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  1. 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:

  3. 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:

  4. 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:

  5. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  20. 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:

  21. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. MHC class II binding predictions are widely used to identify epitope candidates in infectious agents, allergens, cancer and autoantigens. The vast majority of prediction algorithms for human MHC class II to da...

    Authors: Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen and Bjoern Peters
    Citation: BMC Bioinformatics 2010 11:568
    Content type: Research article Published on:

  35. In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part o...

    Authors: Adrienn Szabó, Ádám Novák, István Miklós and Jotun Hein
    Citation: BMC Bioinformatics 2010 11:570
    Content type: Methodology article Published on:

  36. Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA...

    Authors: Gift Nyamundanda, Lorraine Brennan and Isobel Claire Gormley
    Citation: BMC Bioinformatics 2010 11:571
    Content type: Methodology article Published on:

  37. Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be ...

    Authors: Cristian Coarfa, Fuli Yu, Christopher A Miller, Zuozhou Chen, R Alan Harris and Aleksandar Milosavljevic
    Citation: BMC Bioinformatics 2010 11:572
    Content type: Software Published on:

  38. Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, o...

    Authors: Steinar Thorvaldsen, Tor Flå and Nils P Willassen
    Citation: BMC Bioinformatics 2010 11:573
    Content type: Software Published on:

  39. The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among ...

    Authors: Ruchi Chaudhary, Mukul S Bansal, André Wehe, David Fernández-Baca and Oliver Eulenstein
    Citation: BMC Bioinformatics 2010 11:574
    Content type: Software Published on:

  40. The problem of determining the physical conformation of a protein dimer, given the structures of the two interacting proteins in their unbound state, is a difficult one. The location of the docking interface i...

    Authors: Patricia Francis-Lyon, Shengyin Gu, Joel Hass, Nina Amenta and Patrice Koehl
    Citation: BMC Bioinformatics 2010 11:575
    Content type: Research article Published on:

  41. The data from DNA microarrays are increasingly being used in order to understand effects of different conditions, exposures or diseases on the modulation of the expression of various genes in a biological syst...

    Authors: Reuben Thomas, Luis de la Torre, Xiaoqing Chang and Sanjay Mehrotra
    Citation: BMC Bioinformatics 2010 11:576
    Content type: Research article Published on:

  42. Tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. One of the key challenges in database searching is the remarkable increase in comput...

    Authors: Chen Zhou, Hao Chi, Le-Heng Wang, You Li, Yan-Jie Wu, Yan Fu, Rui-Xiang Sun and Si-Min He
    Citation: BMC Bioinformatics 2010 11:577
    Content type: Research article Published on:

  43. Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Althoug...

    Authors: Miguel A Anton, Ander Aramburu and Angel Rubio
    Citation: BMC Bioinformatics 2010 11:578
    Content type: Research article Published on:

  45. To exploit the flood of data from advances in high throughput imaging of optically sectioned nuclei, image analysis methods need to correctly detect thousands of nuclei, ideally in real time. Variability in nu...

    Authors: Anthony Santella, Zhuo Du, Sonja Nowotschin, Anna-Katerina Hadjantonakis and Zhirong Bao
    Citation: BMC Bioinformatics 2010 11:580
    Content type: Methodology article Published on:

  46. Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra...

    Authors: Alexander Pérez-Ruiz, Margarida Julià-Sapé, Guillem Mercadal, Iván Olier, Carles Majós and Carles Arús
    Citation: BMC Bioinformatics 2010 11:581
    Content type: Software Published on:

  47. The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its componen...

    Authors: Peter Li, Joseph O Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick Dunn, Farid Khan, Naglis Malys, Hanan L Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, Jill Wishart, David S Broomhead, Carole A Goble…
    Citation: BMC Bioinformatics 2010 11:582
    Content type: Methodology article Published on:

  49. External stimulations of cells by hormones, cytokines or growth factors activate signal transduction pathways that subsequently induce a re-arrangement of cellular gene expression. The analysis of such changes...

    Authors: Andreas Kowarsch, Florian Blöchl, Sebastian Bohl, Maria Saile, Norbert Gretz, Ursula Klingmüller and Fabian J Theis
    Citation: BMC Bioinformatics 2010 11:585
    Content type: Research article Published on:

  50. High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes. The microarray-based Infinium methylation assay by Illumina is one platform for l...

    Authors: Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A Kibbe, Lifang Hou and Simon M Lin
    Citation: BMC Bioinformatics 2010 11:587
    Content type: Research article Published on:

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