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  1. The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack...

    Authors: Araya Radtanakatikanon, Stefan M. Keller, Nikos Darzentas, Peter F. Moore, Géraldine Folch, Viviane Nguefack Ngoune, Marie-Paule Lefranc and William Vernau

    Citation: BMC Genomics 2020 21:20

    Content type: Research article

    Published on:

  2. Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Inte...

    Authors: Jouni Kvist, Camila Gonçalves Athanàsio, Michael E. Pfrender, James B. Brown, John K. Colbourne and Leda Mirbahai

    Citation: BMC Genomics 2020 21:17

    Content type: Research article

    Published on:

  3. The genus Borrelia comprises spirochaetal bacteria maintained in natural transmission cycles by tick vectors and vertebrate reservoir hosts. The main groups are represented by a species complex including the caus...

    Authors: Konstantin V. Kuleshov, Gabriele Margos, Volker Fingerle, Joris Koetsveld, Irina A. Goptar, Mikhail L. Markelov, Nadezhda M. Kolyasnikova, Denis S. Sarksyan, Nina P. Kirdyashkina, German A. Shipulin, Joppe W. Hovius and Alexander E. Platonov

    Citation: BMC Genomics 2020 21:16

    Content type: Research article

    Published on:

  4. Cotton grows in altering environments that are often unfavorable or stressful for its growth and development. Consequently, the plant must cope with abiotic stresses such as soil salinity, drought, and excessi...

    Authors: Yanchao Xu, Richard Odongo Magwanga, Xiu Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Zhongli Zhou, Kunbo Wang and Fang Liu

    Citation: BMC Genomics 2020 21:15

    Content type: Research article

    Published on:

  5. Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, how...

    Authors: Adam Kawalek, Karolina Kotecka, Magdalena Modrzejewska, Jan Gawor, Grazyna Jagura-Burdzy and Aneta Agnieszka Bartosik

    Citation: BMC Genomics 2020 21:14

    Content type: Research article

    Published on:

  6. Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has n...

    Authors: Qi Yang, Xiaocui Niu, Xiaona Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang and Guojing Li

    Citation: BMC Genomics 2020 21:12

    Content type: Research article

    Published on:

  7. Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future enviro...

    Authors: Le Qin Choo, Thijs M. P. Bal, Marvin Choquet, Irina Smolina, Paula Ramos-Silva, Ferdinand Marlétaz, Martina Kopp, Galice Hoarau and Katja T. C. A. Peijnenburg

    Citation: BMC Genomics 2020 21:11

    Content type: Research article

    Published on:

  8. In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, e...

    Authors: Glenn T. Howe, Keith Jayawickrama, Scott E. Kolpak, Jennifer Kling, Matt Trappe, Valerie Hipkins, Terrance Ye, Stephanie Guida, Richard Cronn, Samuel A. Cushman and Susan McEvoy

    Citation: BMC Genomics 2020 21:9

    Content type: Research article

    Published on:

  9. Pineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological ...

    Authors: Xiaodan Zhang, Mahpara Fatima, Ping Zhou, Qing Ma and Ray Ming

    Citation: BMC Genomics 2020 21:8

    Content type: Research article

    Published on:

  10. The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulen...

    Authors: Carolyn Graham-Taylor, Lars G. Kamphuis and Mark C. Derbyshire

    Citation: BMC Genomics 2020 21:7

    Content type: Research article

    Published on:

  11. Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not alway...

    Authors: Everlyn Kamau, John W. Oketch, Zaydah R. de Laurent, My V. T. Phan, Charles N. Agoti, D. James Nokes and Matthew Cotten

    Citation: BMC Genomics 2020 21:5

    Content type: Methodology article

    Published on:

  12. Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system fo...

    Authors: Yukun Chen, Xiaoping Xu, Zhuanxia Liu, Zihao Zhang, Xu XuHan, Yuling Lin and Zhongxion Lai

    Citation: BMC Genomics 2020 21:4

    Content type: Research article

    Published on:

  13. Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of...

    Authors: Joni Frederick, Fritha Hennessy, Uli Horn, Pilar de la Torre Cortés, Marcel van den Broek, Ulrich Strych, Richard Willson, Charles A. Hefer, Jean-Marc G. Daran, Trevor Sewell, Linda G. Otten and Dean Brady

    Citation: BMC Genomics 2020 21:3

    Content type: Research article

    Published on:

  14. The clinical success of immune checkpoint inhibitors demonstrates that reactivation of the human immune system delivers durable responses for some patients and represents an exciting approach for cancer treatm...

    Authors: Wenyan Zhong, Jeremy S. Myers, Fang Wang, Kai Wang, Justin Lucas, Edward Rosfjord, Judy Lucas, Andrea T. Hooper, Sharon Yang, Lu Anna Lemon, Magali Guffroy, Chad May, Jadwiga R. Bienkowska and Paul A. Rejto

    Citation: BMC Genomics 2020 21:2

    Content type: Research article

    Published on:

  15. Following the publication of the original article [1], the authors reported an error in Fig. 2 of the PDF version of their article.

    Authors: Jason D. Maarsingh, Shanshan Yang, Jin G. Park and Shelley E. Haydel

    Citation: BMC Genomics 2019 21:1

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2019 20:942

  16. Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequ...

    Authors: Kelsi A. Lindblad, Jananan S. Pathmanathan, Sandrine Moreira, John R. Bracht, Robert P. Sebra, Elizabeth R. Hutton and Laura F. Landweber

    Citation: BMC Genomics 2019 20:1037

    Content type: Research article

    Published on:

  17. Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are kn...

    Authors: Sivasubramanian Rajarammohan, Kumar Paritosh, Deepak Pental and Jagreet Kaur

    Citation: BMC Genomics 2019 20:1036

    Content type: Research article

    Published on:

  18. Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing ...

    Authors: Ying Li, Chunxia Zhang, Kebin Yang, Jingjing Shi, Yulong Ding and Zhimin Gao

    Citation: BMC Genomics 2019 20:1035

    Content type: Research article

    Published on:

  19. Grape buds exhibit non-uniform, or delayed, break in early spring in subtropical regions because the accumulation of chilling is insufficient. Hydrogen cyanamide (H2CN2, HC) can partially replace chilling to effe...

    Authors: Dong Liang, Xiaojing Huang, Yanqiu Shen, Tian Shen, Huifen Zhang, Lijin Lin, Jin Wang, Qunxian Deng, Xiulan Lyu and Hui Xia

    Citation: BMC Genomics 2019 20:1034

    Content type: Research article

    Published on:

  20. Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to bette...

    Authors: F. Jehl, C. Désert, C. Klopp, M. Brenet, A. Rau, S. Leroux, M. Boutin, L. Lagoutte, K. Muret, Y. Blum, D. Esquerré, D. Gourichon, T. Burlot, A. Collin, F. Pitel, A. Benani…

    Citation: BMC Genomics 2019 20:1033

    Content type: Research article

    Published on:

  21. MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the ...

    Authors: Jian-fang Bai, Yu-kun Wang, Li-ping Guo, Xiao-ming Guo, Hao-yu Guo, Shao-hua Yuan, Wen-jing Duan, Zihan Liu, Chang-ping Zhao, Feng-ting Zhang and Li-ping Zhang

    Citation: BMC Genomics 2019 20:1032

    Content type: Research article

    Published on:

  22. The proximal femoral head separation (FHS) or epiphysiolysis is a prevalent disorder affecting the chicken femur epiphysis, being considered a risk factor to infection which can cause bacterial chondronecrosis...

    Authors: Jane de Oliveira Peixoto, Igor Ricardo Savoldi, Adriana Mércia Guaratini Ibelli, Maurício Egídio Cantão, Fátima Regina Ferreira Jaenisch, Poliana Fernanda Giachetto, Matthew Lee Settles, Ricardo Zanella, Jorge Augusto Petroli Marchesi, José Rodrigo Pandolfi, Luiz Lehmann Coutinho and Mônica Corrêa Ledur

    Citation: BMC Genomics 2019 20:1031

    Content type: Research article

    Published on:

  23. Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre...

    Authors: Taiana T. Silva-Pereira, Cássia Y. Ikuta, Cristina K. Zimpel, Naila C. S. Camargo, Antônio F. de Souza Filho, José S. Ferreira Neto, Marcos B. Heinemann and Ana M. S. Guimarães

    Citation: BMC Genomics 2019 20:1030

    Content type: Research article

    Published on:

  24. Behavior reflects an organism’s health status. Many organisms display a generalized suite of behaviors that indicate infection or predict infection susceptibility. We apply this concept to honey bee aggression...

    Authors: Clare C. Rittschof, Benjamin E. R. Rubin and Joseph H. Palmer

    Citation: BMC Genomics 2019 20:1029

    Content type: Research article

    Published on:

  25. The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we perfor...

    Authors: Nirupama Benis, Jerry M. Wells, Mari A. Smits, Soumya Kanti Kar, Bart van der Hee, Vitor A. P. Martins dos Santos, Maria Suarez-Diez and Dirkjan Schokker

    Citation: BMC Genomics 2019 20:1028

    Content type: Research article

    Published on:

  26. Europeans and American Indians were major genetic ancestry of Hispanics in the U.S. These ancestral groups have markedly different incidence rates and outcomes in many types of cancers. Therefore, the genetic ...

    Authors: Li-Ju Wang, Catherine W. Zhang, Sophia C. Su, Hung-I H. Chen, Yu-Chiao Chiu, Zhao Lai, Hakim Bouamar, Amelie G. Ramirez, Francisco G. Cigarroa, Lu-Zhe Sun and Yidong Chen

    Citation: BMC Genomics 2019 20(Suppl 12):1007

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  27. The genome architecture mapping (GAM) technique can capture genome-wide chromatin interactions. However, besides the known systematic biases in the raw GAM data, we have found a new type of systematic bias. It...

    Authors: Tong Liu and Zheng Wang

    Citation: BMC Genomics 2019 20(Suppl 12):1006

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  28. The goal of this editorial is to summarize the 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) conference that took place on June 9–11, 2019 in The Ohio State University, Columbu...

    Authors: Ewy Mathé, Chi Zhang, Kai Wang, Xia Ning, Yan Guo and Zhongming Zhao

    Citation: BMC Genomics 2019 20(Suppl 12):1005

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  29. RNA-binding proteins (RBPs) are crucial in modulating RNA metabolism in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Although previous studies on the conservation of RBP targets...

    Authors: Aarthi Ramakrishnan and Sarath Chandra Janga

    Citation: BMC Genomics 2019 20(Suppl 12):1004

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  30. The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the...

    Authors: Nam D. Nguyen, Ian K. Blaby and Daifeng Wang

    Citation: BMC Genomics 2019 20(Suppl 12):1003

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  31. Bacterial cells during many replication cycles accumulate spontaneous mutations, which result in the birth of novel clones. As a result of this clonal expansion, an evolving bacterial population has different clo...

    Authors: Wazim Mohammed Ismail and Haixu Tang

    Citation: BMC Genomics 2019 20(Suppl 12):1002

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  32. Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well char...

    Authors: Maximillian Westphal, David Frankhouser, Carmine Sonzone, Peter G. Shields, Pearlly Yan and Ralf Bundschuh

    Citation: BMC Genomics 2019 20(Suppl 12):1001

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  33. The rapid development of Next-Generation Sequencing technologies enables sequencing genomes with low cost. The dramatically increasing amount of sequencing data raised crucial needs for efficient compression a...

    Authors: Tao Tang, Yuansheng Liu, Buzhong Zhang, Benyue Su and Jinyan Li

    Citation: BMC Genomics 2019 20(Suppl 10):978

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  34. Pseudouridine modification is most commonly found among various kinds of RNA modification occurred in both prokaryotes and eukaryotes. This biochemical event has been proved to occur in multiple types of RNAs,...

    Authors: Thanh-Hoang Nguyen-Vo, Quang H. Nguyen, Trang T.T. Do, Thien-Ngan Nguyen, Susanto Rahardja and Binh P. Nguyen

    Citation: BMC Genomics 2019 20(Suppl 10):971

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  35. Read alignment and transcript assembly are the core of RNA-seq analysis for transcript isoform discovery. Nonetheless, current tools are not designed to be scalable for analysis of full-length bulk or single c...

    Authors: Andrian Yang, Abhinav Kishore, Benjamin Phipps and Joshua W. K. Ho

    Citation: BMC Genomics 2019 20(Suppl 10):927

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  36. Identification of antibiotic resistance genes from environmental samples has been a critical sub-domain of gene discovery which is directly connected to human health. However, it is drawing extraordinary atten...

    Authors: Haobin Yao and Siu-Ming Yiu

    Citation: BMC Genomics 2019 20(Suppl 10):914

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  37. Super-enhancer RNAs (seRNAs) are a kind of noncoding RNA transcribed from super-enhancer regions. The regulation mechanism and functional role of seRNAs are still unclear. Although super-enhancers play a criti...

    Authors: Hao-Chun Chang, Hsuan-Cheng Huang, Hsueh-Fen Juan and Chia-Lang Hsu

    Citation: BMC Genomics 2019 20(Suppl 10):896

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  38. Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can ...

    Authors: Lea Mikkola, Saila Holopainen, Tiina Pessa-Morikawa, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2019 20:1027

    Content type: Research article

    Published on:

  39. Non-key traits (NKTs) in radiata pine (Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external...

    Authors: Yongjun Li, Jaroslav Klápště, Emily Telfer, Phillip Wilcox, Natalie Graham, Lucy Macdonald and Heidi S. Dungey

    Citation: BMC Genomics 2019 20:1026

    Content type: Research article

    Published on:

  40. Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still...

    Authors: Shenghui Zhou, Jinpeng Zhang, Haiming Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li and Lihui Li

    Citation: BMC Genomics 2019 20:1025

    Content type: Research article

    Published on:

  41. Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic ana...

    Authors: Christopher J. Troll, Joshua Kapp, Varsha Rao, Kelly M. Harkins, Charles Cole, Colin Naughton, Jessica M. Morgan, Beth Shapiro and Richard E. Green

    Citation: BMC Genomics 2019 20:1023

    Content type: Methodology article

    Published on:

  42. In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant “priority pathogens” that are posing the greatest threats to human health. Six of these dreaded pathogens a...

    Authors: Tungadri Bose, K. V. Venkatesh and Sharmila S. Mande

    Citation: BMC Genomics 2019 20:1022

    Content type: Research article

    Published on:

  43. The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectur...

    Authors: Wei Gan, Juan Luo, Yi Zhou Li, Jia Li Guo, Min Zhu and Meng Long Li

    Citation: BMC Genomics 2019 20(Suppl 13):980

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  44. Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the develop...

    Authors: Jinho Im, Byungkyu Park and Kyungsook Han

    Citation: BMC Genomics 2019 20(Suppl 13):967

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  45. Proteins play essential roles in almost all life processes. The prediction of protein function is of significance for the understanding of molecular function and evolution. Network alignment provides a fast an...

    Authors: Jialu Hu, Junhao He, Jing Li, Yiqun Gao, Yan Zheng and Xuequn Shang

    Citation: BMC Genomics 2019 20(Suppl 13):932

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  46. To infer gene regulatory networks (GRNs) from gene-expression data is still a fundamental and challenging problem in systems biology. Several existing algorithms formulate GRNs inference as a regression proble...

    Authors: Xiang Chen, Min Li, Ruiqing Zheng, Fang-Xiang Wu and Jianxin Wang

    Citation: BMC Genomics 2019 20(Suppl 13):929

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  47. Identification of protein-protein interactions (PPIs) is crucial for understanding biological processes and investigating the cellular functions of genes. Self-interacting proteins (SIPs) are those in which mo...

    Authors: Zhan-Heng Chen, Zhu-Hong You, Li-Ping Li, Yan-Bin Wang, Yu Qiu and Peng-Wei Hu

    Citation: BMC Genomics 2019 20(Suppl 13):928

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

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