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  1. Time-course microarray experiments are being increasingly used to characterize dynamic biological processes. In these experiments, the goal is to identify genes differentially expressed in time-course data, me...

    Authors: Sudhakar Jonnalagadda and Rajagopalan Srinivasan
    Citation: BMC Bioinformatics 2008 9:267
  2. As in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance ...

    Authors: Ismael A Vergara, Tomás Norambuena, Evandro Ferrada, Alex W Slater and Francisco Melo
    Citation: BMC Bioinformatics 2008 9:265
  3. The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in dif...

    Authors: Zheng Yin, Xiaobo Zhou, Chris Bakal, Fuhai Li, Youxian Sun, Norbert Perrimon and Stephen TC Wong
    Citation: BMC Bioinformatics 2008 9:264
  4. GPR17 is a G-protein-coupled receptor located at intermediate phylogenetic position between two distinct receptor families: the P2Y and CysLT receptors for extracellular nucleotides and cysteinyl-LTs, respecti...

    Authors: Chiara Parravicini, Graziella Ranghino, Maria P Abbracchio and Piercarlo Fantucci
    Citation: BMC Bioinformatics 2008 9:263
  5. Biologically active sequence motifs often have positional preferences with respect to a genomic landmark. For example, many known transcription factor binding sites (TFBSs) occur within an interval [-300, 0] b...

    Authors: Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez and John L Spouge
    Citation: BMC Bioinformatics 2008 9:262
  6. MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixe...

    Authors: Juan R González, Josep L Carrasco, Lluís Armengol, Sergi Villatoro, Lluís Jover, Yutaka Yasui and Xavier Estivill
    Citation: BMC Bioinformatics 2008 9:261
  7. Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of ...

    Authors: Wei Dong, Litao Yang, Kailin Shen, Banghyun Kim, Gijs A Kleter, Hans JP Marvin, Rong Guo, Wanqi Liang and Dabing Zhang
    Citation: BMC Bioinformatics 2008 9:260
  8. Superoxide dismutases (SODs) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecule...

    Authors: Jean Marc Kwasigroch, René Wintjens, Dimitri Gilis and Marianne Rooman
    Citation: BMC Bioinformatics 2008 9:257
  9. Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order h...

    Authors: Yi Shi, Jianjun Zhou, David Arndt, David S Wishart and Guohui Lin
    Citation: BMC Bioinformatics 2008 9:255
  10. Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS) have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactio...

    Authors: Silvana Penco, Massimo Buscema, Maria Cristina Patrosso, Alessandro Marocchi and Enzo Grossi
    Citation: BMC Bioinformatics 2008 9:254
  11. Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic re...

    Authors: Frank M You, Naxin Huo, Yong Qiang Gu, Ming-cheng Luo, Yaqin Ma, Dave Hane, Gerard R Lazo, Jan Dvorak and Olin D Anderson
    Citation: BMC Bioinformatics 2008 9:253
  12. It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although sever...

    Authors: Qian Xiang, Xianhua Dai, Yangyang Deng, Caisheng He, Jiang Wang, Jihua Feng and Zhiming Dai
    Citation: BMC Bioinformatics 2008 9:252
  13. A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only b...

    Authors: Todd H Stokes, JT Torrance, Henry Li and May D Wang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S18

    This article is part of a Supplement: Volume 9 Supplement 6

  14. This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, t...

    Authors: Chang F Quo and May D Wang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S17

    This article is part of a Supplement: Volume 9 Supplement 6

  15. Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular...

    Authors: Lily R Liang, Vinay Mandal, Yi Lu and Deepak Kumar
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S16

    This article is part of a Supplement: Volume 9 Supplement 6

  16. Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence al...

    Authors: Guoqing Lu, Shunpu Zhang and Xiang Fang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S15

    This article is part of a Supplement: Volume 9 Supplement 6

  17. In DNA microarray gene expression profiling studies, a fundamental task is to extract statistically significant genes that meet certain research hypothesis. Currently, Venn diagram is a frequently used method ...

    Authors: Xutao Deng, Jun Xu and Charles Wang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S14

    This article is part of a Supplement: Volume 9 Supplement 6

  18. Tandem mass spectrometry has emerged as a cornerstone of high throughput proteomic studies owing in part to various high throughput search engines which are used to interpret these tandem mass spectra. However...

    Authors: Fang-Xiang Wu, Pierre Gagné, Arnaud Droit and Guy G Poirier
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S13

    This article is part of a Supplement: Volume 9 Supplement 6

  19. The traditional (unweighted) k-means is one of the most popular clustering methods for analyzing gene expression data. However, it suffers three major shortcomings. It is sensitive to initial partitions, its r...

    Authors: Fang-Xiang Wu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S12

    This article is part of a Supplement: Volume 9 Supplement 6

  20. In accordance with the increasing amount of information concerning individual differences in drug response and molecular interaction, the role of in silico prediction of drug interaction on the pathway level is b...

    Authors: Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura and Akihiko Konagaya
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S11

    This article is part of a Supplement: Volume 9 Supplement 6

  21. Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of differe...

    Authors: Hiroyuki Mishima, Andrew C Lidral and Jun Ni
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S10

    This article is part of a Supplement: Volume 9 Supplement 6

  22. Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters t...

    Authors: Mary Qu Yang, James Taylor and Laura Elnitski
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S9

    This article is part of a Supplement: Volume 9 Supplement 6

  23. Analysis of gene expression data for tumor classification is an important application of bioinformatics methods. But it is hard to analyse gene expression data from DNA microarray experiments by commonly used ...

    Authors: Xue-Qiang Zeng, Guo-Zheng Li, Jack Y Yang, Mary Qu Yang and Geng-Feng Wu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S8

    This article is part of a Supplement: Volume 9 Supplement 6

  24. Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimen...

    Authors: Guo-Zheng Li, Hao-Hua Meng, Wen-Cong Lu, Jack Y Yang and Mary Qu Yang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S7

    This article is part of a Supplement: Volume 9 Supplement 6

  25. Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques...

    Authors: George Chin Jr, Daniel G Chavarria, Grant C Nakamura and Heidi J Sofia
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S6

    This article is part of a Supplement: Volume 9 Supplement 6

  26. A protein structural class (PSC) belongs to the most basic but important classification in protein structures. The prediction technique of protein structural class has been developing for decades. Two popular ...

    Authors: Fei Gu, Hang Chen and Jun Ni
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S5

    This article is part of a Supplement: Volume 9 Supplement 6

  27. Inference of evolutionary trees using the maximum likelihood principle is NP-hard. Therefore, all practical methods rely on heuristics. The topological transformations often used in heuristics are Nearest Neig...

    Authors: Mao-Zu Guo, Jian-Fu Li and Yang Liu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S4

    This article is part of a Supplement: Volume 9 Supplement 6

  28. DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we prop...

    Authors: Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chian Chen, Yuh-Jyh Hu and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S3

    This article is part of a Supplement: Volume 9 Supplement 6

  29. Localization of complex traits by genetic linkage analysis may involve exploration of a vast multidimensional parameter space. The posterior probability of linkage (PPL), a class of statistics for complex trai...

    Authors: Manika Govil, Alberto M Segre and Veronica J Vieland
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S2

    This article is part of a Supplement: Volume 9 Supplement 6

  30. The Second Symposium on Computations in Bioinformatics and Bioscience (SCBB07) was held in Iowa City, Iowa, USA, on August 13–15, 2007. This annual event attracted dozens of bioinformatics professionals and st...

    Authors: Guoqing Lu and Jun Ni
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S1

    This article is part of a Supplement: Volume 9 Supplement 6

  31. A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protei...

    Authors: Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom and Baldomero Oliva
    Citation: BMC Bioinformatics 2008 9:249
  32. Association testing is a powerful tool for identifying disease susceptibility genes underlying complex diseases. Technological advances have yielded a dramatic increase in the density of available genetic mark...

    Authors: Ie-Bin Lian, Yi-Hsien Lin, Ying-Chao Lin, Hsin-Chou Yang, Chee-Jang Chang and Cathy SJ Fann
    Citation: BMC Bioinformatics 2008 9:246
  33. We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kin...

    Authors: Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp and Bostjan Kobe
    Citation: BMC Bioinformatics 2008 9:245
  34. The combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies have searched for eQTL by ana...

    Authors: Shameek Biswas, John D Storey and Joshua M Akey
    Citation: BMC Bioinformatics 2008 9:244
  35. Recent advances in global genomic profiling methodologies have enabled multi-dimensional characterization of biological systems. Complete analysis of these genomic profiles require an in depth look at parallel...

    Authors: Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Raymond T Ng, Calum MacAulay and Wan L Lam
    Citation: BMC Bioinformatics 2008 9:243
  36. Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems....

    Authors: W Timothy J White and Michael D Hendy
    Citation: BMC Bioinformatics 2008 9:242
  37. Bioactivity profiling using high-throughput in vitro assays can reduce the cost and time required for toxicological screening of environmental chemicals and can also reduce the need for animal testing. Several pu...

    Authors: Richard Judson, Fathi Elloumi, R Woodrow Setzer, Zhen Li and Imran Shah
    Citation: BMC Bioinformatics 2008 9:241
  38. Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a...

    Authors: Alfredo Braunstein, Roberto Mulet and Andrea Pagnani
    Citation: BMC Bioinformatics 2008 9:240
  39. DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but...

    Authors: Michael C Wendl and Richard K Wilson
    Citation: BMC Bioinformatics 2008 9:239
  40. Multifactor Dimensionality Reduction (MDR) has been introduced previously as a non-parametric statistical method for detecting gene-gene interactions. MDR performs a dimensional reduction by assigning multi-lo...

    Authors: William S Bush, Todd L Edwards, Scott M Dudek, Brett A McKinney and Marylyn D Ritchie
    Citation: BMC Bioinformatics 2008 9:238
  41. With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent resul...

    Authors: Leonid Zaslavsky, Yiming Bao and Tatiana A Tatusova
    Citation: BMC Bioinformatics 2008 9:237

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