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  1. To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of re...

    Authors: Eric CH Chen, Carlos Fernando Buen Abad Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A Albert and David Sankoff
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  2. We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protei...

    Authors: Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth and Gunnar W Klau
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  3. Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available...

    Authors: Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy and Macha Nikolski
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  4. Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic re...

    Authors: Bérénice Batut, David P Parsons, Stephan Fischer, Guillaume Beslon and Carole Knibbe
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  5. Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertice...

    Authors: Owais Mahmudi, Joel Sjöstrand, Bengt Sennblad and Jens Lagergren
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  6. Phylogenomic analyses involving whole-genome or multi-locus data often entail dealing with incongruent gene trees. In this paper, we consider two causes of such incongruence, namely, incomplete lineage sorting...

    Authors: Yun Yu, Nikola Ristic and Luay Nakhleh
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  7. Reconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, su...

    Authors: Manuel Lafond, Magali Semeria, Krister M Swenson, Eric Tannier and Nadia El-Mabrouk
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  8. The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be computed thanks to a pioneering approach of Hannenhalli an...

    Authors: Eyla Willing, Simone Zaccaria, Marília DV Braga and Jens Stoye
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  10. Gene expression is a central process in all living organisms. Central questions in the field are related to the way the expression levels of genes are encoded in the transcripts and affect their evolution, and...

    Authors: Hadas Zur and Tamir Tuller
    Citation: BMC Bioinformatics 2013 14(Suppl 15):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 15

  11. A key goal of systems biology and translational genomics is to utilize high-throughput measurements of cellular states to develop expression-based classifiers for discriminating among different phenotypes. Rec...

    Authors: Noushin Ghaffari, Mohammadmahdi R Yousefi, Charles D Johnson, Ivan Ivanov and Edward R Dougherty
    Citation: BMC Bioinformatics 2013 14:307
    Content type: Research article Published on:

  13. Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surro...

    Authors: Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton and Shu-Dong Zhang
    Citation: BMC Bioinformatics 2013 14:305
    Content type: Software Published on:

  14. Since membrane protein structures are challenging to crystallize, computational approaches are essential for elucidating the sequence-to-structure relationships. Structural modeling of membrane proteins requir...

    Authors: Jhih-Siang Lai, Cheng-Wei Cheng, Allan Lo, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2013 14:304
    Content type: Research article Published on:

  15. Experimentally validated co-expression correlations between miRNAs and genes are a valuable resource to corroborate observations about miRNA/mRNA changes after experimental perturbations, as well as compare mi...

    Authors: Cory B Giles, Reshmi Girija-Devi, Mikhail G Dozmorov and Jonathan D Wren
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S17
    Content type: Proceedings Published on:

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

  16. In drug discovery and development, it is crucial to determine which conformers (instances) of a given molecule are responsible for its observed biological activity and at the same time to recognize the most re...

    Authors: Zhendong Zhao, Gang Fu, Sheng Liu, Khaled M Elokely, Robert J Doerksen, Yixin Chen and Dawn E Wilkins
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S16
    Content type: Proceedings Published on:

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

  17. Pulsed field gel electrophoresis (PFGE) is currently the most widely and routinely used method by the Centers for Disease Control and Prevention (CDC) and state health labs in the United States for Salmonella sur...

    Authors: Wen Zou, Hailin Tang, Weizhong Zhao, Joe Meehan, Steven L Foley, Wei-Jiun Lin, Hung-Chia Chen, Hong Fang, Rajesh Nayak and James J Chen
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S15
    Content type: Proceedings Published on:

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

  18. Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are ...

    Authors: R Shyama Prasad Rao, Dong Xu, Jay J Thelen and Ján A Miernyk
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S14
    Content type: Proceedings Published on:

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

  19. Alternative splicing is an important and widespread mechanism for generating protein diversity and regulating protein expression. High-throughput identification and analysis of alternative splicing in the prot...

    Authors: Fan Zhang and Renee Drabier
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S13
    Content type: Proceedings Published on:

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

  20. In recent years, the use and importance of predicted protein residue-residue contacts has grown considerably with demonstrated applications such as drug design, protein tertiary structure prediction and model ...

    Authors: Jesse Eickholt and Jianlin Cheng
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S12
    Content type: Proceedings Published on:

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

  21. High Content Screening (HCS) has become an important tool for toxicity assessment, partly due to its advantage of handling multiple measurements simultaneously. This approach has provided insight and contribut...

    Authors: Halil Bisgin, Minjun Chen, Yuping Wang, Reagan Kelly, Hong Fang, Xiaowei Xu and Weida Tong
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S11
    Content type: Proceedings Published on:

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

  22. Advances in technology have led to the generation of massive amounts of complex and multifarious biological data in areas ranging from genomics to structural biology. The volume and complexity of such data lea...

    Authors: Rahul Singh, Hui Yang, Ben Dalziel, Daniel Asarnow, William Murad, David Foote, Matthew Gormley, Jonathan Stillman and Susan Fisher
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S10
    Content type: Proceedings Published on:

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

  23. Dicer, an RNase III enzyme, plays a vital role in the processing of pre-miRNAs for generating the miRNAs. The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleav...

    Authors: Firoz Ahmed, Rakesh Kaundal and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S9
    Content type: Proceedings Published on:

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

  24. The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species...

    Authors: Jialiang Yang, Jun Li, Stefan Grünewald and Xiu-Feng Wan
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S8
    Content type: Proceedings Published on:

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

  25. Plastids are an important component of plant cells, being the site of manufacture and storage of chemical compounds used by the cell, and contain pigments such as those used in photosynthesis, starch synthesis...

    Authors: Rakesh Kaundal, Sitanshu S Sahu, Ruchi Verma and Tyler Weirick
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S7
    Content type: Proceedings Published on:

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

  26. An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). α-Fetoprotein (AFP) is a m...

    Authors: Jie Shen, Wenqian Zhang, Hong Fang, Roger Perkins, Weida Tong and Huixiao Hong
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S6
    Content type: Proceedings Published on:

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

  27. The dynamic, decentralized world-wide-web has become an essential part of scientific research and communication. Researchers create thousands of web sites every year to share software, data and services. These...

    Authors: Jason Hennessey and Steven Xijin Ge
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S5
    Content type: Proceedings Published on:

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

  28. Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via c...

    Authors: Shweta S Chavan, Michael A Bauer, Erich A Peterson, Christoph J Heuck and Donald J Johann Jr
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S4
    Content type: Proceedings Published on:

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

  29. Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of ac...

    Authors: Yi Yang, Andrew Maxwell, Xiaowei Zhang, Nan Wang, Edward J Perkins, Chaoyang Zhang and Ping Gong
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S3
    Content type: Proceedings Published on:

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

  30. Even though only 1.5% of the human genome is translated into proteins, recent reports indicate that most of it is transcribed into non-coding RNAs (ncRNAs), which are becoming the subject of increased scientif...

    Authors: Mikhail G Dozmorov, Cory B Giles, Kristi A Koelsch and Jonathan D Wren
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S2
    Content type: Proceedings Published on:

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

  32. Knowledge of which genes are essential to the survival of an organism is critical to understanding the function of genes, and for the identification of potential drug targets for antimicrobial treatment. Previ...

    Authors: Michael A DeJesus and Thomas R Ioerger
    Citation: BMC Bioinformatics 2013 14:303
    Content type: Methodology article Published on:

  33. Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. Th...

    Authors: Chris Schmidt, Stephanie J Irausquin and Homayoun Valafar
    Citation: BMC Bioinformatics 2013 14:302
    Content type: Software Published on:

  35. Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a stable structure in the natural state, they read...

    Authors: Chun Fang, Tamotsu Noguchi, Daisuke Tominaga and Hayato Yamana
    Citation: BMC Bioinformatics 2013 14:300
    Content type: Methodology article Published on:

  36. Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput...

    Authors: George Tucker, Po-Ru Loh and Bonnie Berger
    Citation: BMC Bioinformatics 2013 14:299
    Content type: Methodology article Published on:

  37. Gene expression in the Drosophila embryo is controlled by functional interactions between a large network of protein transcription factors (TFs) and specific sequences in DNA cis-regulatory modules (CRMs). The bi...

    Authors: Jessica L Stringham, Adam S Brown, Robert A Drewell and Jacqueline M Dresch
    Citation: BMC Bioinformatics 2013 14:298
    Content type: Research article Published on:

  38. In recent years, high-throughput microscopy has emerged as a powerful tool to analyze cellular dynamics in an unprecedentedly high resolved manner. The amount of data that is generated, for example in long-ter...

    Authors: Felix Buggenthin, Carsten Marr, Michael Schwarzfischer, Philipp S Hoppe, Oliver Hilsenbeck, Timm Schroeder and Fabian J Theis
    Citation: BMC Bioinformatics 2013 14:297
    Content type: Research article Published on:

  39. Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possi...

    Authors: Cheng-Jin Du, Phillip T Hawkins, Len R Stephens and Till Bretschneider
    Citation: BMC Bioinformatics 2013 14:296
    Content type: Research article Published on:

  41. Segmenting electron microscopy (EM) images of cellular and subcellular processes in the nervous system is a key step in many bioimaging pipelines involving classification and labeling of ultrastructures. Howev...

    Authors: Saket Navlakha, Parvez Ahammad and Eugene W Myers
    Citation: BMC Bioinformatics 2013 14:294
    Content type: Methodology article Published on:

  42. We briefly identify several critical issues in current computational neuroscience, and present our opinions on potential solutions based on bioimage informatics, especially automated image computing.

    Authors: Hanchuan Peng, Badrinath Roysam and Giorgio A Ascoli
    Citation: BMC Bioinformatics 2013 14:293
    Content type: Commentary Published on:

  44. Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effectiv...

    Authors: Jie Zhou, Santosh Lamichhane, Gabriella Sterne, Bing Ye and Hanchuan Peng
    Citation: BMC Bioinformatics 2013 14:291
    Content type: Software Published on:

  45. RNAi screening is a powerful method to study the genetics of intracellular processes in metazoans. Technically, the approach has been largely inspired by techniques and tools developed for compound screening, ...

    Authors: Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau and Frédéric Bard
    Citation: BMC Bioinformatics 2013 14:290
    Content type: Software Published on:

  46. A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima’s D. These statistics are now...

    Authors: Thorfinn Sand Korneliussen, Ida Moltke, Anders Albrechtsen and Rasmus Nielsen
    Citation: BMC Bioinformatics 2013 14:289
    Content type: Methodology article Published on:

  47. The development of new therapies for orphan genetic diseases represents an extremely important medical and social challenge. Drug repositioning, i.e. finding new indications for approved drugs, could be one of...

    Authors: Ivan Molineris, Ugo Ala, Paolo Provero and Ferdinando Di Cunto
    Citation: BMC Bioinformatics 2013 14:288
    Content type: Research article Published on:

  48. Dendritic spines serve as key computational structures in brain plasticity. Much remains to be learned about their spatial and temporal distribution among neurons. Our aim in this study was to perform explorat...

    Authors: Aruna Jammalamadaka, Sourav Banerjee, Bangalore S Manjunath and Kenneth S Kosik
    Citation: BMC Bioinformatics 2013 14:287
    Content type: Research article Published on:

  49. Since the advent of microarray technology, numerous methods have been devised to infer gene regulatory relationships from gene expression data. Many approaches that infer entire regulatory networks. This produ...

    Authors: James D Jensen, Daniel M Jensen, Mark J Clement and Quinn O Snell
    Citation: BMC Bioinformatics 2013 14(Suppl 13):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 13

  50. Identification of the genetic alterations responsible for human disease is a central challenge facing medical genetics. While many algorithms have been developed to predict the degree of damage caused by a giv...

    Authors: Brendan D O'Fallon, Whitney Wooderchak-Donahue, Pinar Bayrak-Toydemir and David Crockett
    Citation: BMC Bioinformatics 2013 14(Suppl 13):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 13

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