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  1. Multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope dilution (SID) is increasingly becoming a widely accepted assay for the quantification of proteins and peptides. These assays have sh...

    Authors: D R Mani, Susan E Abbatiello and Steven A Carr
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  2. Mass Spectrometry utilizing labeling allows multiple specimens to be subjected to mass spectrometry simultaneously. As a result, between-experiment variability is reduced. Here we describe use of fundamental c...

    Authors: Ann L Oberg and Douglas W Mahoney
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S7
    Content type: Review Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  3. Protein structures are comprised of modular elements known as domains. These units are used and re-used over and over in nature, and usually serve some particular function in the structure. Thus it is useful t...

    Authors: Howard J Feldman
    Citation: BMC Bioinformatics 2012 13:286
    Content type: Methodology article Published on:

  4. X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characteri...

    Authors: Zaheer Ul-Haq, Sadaf Iqbal and Syed Tarique Moin
    Citation: BMC Bioinformatics 2012 13:285
    Content type: Research article Published on:

  5. Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be take...

    Authors: Verena Zuber, A Pedro Duarte Silva and Korbinian Strimmer
    Citation: BMC Bioinformatics 2012 13:284
    Content type: Methodology article Published on:

  6. PCR amplification and high-throughput sequencing theoretically enable the characterization of the finest-scale diversity in natural microbial and viral populations, but each of these methods introduces random ...

    Authors: Michael J Rosen, Benjamin J Callahan, Daniel S Fisher and Susan P Holmes
    Citation: BMC Bioinformatics 2012 13:283
    Content type: Research article Published on:

  7. Automated classification of histopathology involves identification of multiple classes, including benign, cancerous, and confounder categories. The confounder tissue classes can often mimic and share attribute...

    Authors: Scott Doyle, Michael D Feldman, Natalie Shih, John Tomaszewski and Anant Madabhushi
    Citation: BMC Bioinformatics 2012 13:282
    Content type: Research article Published on:

  8. Techniques for reconstruction of biological networks which are based on perturbation experiments often predict direct interactions between nodes that do not exist. Transitive reduction removes such relations i...

    Authors: Dragan Bošnački, Maximilian R Odenbrett, Anton Wijs, Willem Ligtenberg and Peter Hilbers
    Citation: BMC Bioinformatics 2012 13:281
    Content type: Software Published on:

  10. Structural variations (SVs) in genomes are commonly observed even in healthy individuals and play key roles in biological functions. To understand their functional impact or to infer molecular mechanisms of SV...

    Authors: Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki and Satoru Miyano
    Citation: BMC Bioinformatics 2012 13:279
    Content type: Methodology article Published on:

  15. Despite our increasing recognition of the mechanisms that specify and propagate epigenetic states of gene expression, the pattern of how epigenetic modifications contribute to the overall genetic variation of ...

    Authors: Zhong Wang, Zuoheng Wang, Jianxin Wang, Yihan Sui, Jian Zhang, Duanping Liao and Rongling Wu
    Citation: BMC Bioinformatics 2012 13:274
    Content type: Methodology article Published on:

  17. Early screening for cancer is arguably one of the greatest public health advances over the last fifty years. However, many cancer screening tests are invasive (digital rectal exams), expensive (mammograms, ima...

    Authors: Héctor Corrada Bravo, Vasyl Pihur, Matthew McCall, Rafael A Irizarry and Jeffrey T Leek
    Citation: BMC Bioinformatics 2012 13:272
    Content type: Research article Published on:

  18. Dysregulation of imprinted genes, which are expressed in a parent-of-origin-specific manner, plays an important role in various human diseases, such as cancer and behavioral disorder. To date, however, fewer t...

    Authors: Hua Li, Xiao Su, Juan Gallegos, Yue Lu, Yuan Ji, Jeffrey J Molldrem and Shoudan Liang
    Citation: BMC Bioinformatics 2012 13:271
    Content type: Research article Published on:

  19. A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list...

    Authors: Argiris Sakellariou, Despina Sanoudou and George Spyrou
    Citation: BMC Bioinformatics 2012 13:270
    Content type: Methodology article Published on:

  20. An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with mo...

    Authors: Shanker Kalyana-Sundaram, Achiraman Shanmugam and Arul M Chinnaiyan
    Citation: BMC Bioinformatics 2012 13:269
    Content type: Methodology article Published on:

  23. Alzheimer’s disease has been known for more than 100 years and the underlying molecular mechanisms are not yet completely understood. The identification of genes involved in the processes in Alzheimer affected...

    Authors: Lena Scheubert, Mitja Luštrek, Rainer Schmidt, Dirk Repsilber and Georg Fuellen
    Citation: BMC Bioinformatics 2012 13:266
    Content type: Research article Published on:

  25. New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of...

    Authors: Thomas J Sharpton, Guillaume Jospin, Dongying Wu, Morgan GI Langille, Katherine S Pollard and Jonathan A Eisen
    Citation: BMC Bioinformatics 2012 13:264
    Content type: Research article Published on:

  26. The generation of focused mutant libraries at hotspot residues is an important strategy in directed protein evolution. Existing methods, such as combinatorial active site testing and residual coupling analysis...

    Authors: Chenghua Wang, Ribo Huang, Bingfang He and Qishi Du
    Citation: BMC Bioinformatics 2012 13:263
    Content type: Research article Published on:

  27. Protein-protein interaction networks are key to a systems-level understanding of cellular biology. However, interaction data can contain a considerable fraction of false positives. Several methods have been pr...

    Authors: Atanas Kamburov, Arndt Grossmann, Ralf Herwig and Ulrich Stelzl
    Citation: BMC Bioinformatics 2012 13:262
    Content type: Methodology article Published on:

  29. RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The i...

    Authors: Rune B Lyngsø, James WJ Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland and Jotun Hein
    Citation: BMC Bioinformatics 2012 13:260
    Content type: Research article Published on:

  31. Clinical Bioinformatics is currently growing and is based on the integration of clinical and omics data aiming at the development of personalized medicine. Thus the introduction of novel technologies able to i...

    Authors: Pietro Hiram Guzzi, Giuseppe Agapito, Maria Teresa Di Martino, Mariamena Arbitrio, Pierfrancesco Tassone, Pierosandro Tagliaferri and Mario Cannataro
    Citation: BMC Bioinformatics 2012 13:258
    Content type: Software Published on:

  35. Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Co...

    Authors: Myles Byrne, Ivo FAC Fokkema, Owen Lancaster, Tomasz Adamusiak, Anni Ahonen-Bishopp, David Atlan, Christophe Béroud, Michael Cornell, Raymond Dalgleish, Andrew Devereau, George P Patrinos, Morris A Swertz, Peter EM Taschner, Gudmundur A Thorisson, Mauno Vihinen, Anthony J Brookes…
    Citation: BMC Bioinformatics 2012 13:254
    Content type: Methodology article Published on:

  36. In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size,...

    Authors: Danielle G Lemay, William F Martin, Angie S Hinrichs, Monique Rijnkels, J Bruce German, Ian Korf and Katherine S Pollard
    Citation: BMC Bioinformatics 2012 13:253
    Content type: Research article Published on:

  38. Signaling systems typically involve large, structured molecules each consisting of a large number of subunits called molecule domains. In modeling such systems these domains can be considered as the main playe...

    Authors: Katrin Kolczyk, Regina Samaga, Holger Conzelmann, Sebastian Mirschel and Carsten Conradi
    Citation: BMC Bioinformatics 2012 13:251
    Content type: Research article Published on:

  39. Transcription factors regulate numerous cellular processes by controlling the rate of production of each gene. The regulatory relations are modeled using transcriptional regulatory networks. Recent studies hav...

    Authors: Günhan Gülsoy, Nirmalya Bandhyopadhyay and Tamer Kahveci
    Citation: BMC Bioinformatics 2012 13:250
    Content type: Research article Published on:

  40. MEDLINE®/PubMed® indexes over 20 million biomedical articles, providing curated annotation of its contents using a controlled vocabulary known as Medical Subject Headings (MeSH). The MeSH vocabulary, developed...

    Authors: Warren A Cheung, BF Francis Ouellette and Wyeth W Wasserman
    Citation: BMC Bioinformatics 2012 13:249
    Content type: Research article Published on:

  43. Inverted repeat genes encode precursor RNAs characterized by hairpin structures. These RNA hairpins are then metabolized by biosynthetic pathways to produce functional small RNAs. In eukaryotic genomes, short ...

    Authors: Sébastien Tempel, Nicolas Pollet and Fariza Tahi
    Citation: BMC Bioinformatics 2012 13:246
    Content type: Research article Published on:

  45. Sporadic Amyotrophic Lateral Sclerosis (sALS) is a devastating, complex disease of unknown etiology. We studied this disease with microarray technology to capture as much biological complexity as possible. The...

    Authors: Cristina Baciu, Kevin J Thompson, Jean-Luc Mougeot, Benjamin R Brooks and Jennifer W Weller
    Citation: BMC Bioinformatics 2012 13:244
    Content type: Research article Published on:

  47. Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the numbe...

    Authors: Bogumil M Konopka, Jean-Christophe Nebel and Malgorzata Kotulska
    Citation: BMC Bioinformatics 2012 13:242
    Content type: Methodology article Published on:

  49. The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user inte...

    Authors: Hiroyuki Mishima, Jan Aerts, Toshiaki Katayama, Raoul J P Bonnal and Koh-ichiro Yoshiura
    Citation: BMC Bioinformatics 2012 13:240
    Content type: Software Published on:

  50. Performing high throughput sequencing on samples pooled from different individuals is a strategy to characterize genetic variability at a small fraction of the cost required for individual sequencing. In certa...

    Authors: Emanuele Raineri, Luca Ferretti, Anna Esteve-Codina, Bruno Nevado, Simon Heath and Miguel Pérez-Enciso
    Citation: BMC Bioinformatics 2012 13:239
    Content type: Methodology article Published on:

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