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  2. Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and re...

    Authors: Harold J Drabkin, Christopher Hollenbeck, David P Hill and Judith A Blake
    Citation: BMC Bioinformatics 2005 6:29
    Content type: Research article Published on:

  3. Normalization is a critical step in analysis of gene expression profiles. For dual-labeled arrays, global normalization assumes that the majority of the genes on the array are non-differentially expressed betw...

    Authors: Yingdong Zhao, Ming-Chung Li and Richard Simon
    Citation: BMC Bioinformatics 2005 6:28
    Content type: Research article Published on:

  4. Microarray-CGH experiments are used to detect and map chromosomal imbalances, by hybridizing targets of genomic DNA from a test and a reference sample to sequences immobilized on a slide. These probes are geno...

    Authors: Franck Picard, Stephane Robin, Marc Lavielle, Christian Vaisse and Jean-Jacques Daudin
    Citation: BMC Bioinformatics 2005 6:27
    Content type: Research article Published on:

  5. A critical step in processing oligonucleotide microarray data is combining the information in multiple probes to produce a single number that best captures the expression level of a RNA transcript. Several sys...

    Authors: Kerby Shedden, Wei Chen, Rork Kuick, Debashis Ghosh, James Macdonald, Kathleen R Cho, Thomas J Giordano, Stephen B Gruber, Eric R Fearon, Jeremy MG Taylor and Samir Hanash
    Citation: BMC Bioinformatics 2005 6:26
    Content type: Research article Published on:

  6. Alternative splicing (AS) is now considered as a major actor in transcriptome/proteome diversity and it cannot be neglected in the annotation process of a new genome. Despite considerable progresses in term of...

    Authors: Sylvain Foissac and Thomas Schiex
    Citation: BMC Bioinformatics 2005 6:25
    Content type: Research article Published on:

  7. Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas.

    Authors: Victor Kunin and Christos A Ouzounis
    Citation: BMC Bioinformatics 2005 6:24
    Content type: Research article Published on:

  9. Post-translational modification by Small Ubiquitin-like Modifiers (SUMO) has been implicated in protein targeting, in the maintenance of genomic integrity and in transcriptional control. But the specific molec...

    Authors: Maria Novatchkova, Andreas Bachmair, Birgit Eisenhaber and Frank Eisenhaber
    Citation: BMC Bioinformatics 2005 6:22
    Content type: Research article Published on:

  10. The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed...

    Authors: John L Moreland, Apostol Gramada, Oleksandr V Buzko, Qing Zhang and Philip E Bourne
    Citation: BMC Bioinformatics 2005 6:21
    Content type: Software Published on:

  12. The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms...

    Authors: Vilmos Ágoston, Masa Cemazar, László Kaján and Sándor Pongor
    Citation: BMC Bioinformatics 2005 6:19
    Content type: Methodology article Published on:

  13. Detection of Loss of Heterozygosity (LOH) is one of the most common molecular applications in the study of human diseases, in particular cancer. The technique is commonly used to examine whether a known tumour...

    Authors: Rifat A Hamoudi, Amina El-Hamidi and Ming-Qing Du
    Citation: BMC Bioinformatics 2005 6:18
    Content type: Software Published on:

  14. Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to estimate a protein's concentration in a sample. Deploying ELISA in a microarray format permits simultaneous estimation of the concentratio...

    Authors: Don Simone Daly, Amanda M White, Susan M Varnum, Kevin K Anderson and Richard C Zangar
    Citation: BMC Bioinformatics 2005 6:17
    Content type: Research article Published on:

  16. Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication of currently availab...

    Authors: Antje Krause, Jens Stoye and Martin Vingron
    Citation: BMC Bioinformatics 2005 6:15
    Content type: Methodology article Published on:

  20. Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative recon...

    Authors: Thomas MacCarthy, Andrew Pomiankowski and Robert Seymour
    Citation: BMC Bioinformatics 2005 6:11
    Content type: Methodology article Published on:

  24. Prediction of the transmembrane strands and topology of β-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing dif...

    Authors: Pantelis G Bagos, Theodore D Liakopoulos and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2005 6:7
    Content type: Research article Published on:

  26. Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software ...

    Authors: Marko Srdanovic, Ulf Schenk, Michael Schwieger and Fabien Campagne
    Citation: BMC Bioinformatics 2005 6:5
    Content type: Methodology article Published on:

  27. Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold recognition. We propose a new automated me...

    Authors: Jean-Christophe Gelly, Laurent Chiche and Jérôme Gracy
    Citation: BMC Bioinformatics 2005 6:4
    Content type: Methodology article Published on:

  31. Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease) or absence (Con...

    Authors: Hao Li, Constance L Wood, Thomas V Getchell, Marilyn L Getchell and Arnold J Stromberg
    Citation: BMC Bioinformatics 2004 5:209
    Content type: Research article Published on:

  32. G protein-coupled receptors (GPCRs) transduce signals from extracellular space into the cell, through their interaction with G proteins, which act as switches forming hetero-trimers composed of different subun...

    Authors: Antigoni L Elefsinioti, Pantelis G Bagos, Ioannis C Spyropoulos and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2004 5:208
    Content type: Database Published on:

  33. Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has ...

    Authors: Jose C Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2004 5:207
    Content type: Research article Published on:

  35. Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to dec...

    Authors: Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu and Drena Dobbs
    Citation: BMC Bioinformatics 2004 5:205
    Content type: Methodology article Published on:

  37. High-density oligonucleotide microarray technology enables the discovery of genes that are transcriptionally modulated in different biological samples due to physiology, disease or intervention. Methods for th...

    Authors: Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci and Paola Ricciardi-Castagnoli
    Citation: BMC Bioinformatics 2004 5:203
    Content type: Methodology article Published on:

  38. Modern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatial...

    Authors: Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan and Sudhir Kumar
    Citation: BMC Bioinformatics 2004 5:202
    Content type: Software Published on:

  39. The main goal in analyzing microarray data is to determine the genes that are differentially expressed across two types of tissue samples or samples obtained under two experimental conditions. Mixture model me...

    Authors: Kayvan Najarian, Maryam Zaheri, Ali A Rad, Siamak Najarian and Javad Dargahi
    Citation: BMC Bioinformatics 2004 5:201
    Content type: Methodology article Published on:

  41. Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understandi...

    Authors: Hong-Wu Ma, Jan Buer and An-Ping Zeng
    Citation: BMC Bioinformatics 2004 5:199
    Content type: Research article Published on:

  42. An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis o...

    Authors: Rohit Ghai, Torsten Hain and Trinad Chakraborty
    Citation: BMC Bioinformatics 2004 5:198
    Content type: Software Published on:

  44. It is a major challenge of computational biology to provide a comprehensive functional classification of all known proteins. Most existing methods seek recurrent patterns in known proteins based on manually-va...

    Authors: Noam Kaplan, Moriah Friedlich, Menachem Fromer and Michal Linial
    Citation: BMC Bioinformatics 2004 5:196
    Content type: Research article Published on:

  45. Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

    Authors: Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel and Steven Bushnell
    Citation: BMC Bioinformatics 2004 5:195
    Content type: Software Published on:

  46. Microarray data normalization is an important step for obtaining data that are reliable and usable for subsequent analysis. One of the most commonly utilized normalization techniques is the locally weighted sc...

    Authors: John A Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K Mitra and Jaakko Astola
    Citation: BMC Bioinformatics 2004 5:194
    Content type: Methodology article Published on:

  47. Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restrict...

    Authors: Thomas Breslin, Patrik Edén and Morten Krogh
    Citation: BMC Bioinformatics 2004 5:193
    Content type: Methodology article Published on:

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