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  3. Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, takin...

    Authors: Yanglan Gan, Jihong Guan, Shuigeng Zhou and Weixiong Zhang
    Citation: BMC Bioinformatics 2012 13:49
    Content type: Research article Published on:

  5. Next generation sequencing provides detailed insight into the variation present within viral populations, introducing the possibility of treatment strategies that are both reactive and predictive. Current soft...

    Authors: John Archer, Greg Baillie, Simon J Watson, Paul Kellam, Andrew Rambaut and David L Robertson
    Citation: BMC Bioinformatics 2012 13:47
    Content type: Software Published on:

  6. Identification of active causal regulators is a crucial problem in understanding mechanism of diseases or finding drug targets. Methods that infer causal regulators directly from primary data have been propose...

    Authors: Chia-Ling Huang, John Lamb, Leonid Chindelevitch, Jarek Kostrowicki, Justin Guinney, Charles DeLisi and Daniel Ziemek
    Citation: BMC Bioinformatics 2012 13:46
    Content type: Methodology article Published on:

  9. Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Ther...

    Authors: Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P Townsend and Jun Yu
    Citation: BMC Bioinformatics 2012 13:43
    Content type: Methodology article Published on:

  10. DNA methylation is essential for normal development and differentiation and plays a crucial role in the development of nearly all types of cancer. Aberrant DNA methylation patterns, including genome-wide hypom...

    Authors: Youngik Yang, Kenneth Nephew and Sun Kim
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  11. A pedigree is a diagram of family relationships, and it is often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. Along with rapidly growing knowledge of genetics and ...

    Authors: Lei Yang, En Cheng and Z Meral Özsoyoğlu
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  12. Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited...

    Authors: Jeremy R Wang, Fernando Pardo-Manuel de Villena and Leonard McMillan
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  13. NCRNAs (noncoding RNAs) play important roles in many biological processes. Existing genome-scale ncRNA search tools identify ncRNAs in local sequence alignments generated by conventional sequence comparison me...

    Authors: Yanni Sun, Osama Aljawad, Jikai Lei and Alex Liu
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  14. Advances in high-throughput technology has led to an increased amount of available data on protein-protein interaction (PPI) data. Detecting and extracting functional modules that are common across multiple ne...

    Authors: Yu-Keng Shih and Srinivasan Parthasarathy
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  15. The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using gr...

    Authors: Boon-Siew Seah, Sourav S Bhowmick, C Forbes Dewey Jr and Hanry Yu
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  16. The normal functioning of a living cell is characterized by complex interaction networks involving many different types of molecules. Associations detected between diseases and perturbations in well-defined pa...

    Authors: Corban G Rivera, Brett M Tyler and TM Murali
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  17. Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one o...

    Authors: Marco Pellegrini, Maria Elena Renda and Alessio Vecchio
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  18. Selecting an appropriate classifier for a particular biological application poses a difficult problem for researchers and practitioners alike. In particular, choosing a classifier depends heavily on the featur...

    Authors: R Mitchell Parry, John H Phan and May D Wang
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  19. We study the relation between genome rearrangements, breakpoints and gene expression. Genome rearrangement research has been concerned with the creation of breakpoints and their position in the chromosome, but...

    Authors: Adriana Muñoz and David Sankoff
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  20. Accurately predicting low energy barrier folding pathways between conformational secondary structures of an RNA molecule can provide valuable information for understanding its catalytic and regulatory function...

    Authors: Yuan Li and Shaojie Zhang
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  21. Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasin...

    Authors: Richard Jang, Xin Gao and Ming Li
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  22. DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify tho...

    Authors: Lu He, Alan M Friedman and Chris Bailey-Kellogg
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  23. Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic n...

    Authors: Ferhat Ay, Michael Dang and Tamer Kahveci
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  24. The relationships between the gene functional similarity and gene expression profile, and between gene function annotation and gene sequence have been studied extensively. However, not much work has considered...

    Authors: Li An, Haibin Ling, Zoran Obradovic, Desmond J Smith and Vasileios Megalooikonomou
    Citation: BMC Bioinformatics 2012 13(Suppl 3):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  25. A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottle...

    Authors: Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field and Karen E Nelson
    Citation: BMC Bioinformatics 2012 13:42
    Content type: Software Published on:

  26. Identification of the residues in protein-protein interaction sites has a significant impact in problems such as drug discovery. Motivated by the observation that the set of interface residues of a protein ten...

    Authors: Rafael A Jordan, Yasser EL-Manzalawy, Drena Dobbs and Vasant Honavar
    Citation: BMC Bioinformatics 2012 13:41
    Content type: Research article Published on:

  27. Prokaryotic ubiquitin-like protein (Pup), the firstly identified post-translational protein modifier in prokaryotes, is an important signal for the selective degradation of proteins. Recently, large-scale prot...

    Authors: Chun-Wei Tung
    Citation: BMC Bioinformatics 2012 13:40
    Content type: Database Published on:

  28. Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a...

    Authors: Paul Ashford, David S Moss, Alexander Alex, Siew K Yeap, Alice Povia, Irene Nobeli and Mark A Williams
    Citation: BMC Bioinformatics 2012 13:39
    Content type: Methodology article Published on:

  29. Retrotransposons are mobile DNA elements that spread through genomes via the action of element-encoded reverse transcriptases. They are ubiquitous constituents of most eukaryotic genomes, especially those of h...

    Authors: Lauren S Mogil, Kamil Slowikowski and Howard M Laten
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  30. Using gene co-expression analysis, researchers were able to predict clusters of genes with consistent functions that are relevant to cancer development and prognosis. We applied a weighted gene co-expression n...

    Authors: Yang Xiang, Cun-Quan Zhang and Kun Huang
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  31. As context is important to gene expression, so is the preprocessing of microarray to transcriptomics. Microarray data suffers from several normalization and significance problems. Arbitrary fold change (FC) cu...

    Authors: Mark R Dalman, Anthony Deeter, Gayathri Nimishakavi and Zhong-Hui Duan
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  32. When flow cytometric data on mixtures of cell populations are collected from samples under different experimental conditions, computational methods are needed (a) to classify the samples into similar groups, a...

    Authors: Ariful Azad, Saumyadipta Pyne and Alex Pothen
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  33. Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment ...

    Authors: Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu and Geoffrey Fox
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  34. Predisposition to complex diseases is explained in part by genetic variation, and complex diseases are frequently comorbid, consistent with pleiotropic genetic variation influencing comorbidity. Genome Wide As...

    Authors: Richard C McEachin, Keerthi S Sannareddy, James D Cavalcoli, Alla Karnovsky, Jacqueline M Vink and Maureen A Sartor
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  35. Many of solved tertiary structures of unknown functions do not have global sequence and structural similarities to proteins of known function. Often functional clues of unknown proteins can be obtained by pred...

    Authors: Lee Sael and Daisuke Kihara
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  36. Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development ...

    Authors: Juan Esquivel-Rodríguez and Daisuke Kihara
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  37. The T box riboswitch controls bacterial transcription by structurally responding to tRNA aminoacylation charging ratios. Knowledge of the thermodynamic stability difference between two competing structural ele...

    Authors: Franziska Jentzsch and Jennifer V Hines
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  38. Results of high throughput experiments can be challenging to interpret. Current approaches have relied on bulk processing the set of expression levels, in conjunction with easily obtained external evidence, su...

    Authors: Fernando Farfán, Jun Ma, Maureen A Sartor, George Michailidis and Hosagrahar V Jagadish
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  39. The DNA binding domain of HMG proteins is known to be important in many diseases, with the Sox sub-family of HMG proteins of particular significance. Numerous natural variants in HMG proteins are associated wi...

    Authors: Jeremy W Prokop, Thomas C Leeper, Zhong-Hui Duan and Amy Milsted
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  40. RNA polymerase II (PolII) is essential in gene transcription and ChIP-seq experiments have been used to study PolII binding patterns over the entire genome. However, since PolII enriched regions in the genome ...

    Authors: Zhi Han, Lu Tian, Thierry Pécot, Tim Huang, Raghu Machiraju and Kun Huang
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  41. Current network-based microarray analysis uses the information of interactions among concerned genes/gene products, but still considers each gene expression individually. We propose an organized knowledge-supe...

    Authors: Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey and Jake Y Chen
    Citation: BMC Bioinformatics 2012 13(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 2

  43. In-vivo single voxel proton magnetic resonance spectroscopy (SV 1H-MRS), coupled with supervised pattern recognition (PR) methods, has been widely used in clinical studies of discrimination of brain tumour types ...

    Authors: Sandra Ortega-Martorell, Paulo JG Lisboa, Alfredo Vellido, Margarida Julià-Sapé and Carles Arús
    Citation: BMC Bioinformatics 2012 13:38
    Content type: Research article Published on:

  44. Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents...

    Authors: Bhakti Dwivedi, Robert Schmieder, Dawn B Goldsmith, Robert A Edwards and Mya Breitbart
    Citation: BMC Bioinformatics 2012 13:37
    Content type: Software Published on:

  45. Expression profiling provides new insights into regulatory and metabolic processes and in particular into pathogenic mechanisms associated with diseases. Besides genes, non-coding transcripts as microRNAs (miR...

    Authors: Cedric Laczny, Petra Leidinger, Jan Haas, Nicole Ludwig, Christina Backes, Andreas Gerasch, Michael Kaufmann, Britta Vogel, Hugo A Katus, Benjamin Meder, Cord Stähler, Eckart Meese, Hans-Peter Lenhof and Andreas Keller
    Citation: BMC Bioinformatics 2012 13:36
    Content type: Software Published on:

  46. Causal graphs are an increasingly popular tool for the analysis of biological datasets. In particular, signed causal graphs--directed graphs whose edges additionally have a sign denoting upregulation or downre...

    Authors: Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger and Daniel Ziemek
    Citation: BMC Bioinformatics 2012 13:35
    Content type: Methodology article Published on:

  47. Recent development of novel technologies paved the way for quantitative proteomics. One of the most important among them is iTRAQ, employing isobaric tags for relative or absolute quantitation. Despite large p...

    Authors: Chris Bauer, Frank Kleinjung, Dorothea Rutishauser, Christian Panse, Alexandra Chadt, Tanja Dreja, Hadi Al-Hasani, Knut Reinert, Ralph Schlapbach and Johannes Schuchhardt
    Citation: BMC Bioinformatics 2012 13:34
    Content type: Methodology article Published on:

  50. Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mi...

    Authors: Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown and Josh D Neufeld
    Citation: BMC Bioinformatics 2012 13:31
    Content type: Software Published on:

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