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  1. Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic mate...

    Authors: Kishor Dhaygude, Abhilash Nair, Helena Johansson, Yannick Wurm and Liselotte Sundström
    Citation: BMC Genomics 2019 20:301
    Content type: Research article Published on:

  2. Temperate bacteriophages are capable of lysogenic conversion of new bacterial hosts. This phenomenon is often ascribed to “moron” elements that are acquired horizontally and transcribed independently from the ...

    Authors: Danielle L. Peters, Jaclyn G. McCutcheon, Paul Stothard and Jonathan J. Dennis
    Citation: BMC Genomics 2019 20:300
    Content type: Research article Published on:

  3. Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the ...

    Authors: A. Santos-Zavaleta, E. Pérez-Rueda, M. Sánchez-Pérez, D. A. Velázquez-Ramírez and J. Collado-Vides
    Citation: BMC Genomics 2019 20:299
    Content type: Research article Published on:

  5. Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or th...

    Authors: Ding Wu, Brett Pepowski, Satoe Takahashi and Stephen J. Kron
    Citation: BMC Genomics 2019 20:290
    Content type: Research article Published on:

  6. Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. villosum accessions, D....

    Authors: Shijin Li, Jing Wang, Kunyang Wang, Jingnan Chen, Ke Wang, Lipu Du, Zhongfu Ni, Zhishan Lin and Xingguo Ye
    Citation: BMC Genomics 2019 20:289
    Content type: Research article Published on:

  7. Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selecti...

    Authors: Yajuan Li, Lingling Zhang, Ruojiao Li, Meiwei Zhang, Yangping Li, Hao Wang, Shi Wang and Zhenmin Bao
    Citation: BMC Genomics 2019 20:288
    Content type: Research article Published on:

  8. The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization ...

    Authors: Jie Xiao, Rui Hu, Ting Gu, Jiapeng Han, Ding Qiu, Peipei Su, Jialu Feng, Junli Chang, Guangxiao Yang and Guangyuan He
    Citation: BMC Genomics 2019 20:287
    Content type: Research article Published on:

  9. Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of ar...

    Authors: Terhi Iso-Touru, Christine Wurmser, Heli Venhoranta, Maya Hiltpold, Tujia Savolainen, Anu Sironen, Konrad Fischer, Krzysztof Flisikowski, Ruedi Fries, Alejandro Vicente-Carrillo, Manuel Alvarez-Rodriguez, Szabolcs Nagy, Mervi Mutikainen, Jaana Peippo, Juhani Taponen, Goutam Sahana…
    Citation: BMC Genomics 2019 20:286
    Content type: Research article Published on:

  10. Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfi...

    Authors: Xiang Jin, Liping Zhu, Chengcheng Tao, Quanliang Xie, Xinyang Xu, Lili Chang, Yanhua Tan, Guohua Ding, Hongbin Li and Xuchu Wang
    Citation: BMC Genomics 2019 20:285
    Content type: Methodology article Published on:

  11. The effect of mutations conferring antibiotic resistance can depend on the genetic background. To determine if a previously de novo acquired antibiotic resistance influences the adaptation to a second antibiot...

    Authors: Marloes Hoeksema, Martijs J. Jonker, Stanley Brul and Benno H. ter Kuile
    Citation: BMC Genomics 2019 20:284
    Content type: Research article Published on:

  12. Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress p...

    Authors: Yuhui Du, Jinjin Ma, Zhiqiu Yin, Kai Liu, Gan Yao, Wenfeng Xu, Lingchao Fan, Binghai Du, Yanqin Ding and Chengqiang Wang
    Citation: BMC Genomics 2019 20:283
    Content type: Research article Published on:

  13. In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical ste...

    Authors: Hua Li, Ling Bai, Hongmei Li, Xinhui Li, Yani Kang, Ningbo Zhang, Jielin Sun and Zhifeng Shao
    Citation: BMC Genomics 2019 20:282
    Content type: Research article Published on:

  14. Ketamine ester analogs, SN 35210 and SN 35563, demonstrate different pharmacological profiles to ketamine in animal models. Both confer hypnosis with predictably rapid offset yet, paradoxically, SN35563 induce...

    Authors: Gregory M. Jacobson, Logan J. Voss, Anica Klockars, Steve Bird, Ivo Dimitrov, William A. Denny, Pawel K. Olszewski, James W. Sleigh and Martyn G. Harvey
    Citation: BMC Genomics 2019 20:281
    Content type: Research article Published on:

  15. Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-ind...

    Authors: Elizabeth A. Malinich, Ken Wang, Prasun K. Mukherjee, Michael Kolomiets and Charles M. Kenerley
    Citation: BMC Genomics 2019 20:280
    Content type: Research article Published on:

  16. Following publication of the original article

    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 2019 20:279
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2018 19:588

  17. The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploi...

    Authors: Vera Vendramin, Danara Ormanbekova, Simone Scalabrin, Davide Scaglione, Marco Maccaferri, Pierluigi Martelli, Silvio Salvi, Irena Jurman, Rita Casadio, Federica Cattonaro, Roberto Tuberosa, Andrea Massi and Michele Morgante
    Citation: BMC Genomics 2019 20:278
    Content type: Research article Published on:

  18. Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are assoc...

    Authors: Katharina May, Carsten Scheper, Kerstin Brügemann, Tong Yin, Christina Strube, Paula Korkuć, Gudrun A. Brockmann and Sven König
    Citation: BMC Genomics 2019 20:277
    Content type: Research article Published on:

  20. The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data fr...

    Authors: Andreas Wallberg, Ignas Bunikis, Olga Vinnere Pettersson, Mai-Britt Mosbech, Anna K. Childers, Jay D. Evans, Alexander S. Mikheyev, Hugh M. Robertson, Gene E. Robinson and Matthew T. Webster
    Citation: BMC Genomics 2019 20:275
    Content type: Research article Published on:

  21. Cotton leaf curl disease (CLCuD), caused by begomoviruses in association with satellite molecules, is a major threat to cotton production causing enormous losses to cotton crop in most of the cotton growing co...

    Authors: Razia Qadir, Zainul A. Khan, Dilip Monga and Jawaid A. Khan
    Citation: BMC Genomics 2019 20:274
    Content type: Research article Published on:

  23. The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well docume...

    Authors: Irene Bassano, Swee Hoe Ong, Maximo Sanz-Hernandez, Michal Vinkler, Adebabay Kebede, Olivier Hanotte, Ebele Onuigbo, Mark Fife and Paul Kellam
    Citation: BMC Genomics 2019 20:272
    Content type: Research article Published on:

  24. Wild birds, in particular pigeons are considered a natural reservoir for stx2f-carrying E. coli. An extensive comparison of isolates from pigeons and humans from the same region is lacking, which hampers justifia...

    Authors: Angela H. A. M. van Hoek, Janieke N. J. van Veldhuizen, Ingrid Friesema, Claudia Coipan, John W. A. Rossen, Indra L. Bergval and Eelco Franz
    Citation: BMC Genomics 2019 20:271
    Content type: Research article Published on:

  25. The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great ...

    Authors: Andrei A. Kudinov, Natalia V. Dementieva, Olga V. Mitrofanova, Olga I. Stanishevskaya, Elena S. Fedorova, Tatiana A. Larkina, Arina I. Mishina, Kirill V. Plemyashov, Darren K. Griffin and Michael N. Romanov
    Citation: BMC Genomics 2019 20:270
    Content type: Research article Published on:

  26. Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperatur...

    Authors: Rongfang Guo, Xingru Wang, Xiaoyun Han, Wenjing Li, Tao Liu, Bingxing Chen, Xiaodong Chen and Gefu Wang-Pruski
    Citation: BMC Genomics 2019 20:269
    Content type: Research article Published on:

  27. Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacit...

    Authors: Joseph L. Sevigny, Derek Rothenheber, Krystalle Sharlyn Diaz, Ying Zhang, Kristin Agustsson, R. Daniel Bergeron and W. Kelley Thomas
    Citation: BMC Genomics 2019 20:268
    Content type: Research article Published on:

  28. Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection an...

    Authors: Shaokun An, Liang Ma and Lin Wan
    Citation: BMC Genomics 2019 20(Suppl 2):224
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  29. Epigenome is highly dynamic during the early stages of embryonic development. Epigenetic modifications provide the necessary regulation for lineage specification and enable the maintenance of cellular identity...

    Authors: Xia Zhang, Yanglan Gan, Guobing Zou, Jihong Guan and Shuigeng Zhou
    Citation: BMC Genomics 2019 20(Suppl 2):221
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  30. The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years....

    Authors: Bipasa Biswas and Yinglei Lai
    Citation: BMC Genomics 2019 20(Suppl 2):195
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  31. A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of ...

    Authors: Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu and Laxmi Parida
    Citation: BMC Genomics 2019 20(Suppl 2):194
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  32. Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage....

    Authors: Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv and Rui Jiang
    Citation: BMC Genomics 2019 20(Suppl 2):193
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  33. Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence th...

    Authors: Qi Tian, Jianxiao Zou, Jianxiong Tang, Yuan Fang, Zhongli Yu and Shicai Fan
    Citation: BMC Genomics 2019 20(Suppl 2):192
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  34. One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial comm...

    Authors: Ko Abe, Masaaki Hirayama, Kinji Ohno and Teppei Shimamura
    Citation: BMC Genomics 2019 20(Suppl 2):191
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  35. Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than second-generation sequencing technologies such as Illumina. The increased read length enables PacBio seq...

    Authors: Nan Du, Jiao Chen and Yanni Sun
    Citation: BMC Genomics 2019 20(Suppl 2):190
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  36. Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as w...

    Authors: Wenhao Qian, Ting Ma, Mao Ye, Zhiyao Li, Yuanhua Liu and Pei Hao
    Citation: BMC Genomics 2019 20(Suppl 2):189
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  37. Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNP...

    Authors: Sungjoon Park, Minsu Kim, Seokjun Seo, Seungwan Hong, Kyoohyung Han, Keewoo Lee, Jung Hee Cheon and Sun Kim
    Citation: BMC Genomics 2019 20(Suppl 2):188
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  38. The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data min...

    Authors: Pengshuo Yang, Shaojun Yu, Lin Cheng and Kang Ning
    Citation: BMC Genomics 2019 20(Suppl 2):187
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  39. Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible i...

    Authors: Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng and Shuaicheng Li
    Citation: BMC Genomics 2019 20(Suppl 2):186
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  40. Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence p...

    Authors: Dongmei Ai, Xiaoxin Li, Hongfei Pan, Jiamin Chen, Jacob A. Cram and Li C. Xia
    Citation: BMC Genomics 2019 20(Suppl 2):185
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  41. Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optim...

    Authors: Shanshan Ren, Nauman Ahmed, Koen Bertels and Zaid Al-Ars
    Citation: BMC Genomics 2019 20(Suppl 2):184
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  43. Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the i...

    Authors: Gurjit S. Randhawa, Kathleen A. Hill and Lila Kari
    Citation: BMC Genomics 2019 20:267
    Content type: Software Article Published on:

  44. The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma...

    Authors: Yuqiong Guo, Chen Zhu, Shanshan Zhao, Shuting Zhang, Wenjian Wang, Haifeng Fu, Xiaozhen Li, Chengzhe Zhou, Lan Chen, Yuling Lin and Zhongxiong Lai
    Citation: BMC Genomics 2019 20:265
    Content type: Research article Published on:

  45. Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa, one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GM...

    Authors: Xiuping Shen, Liai Xu, Yanhong Liu, Heng Dong, Dong Zhou, Yuzhi Zhang, Sue Lin, Jiashu Cao and Li Huang
    Citation: BMC Genomics 2019 20:264
    Content type: Research article Published on:

  46. There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of...

    Authors: Diyan Li, Yan Li, Miao Li, Tiandong Che, Shilin Tian, Binlong Chen, Xuming Zhou, Guolong Zhang, Uma Gaur, Majing Luo, Kai Tian, Mengnan He, Shen He, Zhongxian Xu, Long Jin, Qianzi Tang…
    Citation: BMC Genomics 2019 20:263
    Content type: Research article Published on:

  47. The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its gen...

    Authors: Vanessa Carvalho Cayres Pamponét, Margarete Magalhães Souza, Gonçalo Santos Silva, Fabienne Micheli, Cláusio Antônio Ferreira de Melo, Sarah Gomes de Oliveira, Eduardo Almeida Costa and Ronan Xavier Corrêa
    Citation: BMC Genomics 2019 20:262
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:303

  48. The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to ident...

    Authors: Liang Wang, Yanbo Cheng, Qibin Ma, Yinghui Mu, Zhifeng Huang, Qiuju Xia, Gengyun Zhang and Hai Nian
    Citation: BMC Genomics 2019 20:260
    Content type: Research article Published on:

  49. RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The ...

    Authors: Alberto Berral-Gonzalez, Angela L. Riffo-Campos and Guillermo Ayala
    Citation: BMC Genomics 2019 20:259
    Content type: Methodology article Published on:

  50. Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cow fertility has received much attention in the last decade, while bull fertility has been largely overlooked. The...

    Authors: Juan Pablo Nani, Fernanda M. Rezende and Francisco Peñagaricano
    Citation: BMC Genomics 2019 20:258
    Content type: Research article Published on:

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BMC Genomics

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