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  1. Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigat...

    Authors: Johanna Brodin, Mohan Krishnamoorthy, Gayathri Athreya, Will Fischer, Peter Hraber, Cheryl Gleasner, Lance Green, Bette Korber and Thomas Leitner
    Citation: BMC Bioinformatics 2013 14:255
    Content type: Software Published on:

  2. Time course data from microarrays and high-throughput sequencing experiments require simple, computationally efficient and powerful statistical models to extract meaningful biological signal, and for tasks suc...

    Authors: James Hensman, Neil D Lawrence and Magnus Rattray
    Citation: BMC Bioinformatics 2013 14:252
    Content type: Research article Published on:

  5. Candidate disease gene prediction is a rapidly developing area of bioinformatics research with the potential to deliver great benefits to human health. As experimental studies detecting associations between ge...

    Authors: Sara Ballouz, Jason Y Liu, Richard A George, Naresh Bains, Arthur Liu, Martin Oti, Bruno Gaeta, Diane Fatkin and Merridee A Wouters
    Citation: BMC Bioinformatics 2013 14:249
    Content type: Database Published on:

  7. Dynamic protein phosphorylation is an essential regulatory mechanism in various organisms. In this capacity, it is involved in a multitude of signal transduction pathways. Kinase-specific phosphorylation data ...

    Authors: Liang Zou, Mang Wang, Yi Shen, Jie Liao, Ao Li and Minghui Wang
    Citation: BMC Bioinformatics 2013 14:247
    Content type: Methodology article Published on:

  9. The emergence of high-throughput genomic datasets from different sources and platforms (e.g., gene expression, single nucleotide polymorphisms (SNP), and copy number variation (CNV)) has greatly enhanced our unde...

    Authors: Dongdong Lin, Jigang Zhang, Jingyao Li, Vince D Calhoun, Hong-Wen Deng and Yu-Ping Wang
    Citation: BMC Bioinformatics 2013 14:245
    Content type: Methodology article Published on:

  10. Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a f...

    Authors: Daniel Barker, David EK Ferrier, Peter WH Holland, John BO Mitchell, Heleen Plaisier, Michael G Ritchie and Steven D Smart
    Citation: BMC Bioinformatics 2013 14:243
    Content type: Software Published on:

  11. With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open u...

    Authors: Heinz Koeppl, Marc Hafner and James Lu
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  12. Cell imaging is becoming an indispensable tool for cell and molecular biology research. However, most processes studied are stochastic in nature, and require the observation of many cells and events. Ideally, ...

    Authors: Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja and Andre S Ribeiro
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  13. Diffusion is a key component of many biological processes such as chemotaxis, developmental differentiation and tissue morphogenesis. Since recently, the spatial gradients caused by diffusion can be assessed i...

    Authors: Sabrina Hock, Jan Hasenauer and Fabian J Theis
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  14. High-throughput genome-wide screening to study gene-specific functions, e.g. for drug discovery, demands fast automated image analysis methods to assist in unraveling the full potential of such studies. Image ...

    Authors: Muhammad Farhan, Pekka Ruusuvuori, Mario Emmenlauer, Pauli Rämö, Christoph Dehio and Olli Yli-Harja
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  15. Zebrafish embryos have recently been established as a xenotransplantation model of the metastatic behaviour of primary human tumours. Current tools for automated data extraction from the microscope images are ...

    Authors: Teppo Annila, Eero Lihavainen, Ines J Marques, Darren R Williams, Olli Yli-Harja and Andre Ribeiro
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  16. In this paper we present an algorithm based on the sum-product algorithm that finds elements in the preimage of a feed-forward Boolean networks given an output of the network. Our probabilistic method runs in ...

    Authors: Johannes Georg Klotz, Martin Bossert and Steffen Schober
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  17. The circadian clock is an important molecular mechanism that enables many organisms to anticipate and adapt to environmental change. Pokhilko et al. recently built a deterministic ODE mathematical model of the pl...

    Authors: Catherine F Higham and Dirk Husmeier
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  18. Transcription factor (TF) binding to DNA can be modeled in a number of different ways. It is highly debated which modeling methods are the best, how the models should be built and what can they be applied to. ...

    Authors: Juhani Kähärä and Harri Lähdesmäki
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  19. Classification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a num...

    Authors: Helena Skutkova, Martin Vitek, Petr Babula, Rene Kizek and Ivo Provaznik
    Citation: BMC Bioinformatics 2013 14(Suppl 10):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 10

  20. Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional relationships between genomic intervals. Running Circos requires extra data proc...

    Authors: Hongen Zhang, Paul Meltzer and Sean Davis
    Citation: BMC Bioinformatics 2013 14:244
    Content type: Software Published on:

  22. Accurate recognition of regulatory elements in promoters is an essential prerequisite for understanding the mechanisms of gene regulation at the level of transcription. Composite regulatory elements represent ...

    Authors: Igor V Deyneko, Alexander E Kel, Olga V Kel-Margoulis, Elena V Deineko, Edgar Wingender and Siegfried Weiss
    Citation: BMC Bioinformatics 2013 14:241
    Content type: Methodology article Published on:

  24. The success of targeted anti-cancer drugs are frequently hindered by the lack of knowledge of the individual pathway of the patient and the extreme data requirements on the estimation of the personalized genet...

    Authors: Noah Berlow, Lara E Davis, Emma L Cantor, Bernard Séguin, Charles Keller and Ranadip Pal
    Citation: BMC Bioinformatics 2013 14:239
    Content type: Research article Published on:

  25. Laserscanning recently has become a powerful and common method for plant parameterization and plant growth observation on nearly every scale range. However, 3D measurements with high accuracy, spatial resoluti...

    Authors: Stefan Paulus, Jan Dupuis, Anne-Katrin Mahlein and Heiner Kuhlmann
    Citation: BMC Bioinformatics 2013 14:238
    Content type: Research article Published on:

  28. Constant technological advances have allowed scientists in biology to migrate from conventional single-omics to multi-omics experimental approaches, challenging bioinformatics to bridge this multi-tiered infor...

    Authors: Panagiotis Moulos, Julie Klein, Simon Jupp, Robert Stevens, Jean-Loup Bascands and Joost P Schanstra
    Citation: BMC Bioinformatics 2013 14:235
    Content type: Software Published on:

  30. Assigning a protein into one of its folds is a transitional step for discovering three dimensional protein structure, which is a challenging task in bimolecular (biological) science. The present research focus...

    Authors: Alok Sharma, Kuldip K Paliwal, Abdollah Dehzangi, James Lyons, Seiya Imoto and Satoru Miyano
    Citation: BMC Bioinformatics 2013 14:233
    Content type: Research article Published on:

  32. In addition to probe sequence characteristics, noise in hybridization array data is thought to be influenced by competitive hybridization between probes tiled at high densities. Empirical evaluation of competi...

    Authors: Cali E Willet, Laura Bunbury-Cruickshank, Diane van Rooy, Georgina Child, Mohammad R Shariflou, Peter C Thomson and Claire M Wade
    Citation: BMC Bioinformatics 2013 14:231
    Content type: Research article Published on:

  33. Frequent pattern mining analysis applied on microarray dataset appears to be a promising strategy for identifying relationships between gene expression levels. Unfortunately, too many itemsets (co-expressed ge...

    Authors: Yu-Cheng Liu, Chun-Pei Cheng and Vincent S Tseng
    Citation: BMC Bioinformatics 2013 14:230
    Content type: Methodology article Published on:

  34. Most proteins have evolved in specific cellular compartments that limit their functions and potential interactions. On the other hand, motifs define amino acid arrangements conserved between protein family mem...

    Authors: Marcos Parras-Moltó, Francisco J Campos-Laborie, Juan García-Diéguez, M Rosario Rodríguez-Griñolo and Antonio J Pérez-Pulido
    Citation: BMC Bioinformatics 2013 14:229
    Content type: Research article Published on:

  35. The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these dataset...

    Authors: Stefanie Seltmann, Harald Stachelscheid, Alexander Damaschun, Ludger Jansen, Fritz Lekschas, Jean-Fred Fontaine, Throng Nghia Nguyen-Dobinsky, Ulf Leser and Andreas Kurtz
    Citation: BMC Bioinformatics 2013 14:228
    Content type: Methodology article Published on:

  38. The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Single nucleotide variants (SNVs) inferred from next generation sequencing are...

    Authors: Jiawen Bian, Chenglin Liu, Hongyan Wang, Jing Xing, Priyanka Kachroo and Xiaobo Zhou
    Citation: BMC Bioinformatics 2013 14:225
    Content type: Software Published on:

  42. Mechanistic biosimulation can be used in drug development to form testable hypotheses, develop predictions of efficacy before clinical trial results are available, and elucidate clinical response to therapy. H...

    Authors: Brian J Schmidt, Fergal P Casey, Thomas Paterson and Jason R Chan
    Citation: BMC Bioinformatics 2013 14:221
    Content type: Research article Published on:

  45. The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors in...

    Authors: Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich and Thomas Dandekar
    Citation: BMC Bioinformatics 2013 14:218
    Content type: Software Published on:

  46. Biomolecular pathways and networks are dynamic and complex, and the perturbations to them which cause disease are often multiple, heterogeneous and contingent. Pathway and network visualizations, rendered on a...

    Authors: Paul T Shannon, Mark Grimes, Burak Kutlu, Jan J Bot and David J Galas
    Citation: BMC Bioinformatics 2013 14:217
    Content type: Software Published on:

  48. We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth req...

    Authors: Guy Bresler, Ma'ayan Bresler and David Tse
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  49. Two-dimensional gel electrophoresis (2DE) is a powerful technique for studying protein isoforms and their modifications. Existing commercial 2D image analysis tools rely on spot detection that limits analysis ...

    Authors: Ola Kristoffer Øye, Katarina M Jørgensen, Sigrun M Hjelle, André Sulen, Dag Magne Ulvang and Bjørn Tore Gjertsen
    Citation: BMC Bioinformatics 2013 14:215
    Content type: Software Published on:

  50. The synthesis of information across microarray studies has been performed by combining statistical results of individual studies (as in a mosaic), or by combining data from multiple studies into a large pool t...

    Authors: Márcia M Almeida-de-Macedo, Nick Ransom, Yaping Feng, Jonathan Hurst and Eve Syrkin Wurtele
    Citation: BMC Bioinformatics 2013 14:214
    Content type: Research article Published on:

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