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  1. Dynamic Bayesian network (DBN) is among the mainstream approaches for modeling various biological networks, including the gene regulatory network (GRN). Most current methods for learning DBN employ either loca...

    Authors: Nguyen Xuan Vinh, Madhu Chetty, Ross Coppel and Pramod P Wangikar
    Citation: BMC Bioinformatics 2012 13:131
    Content type: Research article Published on:

  2. An important question in genetic studies is to determine those genetic variants, in particular CNVs, that are specific to different groups of individuals. This could help in elucidating differences in disease ...

    Authors: Juan R González, Carlos Abellán and Juan J Abellán
    Citation: BMC Bioinformatics 2012 13:130
    Content type: Methodology article Published on:

  4. Given genetic networks derived from two genomes, it may be difficult to decide if their local structures are similar enough in both genomes to infer some ancestral configuration or some conserved functional re...

    Authors: Zhenyu Yang and David Sankoff
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  5. Understanding drug bioactivities is crucial for early-stage drug discovery, toxicology studies and clinical trials. Network pharmacology is a promising approach to better understand the molecular mechanisms of...

    Authors: Jingchun Sun, Yonghui Wu, Hua Xu and Zhongming Zhao
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  6. Often protein (or gene) time-course data are collected for multiple replicates. Each replicate generally has sparse data with the number of time points being less than the number of proteins. Usually each repl...

    Authors: Kristopher L Patton, David J John and James L Norris
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  7. Because common complex diseases are affected by multiple genes and environmental factors, it is essential to investigate gene-gene and/or gene-environment interactions to understand genetic architecture of com...

    Authors: Sohee Oh, Jaehoon Lee, Min-Seok Kwon, Bruce Weir, Kyooseob Ha and Taesung Park
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  8. The discovering of interesting patterns in drug-protein interaction data at molecular level can reveal hidden relationship among drugs and proteins and can therefore be of paramount importance for such applica...

    Authors: Weimin Luo and Keith CC Chan
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  9. Identifying gene regulatory network (GRN) from time course gene expression data has attracted more and more attentions. Due to the computational complexity, most approaches for GRN reconstruction are limited o...

    Authors: Xi-Jun Liang, Zhonghang Xia, Li-Wei Zhang and Fang-Xiang Wu
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  10. The growth of the biomedical information requires most information retrieval systems to provide short and specific answers in response to complex user queries. Semantic information in the form of free text tha...

    Authors: Qinmin Hu, Jimmy Xiangji Huang and Xiaohua Hu
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  11. Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals--some researchers conjecture that up to 90% of ...

    Authors: Yann Christinat and Bernard ME Moret
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  13. Most major genome projects and sequence databases provide a GO annotation of their data, either automatically or through human annotators, creating a large corpus of data written in the language of GO. Texts w...

    Authors: Leila Ranandeh Kalankesh, Robert Stevens and Andy Brass
    Citation: BMC Bioinformatics 2012 13:127
    Content type: Methodology article Published on:

  15. Self-incompatibility (SI) is a biological mechanism to avoid inbreeding in allogamous plants. In grasses, this mechanism is controlled by a two-locus system (S-Z). Calculation of male and female gamete frequen...

    Authors: Andrea Arias Aguirre, Bernd Wollenweber, Ursula K Frei and Thomas Lübberstedt
    Citation: BMC Bioinformatics 2012 13:125
    Content type: Software Published on:

  16. The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence...

    Authors: Laura J Anzaldi, Daniel Muñoz-Fernández and Ivan Erill
    Citation: BMC Bioinformatics 2012 13:124
    Content type: Software Published on:

  17. The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in signif...

    Authors: Fenglou Mao, David Williams, Olga Zhaxybayeva, Maria Poptsova, Pascal Lapierre, J Peter Gogarten and Ying Xu
    Citation: BMC Bioinformatics 2012 13:123
    Content type: Software Published on:

  18. Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to...

    Authors: Zsolt L Husz, Nicholas Burton, Bill Hill, Nestor Milyaev and Richard A Baldock
    Citation: BMC Bioinformatics 2012 13:122
    Content type: Software Published on:

  19. Identity by descent (IBD) has played a fundamental role in the discovery of genetic loci underlying human diseases. Both pedigree-based and population-based linkage analyses rely on estimating recent IBD, and ...

    Authors: Shu-Yi Su, Jay Kasberger, Sergio Baranzini, William Byerley, Wilson Liao, Jorge Oksenberg, Elliott Sherr and Eric Jorgenson
    Citation: BMC Bioinformatics 2012 13:121
    Content type: Research article Published on:

  20. Genome-wide association studies (GWAS) with metabolic traits and metabolome-wide association studies (MWAS) with traits of biomedical relevance are powerful tools to identify the contribution of genetic, envir...

    Authors: Ann-Kristin Petersen, Jan Krumsiek, Brigitte Wägele, Fabian J Theis, H-Erich Wichmann, Christian Gieger and Karsten Suhre
    Citation: BMC Bioinformatics 2012 13:120
    Content type: Research article Published on:

  22. Adenosine-5′-triphosphate (ATP) is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is...

    Authors: Ya-Nan Zhang, Dong-Jun Yu, Shu-Sen Li, Yong-Xian Fan, Yan Huang and Hong-Bin Shen
    Citation: BMC Bioinformatics 2012 13:118
    Content type: Research article Published on:

  23. The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of po...

    Authors: Peter W Collingridge and Steven Kelly
    Citation: BMC Bioinformatics 2012 13:117
    Content type: Methodology article Published on:

  24. Gas chromatography–mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data ti...

    Authors: Sean O'Callaghan, David P De Souza, Andrew Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia L Tull, Ute Roessner, Antony Bacic, Malcolm J McConville and Vladimir A Likić
    Citation: BMC Bioinformatics 2012 13:115
    Content type: Software Published on:

  25. A recent large-scale analysis of Gene Expression Omnibus (GEO) data found frequent evidence for spatial defects in a substantial fraction of Affymetrix microarrays in the GEO. Nevertheless, in contrast to qual...

    Authors: Tobias Petri, Evi Berchtold, Ralf Zimmer and Caroline C Friedel
    Citation: BMC Bioinformatics 2012 13:114
    Content type: Research article Published on:

  26. Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial commun...

    Authors: Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo and Jizhong Zhou
    Citation: BMC Bioinformatics 2012 13:113
    Content type: Methodology article Published on:

  27. Detailed and systematic understanding of the biological effects of millions of available compounds on living cells is a significant challenge. As most compounds impact multiple targets and pathways, traditiona...

    Authors: Suleiman A Khan, Ali Faisal, John Patrick Mpindi, Juuso A Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P Kallioniemi, Krister Wennerberg and Samuel Kaski
    Citation: BMC Bioinformatics 2012 13:112
    Content type: Research article Published on:

  29. Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software e...

    Authors: Thomas Laubach, Arndt von Haeseler and Martin J Lercher
    Citation: BMC Bioinformatics 2012 13:110
    Content type: Software Published on:

  30. Identification of protein complexes and functional modules from protein-protein interaction (PPI) networks is crucial to understanding the principles of cellular organization and predicting protein functions. ...

    Authors: Min Li, Xuehong Wu, Jianxin Wang and Yi Pan
    Citation: BMC Bioinformatics 2012 13:109
    Content type: Methodology article Published on:

  31. Research into event-based text mining from the biomedical literature has been growing in popularity to facilitate the development of advanced biomedical text mining systems. Such technology permits advanced se...

    Authors: Makoto Miwa, Paul Thompson, John McNaught, Douglas B Kell and Sophia Ananiadou
    Citation: BMC Bioinformatics 2012 13:108
    Content type: Research article Published on:

  32. Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughp...

    Authors: Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar and Jieping Ye
    Citation: BMC Bioinformatics 2012 13:107
    Content type: Research article Published on:

  33. Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead comp...

    Authors: Kalai Vanii Jayaseelan, Pablo Moreno, Andreas Truszkowski, Peter Ertl and Christoph Steinbeck
    Citation: BMC Bioinformatics 2012 13:106
    Content type: Methodology article Published on:

  34. Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied t...

    Authors: Paul Shealy and Homayoun Valafar
    Citation: BMC Bioinformatics 2012 13:105
    Content type: Software Published on:

  35. Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3–10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods hav...

    Authors: Niall J Haslam and Denis C Shields
    Citation: BMC Bioinformatics 2012 13:104
    Content type: Methodology article Published on:

  36. In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and r...

    Authors: Christopher W Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts and William C Ray
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  37. One of the major goals in biomedical image processing is accurate segmentation of networks embedded in volumetric data sets. Biological networks are composed of a meshwork of thin filaments that span large vol...

    Authors: David Mayerich, Chris Bjornsson, Jonathan Taylor and Badrinath Roysam
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  38. When analyzing metabolomics data, cancer care researchers are searching for differences between known healthy samples and unhealthy samples. By analyzing and understanding these differences, researchers hope t...

    Authors: Philip Livengood, Ross Maciejewski, Wei Chen and David S Ebert
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  39. Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and ...

    Authors: Trevor Paterson, Martin Graham, Jessie Kennedy and Andy Law
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  40. We present HiTSEE (High-Throughput Screening Exploration Environment), a visualization tool for the analysis of large chemical screens used to examine biochemical processes. The tool supports the investigation...

    Authors: Hendrik Strobelt, Enrico Bertini, Joachim Braun, Oliver Deussen, Ulrich Groth, Thomas U Mayer and Dorit Merhof
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  41. Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, ...

    Authors: Adam M Smith, Wen Xu, Yao Sun, James R Faeder and G Elisabeta Marai
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  42. In the search for single-nucleotide polymorphisms which influence the observable phenotype, genome wide association studies have become an important technique for the identification of associations between gen...

    Authors: Julian Heinrich, Corinna Vehlow, Florian Battke, Günter Jäger, Daniel Weiskopf and Kay Nieselt
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 8

  44. Many methods for dimensionality reduction of large data sets such as those generated in microarray studies boil down to the Singular Value Decomposition (SVD). Although singular vectors associated with the lar...

    Authors: András Bodor, István Csabai, Michael W Mahoney and Norbert Solymosi
    Citation: BMC Bioinformatics 2012 13:103
    Content type: Software Published on:

  45. Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis...

    Authors: Thomas Stropp, Timothy McPhillips, Bertram Ludäscher and Mark Bieda
    Citation: BMC Bioinformatics 2012 13:102
    Content type: Software Published on:

  47. As Next-Generation Sequencing data becomes available, existing hardware environments do not provide sufficient storage space and computational power to store and process the data due to their enormous size. Th...

    Authors: Dandi Qiao, Wai-Ki Yip and Christoph Lange
    Citation: BMC Bioinformatics 2012 13:100
    Content type: Methodology article Published on:

  48. Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fet...

    Authors: Dinesh K Barupal, Pradeep K Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L Kothari, Kent E Pinkerton and Oliver Fiehn
    Citation: BMC Bioinformatics 2012 13:99
    Content type: Research article Published on:

  49. In systems biology, the task of reverse engineering gene pathways from data has been limited not just by the curse of dimensionality (the interaction space is huge) but also by systematic error in the data. Th...

    Authors: Weiliang Shi, Grace Wahba, Rafael A Irizarry, Hector Corrada Bravo and Stephen J Wright
    Citation: BMC Bioinformatics 2012 13:98
    Content type: Methodology article Published on:

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