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137 result(s) for 'Genics' within BMC Bioinformatics

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  1. The de novo assembly of genomes and transcriptomes from short sequences is a challenging problem. Because of the high coverage needed to assemble short sequences as well as the overhead of modeling the assembly p...

    Authors: Benjamin G Jackson, Patrick S Schnable and Srinivas Aluru
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  3. Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which ...

    Authors: Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline M Bye, Francisco Camara, Paul Flicek, Elizabeth J Huckle, Genis Parra, David D Shteynberg, Carine Wyss, Jane Rogers, Stylianos E Antonarakis, Ewan Birney, Roderic Guigo and Michael R Brent
    Citation: BMC Bioinformatics 2005 6:131
    Content type: Research article Published on:

  4. The capability of correlating specific genotypes with human diseases is a complex issue in spite of all advantages arisen from high-throughput technologies, such as Genome Wide Association Studies (GWAS). New ...

    Authors: Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca and Luciano Milanesi
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  5. Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian d...

    Authors: Alexander Churbanov, Igor Vořechovský and Chindo Hicks
    Citation: BMC Bioinformatics 2010 11:22
    Content type: Methodology article Published on:

  6. The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This make...

    Authors: James M Eales, John W Pinney, Robert D Stevens and David L Robertson
    Citation: BMC Bioinformatics 2008 9:359
    Content type: Research article Published on:

  7. The BioNLP Gene Regulation Task has attracted a diverse collection of submissions showcasing state-of-the-art systems. However, a principal challenge remains in obtaining a significant amount of recall. We arg...

    Authors: Thomas Provoost and Marie-Francine Moens
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  9. 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 reduc...

    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

  10. The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources r...

    Authors: Coral del Val, Vladimir Yurjevich Kuryshev, Karl-Heinz Glatting, Peter Ernst, Agnes Hotz-Wagenblatt, Annemarie Poustka, Sandor Suhai and Stefan Wiemann
    Citation: BMC Bioinformatics 2006 7:473
    Content type: Software Published on:

  11. The canonical core promoter elements consist of the TATA box, initiator (Inr), downstream core promoter element (DPE), TFIIB recognition element (BRE) and the newly-discovered motif 10 element (MTE). The motif...

    Authors: Victor X Jin, Gregory AC Singer, Francisco J Agosto-Pérez, Sandya Liyanarachchi and Ramana V Davuluri
    Citation: BMC Bioinformatics 2006 7:114
    Content type: Research article Published on:

  13. Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition...

    Authors: Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  14. Genome-wide association studies of common diseases for common, low penetrance causal variants are underway. A proportion of these will alter protein sequences, the most common of which is the non-synonymous si...

    Authors: David F Burke, Catherine L Worth, Eva-Maria Priego, Tammy Cheng, Luc J Smink, John A Todd and Tom L Blundell
    Citation: BMC Bioinformatics 2007 8:301
    Content type: Methodology article Published on:

  15. Various chromatin modifications, identified in large-scale epigenomic analyses, are associated with distinct phenotypes of different cells and disease phases. To improve our understanding of these variations, ...

    Authors: Sung Hee Park, Sun-Min Lee, Young-Joon Kim and Sangsoo Kim
    Citation: BMC Bioinformatics 2016 17(Suppl 16):452
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 16

  16. Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m6A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic pr...

    Authors: Teng Zhang, Shao-Wu Zhang, Lin Zhang and Jia Meng
    Citation: BMC Bioinformatics 2018 19:260
    Content type: Software Published on:

  17. While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, es...

    Authors: Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman and Inanç Birol
    Citation: BMC Bioinformatics 2015 16:230
    Content type: Software Published on:

  18. The development of sequencing techniques and statistical methods provides great opportunities for identifying the impact of rare genetic variation on complex traits. However, there is a lack of knowledge on th...

    Authors: Xinyuan Zhang, Anna O. Basile, Sarah A. Pendergrass and Marylyn D. Ritchie
    Citation: BMC Bioinformatics 2019 20:46
    Content type: Research article Published on:

  19. R-loops are three-stranded nucleic acid structures that usually form during transcription and that may lead to gene regulation or genome instability. DRIP (DNA:RNA Immunoprecipitation)-seq techniques are widel...

    Authors: Marco Russo, Bruno De Lucca, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi and Giovanni Capranico
    Citation: BMC Bioinformatics 2019 20:414
    Content type: Software Published on:

  21. Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative...

    Authors: Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko and Andrew P. Morris
    Citation: BMC Bioinformatics 2017 18:25
    Content type: Software Published on:

  22. The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to...

    Authors: John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas and Peristera Paschou
    Citation: BMC Bioinformatics 2017 18:341
    Content type: Software Published on:

  23. Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging ...

    Authors: M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement and Seth M. Bybee
    Citation: BMC Bioinformatics 2016 17:101
    Content type: Methodology article Published on:

  25. High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Cur...

    Authors: Janna L. Fierst and Duncan A. Murdock
    Citation: BMC Bioinformatics 2017 18:533
    Content type: Methodology Article Published on:

  28. Detection of important functional and/or structural elements and identification of their positions in a large eukaryotic genomic sequence are an active research area. Gene is an important functional and struct...

    Authors: Biswanath Chowdhury, Arnav Garai and Gautam Garai
    Citation: BMC Bioinformatics 2017 18:460
    Content type: Methodology Article Published on:

  30. Short and long range correlations in biological sequences are central in genomic studies of covariation. These correlations can be studied using mutual information because it measures the amount of information...

    Authors: Flavio Lichtenstein, Fernando Antoneli Jr and Marcelo R. S. Briones
    Citation: BMC Bioinformatics 2015 16:409
    Content type: Software Published on:

  31. Because driver mutations provide selective advantage to the mutant clone, they tend to occur at a higher frequency in tumor samples compared to selectively neutral (passenger) mutations. However, mutation freq...

    Authors: Ivan P. Gorlov, Claudio W. Pikielny, Hildreth R. Frost, Stephanie C. Her, Michael D. Cole, Samuel D. Strohbehn, David Wallace-Bradley, Marek Kimmel, Olga Y. Gorlova and Christopher I. Amos
    Citation: BMC Bioinformatics 2018 19:430
    Content type: Research article Published on:

  32. Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant da...

    Authors: Hamid Bagheri, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin and Hridesh Rajan
    Citation: BMC Bioinformatics 2019 20:436
    Content type: Research article Published on:

  33. Current technologies for understanding the transcriptional reprogramming in cells include the transcription factor (TF) chromatin immunoprecipitation (ChIP) experiments and the TF knockout experiments. The ChI...

    Authors: Tzu-Hsien Yang
    Citation: BMC Bioinformatics 2019 20(Suppl 23):630
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  34. RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity a...

    Authors: Soohyun Lee, Chae Hwa Seo, Burak Han Alver, Sanghyuk Lee and Peter J. Park
    Citation: BMC Bioinformatics 2015 16:278
    Content type: Research article Published on:

  35. Large-scale pairwise drug combination analysis has lately gained momentum in drug discovery and development projects, mainly due to the employment of advanced experimental-computational pipelines. This is fort...

    Authors: Efthymia Chantzi, Malin Jarvius, Mia Niklasson, Anna Segerman and Mats G. Gustafsson
    Citation: BMC Bioinformatics 2018 19:453
    Content type: Methodology article Published on:

  36. De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially a...

    Authors: Stanley Kimbung Mbandi, Uljana Hesse, Peter van Heusden and Alan Christoffels
    Citation: BMC Bioinformatics 2015 16:58
    Content type: Methodology article Published on:

  37. Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to de...

    Authors: Maninder Sandhu, V. Sureshkumar, Chandra Prakash, Rekha Dixit, Amolkumar U. Solanke, Tilak Raj Sharma, Trilochan Mohapatra and Amitha Mithra S. V.
    Citation: BMC Bioinformatics 2017 18:432
    Content type: Database Published on:

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