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  1. The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split...

    Authors: Daniel Kleinman-Ruiz, Begoña Martínez-Cruz, Laura Soriano, Maria Lucena-Perez, Fernando Cruz, Beatriz Villanueva, Jesús Fernández and José A. Godoy
    Citation: BMC Genomics 2017 18:556
    Content type: Research article Published on:

  3. While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often as...

    Authors: Robin C. Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A. Mueller, Martina Chovancová, Martin von Bergen and Benno Schwikowski
    Citation: BMC Genomics 2017 18:553
    Content type: Methodology Article Published on:

  4. The association studies on human complex traits are admittedly propitious to identify deleterious genetic markers. Compared to single-trait analyses, multiple-trait analyses can arguably make better use of the...

    Authors: Wei Zhang, Liu Yang, Larry L. Tang, Aiyi Liu, James L. Mills, Yuanchang Sun and Qizhai Li
    Citation: BMC Genomics 2017 18:552
    Content type: Methodology Article Published on:

  5. The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. ed...

    Authors: Susan Araya, Alexandre M Martins, Nilton T V Junqueira, Ana Maria Costa, Fábio G Faleiro and Márcio E Ferreira
    Citation: BMC Genomics 2017 18:549
    Content type: Research article Published on:

  7. The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and i...

    Authors: Irina Ćalić, Jennifer Koch, David Carey, Charles Addo-Quaye, John E. Carlson and David B. Neale
    Citation: BMC Genomics 2017 18:547
    Content type: Research article Published on:

  8. Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and qu...

    Authors: Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A. El-Kassaby and Hui Chen
    Citation: BMC Genomics 2017 18:546
    Content type: Research article Published on:

  10. Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was cont...

    Authors: Daria V. Rakitina, Alexander I. Manolov, Alexandra V. Kanygina, Sofya K. Garushyants, Julia P. Baikova, Dmitry G. Alexeev, Valentina G. Ladygina, Elena S. Kostryukova, Andrei K. Larin, Tatiana A. Semashko, Irina Y. Karpova, Vladislav V. Babenko, Ruzilya K. Ismagilova, Sergei Y. Malanin, Mikhail S. Gelfand, Elena N. Ilina…
    Citation: BMC Genomics 2017 18:544
    Content type: Research article Published on:

  11. Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the ...

    Authors: Maureen A. Carey, Jason A. Papin and Jennifer L. Guler
    Citation: BMC Genomics 2017 18:543
    Content type: Research article Published on:

  12. Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male ...

    Authors: Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao and Baosong Xing
    Citation: BMC Genomics 2017 18:542
    Content type: Research article Published on:

  13. Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.

    Authors: Jason R. Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P. Walenz, Junqi Liu, Robert M. Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G. Maron, Susan R. McCouch, W. Richard McCombie, Michael C. Schatz…
    Citation: BMC Genomics 2017 18:541
    Content type: Methodology article Published on:

  14. The cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their act...

    Authors: Pamela Córdova, Ana-María Gonzalez, David R. Nelson, María-Soledad Gutiérrez, Marcelo Baeza, Víctor Cifuentes and Jennifer Alcaíno
    Citation: BMC Genomics 2017 18:540
    Content type: Research article Published on:

  15. Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a ‘typical’ lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of ...

    Authors: Colleen P. MacMillan, Hannah Birke, Aaron Chuah, Elizabeth Brill, Yukiko Tsuji, John Ralph, Elizabeth S. Dennis, Danny Llewellyn and Filomena A. Pettolino
    Citation: BMC Genomics 2017 18:539
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:261

  16. Histone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in eth...

    Authors: Likai Wang, Fan Zhang, Siddharth Rode, Kevin K. Chin, Eun Esther Ko, Jonghwan Kim, Vishwanath R. Iyer and Hong Qiao
    Citation: BMC Genomics 2017 18:538
    Content type: Research article Published on:

  17. Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation o...

    Authors: Emilie Debladis, Christel Llauro, Marie-Christine Carpentier, Marie Mirouze and Olivier Panaud
    Citation: BMC Genomics 2017 18:537
    Content type: Methodology article Published on:

  19. The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization...

    Authors: Jeanne Wilbrandt, Bernhard Misof and Oliver Niehuis
    Citation: BMC Genomics 2017 18:535
    Content type: Software Published on:

  20. Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar ...

    Authors: Gairu Li, Senlin Ji, Xiaofeng Zhai, Yuxiang Zhang, Jie Liu, Mengyan Zhu, Jiyong Zhou and Shuo Su
    Citation: BMC Genomics 2017 18:534
    Content type: Research article Published on:

  21. The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells. F-box proteins are substrate adaptors within the UPS and are respon...

    Authors: Lauren E. Gonzalez, Kristen Keller, Karen X. Chan, Megan M. Gessel and Bryan C. Thines
    Citation: BMC Genomics 2017 18:533
    Content type: Research article Published on:

  22. The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to ...

    Authors: Timothy D. Read, Robert A. Petit III, Sandeep J. Joseph, Md. Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan and Alistair D. M. Dove
    Citation: BMC Genomics 2017 18:532
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2017 18:755

  23. In Nile tilapia sex determination is governed by a male heterogametic system XX/XY either on LG1 or LG23. The latter carries a Y-specific duplicate of the amh gene, which is a testis-determining factor. Allelic v...

    Authors: Stephan Wessels, Ina Krause, Claudia Floren, Ekkehard Schütz, Jule Beck and Christoph Knorr
    Citation: BMC Genomics 2017 18:531
    Content type: Research article Published on:

  24. Tuberculosis (TB) is caused by Mycobacterium tuberculosis and represents one of the major challenges facing drug discovery initiatives worldwide. The considerable rise in bacterial drug resistance in recent years...

    Authors: Amine Namouchi, Mena Cimino, Sandrine Favre-Rochex, Patricia Charles and Brigitte Gicquel
    Citation: BMC Genomics 2017 18:530
    Content type: Research article Published on:

  25. Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association s...

    Authors: Long Yan, Nicolle Hofmann, Shuxian Li, Marcio Elias Ferreira, Baohua Song, Guoliang Jiang, Shuxin Ren, Charles Quigley, Edward Fickus, Perry Cregan and Qijian Song
    Citation: BMC Genomics 2017 18:529
    Content type: Research article Published on:

  26. Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in i...

    Authors: Katherine H. Tanaka, Antony T. Vincent, Jean-Guillaume Emond-Rheault, Marcin Adamczuk, Michel Frenette and Steve J. Charette
    Citation: BMC Genomics 2017 18:528
    Content type: Research article Published on:

  28. An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks ...

    Authors: Mahesh Iddawela, Oscar Rueda, Jenny Eremin, Oleg Eremin, Jed Cowley, Helena M. Earl and Carlos Caldas
    Citation: BMC Genomics 2017 18:526
    Content type: Research article Published on:

  29. A restricted set of aerobic bacteria dominated by the Acinetobacter genus was identified in murine intestinal colonic crypts. The vicinity of such bacteria with intestinal stem cells could indicate that they prot...

    Authors: Azadeh Saffarian, Marie Touchon, Céline Mulet, Régis Tournebize, Virginie Passet, Sylvain Brisse, Eduardo P. C. Rocha, Philippe J. Sansonetti and Thierry Pédron
    Citation: BMC Genomics 2017 18:525
    Content type: Research article Published on:

  30. The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted ...

    Authors: Bárbara S. F. Müller, Leandro G. Neves, Janeo E. de Almeida Filho, Márcio F. R. Resende Jr, Patricio R. Muñoz, Paulo E. T. dos Santos, Estefano Paludzyszyn Filho, Matias Kirst and Dario Grattapaglia
    Citation: BMC Genomics 2017 18:524
    Content type: Research article Published on:

  32. Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogeno...

    Authors: Wilson H. McKerrow, Yiannis A. Savva, Ali Rezaei, Robert A. Reenan and Charles E. Lawrence
    Citation: BMC Genomics 2017 18:522
    Content type: Methodology Article Published on:

  33. Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes,...

    Authors: Andries Johannes van der Walt, Marc Warwick van Goethem, Jean-Baptiste Ramond, Thulani Peter Makhalanyane, Oleg Reva and Don Arthur Cowan
    Citation: BMC Genomics 2017 18:521
    Content type: Research article Published on:

  34. The placenta is the principal organ regulating intrauterine growth and development, performing critical functions on behalf of the developing fetus. The delineation of functional networks and pathways driving ...

    Authors: Maya A. Deyssenroth, Shouneng Peng, Ke Hao, Luca Lambertini, Carmen J. Marsit and Jia Chen
    Citation: BMC Genomics 2017 18:520
    Content type: Research article Published on:

  35. Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expre...

    Authors: Leonard D. Goldstein, Ying-Jiun Jasmine Chen, Jude Dunne, Alain Mir, Hermann Hubschle, Joseph Guillory, Wenlin Yuan, Jingli Zhang, Jeremy Stinson, Bijay Jaiswal, Kanika Bajaj Pahuja, Ishminder Mann, Thomas Schaal, Leo Chan, Sangeetha Anandakrishnan, Chun-wah Lin…
    Citation: BMC Genomics 2017 18:519
    Content type: Methodology article Published on:

  36. Aldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses...

    Authors: Wei Wang, Wei Jiang, Juge Liu, Yang Li, Junyi Gai and Yan Li
    Citation: BMC Genomics 2017 18:518
    Content type: Research article Published on:

  37. Gastric cancer is the fourth most common cancer and the second leading cause of cancer death worldwide. In order to understand the genetic background, we sequenced the whole exome and the whole genome of one m...

    Authors: Daniela Esser, Niklas Holze, Jochen Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel and Christoph Röcken
    Citation: BMC Genomics 2017 18:517
    Content type: Research article Published on:

  38. Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumb...

    Authors: Marco Pessoa-Filho, Alexandre Magalhães Martins and Márcio Elias Ferreira
    Citation: BMC Genomics 2017 18:516
    Content type: Research article Published on:

  39. RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of expressed mutation...

    Authors: Simon Haile, Richard D. Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, Philip Tsao, Heather Kirk, Helen McDonald, Pawan Pandoh, Miruna Bala, Martin Hirst, Diane Miller, Richard A. Moore, Andrew J. Mungall, Jacquie Schein, Robin J. Coope…
    Citation: BMC Genomics 2017 18:515
    Content type: Methodology article Published on:

  40. Reversible protein acetylation occurring on Lys-Ne has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysi...

    Authors: R. Glen Uhrig, Pascal Schläpfer, Devang Mehta, Matthias Hirsch-Hoffmann and Wilhelm Gruissem
    Citation: BMC Genomics 2017 18:514
    Content type: Research article Published on:

  42. Arthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolu...

    Authors: Umberto Palatini, Pascal Miesen, Rebeca Carballar-Lejarazu, Lino Ometto, Ettore Rizzo, Zhijian Tu, Ronald P. van Rij and Mariangela Bonizzoni
    Citation: BMC Genomics 2017 18:512
    Content type: Research article Published on:

  43. Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet ...

    Authors: E. Y. Scott, T. Mansour, R. R. Bellone, C. T. Brown, M. J. Mienaltowski, M. C. Penedo, P. J. Ross, S. J. Valberg, J. D. Murray and C. J. Finno
    Citation: BMC Genomics 2017 18:511
    Content type: Research article Published on:

  44. Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic sq...

    Authors: Henk Bolhuis, Ana Belén Martín-Cuadrado, Riccardo Rosselli, Lejla Pašić and Francisco Rodriguez-Valera
    Citation: BMC Genomics 2017 18:510
    Content type: Research article Published on:

  45. Nuclear Factor Erythroid-derived 2-like 2 (Nrf2) senses oxidative environments and/or stress and initiates a cytoprotective response through transcriptional activation of antioxidant and detoxification genes. ...

    Authors: Justin M. Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John R. Hoidal and Namakkal S. Rajasekaran
    Citation: BMC Genomics 2017 18:509
    Content type: Research article Published on:

  46. The Cancer Genome Atlas (TCGA) has generated comprehensive molecular profiles. We aim to identify a set of genes whose expression patterns can distinguish diverse tumor types. Those features may serve as bioma...

    Authors: Yuanyuan Li, Kai Kang, Juno M. Krahn, Nicole Croutwater, Kevin Lee, David M. Umbach and Leping Li
    Citation: BMC Genomics 2017 18:508
    Content type: Research article Published on:

  47. Cell elongation and expansion are significant contributors to plant growth and morphogenesis, and are often regulated by environmental cues and endogenous hormones. Auxin is one of the most important phytohorm...

    Authors: Peng He, Peng Zhao, Limin Wang, Yuzhou Zhang, Xiaosi Wang, Hui Xiao, Jianing Yu and Guanghui Xiao
    Citation: BMC Genomics 2017 18:507
    Content type: Research article Published on:

  48. Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measur...

    Authors: Bárbara Silva-Vignato, Luiz L. Coutinho, Aline S. M. Cesar, Mirele D. Poleti, Luciana C. A. Regitano and Júlio C. C. Balieiro
    Citation: BMC Genomics 2017 18:506
    Content type: Research article Published on:

  49. Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inherit...

    Authors: Xiaobo Luo, Liang Xu, Dongyi Liang, Yan Wang, Wei Zhang, Xianwen Zhu, Yuelin Zhu, Haiyan Jiang, Mingjia Tang and Liwang Liu
    Citation: BMC Genomics 2017 18:505
    Content type: Research article Published on:

  50. Edible bird’s nest (EBN), produced from solidified saliva secretions of specific swiftlet species during the breeding season, is one of the most valuable animal by-products in the world. The composition and me...

    Authors: Q. H. Looi, H. Amin, I. Aini, M. Zuki and A. R. Omar
    Citation: BMC Genomics 2017 18:504
    Content type: Research article Published on:

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BMC Genomics

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