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  1. Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to L...

    Authors: Shanshan Dong, Chaoxian Zhao, Fei Chen, Yanhui Liu, Shouzhou Zhang, Hong Wu, Liangsheng Zhang and Yang Liu
    Citation: BMC Genomics 2018 19:614
    Content type: Research article Published on:

  2. Peach (Prunus persica) is an important fruit crop that generally softens rapidly after harvest resulting in a short shelf-life. By contrast, stony hard (SH) peach fruit does not soften and hardly produces ethylen...

    Authors: Shaolei Guo, Shahid Iqbal, Ruijuan Ma, Juan Song, Mingliang Yu and Zhihong Gao
    Citation: BMC Genomics 2018 19:612
    Content type: Research article Published on:

  5. As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequen...

    Authors: Diana I. Cruz-Dávalos, María A. Nieves-Colón, Alexandra Sockell, G. David Poznik, Hannes Schroeder, Anne C. Stone, Carlos D. Bustamante, Anna-Sapfo Malaspinas and María C. Ávila-Arcos
    Citation: BMC Genomics 2018 19:608
    Content type: Methodology article Published on:

  6. Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to n...

    Authors: Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang and Ming Chen
    Citation: BMC Genomics 2018 19:607
    Content type: Research article Published on:

  7. Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some case...

    Authors: Nicolas W. G. Chen, Laurana Serres-Giardi, Mylène Ruh, Martial Briand, Sophie Bonneau, Armelle Darrasse, Valérie Barbe, Lionel Gagnevin, Ralf Koebnik and Marie-Agnès Jacques
    Citation: BMC Genomics 2018 19:606
    Content type: Research article Published on:

  8. It is known that long non-coding RNAs (lncRNAs) play an important role in various biological processes, including cell proliferation, differentiation and apoptosis. However, their functions and profiles in lac...

    Authors: Bing Yang, Beilei Jiao, Wei Ge, Xiaolan Zhang, Shanhe Wang, Hongbo Zhao and Xin Wang
    Citation: BMC Genomics 2018 19:605
    Content type: Research article Published on:

  9. Genome editing by CRISPR-Cas9 technology allows large-scale screening of gene essentiality in cancer. A confounding factor when interpreting CRISPR-Cas9 screens is the high false-positive rate in detecting ess...

    Authors: Francesco Iorio, Fiona M. Behan, Emanuel Gonçalves, Shriram G. Bhosle, Elisabeth Chen, Rebecca Shepherd, Charlotte Beaver, Rizwan Ansari, Rachel Pooley, Piers Wilkinson, Sarah Harper, Adam P. Butler, Euan A. Stronach, Julio Saez-Rodriguez, Kosuke Yusa and Mathew J. Garnett
    Citation: BMC Genomics 2018 19:604
    Content type: Methodology article Published on:

  10. While RNA is often created from linear splicing during transcription, recent studies have found that non-canonical splicing sometimes occurs. Non-canonical splicing joins 3’ and 5’ and forms the so-called circ...

    Authors: Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu and Yufeng Wu
    Citation: BMC Genomics 2018 19(Suppl 6):572
    Content type: Software Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  11. The Human Phenotype Ontology (HPO) is one of the most popular bioinformatics resources. Recently, HPO-based phenotype semantic similarity has been effectively applied to model patient phenotype data. However, ...

    Authors: Jiajie Peng, Hansheng Xue, Weiwei Hui, Junya Lu, Bolin Chen, Qinghua Jiang, Xuequn Shang and Yadong Wang
    Citation: BMC Genomics 2018 19(Suppl 6):571
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  12. Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orth...

    Authors: Eliran Avni and Sagi Snir
    Citation: BMC Genomics 2018 19(Suppl 6):570
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  13. Single cell transcriptomics is critical for understanding cellular heterogeneity and identification of novel cell types. Leveraging the recent advances in single cell RNA sequencing (scRNA-Seq) technology requ...

    Authors: Marmar Moussa and Ion I. Măndoiu
    Citation: BMC Genomics 2018 19(Suppl 6):569
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  14. Viral infection involves a large number of protein-protein interactions (PPIs) between virus and its host. These interactions range from the initial binding of viral coat proteins to host membrane receptor to ...

    Authors: Xiang Zhou, Byungkyu Park, Daesik Choi and Kyungsook Han
    Citation: BMC Genomics 2018 19(Suppl 6):568
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  16. Repeat elements are important components of most eukaryotic genomes. Most existing tools for repeat analysis rely either on high quality reference genomes or existing repeat libraries. Thus, it is still challe...

    Authors: Chong Chu, Jingwen Pei and Yufeng Wu
    Citation: BMC Genomics 2018 19(Suppl 6):566
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  17. With the developments of DNA sequencing technology, large amounts of sequencing data have been produced that provides unprecedented opportunities for advanced association studies between somatic mutations and ...

    Authors: Yuchen Yuan, Yi Shi, Xianbin Su, Xin Zou, Qing Luo, David Dagan Feng, Weidong Cai and Ze-Guang Han
    Citation: BMC Genomics 2018 19(Suppl 6):565
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  18. Alternative splicing is a ubiquitous post-transcriptional regulation mechanism in most eukaryotic genes. Aberrant splicing isoforms and abnormal isoform ratios can contribute to cancer development. Kinase gene...

    Authors: Huijuan Feng, Tingting Li and Xuegong Zhang
    Citation: BMC Genomics 2018 19(Suppl 6):564
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  19. Following publication of the original article [1], the authors reported that one of the authors’ names was erroneously changed during proofing and published incorrectly. In this Correction the incorrect and co...

    Authors: Margarida Espada, Sebastian Eves-van den Akker, Tom Maier, Paramasivan Vijayapalani, Thomas Baum, Manuel Mota and John T. Jones
    Citation: BMC Genomics 2018 19:603
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2018 19:553

  20. While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads ...

    Authors: Mikhail I. Schelkunov, Aleksey A. Penin and Maria D. Logacheva
    Citation: BMC Genomics 2018 19:602
    Content type: Research article Published on:

  21. Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal

    Authors: Michael Pietsch, Alexandra Irrgang, Nicole Roschanski, Geovana Brenner Michael, Axel Hamprecht, Heime Rieber, Annemarie Käsbohrer, Stefan Schwarz, Uwe Rösler, Lothar Kreienbrock, Yvonne Pfeifer, Stephan Fuchs and Guido Werner
    Citation: BMC Genomics 2018 19:601
    Content type: Research article Published on:

  22. Direct molecular cloning of full-length cDNAs derived from viral RNA is an approach to identify the individual viral genomes within a virus population. This enables characterization of distinct viral haplotype...

    Authors: Camille Melissa Johnston, Ulrik Fahnøe, Graham J. Belsham and Thomas Bruun Rasmussen
    Citation: BMC Genomics 2018 19:600
    Content type: Methodology article Published on:

  23. Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family gen...

    Authors: Muhammad Shaban, Muhammad Mahmood Ahmed, Heng Sun, Abid Ullah and Longfu Zhu
    Citation: BMC Genomics 2018 19:599
    Content type: Research article Published on:

  24. Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Bei...

    Authors: Mengmeng Zhang, Wei Han, Hui Tang, Guohui Li, Minjie Zhang, Ran Xu, Yijun Liu, Tao Yang, Wenting Li, Jianmin Zou and Keliang Wu
    Citation: BMC Genomics 2018 19:598
    Content type: Research article Published on:

  26. Though it is toxic to humans, dichlorvos is a widely used chemical pesticide and plays an important role in the control of plant pests. The application of a combination of the biocontrol agent Trichoderma with di...

    Authors: Qiong Wu, Mi Ni, Guisheng Wang, Qianqian Liu, Meixia Yu and Jun Tang
    Citation: BMC Genomics 2018 19:596
    Content type: Research article Published on:

  27. The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majori...

    Authors: K. Blighe, L. DeDionisio, K. A. Christie, B. Chawes, S. Shareef, T. Kakouli-Duarte, C. Chao-Shern, V. Harding, R. S. Kelly, L. Castellano, J. Stebbing, J. A. Lasky-Su, M. A. Nesbit and C. B. T. Moore
    Citation: BMC Genomics 2018 19:595
    Content type: Review Published on:

  28. The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression ...

    Authors: Stephen J. Bush, Lucy Freem, Amanda J. MacCallum, Jenny O’Dell, Chunlei Wu, Cyrus Afrasiabi, Androniki Psifidi, Mark P. Stevens, Jacqueline Smith, Kim M. Summers and David A. Hume
    Citation: BMC Genomics 2018 19:594
    Content type: Methodology article Published on:

  29. Nematode sperm have unique and highly diverged morphology and molecular biology. In particular, nematode sperm contain subcellular vesicles known as membranous organelles that are necessary for male fertility,...

    Authors: Katja R. Kasimatis, Megan J. Moerdyk-Schauwecker, Nadine Timmermeyer and Patrick C. Phillips
    Citation: BMC Genomics 2018 19:593
    Content type: Research article Published on:

  30. Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating an...

    Authors: C. Llorens, S. C. Arcos, L. Robertson, R. Ramos, R. Futami, B. Soriano, S. Ciordia, M. Careche, M. González-Muñoz, Y. Jiménez-Ruiz, N. Carballeda-Sangiao, I. Moneo, J. P. Albar, M. Blaxter and A. Navas
    Citation: BMC Genomics 2018 19:592
    Content type: Research article Published on:

  31. Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss.; DD) and has novel sources of genetic diversity for bro...

    Authors: Madhav Bhatta, Alexey Morgounov, Vikas Belamkar, Jesse Poland and P. Stephen Baenziger
    Citation: BMC Genomics 2018 19:591
    Content type: Research article Published on:

  32. The expression of microRNAs (miRNAs) is essential for the proper development of the mammalian embryo. A maternal exposure to endocrine disrupting chemicals during preimplantation bears the potential for transg...

    Authors: Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs and Susanne E. Ulbrich
    Citation: BMC Genomics 2018 19:590
    Content type: Research article Published on:

  33. The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strain...

    Authors: Jon Bohlin, Vegard Eldholm, Ola Brynildsrud, John H.-O. Petterson and Kristian Alfsnes
    Citation: BMC Genomics 2018 19:589
    Content type: Research article Published on:

  34. Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over...

    Authors: Hengfu Yin, Hao-Bo Guo, David J. Weston, Anne M. Borland, Priya Ranjan, Paul E. Abraham, Sara S. Jawdy, James Wachira, Gerald A. Tuskan, Timothy J. Tschaplinski, Stan D. Wullschleger, Hong Guo, Robert L. Hettich, Stephen M. Gross, Zhong Wang, Axel Visel…
    Citation: BMC Genomics 2018 19:588
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:279

  35. Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a power...

    Authors: Alessandra Di Canito, Jessica Zampolli, Alessandro Orro, Pasqualina D’Ursi, Luciano Milanesi, Guido Sello, Alexander Steinbüchel and Patrizia Di Gennaro
    Citation: BMC Genomics 2018 19:587
    Content type: Research article Published on:

  36. Allopolyploids require rapid genetic and epigenetic modifications to reconcile two or more sets of divergent genomes. To better understand the fate of duplicate genes following genomic mergers and doubling dur...

    Authors: Jian Wu, Li Lin, Meiling Xu, Peipei Chen, Dongxiao Liu, Qinfu Sun, Liping Ran and Youping Wang
    Citation: BMC Genomics 2018 19:586
    Content type: Research article Published on:

  37. Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options f...

    Authors: Vania Michelotti, Antonella Lamontanara, Giampaolo Buriani, Luigi Orrù, Antonio Cellini, Irene Donati, Joel L. Vanneste, Luigi Cattivelli, Gianni Tacconi and Francesco Spinelli
    Citation: BMC Genomics 2018 19:585
    Content type: Research article Published on:

  38. Following the publication of this article [1], the authors found that the primers listed for CREB-binding protein were not correct. This mistake occurred during assembly of the primer table and the authors apo...

    Authors: Amit Roy, Smitha George and Subba Reddy Palli
    Citation: BMC Genomics 2018 19:584
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2017 18:996

  39. Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infe...

    Authors: Xing Wang, Chunyan Cheng, Kaijing Zhang, Zhen Tian, Jian Xu, Shuqiong Yang, Qunfeng Lou, Ji Li and Jin-Feng Chen
    Citation: BMC Genomics 2018 19:583
    Content type: Research article Published on:

  40. Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4...

    Authors: Weijing Cai, Dapeng Zhou, Weibo Wu, Wen Ling Tan, Jiaqian Wang, Caicun Zhou and Yanyan Lou
    Citation: BMC Genomics 2018 19:582
    Content type: Research article Published on:

  41. Severe equine asthma, also known as recurrent airway obstruction (RAO), is a debilitating, performance limiting, obstructive respiratory condition in horses that is phenotypically similar to human asthma. Past...

    Authors: Victor C. Mason, Robert J. Schaefer, Molly E. McCue, Tosso Leeb and Vinzenz Gerber
    Citation: BMC Genomics 2018 19:581
    Content type: Research article Published on:

  42. 3,4-methylenedioxymethamphetamine (MDMA, “ecstasy”) is a widely used entactogenic drug known to impair cognitive functions on the long-run. Both hippocampal and frontal cortical regions have well established r...

    Authors: Peter Petschner, Viola Tamasi, Csaba Adori, Eszter Kirilly, Romeo D. Ando, Laszlo Tothfalusi and Gyorgy Bagdy
    Citation: BMC Genomics 2018 19:580
    Content type: Research article Published on:

  43. The 14–3-3 family of ubiquitous proteins in eukaryotes plays important roles in the regulation of various plant biological processes. However, less information is known about this family in grape fruit.

    Authors: Cheng Cheng, Yi Wang, Fengmei Chai, Shaohua Li, Haiping Xin and Zhenchang Liang
    Citation: BMC Genomics 2018 19:579
    Content type: Research article Published on:

  44. Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtrop...

    Authors: Yung-I Lee, Jing Wei Yap, Shairul Izan, Ilia J. Leitch, Michael F. Fay, Yi-Ching Lee, Oriane Hidalgo, Steven Dodsworth, Marinus J. M. Smulders, Barbara Gravendeel and Andrew R. Leitch
    Citation: BMC Genomics 2018 19:578
    Content type: Research article Published on:

  45. Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCM...

    Authors: Timokratis Karamitros, Bonnie van Wilgenburg, Mark Wills, Paul Klenerman and Gkikas Magiorkinis
    Citation: BMC Genomics 2018 19:577
    Content type: Research article Published on:

  46. The Mediterranean diet is considered one of the healthier food habits and olive oil is one of its key components. Olive oil polyphenols are known to induce beneficial effects in several pathological conditions...

    Authors: Marcella Sabino, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Ilaria Biasato, Andrea Verini-Supplizi, Andrea Valiani and Massimo Trabalza-Marinucci
    Citation: BMC Genomics 2018 19:576
    Content type: Research article Published on:

  48. N6-methyladenosine (m6A) is an important epigenetic modification which plays various roles in mRNA metabolism and embryogenesis directly related to human diseases. To identify m6A in a large scale, machine learni...

    Authors: Zhixun Zhao, Hui Peng, Chaowang Lan, Yi Zheng, Liang Fang and Jinyan Li
    Citation: BMC Genomics 2018 19:574
    Content type: Research article Published on:

  49. Human neutrophils are central players in innate immunity, a major component of inflammatory responses, and a leading model for cell motility and chemotaxis. However, primary neutrophils are short-lived, limiti...

    Authors: Esther Rincón, Briana L. Rocha-Gregg and Sean R. Collins
    Citation: BMC Genomics 2018 19:573
    Content type: Research article Published on:

  50. Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 ...

    Authors: Wiebke Sannemann, Antonia Lisker, Andreas Maurer, Jens Léon, Ebrahim Kazman, Hilmar Cöster, Josef Holzapfel, Hubert Kempf, Viktor Korzun, Erhard Ebmeyer and Klaus Pillen
    Citation: BMC Genomics 2018 19:559
    Content type: Research article Published on:

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BMC Genomics

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