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  1. Content type: Research

    Glyoxalase pathway is a reactive carbonyl species (RCS) scavenging mechanism involved in the detoxification of methylglyoxal (MG), which is a reactive α-ketoaldehyde. In plants under abiotic stress, the cellul...

    Authors: Vadakkancherry Mohanan Manoj, Pushpanathan Anunanthini, Peter Clarancia Swathik, Selvarajan Dharshini, Jayanarayanan Ashwin Narayan, Markandan Manickavasagam, Ramalingam Sathishkumar, Giriyapura Shivalingamurthy Suresha, Govind Hemaprabha, Bakshi Ram and Chinnaswamy Appunu

    Citation: BMC Genomics 2019 19(Suppl 9):986

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  2. Content type: Database

    Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as comm...

    Authors: Rajesh Kumar, Gandharva Nagpal, Vinod Kumar, Salman Sadullah Usmani, Piyush Agrawal and Gajendra P. S. Raghava

    Citation: BMC Genomics 2019 19(Suppl 9):985

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  3. Content type: Research

    Post-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis. In the recent times, there has been many reported P...

    Authors: Abel Avitesh Chandra, Alok Sharma, Abdollah Dehzangi and Tatushiko Tsunoda

    Citation: BMC Genomics 2019 19(Suppl 9):984

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  4. Content type: Research

    MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and...

    Authors: Junqiang Guo, Qingyi Wang, Li Liu, Shuchao Ren, Shipeng Li, Peiran Liao, Zhigang Zhao, Chenyu Lu, Bingbing Jiang, Ramanjulu Sunkar and Yun Zheng

    Citation: BMC Genomics 2019 19(Suppl 9):983

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  5. Content type: Research

    Post-translational modifications are viewed as an important mechanism for controlling protein function and are believed to be involved in multiple important diseases. However, their profiling using laboratory-...

    Authors: Alok Sharma, Artem Lysenko, Yosvany López, Abdollah Dehzangi, Ronesh Sharma, Hamendra Reddy, Abdul Sattar and Tatsuhiko Tsunoda

    Citation: BMC Genomics 2019 19(Suppl 9):982

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  6. Content type: Correction

    .

    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 20:303

    Published on:

    The original article was published in BMC Genomics 2019 20:262

  7. Content type: Research article

    Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation b...

    Authors: Marie Pégard, Odile Rogier, Aurélie Bérard, Patricia Faivre-Rampant, Marie-Christine Le Paslier, Catherine Bastien, Véronique Jorge and Leopoldo Sánchez

    Citation: BMC Genomics 2019 20:302

    Published on:

  8. Content type: Introduction

    InCoB, one of the largest annual bioinformatics conferences in the Asia-Pacific region since its launch in 2002, returned to New Delhi, India after 12 years, with a conference attendance of 314 delegates. The ...

    Authors: Shandar Ahmad, Michael M. Gromiha, Gajendra P. S. Raghava, Christian Schönbach and Shoba Ranganathan

    Citation: BMC Genomics 2019 19(Suppl 9):266

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  9. Content type: Research

    With the rapid increase in genome sequencing projects for non-model organisms, numerous genome assemblies are currently in progress or available as drafts, but not made available as satisfactory, usable genome...

    Authors: Li-An Yang, Yu-Jung Chang, Shu-Hwa Chen, Chung-Yen Lin and Jan-Ming Ho

    Citation: BMC Genomics 2019 19(Suppl 9):238

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

    Published on:

  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Research article

    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

    Published on:

  16. Content type: Research article

    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

    Published on:

  17. Content type: Research article

    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

    Published on:

  18. Content type: Methodology article

    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

    Published on:

  19. Content type: Research article

    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

    Published on:

  20. Content type: Research article

    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

    Published on:

  21. Content type: Research article

    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

    Published on:

  22. Content type: Research article

    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

    Published on:

  23. Content type: Research article

    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

    Published on:

  24. Content type: Correction

    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

    Published on:

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

  25. Content type: Research article

    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

    Published on:

  26. Content type: Research article

    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

    Published on:

  27. Content type: Research article

    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

    Published on:

  28. Content type: Research article

    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

    Published on:

  29. Content type: Research article

    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

    Published on:

  30. Content type: Research article

    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

    Published on:

  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Research article

    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

    Published on:

  34. Content type: Research

    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

    Published on:

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

  35. Content type: Research

    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

    Published on:

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

  36. Content type: Research

    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

    Published on:

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

  37. Content type: Research

    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

    Published on:

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

  38. Content type: Research

    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

    Published on:

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

  39. Content type: Research

    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

    Published on:

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

  40. Content type: Research

    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

    Published on:

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

  41. Content type: Research

    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

    Published on:

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

  42. Content type: Research

    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

    Published on:

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

  43. Content type: Research

    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

    Published on:

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

  44. Content type: Research

    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

    Published on:

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

  45. Content type: Research

    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

    Published on:

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

  46. Content type: Research

    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

    Published on:

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

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