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  1. Protein structure prediction and computational protein design require efficient yet sufficiently accurate descriptions of aqueous solvent. We continue to evaluate the performance of the Coulomb/Accessible Surf...

    Authors: Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt and Thomas Simonson
    Citation: BMC Bioinformatics 2008 9:148
    Content type: Research article Published on:

  2. Many microarray experiments produce temporal profiles in different biological conditions but common cluster techniques are not able to analyze the data conditional on the biological conditions.

    Authors: Ling Wang, Monty Montano, Matt Rarick and Paola Sebastiani
    Citation: BMC Bioinformatics 2008 9:147
    Content type: Methodology article Published on:

  3. The risk of common diseases is likely determined by the complex interplay between environmental and genetic factors, including single nucleotide polymorphisms (SNPs). Traditional methods of data analysis are p...

    Authors: Leah E Mechanic, Brian T Luke, Julie E Goodman, Stephen J Chanock and Curtis C Harris
    Citation: BMC Bioinformatics 2008 9:146
    Content type: Methodology article Published on:

  5. An important goal of whole-genome studies concerned with single nucleotide polymorphisms (SNPs) is the identification of SNPs associated with a covariate of interest such as the case-control status or the type...

    Authors: Holger Schwender and Katja Ickstadt
    Citation: BMC Bioinformatics 2008 9:144
    Content type: Methodology article Published on:

  6. Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biom...

    Authors: Ali Cakmak and Gultekin Ozsoyoglu
    Citation: BMC Bioinformatics 2008 9:143
    Content type: Research article Published on:

  7. Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expres...

    Authors: Yuan-De Tan, Myriam Fornage and Hongyan Xu
    Citation: BMC Bioinformatics 2008 9:142
    Content type: Methodology article Published on:

  8. Modern proteomes evolved by modification of pre-existing ones. It is extremely important to comparative biology that related proteins be identified as members of the same cognate group, since a characterized p...

    Authors: Adriano Barbosa-Silva, Venkata P Satagopam, Reinhard Schneider and J Miguel Ortega
    Citation: BMC Bioinformatics 2008 9:141
    Content type: Software Published on:

  10. The topology of signaling cascades has been studied in quite some detail. However, how information is processed exactly is still relatively unknown. Since quite diverse information has to be transported by one...

    Authors: Jürgen Pahle, Anne K Green, C Jane Dixon and Ursula Kummer
    Citation: BMC Bioinformatics 2008 9:139
    Content type: Research article Published on:

  11. Genome wide association (GWA) studies are now being widely undertaken aiming to find the link between genetic variations and common diseases. Ideally, a well-powered GWA study will involve the measurement of h...

    Authors: Fredrik Pettersson, Andrew P Morris, Michael R Barnes and Lon R Cardon
    Citation: BMC Bioinformatics 2008 9:138
    Content type: Software Published on:

  13. Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In the past years, many technologies to syste...

    Authors: Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz and Ulf Leser
    Citation: BMC Bioinformatics 2008 9:136
    Content type: Research article Published on:

  15. With the abundant information produced by microarray technology, various approaches have been proposed to infer transcriptional regulatory networks. However, few approaches have studied subtle and indirect int...

    Authors: Grace S Shieh, Chung-Ming Chen, Ching-Yun Yu, Juiling Huang, Woei-Fuh Wang and Yi-Chen Lo
    Citation: BMC Bioinformatics 2008 9:134
    Content type: Research article Published on:

  16. A Java™ application is presented, which compares large numbers (n > 100) of raw FTICR mass spectra from patients and controls. Two peptide profile matrices can be produced simultaneously, one with occurrences ...

    Authors: Mark K Titulaer, Dana AN Mustafa, Ivar Siccama, Marco Konijnenburg, Peter C Burgers, Arno C Andeweg, Peter AE Sillevis Smitt, Johan M Kros and Theo M Luider
    Citation: BMC Bioinformatics 2008 9:133
    Content type: Software Published on:

  18. Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally annotated RNA families. Unfortunately, sea...

    Authors: Stefan Janssen, Jens Reeder and Robert Giegerich
    Citation: BMC Bioinformatics 2008 9:131
    Content type: Research article Published on:

  19. Risk for complex disease is thought to be controlled by multiple genetic risk factors, each with small individual effects. Meta-analyses of several independent studies may be helpful to increase the ability to...

    Authors: Kristin K Nicodemus
    Citation: BMC Bioinformatics 2008 9:130
    Content type: Software Published on:

  20. Predictive classification on the base of gene expression profiles appeared recently as an attractive strategy for identifying the biological functions of genes. Gene Ontology (GO) provides a valuable source of...

    Authors: Wensheng Zhang, Sige Zou and Jiuzhou Song
    Citation: BMC Bioinformatics 2008 9:129
    Content type: Research article Published on:

  24. There is an urgent need for new prognostic markers of breast cancer metastases to ensure that newly diagnosed patients receive appropriate therapy. Recent studies have demonstrated the potential value of gene ...

    Authors: Lei Xu, Aik Choon Tan, Raimond L Winslow and Donald Geman
    Citation: BMC Bioinformatics 2008 9:125
    Content type: Research article Published on:

  26. Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have add...

    Authors: Kjetil Klepper, Geir K Sandve, Osman Abul, Jostein Johansen and Finn Drablos
    Citation: BMC Bioinformatics 2008 9:123
    Content type: Research article Published on:

  27. Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA gene...

    Authors: Andreas R Gruber, Stephan H Bernhart, Ivo L Hofacker and Stefan Washietl
    Citation: BMC Bioinformatics 2008 9:122
    Content type: Research article Published on:

  28. The exponential growth of research in molecular biology has brought concomitant proliferation of databases for stocking its findings. A variety of protein sequence databases exist. While all of these strive fo...

    Authors: Riadh Hammami, Abdelmajid Zouhir, Karim Naghmouchi, Jeannette Ben Hamida and Ismail Fliss
    Citation: BMC Bioinformatics 2008 9:121
    Content type: Software Published on:

  29. In real-time quantitative PCR studies using absolute plasmid DNA standards, a calibration curve is developed to estimate an unknown DNA concentration. However, potential differences in the amplification perfor...

    Authors: Mano Sivaganesan, Shawn Seifring, Manju Varma, Richard A Haugland and Orin C Shanks
    Citation: BMC Bioinformatics 2008 9:120
    Content type: Methodology article Published on:

  30. Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge about protein function. The resul...

    Authors: Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia and Charles DeLisi
    Citation: BMC Bioinformatics 2008 9:119
    Content type: Research article Published on:

  31. Previous studies comparing quantitative proteomics and microarray data have generally found poor correspondence between the two. We hypothesised that this might in part be because the different assays were tar...

    Authors: Danny A Bitton, Michał J Okoniewski, Yvonne Connolly and Crispin J Miller
    Citation: BMC Bioinformatics 2008 9:118
    Content type: Methodology article Published on:

  32. Choosing the appropriate sample size is an important step in the design of a microarray experiment, and recently methods have been proposed that estimate sample sizes for control of the False Discovery Rate (F...

    Authors: Tommy S Jørstad, Herman Midelfart and Atle M Bones
    Citation: BMC Bioinformatics 2008 9:117
    Content type: Methodology article Published on:

  33. Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are be...

    Authors: Jonathan D Moore, Shelagh P Kell, Jose M Iriondo, Brian V Ford-Lloyd and Nigel Maxted
    Citation: BMC Bioinformatics 2008 9:116
    Content type: Software Published on:

  36. Promoter region plays an important role in determining where the transcription of a particular gene should be initiated. Computational prediction of eukaryotic Pol II promoter sequences is one of the most sign...

    Authors: Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh and Li-Qian Zhou
    Citation: BMC Bioinformatics 2008 9:113
    Content type: Methodology article Published on:

  37. Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can n...

    Authors: Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao and Toshihiko Ishida
    Citation: BMC Bioinformatics 2008 9:112
    Content type: Software Published on:

  39. Biological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The...

    Authors: Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh and Ron Shamir
    Citation: BMC Bioinformatics 2008 9:110
    Content type: Software Published on:

  40. As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the ques...

    Authors: Wolfram Gronwald, Tim Hohm and Daniel Hoffmann
    Citation: BMC Bioinformatics 2008 9:109
    Content type: Research article Published on:

  41. Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate informat...

    Authors: Graham L Poulter, Daniel L Rubin, Russ B Altman and Cathal Seoighe
    Citation: BMC Bioinformatics 2008 9:108
    Content type: Research article Published on:

  42. Last years' mapping of diverse genomes has generated huge amounts of biological data which are currently dispersed through many databases. Integration of the information available in the various databases is r...

    Authors: Francisco J Lopez, Armando Blanco, Fernando Garcia, Carlos Cano and Antonio Marin
    Citation: BMC Bioinformatics 2008 9:107
    Content type: Research article Published on:

  43. Kernel-based classification and regression methods have been successfully applied to modelling a wide variety of biological data. The Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method of...

    Authors: Max Bylesjö, Mattias Rantalainen, Jeremy K Nicholson, Elaine Holmes and Johan Trygg
    Citation: BMC Bioinformatics 2008 9:106
    Content type: Software Published on:

  44. Modelling the time-related behaviour of biological systems is essential for understanding their dynamic responses to perturbations. In metabolic profiling studies, the sampling rate and number of sampling poin...

    Authors: Mattias Rantalainen, Olivier Cloarec, Timothy MD Ebbels, Torbjörn Lundstedt, Jeremy K Nicholson, Elaine Holmes and Johan Trygg
    Citation: BMC Bioinformatics 2008 9:105
    Content type: Methodology article Published on:

  45. Target identification is important for modern drug discovery. With the advances in the development of molecular docking, potential binding proteins may be discovered by docking a small molecule to a repository...

    Authors: Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang and Hualiang Jiang
    Citation: BMC Bioinformatics 2008 9:104
    Content type: Database Published on:

  46. The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant...

    Authors: Indra Neil Sarkar, Mary G Egan, Gloria Coruzzi, Ernest K Lee and Rob DeSalle
    Citation: BMC Bioinformatics 2008 9:103
    Content type: Software Published on:

  48. As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequ...

    Authors: Yong-Zi Chen, Yu-Rong Tang, Zhi-Ya Sheng and Ziding Zhang
    Citation: BMC Bioinformatics 2008 9:101
    Content type: Research article Published on:

  49. The analysis of high-throughput gene expression data sets derived from microarray experiments still is a field of extensive investigation. Although new approaches and algorithms are published continuously, mos...

    Authors: Dominik Lutter, Peter Ugocsai, Margot Grandl, Evelyn Orso, Fabian Theis, Elmar W Lang and Gerd Schmitz
    Citation: BMC Bioinformatics 2008 9:100
    Content type: Research article Published on:

  50. The integration of biomedical information is essential for tackling medical problems. We describe a data model in the domain of flow cytometry (FC) allowing for massive management, analysis and integration wit...

    Authors: John Drakos, Marina Karakantza, Nicholas C Zoumbos, John Lakoumentas, George C Nikiforidis and George C Sakellaropoulos
    Citation: BMC Bioinformatics 2008 9:99
    Content type: Research article Published on:

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