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  1. Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe rust resistance genes and cultivation of resistant cultiv...

    Authors: Yuqi Wang, Can Yu, Yukun Cheng, Fangjie Yao, Li Long, Yu Wu, Jing Li, Hao Li, Jirui Wang, Qiantao Jiang, Wei Li, Zhien Pu, Pengfei Qi, Jian Ma, Mei Deng, Yuming Wei…

    Citation: BMC Genomics 2021 22:34

    Content type: Research article

    Published on:

  2. Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resol...

    Authors: Sonia Rey, Xingkun Jin, Børge Damsgård, Marie-Laure Bégout and Simon Mackenzie

    Citation: BMC Genomics 2021 22:33

    Content type: Research article

    Published on:

  3. Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the impor...

    Authors: Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulin and Petri Auvinen

    Citation: BMC Genomics 2021 22:28

    Content type: Research article

    Published on:

  4. Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progress...

    Authors: Yao Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu and Haiyun Wang

    Citation: BMC Genomics 2021 22:27

    Content type: Research article

    Published on:

  5. Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect...

    Authors: Peng Xu, Qi Guo, Shan Meng, Xianggui Zhang, Zhenzhen Xu, Wangzhen Guo and Xinlian Shen

    Citation: BMC Genomics 2021 22:26

    Content type: Research article

    Published on:

  6. Olfactory systems take on important tasks to distinguish salient information from a complex olfactory environment, such as locating hosts, mating, aggression, selecting oviposition sites, and avoiding predator...

    Authors: Li Xu, Kai-Yue Tang, Xiao-Feng Chen, Yong Tao, Hong-Bo Jiang and Jin-Jun Wang

    Citation: BMC Genomics 2021 22:25

    Content type: Research article

    Published on:

  7. Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 ...

    Authors: Juanjuan Feng, Xuexian Zhang, Meng Zhang, Liping Guo, Tingxiang Qi, Huini Tang, Haiyong Zhu, Hailin Wang, Xiuqin Qiao, Chaozhu Xing and Jianyong Wu

    Citation: BMC Genomics 2021 22:24

    Content type: Research article

    Published on:

  8. Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heteroch...

    Authors: Stéphane Deschamps, John A. Crow, Nadia Chaidir, Brooke Peterson-Burch, Sunil Kumar, Haining Lin, Gina Zastrow-Hayes and Gregory D. May

    Citation: BMC Genomics 2021 22:23

    Content type: Research article

    Published on:

  9. The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 G...

    Authors: Jiseong Jeong, Sunhee Park, Jeong Hui Im and Hankuil Yi

    Citation: BMC Genomics 2021 22:22

    Content type: Research article

    Published on:

  10. Cadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfi...

    Authors: Hongrui Lv, Jing Xu, Tao Bo and Wei Wang

    Citation: BMC Genomics 2021 22:21

    Content type: Research article

    Published on:

  11. Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety...

    Authors: Admas Alemu, Tileye Feyissa, Marco Maccaferri, Giuseppe Sciara, Roberto Tuberosa, Karim Ammar, Ayele Badebo, Maricelis Acevedo, Tesfaye Letta and Bekele Abeyo

    Citation: BMC Genomics 2021 22:20

    Content type: Research article

    Published on:

  12. Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed mode...

    Authors: Osval Antonio Montesinos-López, Abelardo Montesinos-López, Paulino Pérez-Rodríguez, José Alberto Barrón-López, Johannes W. R. Martini, Silvia Berenice Fajardo-Flores, Laura S. Gaytan-Lugo, Pedro C. Santana-Mancilla and José Crossa

    Citation: BMC Genomics 2021 22:19

    Content type: Review

    Published on:

  13. The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). Howeve...

    Authors: Nancy Dong, Julia Bandura, Zhaolei Zhang, Yan Wang, Karine Labadie, Benjamin Noel, Angus Davison, Joris M. Koene, Hong-Shuo Sun, Marie-Agnès Coutellec and Zhong-Ping Feng

    Citation: BMC Genomics 2021 22:18

    Content type: Research article

    Published on:

  14. Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences b...

    Authors: Ricardo Nilo-Poyanco, Carol Moraga, Gianfranco Benedetto, Ariel Orellana and Andrea Miyasaka Almeida

    Citation: BMC Genomics 2021 22:17

    Content type: Research article

    Published on:

  15. Asarum heterotropides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. is an important medicinal and industrial plant, which is used in the treatment of various diseases. The main bioactive ingredient is the volatil...

    Authors: Zhiqing Wang, Haiqin Ma, Min Zhang, Ziqing Wang, Yixin Tian, Wei Li and Yingping Wang

    Citation: BMC Genomics 2021 22:16

    Content type: Research article

    Published on:

  16. Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease ...

    Authors: Shan Feng, Hongcheng Fang, Xia Liu, Yuhui Dong, Qingpeng Wang and Ke Qiang Yang

    Citation: BMC Genomics 2021 22:15

    Content type: Research article

    Published on:

  17. Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of...

    Authors: Dayle Johnston, JaeWoo Kim, Jeremy F. Taylor, Bernadette Earley, Matthew S. McCabe, Ken Lemon, Catherine Duffy, Michael McMenamy, S. Louise Cosby and Sinéad M. Waters

    Citation: BMC Genomics 2021 22:14

    Content type: Research article

    Published on:

  18. Actinidia eriantha is a precious material to study the metabolism and regulation of ascorbic acid (AsA) because of its high AsA content. Although the pathway of AsA biosynthesis in kiwifruit has been identified, ...

    Authors: Guanglian Liao, Lu Chen, Yanqun He, Xishi Li, Zhengxin Lv, Shuyao Yi, Min Zhong, Chunhui Huang, Dongfeng Jia, Xueyan Qu and Xiaobiao Xu

    Citation: BMC Genomics 2021 22:13

    Content type: Research article

    Published on:

  19. Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome...

    Authors: Shenping Zhou, Rongrong Ding, Fanming Meng, Xingwang Wang, Zhanwei Zhuang, Jianping Quan, Qian Geng, Jie Wu, Enqin Zheng, Zhenfang Wu, Jianhui Yang and Jie Yang

    Citation: BMC Genomics 2021 22:12

    Content type: Research article

    Published on:

  20. The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [al...

    Authors: Mingqun Lin, Qingming Xiong, Matthew Chung, Sean C. Daugherty, Sushma Nagaraj, Naomi Sengamalay, Sandra Ott, Al Godinez, Luke J. Tallon, Lisa Sadzewicz, Claire Fraser, Julie C. Dunning Hotopp and Yasuko Rikihisa

    Citation: BMC Genomics 2021 22:11

    Content type: Research article

    Published on:

  23. DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Here...

    Authors: Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng and Jie Wen

    Citation: BMC Genomics 2021 22:8

    Content type: Research article

    Published on:

  24. Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This st...

    Authors: E. F. Dzomba, M. Chimonyo, R. Pierneef and F. C. Muchadeyi

    Citation: BMC Genomics 2021 22:7

    Content type: Research article

    Published on:

  25. DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epi...

    Authors: Victor Yuan, Desmond Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain and Wendy P. Robinson

    Citation: BMC Genomics 2021 22:6

    Content type: Research article

    Published on:

  26. Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complex...

    Authors: Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac Neuhaus, Alice M. Walsh and Zachary W. Pitluk

    Citation: BMC Genomics 2021 22:5

    Content type: Database

    Published on:

  27. Long noncoding RNAs (lncRNAs) have emerged as an important class of transcriptional regulators in cellular processes. The past decades have witnessed great progress in lncRNA studies in a variety of organisms....

    Authors: Longsheng Xing, Yu Xi, Xi Qiao, Cong Huang, Qiang Wu, Nianwan Yang, Jianyang Guo, Wanxue Liu, Wei Fan, Fanghao Wan and Wanqiang Qian

    Citation: BMC Genomics 2021 22:4

    Content type: Research article

    Published on:

  28. Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the imp...

    Authors: Christine Drengenes, Tomas M. L. Eagan, Ingvild Haaland, Harald G. Wiker and Rune Nielsen

    Citation: BMC Genomics 2021 22:3

    Content type: Research article

    Published on:

  29. Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of ...

    Authors: Shamseldeen Eltaher, P. Stephen Baenziger, Vikas Belamkar, Hamdy A. Emara, Ahmed A. Nower, Khaled F. M. Salem, Ahmad M. Alqudah and Ahmed Sallam

    Citation: BMC Genomics 2021 22:2

    Content type: Research article

    Published on:

  30. Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examina...

    Authors: Marina Braun, Annika Lehmbecker, Deborah Eikelberg, Maren Hellige, Andreas Beineke, Julia Metzger and Ottmar Distl

    Citation: BMC Genomics 2021 22:1

    Content type: Research article

    Published on:

  32. Genome-wide association studies (GWAS) have identified many individual genes associated with brain imaging quantitative traits (QTs) in Alzheimer’s disease (AD). However single marker level association discove...

    Authors: Xianglian Meng, Jin Li, Qiushi Zhang, Feng Chen, Chenyuan Bian, Xiaohui Yao, Jingwen Yan, Zhe Xu, Shannon L. Risacher, Andrew J. Saykin, Hong Liang and Li Shen

    Citation: BMC Genomics 2020 21(Suppl 11):896

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  34. Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular metho...

    Authors: Haicang Zhang and Yufeng Shen

    Citation: BMC Genomics 2020 21(Suppl 11):878

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  35. Abnormal metabolic pathways have been considered as one of the hallmarks of cancer. While numerous metabolic pathways have been studied in various cancers, the direct link between metabolic pathway gene expres...

    Authors: Dan Zhang, Yan Guo and Ni Xie

    Citation: BMC Genomics 2020 21(Suppl 11):860

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  36. Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of ...

    Authors: Shouguo Gao, Zhijie Wu, Xingmin Feng, Sachiko Kajigaya, Xujing Wang and Neal S. Young

    Citation: BMC Genomics 2020 21(Suppl 11):849

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  37. In this introduction article, we summarize the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference which was held on August 9–10, 2020 (virtual conference). We then briefl...

    Authors: Wei Zhang, Zhongming Zhao, Kai Wang, Li Shen and Xinghua Shi

    Citation: BMC Genomics 2020 21(Suppl 11):831

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  38. Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at i...

    Authors: Adam Cornish, Shrabasti Roychoudhury, Krishna Sarma, Suravi Pramanik, Kishor Bhakat, Andrew Dudley, Nitish K. Mishra and Chittibabu Guda

    Citation: BMC Genomics 2020 21(Suppl 11):830

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  39. RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions. Gene expression is regulated ...

    Authors: Yingying Cao, Simo Kitanovski and Daniel Hoffmann

    Citation: BMC Genomics 2020 21(Suppl 11):802

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  40. Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that ...

    Authors: Qian Liu, Yu Hu, Andres Stucky, Li Fang, Jiang F. Zhong and Kai Wang

    Citation: BMC Genomics 2020 21(Suppl 11):793

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  41. Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is ...

    Authors: Johannes Balkenhol, Kristin V. Kaltdorf, Elmina Mammadova-Bach, Attila Braun, Bernhard Nieswandt, Marcus Dittrich and Thomas Dandekar

    Citation: BMC Genomics 2020 21:897

    Content type: Research article

    Published on:

  42. Third-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstre...

    Authors: Haowen Zhang, Chirag Jain and Srinivas Aluru

    Citation: BMC Genomics 2020 21(Suppl 6):889

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  43. Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to...

    Authors: Musfiqur Sazal, Kalai Mathee, Daniel Ruiz-Perez, Trevor Cickovski and Giri Narasimhan

    Citation: BMC Genomics 2020 21(Suppl 6):663

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  44. Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen...

    Authors: Chi-Ming Leung, Dinghua Li, Yan Xin, Wai-Chun Law, Yifan Zhang, Hing-Fung Ting, Ruibang Luo and Tak-Wah Lam

    Citation: BMC Genomics 2020 21(Suppl 6):500

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  45. Analysis of heterogeneous populations such as viral quasispecies is one of the most challenging bioinformatics problems. Although machine learning models are becoming to be widely employed for analysis of sequ...

    Authors: Sunitha Basodi, Pelin Icer Baykal, Alex Zelikovsky, Pavel Skums and Yi Pan

    Citation: BMC Genomics 2020 21(Suppl 6):405

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  46. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi and Bo Zheng

    Citation: BMC Genomics 2020 21:895

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:709

  48. Researchers discover LncRNA–miRNA regulatory paradigms modulate gene expression patterns and drive major cellular processes. Identification of lncRNA-miRNA interactions (LMIs) is critical to reveal the mechani...

    Authors: Chengshuai Zhao, Yang Qiu, Shuang Zhou, Shichao Liu, Wen Zhang and Yanqing Niu

    Citation: BMC Genomics 2020 21(Suppl 13):867

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  49. RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification ...

    Authors: Lei Deng, Youzhi Liu, Yechuan Shi, Wenhao Zhang, Chun Yang and Hui Liu

    Citation: BMC Genomics 2020 21(Suppl 13):866

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  50. Many transcripts have been generated due to the development of sequencing technologies, and lncRNA is an important type of transcript. Predicting lncRNAs from transcripts is a challenging and important task. T...

    Authors: Yanzhen Xu, Xiaohan Zhao, Shuai Liu and Wen Zhang

    Citation: BMC Genomics 2020 21(Suppl 13):865

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

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