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  1. Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription. It is critical to locate these TF-DNA interactions to understand transcriptional re...

    Authors: Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon and Anthony Mathelier

    Citation: BMC Genomics 2021 22:482

    Content type: Research

    Published on:

  2. Low conception rate (CR) despite insemination with morphologically normal spermatozoa is a common reproductive restraint that limits buffalo productivity. This accounts for a significant loss to the farmers an...

    Authors: Vipul Batra, Vanya Bhushan, Syed Azmal Ali, Parul Sarwalia, Ankit Pal, Seema Karanwal, Subhash Solanki, Arumugam Kumaresan, Rakesh Kumar and Tirtha Kumar Datta

    Citation: BMC Genomics 2021 22:480

    Content type: Research

    Published on:

  3. Identifying differentially expressed genes between the same or different species is an urgent demand for biological and medical research. For RNA-seq data, systematic technical effects and different sequencing...

    Authors: Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu and Guoliang Tian

    Citation: BMC Genomics 2021 22:479

    Content type: Methodology article

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  4. Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant ...

    Authors: Gehendra Bhattarai, Wei Yang, Ainong Shi, Chunda Feng, Braham Dhillon, James C. Correll and Beiquan Mou

    Citation: BMC Genomics 2021 22:478

    Content type: Research article

    Published on:

  5. Glaucoma is a leading cause of visual disability and blindness. Release of iris pigment within the eye, pigment dispersion syndrome (PDS), can lead to one type of glaucoma known as pigmentary glaucoma. PDS has...

    Authors: Carly van der Heide, Wes Goar, Kacie J. Meyer, Wallace L. M. Alward, Erin A. Boese, Nathan C. Sears, Ben R. Roos, Young H. Kwon, Adam P. DeLuca, Owen M. Siggs, Claudia Gonzaga-Jauregui, Val C. Sheffield, Kai Wang, Edwin M. Stone, Robert F. Mullins, Michael G. Anderson…

    Citation: BMC Genomics 2021 22:477

    Content type: Research

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  6. The sequence content of the 3′ UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging.

    Authors: Raeann Goering, Krysta L. Engel, Austin E. Gillen, Nova Fong, David L. Bentley and J. Matthew Taliaferro

    Citation: BMC Genomics 2021 22:476

    Content type: Methodology article

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  7. Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction...

    Authors: Valentine Murigneux, Leah W. Roberts, Brian M. Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D. Irwin, Patrick N. A. Harris, David L. Paterson, Mark A. Schembri, David M. Whiley and Scott A. Beatson

    Citation: BMC Genomics 2021 22:474

    Content type: Software

    Published on:

  8. Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. Howeve...

    Authors: Jenni Harmoinen, Alina von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo K. Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho…

    Citation: BMC Genomics 2021 22:473

    Content type: Research article

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  9. Ventilator-induced diaphragmatic dysfunction (VIDD) is associated with weaning difficulties, intensive care unit hospitalization (ICU), infant mortality, and poor long-term clinical outcomes. The expression pa...

    Authors: Ruining Liu, Gang Li, Haoli Ma, Xianlong Zhou, Pengcheng Wang and Yan Zhao

    Citation: BMC Genomics 2021 22:472

    Content type: Research article

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  10. The identification of differentially expressed genes (DEGs) is an important task in many biological studies. The currently widely used methods often calculate a score for each gene by estimating the significan...

    Authors: Bolin Chen, Li Gao and Xuequn Shang

    Citation: BMC Genomics 2021 22(Suppl 1):471

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 1

  11. Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially t...

    Authors: Maria Buerstmayr, Christian Wagner, Tetyana Nosenko, Jimmy Omony, Barbara Steiner, Thomas Nussbaumer, Klaus F. X. Mayer and Hermann Buerstmayr

    Citation: BMC Genomics 2021 22:470

    Content type: Research

    Published on:

  12. The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functio...

    Authors: Qi Zheng, Cuiyun Zhu, Jing Jing, Yinghui Ling, Shuaiqi Qin, Jiao Wang, Lisha Zha, Ya Liu and Fugui Fang

    Citation: BMC Genomics 2021 22:469

    Content type: Research

    Published on:

  13. Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in te...

    Authors: Yuxin Yang, Xueying Zhang, Lifen Wu, Lichao Zhang, Guoxiang Liu, Chuan Xia, Xu Liu and Xiuying Kong

    Citation: BMC Genomics 2021 22:468

    Content type: Research article

    Published on:

  14. Amber-like compounds form in tobacco (Nicotiana tabacum) during leaf curing and impact aromatic quality. In particular, cis-abienol, a polycyclic labdane-related diterpenoid, is of research interest as a precurso...

    Authors: Lingxiao He, Huabing Liu, Changhe Cheng, Min Xu, Lei He, Lihua Li, Jian Yao, Wenjun Zhang, Zhengguang Zhai, Qinzhan Luo, Jutao Sun, Tiezhao Yang and Shixiao Xu

    Citation: BMC Genomics 2021 22:467

    Content type: Research article

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  15. Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and fun...

    Authors: Razgar Seyed Rahmani, Tao Shi, Dongzhi Zhang, Xiaoping Gou, Jing Yi, Giles Miclotte, Kathleen Marchal and Jia Li

    Citation: BMC Genomics 2021 22:465

    Content type: Research article

    Published on:

  16. Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindro...

    Authors: Erika Berenice Martínez-Ruiz, Myriel Cooper, Jimena Barrero-Canosa, Mindia A. S. Haryono, Irina Bessarab, Rohan B. H. Williams and Ulrich Szewzyk

    Citation: BMC Genomics 2021 22:464

    Content type: Research article

    Published on:

  17. The amino acid/auxin permease (AAAP) family represents a class of proteins that transport amino acids across cell membranes. Members of this family are widely distributed in different organisms and participate...

    Authors: Xiaoxue Pan, Mingyu Hu, Zhongwei Wang, Ling Guan, Xiaoying Jiang, Wenqin Bai, Hong Wu and Kairong Lei

    Citation: BMC Genomics 2021 22:463

    Content type: Research article

    Published on:

  18. Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation’s food security. The pathogen, a highly pathogenic strain of a v...

    Authors: Bahiyah Azli, Sharanya Ravi, Mohd Hair-Bejo, Abdul Rahman Omar, Aini Ideris and Nurulfiza Mat Isa

    Citation: BMC Genomics 2021 22:461

    Content type: Research

    Published on:

  19. Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of ...

    Authors: Chendan Wei, Zhenyi Wang, Jianyu Wang, Jia Teng, Shaoqi Shen, Qimeng Xiao, Shoutong Bao, Yishan Feng, Yan Zhang, Yuxian Li, Sangrong Sun, Yuanshuai Yue, Chunyang Wu, Yanli Wang, Tianning Zhou, Wenbo Xu…

    Citation: BMC Genomics 2021 22:460

    Content type: Research

    Published on:

  20. Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes have described accessible chromatin regions, but little work has been done in f...

    Authors: Aileen R. Ferraro, Abigail J. Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz and Zachary A. Lewis

    Citation: BMC Genomics 2021 22:459

    Content type: Research article

    Published on:

  21. Brain cancer is one of the eight most common cancers occurring in people aged 40+ and is the fifth-leading cause of cancer-related deaths for males aged 40–59. Accurate subtype identification is crucial for pr...

    Authors: Min Zhao, Yining Liu, Guiqiong Ding, Dacheng Qu and Hong Qu

    Citation: BMC Genomics 2021 22:458

    Content type: Research

    Published on:

  22. A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole...

    Authors: Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongzhi Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, Patrice Humblot and Gilles Charpigny

    Citation: BMC Genomics 2021 22:451

    Content type: Research article

    Published on:

    The Research article to this article has been published in BMC Genomics 2021 22:450

  23. In post-partum dairy cows, the energy needs to satisfy high milk production induces a status of more or less pronounced Negative Energy Balance (NEB). NEB associated with fat mobilization impairs reproductive ...

    Authors: Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongzhi Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, Patrice Humblot and Gilles Charpigny

    Citation: BMC Genomics 2021 22:450

    Content type: Research article

    Published on:

    The Research article to this article has been published in BMC Genomics 2021 22:451

  24. Animal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes. In some cases, wel...

    Authors: Swati Jivanji, Chad Harland, Sally Cole, Brigid Brophy, Dorian Garrick, Russell Snell, Mathew Littlejohn and Götz Laible

    Citation: BMC Genomics 2021 22:457

    Content type: Research

    Published on:

  25. Anthocyanin, chlorophyll, and carotenoid pigments are widely distributed in plants, producing various colors. Ornamental kale (Brassica oleracea var. acephala DC) which has colorful inner leaves is an ideal plant...

    Authors: Yang Liu, Xin Feng, Yuting Zhang, Fuhui Zhou and Pengfang Zhu

    Citation: BMC Genomics 2021 22:455

    Content type: Research

    Published on:

  26. Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealin...

    Authors: Hengyou Zhang, Zhenbin Hu, Yuming Yang, Xiaoqian Liu, Haiyan Lv, Bao-Hua Song, Yong-qiang Charles An, Zhimin Li and Dan Zhang

    Citation: BMC Genomics 2021 22:453

    Content type: Research article

    Published on:

  27. Maintenance of the corpus luteum (CL) beyond the time of luteolysis is essential for establishing pregnancy. Identifying the distinct features of early pregnancy CL remains unresolved, hence we analyzed here t...

    Authors: Raghavendra Basavaraja, Jessica N. Drum, Jackson Sapuleni, Lonice Bibi, Gilgi Friedlander, Sai Kumar, Roberto Sartori and Rina Meidan

    Citation: BMC Genomics 2021 22:452

    Content type: Research

    Published on:

  28. Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endos...

    Authors: Heidi Kaech, Alice B. Dennis and Christoph Vorburger

    Citation: BMC Genomics 2021 22:449

    Content type: Research

    Published on:

  29. Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage o...

    Authors: Gregory M. Weber, Jill Birkett, Kyle Martin, Doug Dixon II, Guangtu Gao, Timothy D. Leeds, Roger L. Vallejo and Hao Ma

    Citation: BMC Genomics 2021 22:448

    Content type: Research article

    Published on:

  30. Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important mari...

    Authors: Xianhui Ning and Li Sun

    Citation: BMC Genomics 2021 22:447

    Content type: Research article

    Published on:

  31. The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylat...

    Authors: Dorothea Seiler Vellame, Isabel Castanho, Aisha Dahir, Jonathan Mill and Eilis Hannon

    Citation: BMC Genomics 2021 22:446

    Content type: Research

    Published on:

  32. In mammals, the ovary is the essential system of female reproduction for the onset of puberty, and the abnormal puberty has negative outcomes on health. CircRNA is a non-coding RNA produced by non-canonical al...

    Authors: Xiangchun Pan, Wentao Gong, Yingting He, Nian Li, Hao Zhang, Zhe Zhang, Jiaqi Li and Xiaolong Yuan

    Citation: BMC Genomics 2021 22:445

    Content type: Research

    Published on:

  33. Autophagy is an evolutionary ancient mechanism that sequesters substrates for degradation within autolysosomes. The process is driven by many autophagy-related (ATG) proteins, including the core members ATG9 a...

    Authors: Qiuhong Xiong, Ning Song, Ping Li, Sarah Fischer, Roman Konertz, Prerana Wagle, Gernot Glöckner, Changxin Wu and Ludwig Eichinger

    Citation: BMC Genomics 2021 22:444

    Content type: Research

    Published on:

    The Correction to this article has been published in BMC Genomics 2021 22:555

  34. An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. Th...

    Authors: Luyao Wang, Jin Han, Kening Lu, Menglin Li, Mengtao Gao, Zeyi Cao, Ting Zhao, Xue Chen, Xiaoyuan Tao, Quanjia Chen and Xueying Guan

    Citation: BMC Genomics 2021 22:443

    Content type: Research article

    Published on:

  35. Rutabaga or swede (Brassica napus ssp. napobrassica (L.) Hanelt) varies in root and leaf shape and colour, flesh colour, foliage growth habits, maturity date, seed quality parameters, disease resistance and other...

    Authors: Zhiyu Yu, Rudolph Fredua-Agyeman, Sheau-Fang Hwang and Stephen E. Strelkov

    Citation: BMC Genomics 2021 22:442

    Content type: Research

    Published on:

  36. Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and ...

    Authors: Liyuan Wang, Yawen Zhang, Bo Zhang, Haian Zhong, Yunfeng Lu and Hao Zhang

    Citation: BMC Genomics 2021 22:441

    Content type: Research

    Published on:

  37. Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic muta...

    Authors: Xue Lin, Yingying Hua, Shuanglin Gu, Li Lv, Xingyu Li, Pin Chen, Peng Dai, Yunyun Hu, Anna Liu and Jian Li

    Citation: BMC Genomics 2021 22:440

    Content type: Software

    Published on:

  38. B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as i...

    Authors: Zhen Feng, Mengyu Li, Yi Li, Xu Yang, Hengling Wei, Xiaokang Fu, Liang Ma, Jianhua Lu, Hantao Wang and Shuxun Yu

    Citation: BMC Genomics 2021 22:439

    Content type: Research

    Published on:

  39. Myofibrillar myopathy in humans causes protein aggregation, degeneration, and weakness of skeletal muscle. In horses, myofibrillar myopathy is a late-onset disease of unknown origin characterized by poor perfo...

    Authors: Zoë J. Williams, Deborah Velez-Irizarry, Keri Gardner and Stephanie J. Valberg

    Citation: BMC Genomics 2021 22:438

    Content type: Research

    Published on:

  40. Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for a...

    Authors: Tejaswi Yarra, Kirti Ramesh, Mark Blaxter, Anne Hüning, Frank Melzner and Melody S. Clark

    Citation: BMC Genomics 2021 22:437

    Content type: Research article

    Published on:

  41. Gene interaction patterns, including modules and motifs, can be used to identify cancer specific biomarkers and to reveal the mechanism of tumorigenesis. Most of the existing module network inferencing methods...

    Authors: Xinguo Lu, Fang Liu, Qiumai Miao, Ping Liu, Yan Gao and Keren He

    Citation: BMC Genomics 2021 22(Suppl 1):436

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 1

  42. Formation of triploid organism is useful in genetics and breeding. In this study, autotriploid Carassius auratus (3nRR, 3n = 150) was generated from Carassius auratus red var. (RCC, 2n = 100) (♀) and autotetraplo...

    Authors: Chongqing Wang, Xiang Luo, Huan Qin, Chun Zhao, Li Yang, Tingting Yu, Yuxin Zhang, Xu Huang, Xidan Xu, Qinbo Qin and Shaojun Liu

    Citation: BMC Genomics 2021 22:435

    Content type: Research

    Published on:

  43. Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, sh...

    Authors: Lingtong Ren, Anfang Liu, Qigui Wang, Honggan Wang, Deqiang Dong and Lingbin Liu

    Citation: BMC Genomics 2021 22:431

    Content type: Research article

    Published on:

  44. Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken li...

    Authors: Junxiao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li and Xiaojun Liu

    Citation: BMC Genomics 2021 22:428

    Content type: Research article

    Published on:

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