Skip to main content

Articles

Page 151 of 338

  1. Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in human...

    Authors: Alyce Taylor-Brown, Nathan L. Bachmann, Nicole Borel and Adam Polkinghorne
    Citation: BMC Genomics 2016 17:710
    Content type: Research article Published on:

  2. Early in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprise...

    Authors: Camilo Gómez-Garzón, Alejandra Hernández-Santana and Jenny Dussán
    Citation: BMC Genomics 2016 17:709
    Content type: Research article Published on:

  3. Ebola virus is the causative agent of a severe syndrome in humans with a fatality rate that can approach 90 %. During infection, the host immune response is thought to become dysregulated, but the mechanisms t...

    Authors: Ignacio S. Caballero, Anna N. Honko, Stephen K. Gire, Sarah M. Winnicki, Marta Melé, Chiara Gerhardinger, Aaron E. Lin, John L. Rinn, Pardis C. Sabeti, Lisa E. Hensley and John H. Connor
    Citation: BMC Genomics 2016 17:707
    Content type: Research article Published on:

  4. Felid herpesvirus 1 (FHV-1) causes upper respiratory tract diseases in cats worldwide, including nasal and ocular discharge, conjunctivitis and oral ulceration. The nature and severity of disease can vary betw...

    Authors: Paola K. Vaz, Natalie Job, Jacquelyn Horsington, Nino Ficorilli, Michael J. Studdert, Carol A. Hartley, James R. Gilkerson, Glenn F. Browning and Joanne M. Devlin
    Citation: BMC Genomics 2016 17:704
    Content type: Research article Published on:

  6. To develop a set of transcriptome sequences to support research on environmental stress responses in green ash (Fraxinus pennsylvanica), we undertook deep RNA sequencing of green ash tissues under various stress ...

    Authors: Thomas Lane, Teodora Best, Nicole Zembower, Jack Davitt, Nathan Henry, Yi Xu, Jennifer Koch, Haiying Liang, John McGraw, Stephan Schuster, Donghwan Shim, Mark V. Coggeshall, John E. Carlson and Margaret E. Staton
    Citation: BMC Genomics 2016 17:702
    Content type: Research article Published on:

  7. The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comp...

    Authors: I. C. R. M. Kolder, S. J. van der Plas-Duivesteijn, G. Tan, G. F. Wiegertjes, M. Forlenza, A. T. Guler, D. Y. Travin, M. Nakao, T. Moritomo, I. Irnazarow, J. T. den Dunnen, S. Y. Anvar, H. J. Jansen, R. P. Dirks, M. Palmblad, B. Lenhard…
    Citation: BMC Genomics 2016 17:701
    Content type: Research article Published on:

  8. Copy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioin...

    Authors: Jacob L. Steenwyk, John S. Soghigian, John R. Perfect and John G. Gibbons
    Citation: BMC Genomics 2016 17:700
    Content type: Research article Published on:

  9. Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extrace...

    Authors: Yongil Yang, Jessy Labbé, Wellington Muchero, Xiaohan Yang, Sara S. Jawdy, Megan Kennedy, Jenifer Johnson, Avinash Sreedasyam, Jeremy Schmutz, Gerald A. Tuskan and Jin-Gui Chen
    Citation: BMC Genomics 2016 17:699
    Content type: Research article Published on:

  10. Radio-Adaptive Response (RAR) is a biological defense mechanism whereby exposure to low dose ionizing radiation (IR) mitigates the detrimental effects of high dose irradiation. RAR has been widely observed in ...

    Authors: Pilar López-Nieva, Manuel Malavé, Laura González-Sánchez, José Fernández-Piqueras, Pablo Fernández-Navarro and Javier Santos
    Citation: BMC Genomics 2016 17:698
    Content type: Research article Published on:

  11. Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibr...

    Authors: Xiao Zhang, Hua Zhang, Lujiang Li, Hai Lan, Zhiyong Ren, Dan Liu, Ling Wu, Hailan Liu, Jennifer Jaqueth, Bailin Li, Guangtang Pan and Shibin Gao
    Citation: BMC Genomics 2016 17:697
    Content type: Research article Published on:

  12. The generalization of the second Chargaff rule states that counts of any string of nucleotides of length k on a single chromosomal strand equal the counts of its inverse (reverse-complement) k-mer. This Invers...

    Authors: Sagi Shporer, Benny Chor, Saharon Rosset and David Horn
    Citation: BMC Genomics 2016 17:696
    Content type: Research article Published on:

  13. Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This is usually inferred from microarray expression data. Wide availability of NGS technology ...

    Authors: Yvette Temate-Tiagueu, Sahar Al Seesi, Meril Mathew, Igor Mandric, Alex Rodriguez, Kayla Bean, Qiong Cheng, Olga Glebova, Ion Măndoiu, Nicole B. Lopanik and Alexander Zelikovsky
    Citation: BMC Genomics 2016 17(Suppl 5):542
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  14. The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstr...

    Authors: Jiajie Peng, Hongxiang Li, Yongzhuang Liu, Liran Juan, Qinghua Jiang, Yadong Wang and Jin Chen
    Citation: BMC Genomics 2016 17(Suppl 5):530
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

    The Erratum to this article has been published in BMC Genomics 2017 18:262

  15. De novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more eff...

    Authors: Binghang Liu, Chi-Man Liu, Dinghua Li, Yingrui Li, Hing-Fung Ting, Siu-Ming Yiu, Ruibang Luo and Tak-Wah Lam
    Citation: BMC Genomics 2016 17(Suppl 5):499
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  16. Therecent development and availability of different genotype by sequencing (GBS) protocols provided a cost-effective approach to perform high-resolution genomic analysis of entire populations in different spec...

    Authors: Claudia Perea, Juan Fernando De La Hoz, Daniel Felipe Cruz, Juan David Lobaton, Paulo Izquierdo, Juan Camilo Quintero, Bodo Raatz and Jorge Duitama
    Citation: BMC Genomics 2016 17(Suppl 5):498
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  17. Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emergin...

    Authors: Kun Zhao, Robert M. Wohlhueter and Yu Li
    Citation: BMC Genomics 2016 17(Suppl 5):497
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  18. Insertions and Deletions (Indels) are the most common form of structural variation in human genome. Indels not only contribute to genetic diversity but also cause diseases. Therefore assessing indels in human ...

    Authors: Mohammad Shabbir Hasan and Liqing Zhang
    Citation: BMC Genomics 2016 17(Suppl 5):496
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  19. The retina as a model system with extensive information on genes involved in development/maintenance is of great value for investigations employing deep sequencing to capture transcriptome change over time. Th...

    Authors: Devi Krishna Priya Karunakaran, Sahar Al Seesi, Abdul Rouf Banday, Marybeth Baumgartner, Anouk Olthof, Christopher Lemoine, Ion I. Măndoiu and Rahul N. Kanadia
    Citation: BMC Genomics 2016 17(Suppl 5):495
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  20. Two types of approaches are mainly considered for the repeat number estimation in short tandem repeat (STR) regions from high-throughput sequencing data: approaches directly counting repeat patterns included i...

    Authors: Kaname Kojima, Yosuke Kawai, Naoki Nariai, Takahiro Mimori, Takanori Hasegawa and Masao Nagasaki
    Citation: BMC Genomics 2016 17(Suppl 5):494
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  21. Parkinson disease (PD) is a severe neurodegenerative disease without curative drugs. The highly complex and heterogeneous disease mechanisms are still unclear. Detecting novel PD associated genes not only cont...

    Authors: Yang Chen and Rong Xu
    Citation: BMC Genomics 2016 17(Suppl 5):493
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  22. Beta-catenin has two major functions: coordinating cell-cell adhesion by interacting with cadherin in cadherin junction formation pathway; and regulating gene expression through Wnt signaling pathway. Accompli...

    Authors: Bi Zhao and Bin Xue
    Citation: BMC Genomics 2016 17(Suppl 5):484
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 5

  23. Genome-wide association studies provide important insights to the genetic component of disease risks. However, an existing challenge is how to incorporate collective effects of interactions beyond the level of...

    Authors: Hyung Jun Woo, Chenggang Yu, Kamal Kumar, Bert Gold and Jaques Reifman
    Citation: BMC Genomics 2016 17:695
    Content type: Methodology Article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:752

  24. MicroRNAs (miRNA) are ~19–25 nucleotide long RNA molecules that fine tune gene expression through the inhibition of translation or degradation of the mRNA through incorporation into the RNA induced silencing c...

    Authors: Aaron Smith, John Calley, Sachin Mathur, Hui-Rong Qian, Han Wu, Mark Farmen, Florian Caiment, Pierre R. Bushel, Jianying Li, Craig Fisher, Patrick Kirby, Erik Koenig, David G. Hall and David E Watson
    Citation: BMC Genomics 2016 17:694
    Content type: Research article Published on:

  25. The motif ACTAYRNNNCCCR (Y being C or T, R being A or G, and N any nucleotide), called M4, was discovered as a putative cis-regulatory element, present 520 times in human promoter regions. Of these, 317 (61 %)...

    Authors: Ngo Tat Trung, Elisabeth Kremmer and Gerhard Mittler
    Citation: BMC Genomics 2016 17:693
    Content type: Research article Published on:

  27. The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to ...

    Authors: Cristian A. Velandia-Huerto, Adriaan A. Gittenberger, Federico D. Brown, Peter F. Stadler and Clara I. Bermúdez-Santana
    Citation: BMC Genomics 2016 17:691
    Content type: Research Article Published on:

  29. Riemerella anatipestifer infection is a contagious disease that has resulted in major economic losses in the duck industry worldwide. This study attempted to characterize CRISPR-Cas sy...

    Authors: De-Kang Zhu, Xue-Qin Yang, Yang He, Wang-Shu Zhou, Xiao-Heng Song, Jiang-Bo Wang, Yu Zhang, Ma-Feng Liu, Ming-Shu Wang, Ren-Yong Jia, Shun Chen, Kun-Feng Sun, Qiao Yang, Ying Wu, Xiao-Yue Chen and An-Chun Cheng
    Citation: BMC Genomics 2016 17:689
    Content type: Research article Published on:

  30. LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds...

    Authors: Andrew S. Mason, Janet E. Fulton, Paul M. Hocking and David W. Burt
    Citation: BMC Genomics 2016 17:688
    Content type: Research article Published on:

  31. Early maturity is one of the most important and complex agronomic traits in upland cotton (Gossypium hirsutum L). To dissect the genetic architecture of this agronomically important trait, a population consisting...

    Authors: Junji Su, Chaoyou Pang, Hengling Wei, Libei Li, Bing Liang, Caixiang Wang, Meizhen Song, Hantao Wang, Shuqi Zhao, Xiaoyun Jia, Guangzhi Mao, Long Huang, Dandan Geng, Chengshe Wang, Shuli Fan and Shuxun Yu
    Citation: BMC Genomics 2016 17:687
    Content type: Research article Published on:

  32. The goal of most programs developed to find transcription factor binding sites (TFBSs) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences wher...

    Authors: Patricia Oliver, Martín Peralta-Gil, María-Luisa Tabche and Enrique Merino
    Citation: BMC Genomics 2016 17:686
    Content type: Methodology article Published on:

  33. Taste receptors (TASRs) are essential for the body’s recognition of chemical compounds. In the tongue, TASRs sense the sweet and umami and the toxin-related bitter taste thus promoting a particular eating beha...

    Authors: Alex Clop, Abdoallah Sharaf, Anna Castelló, Sebastián Ramos-Onsins, Susanna Cirera, Anna Mercadé, Sophia Derdak, Sergi Beltran, Abe Huisman, Merete Fredholm, Pieter van As and Armand Sánchez
    Citation: BMC Genomics 2016 17:685
    Content type: Research article Published on:

  34. MicroRNAs (miRNAs) play important roles in plant growth and development. MiRNAs and their targets have been widely studied in model plants, but limited knowledge is available concerning this small RNA populati...

    Authors: Jihong Hu, Jing Jin, Qian Qian, Keke Huang and Yi Ding
    Citation: BMC Genomics 2016 17:684
    Content type: Research article Published on:

  35. Dysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes wer...

    Authors: Marie-Pier Tremblay, Victoria E. S. Armero, Andréa Allaire, Simon Boudreault, Camille Martenon-Brodeur, Mathieu Durand, Elvy Lapointe, Philippe Thibault, Maude Tremblay-Létourneau, Jean-Pierre Perreault, Michelle S. Scott and Martin Bisaillon
    Citation: BMC Genomics 2016 17:683
    Content type: Research article Published on:

  36. Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about ...

    Authors: Moritz Hess, Henning Wildhagen, Laura Verena Junker and Ingo Ensminger
    Citation: BMC Genomics 2016 17:682
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:780

  37. Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited duri...

    Authors: Oz Solomon, Vered Kunik, Amos Simon, Nitzan Kol, Ortal Barel, Atar Lev, Ninette Amariglio, Raz Somech, Gidi Rechavi and Eran Eyal
    Citation: BMC Genomics 2016 17:681
    Content type: Software Published on:

  38. The intestinal epithelium plays a critical role in nutrient absorption and innate immune defense. Recent studies showed that metabolic stress pathways, in particular the integrated stress response (ISR), contr...

    Authors: Jessica Tsalikis, Qun Pan, Ivan Tattoli, Charles Maisonneuve, Benjamin J. Blencowe, Dana J. Philpott and Stephen E. Girardin
    Citation: BMC Genomics 2016 17:680
    Content type: Research article Published on:

  40. Nasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral gene...

    Authors: Alfredo Rago, Donald G. Gilbert, Jeong-Hyeon Choi, Timothy B. Sackton, Xu Wang, Yogeshwar D. Kelkar, John H. Werren and John K. Colbourne
    Citation: BMC Genomics 2016 17:678
    Content type: Research article Published on:

  41. Analysis of codon usage bias is an extremely versatile method using in furthering understanding of the genetic and evolutionary paths of species. Codon usage bias of envelope glycoprotein genes in nuclear poly...

    Authors: Yongchao Zhao, Hao Zheng, Anying Xu, Donghua Yan, Zijian Jiang, Qi Qi and Jingchen Sun
    Citation: BMC Genomics 2016 17:677
    Content type: Research article Published on:

  42. Rhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still in its infancy. Whole-genome sequence (WGS) data i...

    Authors: Benjamin N. Bimber, Michael J. Raboin, John Letaw, Kimberly A. Nevonen, Jennifer E. Spindel, Susan R. McCouch, Rita Cervera-Juanes, Eliot Spindel, Lucia Carbone, Betsy Ferguson and Amanda Vinson
    Citation: BMC Genomics 2016 17:676
    Content type: Methodology article Published on:

  43. The sea lamprey (Petromyzon marinus) is a jawless vertebrate that parasitizes fish as an adult and, with overfishing, was responsible for the decline in lake trout (Salvelinus namaycush) populations in the Great ...

    Authors: Frederick Goetz, Sara E. Smith, Giles Goetz and Cheryl A. Murphy
    Citation: BMC Genomics 2016 17:675
    Content type: Research article Published on:

  45. Chrysanthemum is a leading cut flower species. Most conventional cultivars flower during the fall, but the Chrysanthemum morifolium ‘Yuuka’ flowers during the summer, thereby filling a gap in the market. To date,...

    Authors: Liping Ren, Tao Liu, Yue Cheng, Jing Sun, Jiaojiao Gao, Bin Dong, Sumei Chen, Fadi Chen and Jiafu Jiang
    Citation: BMC Genomics 2016 17:673
    Content type: Research article Published on:

  46. Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Availabl...

    Authors: Fabian Grandke, Priyanka Singh, Henri C. M. Heuven, Jorn R. de Haan and Dirk Metzler
    Citation: BMC Genomics 2016 17:672
    Content type: Methodology Article Published on:

  47. Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The C...

    Authors: Anne Abot, Gregory Arnal, Lucas Auer, Adèle Lazuka, Delphine Labourdette, Sophie Lamarre, Lidwine Trouilh, Elisabeth Laville, Vincent Lombard, Gabrielle Potocki-Veronese, Bernard Henrissat, Michael O’Donohue, Guillermina Hernandez-Raquet, Claire Dumon and Véronique Anton Leberre
    Citation: BMC Genomics 2016 17:671
    Content type: Research article Published on:

  48. Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fu...

    Authors: Adriaan Vanheule, Kris Audenaert, Sven Warris, Henri van de Geest, Elio Schijlen, Monica Höfte, Sarah De Saeger, Geert Haesaert, Cees Waalwijk and Theo van der Lee
    Citation: BMC Genomics 2016 17:670
    Content type: Research article Published on:

  49. Major depressive disorder (MDD) is a heterogeneous disease at the level of clinical symptoms, and this heterogeneity is likely reflected at the level of biology. Two clinical subtypes within MDD that have garn...

    Authors: Yashu Liu, Lynn Yieh, Tao Yang, Wilhelmus Drinkenburg, Pieter Peeters, Thomas Steckler, Vaibhav A. Narayan, Gayle Wittenberg and Jieping Ye
    Citation: BMC Genomics 2016 17:669
    Content type: Methodology article Published on:

  50. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by inflammation and destruction of synovial joints. RA affects up to 1 % of the population worldwide. Currently, there are no drugs that ...

    Authors: Rong Xu and QuanQiu Wang
    Citation: BMC Genomics 2016 17(Suppl 7):518
    Content type: Research Published on:

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

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 3.5
    5-year Journal Impact Factor: 4.1
    Source Normalized Impact per Paper (SNIP): 1.083
    SCImago Journal Rank (SJR): 1.047

    Speed 2023
    Submission to first editorial decision (median days): 21
    Submission to acceptance (median days): 137

    Usage 2023
    Downloads: 7,167,242
    Altmetric mentions: 4,454

Follow

Sign up for article alerts and news from this journal

BMC Genomics

ISSN: 1471-2164

Contact us