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

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  1. The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation h...

    Authors: Eran Elhaik, Matteo Pellegrini and Tatiana V Tatarinova
    Citation: BMC Bioinformatics 2014 15:23
    Content type: Methodology article Published on:

  2. We have proposed a novel approach, based on a piece-wise function – to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for gene...

    Authors: Srinka Ghosh, Heather A Hirsch, Edward A Sekinger, Philipp Kapranov, Kevin Struhl and Thomas R Gingeras
    Citation: BMC Bioinformatics 2007 8:359
    Content type: Methodology article Published on:

  3. Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until rece...

    Authors: Dadakhalandar Doddamani, Mohan AVSK Katta, Aamir W Khan, Gaurav Agarwal, Trushar M Shah and Rajeev K Varshney
    Citation: BMC Bioinformatics 2014 15:212
    Content type: Database Published on:

  4. The RACS computational pipeline presented in this report is an efficient and reliable tool to analyze genome-wide raw ChIP-Seq data generated in model organisms with poorly annotated contig-based genome sequence....

    Authors: Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah and Jeffrey Fillingham
    Citation: BMC Bioinformatics 2019 20:533
    Content type: Methodology Article Published on:

  5. Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant l...

    Authors: Michael J. Cormier, Brent S. Pedersen, Pinar Bayrak-Toydemir and Aaron R. Quinlan
    Citation: BMC Bioinformatics 2022 23:482
    Content type: Research Published on:

  6. We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. Th...

    Authors: Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte, Philippe Bessières and Claire Nédellec
    Citation: BMC Bioinformatics 2012 13(Suppl 11):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 11

  9. Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not be...

    Authors: Noel Cabañas, Arturo Becerra, David Romero, Tzipe Govezensky, Jesús Javier Espinosa-Aguirre and Rafael Camacho-Carranza
    Citation: BMC Bioinformatics 2020 21:197
    Content type: Research article Published on:

  10. Analyzing regions of the genome where genetic variation is free from the confounding effects of natural selection is essential for many population genetic studies. Several recent studies in humans have stresse...

    Authors: Leonardo Arbiza, Elaine Zhong and Alon Keinan
    Citation: BMC Bioinformatics 2012 13:301
    Content type: Software Published on:

  12. Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing ...

    Authors: Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda and Peter J Park
    Citation: BMC Bioinformatics 2007 8:219
    Content type: Research article Published on:

  14. Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription ...

    Authors: Samuel J. Roth, Sven Heinz and Christopher Benner
    Citation: BMC Bioinformatics 2020 21:214
    Content type: Software Published on:

  15. Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserv...

    Authors: Joseph MEX Lucas, Matthieu Muffato and Hugues Roest Crollius
    Citation: BMC Bioinformatics 2014 15:268
    Content type: Research article Published on:

  16. Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics sk...

    Authors: Ilenia Boria, Lara Boatti, Graziano Pesole and Flavio Mignone
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  17. Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisa...

    Authors: Carlos Willian Dias Dantas, Sebastião Rodrigues da Costa Neto, Sandy Ingrid Aguiar Alves, Kenny da Costa Pinheiro, Edian Franklin Franco De Los Santos and Rommel Thiago Jucá Ramos
    Citation: BMC Bioinformatics 2024 25:217
    Content type: Software Published on:

  18. There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources,...

    Authors: Erdahl T Teber, Edward Crawford, Kent B Bolton, Derek Van Dyk, Peter R Schofield, Vimal Kapoor and W Bret Church
    Citation: BMC Bioinformatics 2006 7:33
    Content type: Software Published on:

  19. Transcription Factors (TFs) and microRNAs (miRNAs) are key players for gene expression regulation in higher eukaryotes. In the last years, a large amount of bioinformatic studies were devoted to the elucidatio...

    Authors: Olivier Friard, Angela Re, Daniela Taverna, Michele De Bortoli and Davide Corá
    Citation: BMC Bioinformatics 2010 11:435
    Content type: Database Published on:

  20. Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs ...

    Authors: Ludwig Mann, Kathrin M. Seibt, Beatrice Weber and Tony Heitkam
    Citation: BMC Bioinformatics 2022 23:40
    Content type: Software Published on:

  22. Performing a statistical test requires a null hypothesis. In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis fo...

    Authors: Erik N. Bergstrom, Mark Barnes, Iñigo Martincorena and Ludmil B. Alexandrov
    Citation: BMC Bioinformatics 2020 21:438
    Content type: Software Published on:

  23. Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cl...

    Authors: Giltae Song, Chih-Hao Hsu, Cathy Riemer and Webb Miller
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S45
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  24. Our results show that SNPs associated with complement activation and inflammation significantly contribute to AMD risk, separately from the risk explained by the 19 known risk SNPs. We found that SNPs within 50 k...

    Authors: Jacob B. Hall, Jessica N. Cooke Bailey, Joshua D. Hoffman, Margaret A. Pericak-Vance, William K. Scott, Jaclyn L. Kovach, Stephen G. Schwartz, Anita Agarwal, Milam A. Brantley Jr., Jonathan L. Haines and William S. Bush
    Citation: BMC Bioinformatics 2015 16:329
    Content type: Research article Published on:

  25. Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions....

    Authors: Giovanni Spirito, Damiano Mangoni, Remo Sanges and Stefano Gustincich
    Citation: BMC Bioinformatics 2019 20(Suppl 9):495
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  26. Global run-on coupled with deep sequencing (GRO-seq) provides extensive information on the location and function of coding and non-coding transcripts, including primary microRNAs (miRNAs), long non-coding RNAs...

    Authors: Minho Chae, Charles G. Danko and W. Lee Kraus
    Citation: BMC Bioinformatics 2015 16:222
    Content type: Software Published on:

  27. With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic regi...

    Authors: Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam and Eve Syrkin Wurtele
    Citation: BMC Bioinformatics 2019 20:440
    Content type: Software Published on:

  28. The environment has been playing an instrumental role in shaping and maintaining the morphological, physiological and biochemical diversities of prokaryotes. It has been debatable whether the whole-genome Guanine...

    Authors: Hao Zheng and Hongwei Wu
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  29. Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current a...

    Authors: Michael Hackenberg, Christopher Previti, Pedro Luis Luque-Escamilla, Pedro Carpena, José Martínez-Aroza and José L Oliver
    Citation: BMC Bioinformatics 2006 7:446
    Content type: Research article Published on:

  30. The availability of multiple whole genome sequences has facilitated in silico identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and fore...

    Authors: Vipin Singh and Rakesh K Mishra
    Citation: BMC Bioinformatics 2010 11:609
    Content type: Research article Published on:

  32. Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting bot...

    Authors: Sophie Coutant, Chloé Cabot, Arnaud Lefebvre, Martine Léonard, Elise Prieur-Gaston, Dominique Campion, Thierry Lecroq and Hélène Dauchel
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S9
    Content type: Research Published on:

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

  34. Simulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common implementation is by using the converse of the probabilistic approach used to i...

    Authors: Carlos J. Rivera-Rivera and Djordje Grbic
    Citation: BMC Bioinformatics 2023 24:247
    Content type: Software Published on:

  36. Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to under...

    Authors: Terry H Shen, Christopher S Carlson and Peter Tarczy-Hornoch
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  37. Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional ...

    Authors: Chuan Jiang, Chao Chen, Ziyue Huang, Renyi Liu and Jerome Verdier
    Citation: BMC Bioinformatics 2015 16:72
    Content type: Methodology article Published on:

  38. This study demonstrates that exonic sequencing datasets, collected both in population based and medical sequencing projects, will be a useful substrate for detecting genic CNV events, particularly deletions. Base...

    Authors: Jiantao Wu, Krzysztof R Grzeda, Chip Stewart, Fabian Grubert, Alexander E Urban, Michael P Snyder and Gabor T Marth
    Citation: BMC Bioinformatics 2012 13:305
    Content type: Methodology article Published on:

  39. We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bac...

    Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières and Claire Nédellec
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S1
    Content type: Research Published on:

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

  40. Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming...

    Authors: Ate van der Burgt, Edouard Severing, Jérôme Collemare and Pierre JGM de Wit
    Citation: BMC Bioinformatics 2014 15:19
    Content type: Methodology article Published on:

  41. Accurate computational identification of eukaryotic gene organization is a long-standing problem. Despite the fundamental importance of precise annotation of genes encoded in newly sequenced genomes, the accur...

    Authors: Osamu Gotoh, Mariko Morita and David R Nelson
    Citation: BMC Bioinformatics 2014 15:189
    Content type: Research article Published on:

  42. Genome-wide association studies (GWAS) have effectively identified genetic factors for many diseases. Many diseases, including Alzheimer’s disease (AD), have epistatic causes, requiring more sophisticated anal...

    Authors: Paul M. Bodily, M. Stanley Fujimoto, Justin T. Page, Mark J. Clement, Mark T. W. Ebbert and Perry G. Ridge
    Citation: BMC Bioinformatics 2016 17(Suppl 7):268
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  44. Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across...

    Authors: Konstantin Yuditskiy, Igor Bezdvornykh, Anastasiya Kazantseva, Alexander Kanapin and Anastasia Samsonova
    Citation: BMC Bioinformatics 2024 25:96
    Content type: Software Published on:

  46. Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can n...

    Authors: Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao and Toshihiko Ishida
    Citation: BMC Bioinformatics 2008 9:112
    Content type: Software Published on:

  47. It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature ...

    Authors: Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian and Henry Horng-Shing Lu
    Citation: BMC Bioinformatics 2016 17(Suppl 13):381
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 13

  50. Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains pattern...

    Authors: Nicholas J Hudson, Laercio R Porto-Neto, James Kijas, Sean McWilliam, Ryan J Taft and Antonio Reverter
    Citation: BMC Bioinformatics 2014 15:66
    Content type: Research article Published on:

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