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

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  1. MTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multipl...

    Authors: Wen Huang, Naoki Takebayashi, Yan Qi and Michael J Hickerson
    Citation: BMC Bioinformatics 2011 12:1
    Content type: Software Published on:

  2. Transcriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species ...

    Authors: Anagha Joshi
    Citation: BMC Bioinformatics 2014 15:412
    Content type: Research article Published on:

  3. The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between ...

    Authors: Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens and Robert A Edwards
    Citation: BMC Bioinformatics 2010 11:319
    Content type: Software Published on:

  4. Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and id...

    Authors: Alberto García S. and Juan Carlos Casamayor
    Citation: BMC Bioinformatics 2021 22(Suppl 13):353
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 13

  5. Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how t...

    Authors: Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus and Isobel Claire Gormley
    Citation: BMC Bioinformatics 2019 20:466
    Content type: Research Article Published on:

  6. Accurate classification of diffuse gliomas, the most common tumors of the central nervous system in adults, is important for appropriate treatment. However, detection of isocitrate dehydrogenase (IDH) mutation an...

    Authors: Sean Chun-Chang Chen, Chung-Ming Lo, Shih-Hua Wang and Emily Chia-Yu Su
    Citation: BMC Bioinformatics 2019 20(Suppl 19):659
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 19

  7. Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues...

    Authors: Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro Santibanez-Koref, David J. Elliott and Michael S. Jackson
    Citation: BMC Bioinformatics 2016 17:31
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:92

  8. Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of ...

    Authors: Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang and Ying Xu
    Citation: BMC Bioinformatics 2015 16:356
    Content type: Research article Published on:

  10. Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotate...

    Authors: Joseph Guhlin, Kevin A. T. Silverstein, Peng Zhou, Peter Tiffin and Nevin D. Young
    Citation: BMC Bioinformatics 2017 18:367
    Content type: Software Published on:

  11. Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for most non-model organisms lacking co...

    Authors: Sung-Gwon Lee, Dokyun Na and Chungoo Park
    Citation: BMC Bioinformatics 2021 22(Suppl 11):310
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  12. An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with mo...

    Authors: Shanker Kalyana-Sundaram, Achiraman Shanmugam and Arul M Chinnaiyan
    Citation: BMC Bioinformatics 2012 13:269
    Content type: Methodology article Published on:

  14. Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functi...

    Authors: Anthony R. Soltis, Clifton L. Dalgard, Harvey B. Pollard and Matthew D. Wilkerson
    Citation: BMC Bioinformatics 2020 21:338
    Content type: Software Published on:

  15. DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional...

    Authors: Sheng Li, Francine E Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross Levine, Bik L To, Ian D Lewis, Anna L Brown, Richard J D'Andrea, Ari Melnick and Christopher E Mason
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  16. It has been apparent in the last few years that small non coding RNAs (ncRNA) play a very significant role in biological regulation. Among these microRNAs (miRNAs), 22-23 nucleotide small regulatory RNAs, have...

    Authors: Sumeet Agarwal, Candida Vaz, Alok Bhattacharya and Ashwin Srinivasan
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S29
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  17. In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mu...

    Authors: Adam Hilterbrand, Joseph Saelens and Catherine Putonti
    Citation: BMC Bioinformatics 2012 13:62
    Content type: Database Published on:

  18. DNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to inve...

    Authors: Robert Lowe and Vardhman K Rakyan
    Citation: BMC Bioinformatics 2013 14:359
    Content type: Database Published on:

  20. Neurogenesis in the murine cerebral cortex involves the coordinated divisions of two main types of progenitor cells, whose numbers, division modes and cell cycle durations set up the final neuronal output. To ...

    Authors: Marie Postel, Alice Karam, Guillaume Pézeron, Sylvie Schneider-Maunoury and Frédérique Clément
    Citation: BMC Bioinformatics 2019 20:470
    Content type: Research Article Published on:

  21. Alternative splicing (AS) is a process which generates several distinct mRNA isoforms from the same gene by splicing different portions out of the precursor transcript. Due to the (patho-)physiological importa...

    Authors: Johannes Eichner, Georg Zeller, Sascha Laubinger and Gunnar Rätsch
    Citation: BMC Bioinformatics 2011 12:55
    Content type: Research article Published on:

  22. Ancestral recombinations graph (ARG) is a topological structure that captures the relationship between the extant genomic sequences in terms of genetic events including recombinations. IRiS is a system that es...

    Authors: Filippo Utro, Omar Eduardo Cornejo, Donald Livingstone, Juan Carlos Motamayor and Laxmi Parida
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  23. Un-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequ...

    Authors: Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-Hong Chen and Wen-chang Lin
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S9
    Content type: Research Published on:

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

  24. In studies that use DNA arrays to assess changes in gene expression, it is preferable to measure the significance of treatment effects on a group of genes from a pathway or functional category such as gene ont...

    Authors: Taewon Lee, Varsha G Desai, Cruz Velasco, Robert J S Reis and Robert R Delongchamp
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S20
    Content type: Proceedings Published on:

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

  25. 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:

  26. Spliced leader (SL) trans-splicing replaces the 5′ end of pre-mRNAs with the spliced leader, an exon derived from a specialised non-coding RNA originating from elsewhere in the genome. This process is essential f...

    Authors: Marius A. Wenzel, Berndt Müller and Jonathan Pettitt
    Citation: BMC Bioinformatics 2021 22:140
    Content type: Software Published on:

  27. Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barri...

    Authors: Kevin Riehle, Cristian Coarfa, Andrew Jackson, Jun Ma, Arpit Tandon, Sameer Paithankar, Sriram Raghuraman, Toni-Ann Mistretta, Delphine Saulnier, Sabeen Raza, Maria Alejandra Diaz, Robert Shulman, Kjersti Aagaard, James Versalovic and Aleksandar Milosavljevic
    Citation: BMC Bioinformatics 2012 13(Suppl 13):S11
    Content type: Research Published on:

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

  28. Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence...

    Authors: Arthur Chun-Chieh Shih, DT Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao and Mu-Fen Hsieh
    Citation: BMC Bioinformatics 2006 7:103
    Content type: Software Published on:

  30. An important initial phase of arguably most homology search and alignment methods such as required for genome alignments is seed finding. The seed finding step is crucial to curb the runtime as potential alignmen...

    Authors: Matthis Ebel, Giovanna Migliorelli and Mario Stanke
    Citation: BMC Bioinformatics 2022 23:225
    Content type: Research article Published on:

  32. The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research co...

    Authors: Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin TR Kuiper and Pierre Hilson
    Citation: BMC Bioinformatics 2007 8:400
    Content type: Research article Published on:

  33. Assigning chromatin states genome-wide (e.g. promoters, enhancers, etc.) is commonly performed to improve functional interpretation of these states. However, computational methods to assign chromatin state suf...

    Authors: Tara Eicher, Jany Chan, Han Luu, Raghu Machiraju and Ewy A. Mathé
    Citation: BMC Bioinformatics 2021 22:35
    Content type: Methodology article Published on:

  34. Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutati...

    Authors: Yiyun Rao, Nabeel Ahmed, Justin Pritchard and Edward P. O’Brien
    Citation: BMC Bioinformatics 2023 24:462
    Content type: Research Published on:

  35. SAGE has been used widely to study the expression of known transcripts, but much less to annotate new transcribed regions. LongSAGE produces tags that are sufficiently long to be reliably mapped to a whole-gen...

    Authors: Céline Keime, Marie Sémon, Dominique Mouchiroud, Laurent Duret and Olivier Gandrillon
    Citation: BMC Bioinformatics 2007 8:154
    Content type: Research article Published on:

  36. Genome-wide association studies have been successful in finding common variants influencing common traits. However, these associations only account for a fraction of trait heritability. There has been a shift ...

    Authors: Robert Lawrence, Aaron G Day-Williams, Katherine S Elliott, Andrew P Morris and Eleftheria Zeggini
    Citation: BMC Bioinformatics 2010 11:527
    Content type: Software Published on:

  37. Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repe...

    Authors: Marco Pellegrini, Maria Elena Renda and Alessio Vecchio
    Citation: BMC Bioinformatics 2012 13(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 4

  38. Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes th...

    Authors: Leroy Bondhus, Angela Wei and Valerie A. Arboleda
    Citation: BMC Bioinformatics 2022 23:364
    Content type: Software Published on:

  39. The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-ba...

    Authors: Angus Roberts, Robert Gaizauskas, Mark Hepple and Yikun Guo
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  40. Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable "balls in a bag", as may be appropriate for transcripts in mi...

    Authors: Stefan M Stanley, Timothy L Bailey and John S Mattick
    Citation: BMC Bioinformatics 2006 7:94
    Content type: Methodology article Published on:

  42. The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological s...

    Authors: Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman and Cathy H Wu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  43. Long non-coding RNAs (lncRNA) are a major class of non-coding RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and DNA methylation. Through these mechanisms the...

    Authors: Swaraj Basu, Ferenc Müller and Remo Sanges
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S14
    Content type: Research Published on:

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

  44. A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost an...

    Authors: Zhong Ren, Gundula Povysil, Joseph A. Hostyk, Hongzhu Cui, Nitin Bhardwaj and David B. Goldstein
    Citation: BMC Bioinformatics 2021 22:149
    Content type: Software Published on:

  45. Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specif...

    Authors: Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi and David M Gilbert
    Citation: BMC Bioinformatics 2008 9:530
    Content type: Database Published on:

  46. Biomedical event extraction has attracted substantial attention as it can assist researchers in understanding the plethora of interactions among genes that are described in publications in molecular biology. W...

    Authors: Andreas Vlachos and Mark Craven
    Citation: BMC Bioinformatics 2012 13(Suppl 11):S5
    Content type: Proceedings Published on:

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

  47. Genome-wide expression studies have developed exponentially in recent years as a result of extensive use of microarray technology. However, expression signals are typically calculated using the assignment of "...

    Authors: Alberto Risueño, Celia Fontanillo, Marcel E Dinger and Javier De Las Rivas
    Citation: BMC Bioinformatics 2010 11:221
    Content type: Database Published on:

  49. In somatic cancer genomes, delineating genuine driver mutations against a background of multiple passenger events is a challenging task. The difficulty of determining function from sequence data and the low fr...

    Authors: Simon Kebede Merid, Daria Goranskaya and Andrey Alexeyenko
    Citation: BMC Bioinformatics 2014 15:308
    Content type: Methodology article Published on:

  50. Identification of deleterious genetic variants using DNA sequencing data relies on increasingly detailed filtering strategies to isolate the small subset of variants that are more likely to underlie a disease ...

    Authors: Thomas J. Nicholas, Michael J. Cormier and Aaron R. Quinlan
    Citation: BMC Bioinformatics 2022 23:490
    Content type: Software Published on:

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