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  1. Visualization of DNA microarray data in two or three dimensional spaces is an important exploratory analysis step in order to detect quality issues or to generate new hypotheses. Principal Component Analysis (...

    Authors: Christoph Bartenhagen, Hans-Ulrich Klein, Christian Ruckert, Xiaoyi Jiang and Martin Dugas
    Citation: BMC Bioinformatics 2010 11:567
    Content type: Research article Published on:

  2. Tissue MicroArray technology aims to perform immunohistochemical staining on hundreds of different tissue samples simultaneously. It allows faster analysis, considerably reducing costs incurred in staining. A ...

    Authors: Federica Viti, Ivan Merelli, Mieke Timmermans, Michael den Bakker, Francesco Beltrame, Peter Riegman and Luciano Milanesi
    Citation: BMC Bioinformatics 2010 11:566
    Content type: Research article Published on:

  3. Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroug...

    Authors: Francis C Weng, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Huai-Kuang Tsai and Daryi Wang
    Citation: BMC Bioinformatics 2010 11:565
    Content type: Research article Published on:

  4. Recent technological advancements have made high throughput sequencing an increasingly popular approach for transcriptome analysis. Advantages of sequencing-based transcriptional profiling over microarrays hav...

    Authors: Zhijin Wu, Bethany D Jenkins, Tatiana A Rynearson, Sonya T Dyhrman, Mak A Saito, Melissa Mercier and LeAnn P Whitney
    Citation: BMC Bioinformatics 2010 11:564
    Content type: Research article Published on:

  7. Bioinformatics data analysis often deals with additive mixtures of signals for which only class labels are known. Then, the overall goal is to estimate class related signals for data mining purposes. A conveni...

    Authors: Carsten Henneges, Pavel Laskov, Endang Darmawan, Jürgen Backhaus, Bernd Kammerer and Andreas Zell
    Citation: BMC Bioinformatics 2010 11:561
    Content type: Methodology article Published on:

  8. Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on ...

    Authors: Vamsi K Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn and Vishal Thapar
    Citation: BMC Bioinformatics 2010 11:560
    Content type: Research article Published on:

  9. Liquid chromatography-mass spectrometry (LC-MS) is one of the major techniques for the quantification of metabolites in complex biological samples. Peak modeling is one of the key components in LC-MS data pre-...

    Authors: Tianwei Yu and Hesen Peng
    Citation: BMC Bioinformatics 2010 11:559
    Content type: Methodology article Published on:

  10. Leukocytes play an important role in the human immune system. The family of leukocytes is comprised of lymphocytes, monocytes, eosinophils, basophils, and neutrophils. Any infection or acute stress may increas...

    Authors: Yung-Kuan Chan, Meng-Hsiun Tsai, Der-Chen Huang, Zong-Han Zheng and Kun-Ding Hung
    Citation: BMC Bioinformatics 2010 11:558
    Content type: Methodology article Published on:

  12. Recent advances in antibody microarray technology have made it possible to measure the expression of hundreds of proteins simultaneously in a competitive dual-colour approach similar to dual-colour gene expres...

    Authors: Martin Sill, Christoph Schröder, Jörg D Hoheisel, Axel Benner and Manuela Zucknick
    Citation: BMC Bioinformatics 2010 11:556
    Content type: Methodology article Published on:

  13. There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However...

    Authors: Mark Moll, Drew H Bryant and Lydia E Kavraki
    Citation: BMC Bioinformatics 2010 11:555
    Content type: Methodology article Published on:

  16. Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such te...

    Authors: Bo Chen, Minhua Chen, John Paisley, Aimee Zaas, Christopher Woods, Geoffrey S Ginsburg, Alfred Hero III, Joseph Lucas, David Dunson and Lawrence Carin
    Citation: BMC Bioinformatics 2010 11:552
    Content type: Research article Published on:

  17. Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biol...

    Authors: Fernando Garcia-Alcalde, Armando Blanco and Adrian J Shepherd
    Citation: BMC Bioinformatics 2010 11:551
    Content type: Research article Published on:

  18. The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues...

    Authors: Liya Wang and Lincoln D Stein
    Citation: BMC Bioinformatics 2010 11:550
    Content type: Research article Published on:

  19. In recent years, the number of High Throughput Screening (HTS) assays deposited in PubChem has grown quickly. As a result, the volume of both the structured information (i.e. molecular structure, bioactivities...

    Authors: Lianyi Han, Tugba O Suzek, Yanli Wang and Steve H Bryant
    Citation: BMC Bioinformatics 2010 11:549
    Content type: Research article Published on:

  20. Many newly detected point mutations are located in protein-coding regions of the human genome. Knowledge of their effects on the protein's 3D structure provides insight into the protein's mechanism, can aid th...

    Authors: Hanka Venselaar, Tim AH te Beek, Remko KP Kuipers, Maarten L Hekkelman and Gert Vriend
    Citation: BMC Bioinformatics 2010 11:548
    Content type: Methodology article Published on:

  22. In a high throughput setting, effective flow cytometry data analysis depends heavily on proper data preprocessing. While usual preprocessing steps of quality assessment, outlier removal, normalization, and gat...

    Authors: Greg Finak, Juan-Manuel Perez, Andrew Weng and Raphael Gottardo
    Citation: BMC Bioinformatics 2010 11:546
    Content type: Methodology article Published on:

  23. Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA), we have developed a conformational generation metho...

    Authors: Fang Bai, Xiaofeng Liu, Jiabo Li, Haoyun Zhang, Hualiang Jiang, Xicheng Wang and Honglin Li
    Citation: BMC Bioinformatics 2010 11:545
    Content type: Methodology article Published on:

  24. Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because t...

    Authors: David R Kelley and Steven L Salzberg
    Citation: BMC Bioinformatics 2010 11:544
    Content type: Methodology article Published on:

  25. Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligom...

    Authors: Jeffry D Sander, Deepak Reyon, Morgan L Maeder, Jonathan E Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R Regan, Elizabeth J Dahlborg, Mathew J Goodwin, Fengli Fu, Daniel F Voytas, J Keith Joung and Drena Dobbs
    Citation: BMC Bioinformatics 2010 11:543
    Content type: Methodology article Published on:

  26. In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manua...

    Authors: Wei Tan, Ravi Madduri, Alexandra Nenadic, Stian Soiland-Reyes, Dinanath Sulakhe, Ian Foster and Carole A Goble
    Citation: BMC Bioinformatics 2010 11:542
    Content type: Software Published on:

  28. Circadian rhythms are 24 hour oscillations in many behavioural, physiological, cellular and molecular processes that are controlled by an endogenous clock which is entrained to environmental factors including ...

    Authors: Meric A Ovacik, Siddharth Sukumaran, Richard R Almon, Debra C DuBois, William J Jusko and Ioannis P Androulakis
    Citation: BMC Bioinformatics 2010 11:540
    Content type: Research article Published on:

  29. Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comp...

    Authors: Zhengdong D Zhang and Mark B Gerstein
    Citation: BMC Bioinformatics 2010 11:539
    Content type: Methodology article Published on:

  30. Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied...

    Authors: Frederick A Matsen, Robin B Kodner and E Virginia Armbrust
    Citation: BMC Bioinformatics 2010 11:538
    Content type: Methodology article Published on:

  32. While occurring enzymatically in biological systems, O-linked glycosylation affects protein folding, localization and trafficking, protein solubility, antigenicity, biological activity, as well as cell-cell in...

    Authors: Shu-An Chen, Tzong-Yi Lee and Yu-Yen Ou
    Citation: BMC Bioinformatics 2010 11:536
    Content type: Research article Published on:

  34. In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1) retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of trans...

    Authors: Eric Rouchka, Diego E Montoya-Durango, Vilius Stribinskis, Kenneth Ramos and Ted Kalbfleisch
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  35. Mouse xenograft models, in which human cancer cells are implanted in immune-suppressed mice, have been popular for studying the mechanisms of novel therapeutic targets, tumor progression and metastasis. We hyp...

    Authors: Xinan Yang, Younghee Lee, Yong Huang, James L Chen, Rosie H Xing and Yves A Lussier
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  36. In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with ...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch, James I Hoath, Ira J Kalet and David L Veenstra
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  37. A key challenge in pharmacogenomics is the identification of genes whose variants contribute to drug response phenotypes, which can include severe adverse effects. Pharmacogenomics GWAS attempt to elucidate ge...

    Authors: Nicholas P Tatonetti, Joel T Dudley, Hersh Sagreiya, Atul J Butte and Russ B Altman
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  38. The amount of data deposited in the Gene Expression Omnibus (GEO) has expanded significantly. It is important to ensure that these data are properly annotated with clinical data and descriptions of experimenta...

    Authors: Ronilda Lacson, Michael Mbagwu, Hisham Yousif and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  39. Multi-item adverse drug event (ADE) associations are associations relating multiple drugs to possibly multiple adverse events. The current standard in pharmacovigilance is bivariate association analysis, where...

    Authors: Rave Harpaz, Herbert S Chase and Carol Friedman
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  40. Combining the results of studies using highly parallelized measurements of gene expression such as microarrays and RNAseq offer unique challenges in meta analysis. Motivated by a need for a deeper understandin...

    Authors: Alexander A Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M Sarwal and Atul J Butte
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  41. Chronic lymphocytic leukemia (CLL) is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Im...

    Authors: Jie Zhang, Yang Xiang, Liya Ding, Kristin Keen-Circle, Tara B Borlawsky, Hatice Gulcin Ozer, Ruoming Jin, Philip Payne and Kun Huang
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  42. Diagnosis and treatment of patients in the clinical setting is often driven by known symptomatic factors that distinguish one particular condition from another. Treatment based on noticeable symptoms, however,...

    Authors: David P Chen, Joel T Dudley and Atul J Butte
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  43. Given the rapid growth of translational research and personalized healthcare paradigms, the ability to relate and reason upon networks of bio-molecular and phenotypic variables at various levels of granularity...

    Authors: Philip RO Payne, Kun Huang, Kristin Keen-Circle, Abhisek Kundu, Jie Zhang and Tara B Borlawsky
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  44. Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene exp...

    Authors: Hsun-Hsien Chang, Michael McGeachie, Gil Alterovitz and Marco F Ramoni
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 9

  46. The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the p...

    Authors: Joel Hedlund, Hans Jörnvall and Bengt Persson
    Citation: BMC Bioinformatics 2010 11:534
    Content type: Research article Published on:

  47. Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-...

    Authors: Shandar Ahmad, Yumlembam Hemajit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita and Kenji Mizuguchi
    Citation: BMC Bioinformatics 2010 11:533
    Content type: Research article Published on:

  48. The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Le...

    Authors: Christian Widmer, Nora C Toussaint, Yasemin Altun and Gunnar Rätsch
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  49. Quantitative phenotypes emerge everywhere in systems biology and biomedicine due to a direct interest for quantitative traits, or to high individual variability that makes hard or impossible to classify sample...

    Authors: Giorgio Guzzetta, Giuseppe Jurman and Cesare Furlanello
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

  50. We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are ...

    Authors: Pavel P Kuksa and Vladimir Pavlovic
    Citation: BMC Bioinformatics 2010 11(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 8

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