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  1. A new class of regulatory elements called super-enhancers, comprised of multiple neighboring enhancers, have recently been reported to be the key transcriptional drivers of cellular, developmental, and disease...

    Authors: Yueh-Hua Tu, Hsueh-Fen Juan and Hsuan-Cheng Huang
    Citation: BMC Genomics 2021 22(Suppl 3):787
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  2. Eggshell is a bio-ceramic material comprising columnar calcite (CaCO3) crystals and organic proteinaceous matrix. The size, shape and orientation of the CaCO3 crystals influence the microstructural properties of ...

    Authors: Quanlin Li, Zhongyi Duan, Congjiao Sun, Jiangxia Zheng, Guiyun Xu and Ning Yang
    Citation: BMC Genomics 2021 22:786
    Content type: Research Published on:

  3. The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitu...

    Authors: Andrew Catanach, Mike Ruigrok, Deepa Bowatte, Marcus Davy, Roy Storey, Noémie Valenza-Troubat, Elena López-Girona, Elena Hilario, Matthew J. Wylie, David Chagné and Maren Wellenreuther
    Citation: BMC Genomics 2021 22:785
    Content type: Research Published on:

  4. The Myxococcales are well known for their predatory and developmental social processes, and for the molecular complexity of regulation of these processes. Many species within this order have unusually large ge...

    Authors: Anna L. McLoon, Max E. Boeck, Marc Bruckskotten, Alexander C. Keyel and Lotte Søgaard-Andersen
    Citation: BMC Genomics 2021 22:784
    Content type: Research Published on:

  5. Barnacles are sessile crustaceans that attach to underwater surfaces using barnacle cement proteins. Barnacles have a calcareous or chitinous membranous base, and their substratum varies from biotic (e.g. cora...

    Authors: Hsiu-Chin Lin, Yue Him Wong, Chia-Hsuan Sung and Benny Kwok Kan Chan
    Citation: BMC Genomics 2021 22:783
    Content type: Research Published on:

  6. Historically, geneticists have relied on genotyping arrays and imputation to study human genetic variation. However, an underrepresentation of diverse populations has resulted in arrays that poorly capture glo...

    Authors: Anne-Katrin Emde, Amanda Phipps-Green, Murray Cadzow, C. Scott Gallagher, Tanya J. Major, Marilyn E. Merriman, Ruth K. Topless, Riku Takei, Nicola Dalbeth, Rinki Murphy, Lisa K. Stamp, Janak de Zoysa, Philip L. Wilcox, Keolu Fox, Kaja A. Wasik, Tony R. Merriman…
    Citation: BMC Genomics 2021 22:666
    Content type: Research article Published on:

  7. Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally establis...

    Authors: Adriano Di Pasquale, Nicolas Radomski, Iolanda Mangone, Paolo Calistri, Alessio Lorusso and Cesare Cammà
    Citation: BMC Genomics 2021 22:782
    Content type: Research article Published on:

  8. Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understandi...

    Authors: Panpan Wang, Yong Mao, Yongquan Su and Jun Wang
    Citation: BMC Genomics 2021 22:781
    Content type: Research article Published on:

  9. The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental p...

    Authors: Lihe Liu, Rocío Amorín, Philipe Moriel, Nicolás DiLorenzo, Phillip A. Lancaster and Francisco Peñagaricano
    Citation: BMC Genomics 2021 22:780
    Content type: Research Published on:

  10. The molecular complexity of neural retina development remains poorly studied. Knowledge of retinal neurogenesis regulation sheds light on retinal degeneration therapy exploration. Therefore, we integrated the ...

    Authors: Gang Chen, Hong-Mei Qian, Jing Chen, Jie Wang, Ji-Tian Guan and Zai-Long Chi
    Citation: BMC Genomics 2021 22:779
    Content type: Research Published on:

  11. Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. Howev...

    Authors: Yu Fan, Dili Lai, Hao Yang, Guoxing Xue, Ailing He, Long Chen, Liang Feng, Jingjun Ruan, Dabing Xiang, Jun Yan and Jianping Cheng
    Citation: BMC Genomics 2021 22:778
    Content type: Research Published on:

  12. Viral vectors, including adenovirus (Ad) and modified vaccinia Ankara (MVA), have gained increasing attention as vaccine platforms in recent years due to their capacity to express antigens from a wide array of...

    Authors: Dylan Sheerin, Christina Dold, Daniel O’Connor, Andrew J. Pollard and Christine S. Rollier
    Citation: BMC Genomics 2021 22:777
    Content type: Research Published on:

  13. Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequentl...

    Authors: Neetu Goyal, Garima Bhatia, Naina Garewal, Anuradha Upadhyay and Kashmir Singh
    Citation: BMC Genomics 2021 22:776
    Content type: Research article Published on:

  14. The gut microbiome is a diverse network of bacteria which inhabit our digestive tract and is crucial for efficient cellular metabolism, nutrient absorption, and immune system development. Spinal cord injury (S...

    Authors: Adam Doelman, Seth Tigchelaar, Brian McConeghy, Sunita Sinha, Martin S. Keung, Neda Manouchehri, Megan Webster, Shera Fisk, Charlotte Morrison, Femke Streijger, Corey Nislow and Brian K. Kwon
    Citation: BMC Genomics 2021 22:775
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:879

  16. High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Her...

    Authors: Seema Yadav, Elizabeth M. Ross, Karen S. Aitken, Lee T. Hickey, Owen Powell, Xianming Wei, Kai P. Voss-Fels and Ben J. Hayes
    Citation: BMC Genomics 2021 22:773
    Content type: Research Published on:

  17. Histone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for maintaining chro...

    Authors: Bowei Chen, Shahid Ali, Xu Zhang, Yonglan Zhang, Min Wang, Qingzhu Zhang and Linan Xie
    Citation: BMC Genomics 2021 22:772
    Content type: Research Published on:

  18. Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the co...

    Authors: Yu Bai, Emmanuel Caussinus, Stefano Leo, Fritz Bosshardt, Faina Myachina, Gregor Rot, Mark D. Robinson and Christian F. Lehner
    Citation: BMC Genomics 2021 22:771
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:241

  19. Long non-coding RNAs (lncRNAs) are involved in several immune processes, including the immune response to vaccination, but most of them remain uncharacterised in livestock species. The mechanism of action of a...

    Authors: Martin Bilbao-Arribas, Endika Varela-Martínez, Naiara Abendaño, Damián de Andrés, Lluís Luján and Begoña M. Jugo
    Citation: BMC Genomics 2021 22:770
    Content type: Research Published on:

  20. There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting th...

    Authors: Jiazhong Guo, Rui Jiang, Ayi Mao, George E. Liu, Siyuan Zhan, Li Li, Tao Zhong, Linjie Wang, Jiaxue Cao, Yu Chen, Guojun Zhang and Hongping Zhang
    Citation: BMC Genomics 2021 22:769
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:117

  21. Colon cancer (CC) is one of the most common cancers whose progression is regulated by a number of factors, including circular RNAs (circRNAs). Nonetheless, circ_0038718 is a novel circRNA, and its regulatory m...

    Authors: Haitao Gu, Zhiquan Xu, Jianbo Zhang, Yanbing Wei, Ling Cheng and Jijian Wang
    Citation: BMC Genomics 2021 22:768
    Content type: Research Published on:

  22. SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiatio...

    Authors: Yanhui Liu, Mohammad Aslam, Li-Ang Yao, Man Zhang, Lulu Wang, Huihuang Chen, Youmei Huang, Yuan Qin and Xiaoping Niu
    Citation: BMC Genomics 2021 22:767
    Content type: Research Published on:

  23. The phytopatogen Claviceps paspali is the causal agent of Ergot disease in Paspalum spp., which includes highly productive forage grasses such as P. dilatatum. This disease impacts dairy and beef production by af...

    Authors: H. Oberti, G. Spangenberg, N. Cogan, R. Reyno, M. Feijoo, S. Murchio and M. Dalla-Rizza
    Citation: BMC Genomics 2021 22:766
    Content type: Research article Published on:

  25. miRNAs regulate circadian patterns by modulating the biological clocks of animals. In our previous study, we found that the clock gene exhibited a cosine expression pattern in the fallopian tube of chicken ute...

    Authors: Zhifu Cui, Zhichao Zhang, Felix Kwame Amevor, Xiaxia Du, Liang Li, Yaofu Tian, Xincheng Kang, Gang Shu, Qing Zhu, Yan Wang, Diyan Li, Yao Zhang and Xiaoling Zhao
    Citation: BMC Genomics 2021 22:764
    Content type: Research Published on:

  26. Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cry...

    Authors: Simin Chai, Xin Huang, Tianzhen Wu, Shixia Xu, Wenhua Ren and Guang Yang
    Citation: BMC Genomics 2021 22:763
    Content type: Research Published on:

  27. Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known ...

    Authors: Xiaomin Yan, Dan Bai, Hongtao Song, Kui Lin and Erli Pang
    Citation: BMC Genomics 2021 22:762
    Content type: Research Published on:

  28. Xyloglucan endotransglycosylase/hydrolases (XTH) can disrupt and reconnect the xyloglucan chains, modify the cellulose-xyloglucan complex structure in the cell wall to reconstruct the cell wall. Previous studi...

    Authors: Zichen Wu, Chuanlei Cui, Anqi Xing, Xiaohan Xu, Yi Sun, Zhiqiang Tian, Xuyan Li, Jiangyuan Zhu, Genmei Wang and Yuhua Wang
    Citation: BMC Genomics 2021 22:761
    Content type: Research Published on:

  29. Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a re...

    Authors: Nguyen Hoai Nguyen, Benny Jian Rong Sng, Hock Chuan Yeo and In-Cheol Jang
    Citation: BMC Genomics 2021 22:760
    Content type: Research Published on:

  30. Archival formalin-fixed, paraffin-embedded (FFPE) tissue samples with clinical and histological data are a singularly valuable resource for developing new molecular biomarkers. However, transcriptome analysis ...

    Authors: Jin Sung Jang, Eileen Holicky, Julie Lau, Samantha McDonough, Mark Mutawe, Matthew J. Koster, Kenneth J. Warrington and Julie M. Cuninngham
    Citation: BMC Genomics 2021 22:759
    Content type: Methodology article Published on:

  31. Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molec...

    Authors: Paola Lisotto, Erwin C. Raangs, Natacha Couto, Sigrid Rosema, Mariëtte Lokate, Xuewei Zhou, Alexander W. Friedrich, John W. A. Rossen, Hermie J. M. Harmsen, Erik Bathoorn and Monika A. Chlebowicz-Fliss
    Citation: BMC Genomics 2021 22:758
    Content type: Research Published on:

  32. The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understand...

    Authors: Pierce Rafter, Isobel Claire Gormley, Deirdre Purfield, Andrew C. Parnell, Saeid Naderi and Donagh P. Berry
    Citation: BMC Genomics 2021 22:757
    Content type: Research Published on:

  33. Much of the complex anatomy of a holometabolous insect is built from disc-shaped epithelial structures found inside the larva, i.e., the imaginal discs, which undergo a rapid differentiation during metamorphos...

    Authors: Michelle Prioli Miranda Soares, Daniel Guariz Pinheiro, Flávia Cristina de Paula Freitas, Zilá Luz Paulino Simões and Márcia Maria Gentile Bitondi
    Citation: BMC Genomics 2021 22:756
    Content type: Research Published on:

  34. Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Her...

    Authors: Mingsheng Yang, Junhao Li, Silin Su, Hongfei Zhang, Zhengbing Wang, Weili Ding and Lili Li
    Citation: BMC Genomics 2021 22:755
    Content type: Research Published on:

  35. Various epigenetic factors are responsible for the non-genetic regulation on gene expression. The epigenetically dysregulated oncogenes or tumor suppressors by miRNA and/or DNA methylation are often observed i...

    Authors: Manu Shivakumar, Seonggyun Han, Younghee Lee and Dokyoon Kim
    Citation: BMC Genomics 2021 22(Suppl 3):754
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  36. Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis, an important poultry disease whose significance is underlined by the absence of any treatment and prophylaxis. The recent su...

    Authors: Nicola Palmieri, Marcelo de Jesus Ramires, Michael Hess and Ivana Bilic
    Citation: BMC Genomics 2021 22:753
    Content type: Research article Published on:

  37. The outcome of cervical artificial insemination (AI) with frozen-thawed semen in sheep is limited by the inability of sperm to traverse the cervix of some ewe breeds. Previous research has demonstrated that ce...

    Authors: Laura Abril-Parreño, Kieran G. Meade, Anette Kristine Krogenæs, Xavier Druart, Sean Fair and Paul Cormican
    Citation: BMC Genomics 2021 22:752
    Content type: Research Published on:

  38. The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging...

    Authors: César Arenas-Mena, Sofija Miljovska, Edward J. Rice, Justin Gurges, Tanvi Shashikant, Zihe Wang, Sevinç Ercan and Charles G. Danko
    Citation: BMC Genomics 2021 22:751
    Content type: Research Published on:

  39. Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern He...

    Authors: Yu-He Zhao, Tong Zhou, Jiu-Xia Wang, Yan Li, Min-Feng Fang, Jian-Ni Liu and Zhong-Hu Li
    Citation: BMC Genomics 2021 22:750
    Content type: Research article Published on:

  40. Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, or an exocrine manner. The unique properties of the EVs protect the cargo...

    Authors: S. Shome, R. L. Jernigan, D. C. Beitz, S. Clark and E. D. Testroet
    Citation: BMC Genomics 2021 22:749
    Content type: Research Published on:

  41. In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress response...

    Authors: Shutao He, Xiaomeng Hao, Shuli He, Xiaoge Hao, Peng Zhang and Xiaonan Chen
    Citation: BMC Genomics 2021 22:748
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:139

  42. Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behavio...

    Authors: Dengying Liu, Zhenliang Chen, Wei Zhao, Longyu Guo, Hao Sun, Kai Zhu, Guanglei Liu, Xiuping Shen, Xiaoduo Zhao, Qishan Wang, Peipei Ma and Yuchun Pan
    Citation: BMC Genomics 2021 22:747
    Content type: Research Published on:

  43. Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information o...

    Authors: Shuya Liu, Yichao Wang, Qing Xu, Mengjia Zhang and Nansheng Chen
    Citation: BMC Genomics 2021 22:746
    Content type: Research Published on:

  45. Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these...

    Authors: Qianyun Ge, Yongbo Guo, Wangshan Zheng, Yuan Cai, Xuebin Qi and Shengguo Zhao
    Citation: BMC Genomics 2021 22:744
    Content type: Research article Published on:

  46. Fruit ripening is an intricate developmental process driven by a highly coordinated action of complex hormonal networks. Ethylene is considered as the main phytohormone that regulates the ripening of climacter...

    Authors: Zahra Iqbal, Mohammed Shariq Iqbal, Lalida Sangpong, Gholamreza Khaksar, Supaart Sirikantaramas and Teerapong Buaboocha
    Citation: BMC Genomics 2021 22:743
    Content type: Research Published on:

  47. Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including...

    Authors: Ana C. Ayupe, Felipe Beckedorff, Konstantin Levay, Benito Yon, Yadira Salgueiro, Ramin Shiekhattar and Kevin K. Park
    Citation: BMC Genomics 2021 22:741
    Content type: Research Published on:

  48. Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in euka...

    Authors: Changzi Yuan, Junxia Mao, Hongyan Sun, Yiying Wang, Ming Guo, Xubo Wang, Ying Tian, Zhenlin Hao, Jun Ding and Yaqing Chang
    Citation: BMC Genomics 2021 22:740
    Content type: Research Published on:

  49. Long non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. On...

    Authors: Shiye Sang, Wen Chen, Di Zhang, Xuan Zhang, Wenjing Yang and Changning Liu
    Citation: BMC Genomics 2021 22(Suppl 3):739
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  50. Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically...

    Authors: Kuiyin Li, Lili Duan, Yubo Zhang, Miaoxiao Shi, Songshu Chen, Mingfang Yang, Yanqing Ding, Yashu Peng, Yabing Dong, Hao Yang, Zhenhua Li, Liyi Zhang, Yu Fan and Mingjian Ren
    Citation: BMC Genomics 2021 22:738
    Content type: Research Published on:

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BMC Genomics

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