judit Zádor, Tamás Turányi and Béla Novák
    Citation: BMC Bioinformatics 2006 7:494
  15. The rapid proliferation of biomedical text makes it increasingly difficult for researchers to identify, synthesize, and utilize developed knowledge in their fields of interest. Automated information extraction...

    Authors: Yang Jin, Ryan T McDonald, Kevin Lerman, Mark A Mandel, Steven Carroll, Mark Y Liberman, Fernando C Pereira, Raymond S Winters and Peter S White
    Citation: BMC Bioinformatics 2006 7:492
  16. Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involve...

    Authors: Philipp N Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar and Robert Giegerich
    Citation: BMC Bioinformatics 2006 7:490
  17. Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the comple...

    Authors: Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert Jr, Joseph White, Patricia L Whetzel…
    Citation: BMC Bioinformatics 2006 7:489
  18. RNA-dependent gene silencing is becoming a routine tool used in laboratories worldwide. One of the important remaining hurdles in the selection of the target sequence, if not the most important one, is the des...

    Authors: Jean-François Lucier, Lucien Junior Bergeron, Francis P Brière, Rodney Ouellette, Sherif Abou Elela and Jean-Pierre Perreault
    Citation: BMC Bioinformatics 2006 7:480
  19. Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However, these methods cannot identify prot...

    Authors: Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga and Masaru Tomita
    Citation: BMC Bioinformatics 2006 7:479
  20. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmenta...

    Authors: Illés J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar and Zoltán N Oltvai
    Citation: BMC Bioinformatics 2006 7:478
  21. A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires speciali...

    Authors: Patrick Durand, Frédéric Mahé, Anne-Sophie Valin and Jacques Nicolas
    Citation: BMC Bioinformatics 2006 7:477
  22. Two-Dimensional Difference In Gel Electrophoresis (2D-DIGE) is a powerful tool for measuring differences in protein expression between samples or conditions. However, to remove systematic variability within an...

    Authors: Kim Kultima, Birger Scholz, Henrik Alm, Karl Sköld, Marcus Svensson, Alan R Crossman, Erwan Bezard, Per E Andrén and Ingrid Lönnstedt
    Citation: BMC Bioinformatics 2006 7:475
  23. Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires sp...

    Authors: Oleksiy Kohany, Andrew J Gentles, Lukasz Hankus and Jerzy Jurka
    Citation: BMC Bioinformatics 2006 7:474
  24. The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources r...

    Authors: Coral del Val, Vladimir Yurjevich Kuryshev, Karl-Heinz Glatting, Peter Ernst, Agnes Hotz-Wagenblatt, Annemarie Poustka, Sandor Suhai and Stefan Wiemann
    Citation: BMC Bioinformatics 2006 7:473
  25. The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculatio...

    Authors: Ikuo Uchiyama, Toshio Higuchi and Ichizo Kobayashi
    Citation: BMC Bioinformatics 2006 7:472
  26. Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for t...

    Authors: Vidar Beisvag, Frode KR Jünge, Hallgeir Bergum, Lars Jølsum, Stian Lydersen, Clara-Cecilie Günther, Heri Ramampiaro, Mette Langaas, Arne K Sandvik and Astrid Lægreid
    Citation: BMC Bioinformatics 2006 7:470
  27. Single nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the ava...

    Authors: Lakshmi K Matukumalli, John J Grefenstette, David L Hyten, Ik-Young Choi, Perry B Cregan and Curtis P Van Tassell
    Citation: BMC Bioinformatics 2006 7:468
  28. Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packag...

    Authors: Sophie Lemoine, Florence Combes, Nicolas Servant and Stéphane Le Crom
    Citation: BMC Bioinformatics 2006 7:467
  29. Many attempts are being made to understand biological subjects at a systems level. A major resource for these approaches are biological databases, storing manifold information about DNA, RNA and protein sequen...

    Authors: Stephan Weise, Ivo Grosse, Christian Klukas, Dirk Koschützki, Uwe Scholz, Falk Schreiber and Björn H Junker
    Citation: BMC Bioinformatics 2006 7:465
  30. Many of the most popular pre-processing methods for Affymetrix expression arrays, such as RMA, gcRMA, and PLIER, simultaneously analyze data across a set of predetermined arrays to improve precision of the fin...

    Authors: Simon Katz, Rafael A Irizarry, Xue Lin, Mark Tripputi and Mark W Porter
    Citation: BMC Bioinformatics 2006 7:464
  31. The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope scr...

    Authors: Ji Wan, Wen Liu, Qiqi Xu, Yongliang Ren, Darren R Flower and Tongbin Li
    Citation: BMC Bioinformatics 2006 7:463

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