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Non-human and non-rodent vertebrate genomics

Section edited by Shane Burgess and Jacqueline Smith

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

Page 1 of 16

  1. Content type: Research article

    To reduce costs of rearing replacement heifers, researchers have focused on decreasing age at breeding and first calving. To increase returns upon initiation of lactation the focus has been on increasing mamma...

    Authors: M. Vailati-Riboni, R. E. Bucktrout, S. Zhan, A. Geiger, J. C. McCann, R. M. Akers and J. J. Loor

    Citation: BMC Genomics 2018 19:900

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  2. Content type: Research article

    Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening...

    Authors: Yun Xia, Wei Luo, Siqi Yuan, Yuchi Zheng and Xiaomao Zeng

    Citation: BMC Genomics 2018 19:886

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  3. Content type: Research article

    The health and resilience of species in natural environments is increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination...

    Authors: Kurt A. Gust, Vijender Chaitankar, Preetam Ghosh, Mitchell S. Wilbanks, Xianfeng Chen, Natalie D. Barker, Don Pham, Leona D. Scanlan, Arun Rawat, Larry G. Talent, Michael J. Quinn Jr, Christopher D. Vulpe, Mohamed O. Elasri, Mark S. Johnson, Edward J. Perkins and Craig A. McFarland

    Citation: BMC Genomics 2018 19:877

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  4. Content type: Research article

    The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-codin...

    Authors: Yong Liu, Bing Qi, Juan Xie, Xiaoqing Wu, Yinghui Ling, Xinyan Cao, Feng Kong, Jing Xin, Xin Jiang, Qiaoqin Wu, Wenying Wang, Qingmei Li, Shengnan Zhang, Fengrui Wu, Di Zhang, Rong Wang…

    Citation: BMC Genomics 2018 19:866

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  5. Content type: Research article

    Corn dried distillers grains with solubles (cDDGS) are a byproduct of biofuel and alcohol production. cDDGS have been used in pig feed for many years, because they are readily available and rich in protein, fi...

    Authors: Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Klaudia Pawlina-Tyszko, Artur Gurgul and Tomasz Ząbek

    Citation: BMC Genomics 2018 19:864

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  6. Content type: Research article

    The dramatic increase in myotomal muscle mass in post-hatching fish is related to their ability to lastingly produce new muscle fibres, a process termed hyperplasia. The molecular and cellular mechanisms under...

    Authors: Sabrina Jagot, Nathalie Sabin, Aurélie Le Cam, Jérôme Bugeon, Pierre-Yves Rescan and Jean-Charles Gabillard

    Citation: BMC Genomics 2018 19:865

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  7. Content type: Research article

    Increased attention is being paid to breast muscle yield and meat quality in the duck breeding industry. Our previous report has demonstrated that dietary Clostridium butyricum (C. butyricum) can improve meat qua...

    Authors: Yanhan Liu, Yaxiong Jia, Cun Liu, Limin Ding and Zhaofei Xia

    Citation: BMC Genomics 2018 19:844

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  8. Content type: Research article

    Skeletal muscle satellite cells (MSC) are crucial for postnatal growth and regeneration of skeletal muscle. An interaction exists between MSC and intramuscular preadipocytes (IMPA). This study is the first to ...

    Authors: Liping Guo, Huanxian Cui, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng, Yuming Guo and Jie Wen

    Citation: BMC Genomics 2018 19:838

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  9. Content type: Research article

    Gene ontology analysis using the microarray database generated in a previous study by this laboratory was used to further evaluate how maternal dietary supplementation with pyridoxine combined with different s...

    Authors: Danyel Bueno Dalto, Stephen Tsoi, Michael K. Dyck and Jean-Jacques Matte

    Citation: BMC Genomics 2018 19:836

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  10. Content type: Research article

    Fertility is a complex trait that has a major impact on the development of the buffalo industry. Genome-wide association study (GWAS) has increased the ability to detect genes influencing complex traits, and m...

    Authors: Jun Li, Jiajia Liu, Giuseppe Campanile, Graham Plastow, Chunyan Zhang, Zhiquan Wang, Martino Cassandro, Bianca Gasparrini, Angela Salzano, Guohua Hua, Aixin Liang and Liguo Yang

    Citation: BMC Genomics 2018 19:814

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  11. Content type: Research article

    Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. While we know many of these regulators, our understanding of how they...

    Authors: Stacey E. Wahl, Brent H. Wyatt, Stephen D. Turner and Amanda J. G. Dickinson

    Citation: BMC Genomics 2018 19:795

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  12. Content type: Research article

    Dependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products ...

    Authors: Albert Caballero-Solares, Xi Xue, Christopher C. Parrish, Maryam Beheshti Foroutani, Richard G. Taylor and Matthew L. Rise

    Citation: BMC Genomics 2018 19:796

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  13. Content type: Research article

    The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple indivi...

    Authors: Majid Khansefid, Jennie E. Pryce, Sunduimijid Bolormaa, Yizhou Chen, Catriona A. Millen, Amanda J. Chamberlain, Christy J. Vander Jagt and Michael E. Goddard

    Citation: BMC Genomics 2018 19:793

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  14. Content type: Research article

    Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to ...

    Authors: Justyna Horodyska, Klaus Wimmers, Henry Reyer, Nares Trakooljul, Anne Maria Mullen, Peadar G. Lawlor and Ruth M. Hamill

    Citation: BMC Genomics 2018 19:791

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  15. Content type: Research article

    MicroRNAs (miRNAs) are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes. Koi carp exhibit diverse color patterns, making it an ideal subject for ...

    Authors: Mingkun Luo, Lanmei Wang, Wenbin Zhu, Jianjun Fu, Feibiao Song, Min Fang, Juanjuan Dong and Zaijie Dong

    Citation: BMC Genomics 2018 19:779

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  16. Content type: Research article

    Disrupted diurnal rhythms cause accelerated aging and an increased incidence in age-related disease and morbidity. The circadian clock governs cell physiology and metabolism by controlling transcription and ch...

    Authors: Jinhee Park and William J. Belden

    Citation: BMC Genomics 2018 19:777

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  17. Content type: Research article

    The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with ...

    Authors: Yung-Chih Lai, Ya-Chen Liang, Ting-Xin Jiang, Randall B. Widelitz, Ping Wu and Cheng-Ming Chuong

    Citation: BMC Genomics 2018 19:780

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  18. Content type: Research article

    In the past years, our laboratory successfully generated transgenic rainbow trout bearing cecropin P1 transgene. These fish exhibited resistant characteristic to infection by Aeromonas salmonicida, Infectious Hem...

    Authors: Yueh-Chiang Han, Chun-Mean Lin and Thomas T. Chen

    Citation: BMC Genomics 2018 19:760

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  19. Content type: Research article

    Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine...

    Authors: Arash Akbarzadeh, Oliver P Günther, Aimee Lee Houde, Shaorong Li, Tobi J Ming, Kenneth M Jeffries, Scott G Hinch and Kristina M Miller

    Citation: BMC Genomics 2018 19:749

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  20. Content type: Research article

    This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, ...

    Authors: Claudia A Sevillano, Jan ten Napel, Simone E F Guimarães, Fabyano F Silva and Mario P L Calus

    Citation: BMC Genomics 2018 19:740

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  21. Content type: Research article

    Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even af...

    Authors: Sarah R. McCoski, McCauley T. Vailes, Connor E. Owens, Rebecca R. Cockrum and Alan D. Ealy

    Citation: BMC Genomics 2018 19:737

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  22. Content type: Research article

    Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.

    Authors: Bi Jun Li, Dan Li Jiang, Zi Ning Meng, Yong Zhang, Zong Xian Zhu, Hao Ran Lin and Jun Hong Xia

    Citation: BMC Genomics 2018 19:729

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  23. Content type: Research article

    Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immun...

    Authors: Amy R Ellison, Tamsyn M Uren Webster, Olivier Rey, Carlos Garcia de Leaniz, Sofia Consuegra, Pablo Orozco-terWengel and Jo Cable

    Citation: BMC Genomics 2018 19:723

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  24. Content type: Research article

    Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular ...

    Authors: Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss and Jean Paul Delgado

    Citation: BMC Genomics 2018 19:704

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  25. Content type: Research article

    Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficie...

    Authors: Leticia P Sanglard, Moysés Nascimento, Philipe Moriel, Jeffrey Sommer, Melissa Ashwell, Matthew H Poore, Márcio de S Duarte and Nick V L Serão

    Citation: BMC Genomics 2018 19:702

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  26. Content type: Research article

    Natural antibodies (NAb) are an important component of the innate immune system, and fight infections as a part of the first line defence. NAb are poly-reactive and can respond non-specifically to antigens. Th...

    Authors: Britt de Klerk, Mehdi Emam, Kathleen A. Thompson-Crispi, Mehdi Sargolzaei, Johan J. van der Poel and Bonnie A. Mallard

    Citation: BMC Genomics 2018 19:694

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  27. Content type: Research article

    Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the emb...

    Authors: Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang and Harold B. White III

    Citation: BMC Genomics 2018 19:695

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  28. Content type: Research article

    Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We us...

    Authors: C. Reimer, C.-J. Rubin, A. R. Sharifi, N.-T. Ha, S. Weigend, K.-H. Waldmann, O. Distl, S. D. Pant, M. Fredholm, M. Schlather and H. Simianer

    Citation: BMC Genomics 2018 19:687

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  29. Content type: Research article

    Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in far...

    Authors: Colin Kern, Ying Wang, James Chitwood, Ian Korf, Mary Delany, Hans Cheng, Juan F. Medrano, Alison L. Van Eenennaam, Catherine Ernst, Pablo Ross and Huaijun Zhou

    Citation: BMC Genomics 2018 19:684

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  30. Content type: Research article

    Environmental changes of biotic or abiotic nature during critical periods of early development may exert a profound influence on physiological functions later in life. This process, named developmental program...

    Authors: Vincent Veron, Lucie Marandel, Jingwei Liu, Emilio J. Vélez, Olivier Lepais, Stéphane Panserat, Sandrine Skiba and Iban Seiliez

    Citation: BMC Genomics 2018 19:677

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  31. Content type: Research article

    Genetically selected modern broiler chickens have acquired outstanding production efficiency through rapid growth and improved feed efficiency compared to unselected chicken breeds. Recently, we analyzed the t...

    Authors: Bhuwan Khatri, Dongwon Seo, Stephanie Shouse, Jeong Hoon Pan, Nicholas J. Hudson, Jae Kyeom Kim, Walter Bottje and Byungwhi C. Kong

    Citation: BMC Genomics 2018 19:683

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  32. Content type: Research article

    The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages...

    Authors: Elisa Peripolli, Julia Metzger, Marcos Vinícius Antunes de Lemos, Nedenia Bonvino Stafuzza, Sabrina Kluska, Bianca Ferreira Olivieri, Fabieli Louise Braga Feitosa, Mariana Piatto Berton, Fernando Brito Lopes, Danísio Prado Munari, Raysildo Barbosa Lôbo, Cláudio de Ulhoa Magnabosco, Fernando Di Croce, Jason Osterstock, Sue Denise, Angélica Simone Cravo Pereira…

    Citation: BMC Genomics 2018 19:680

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  33. Content type: Research article

    Improving resistance to mastitis, one of the costliest diseases in dairy production, has become an important objective in dairy cattle breeding. However, mastitis resistance is influenced by many genes involve...

    Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

    Citation: BMC Genomics 2018 19:656

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  34. Content type: Research article

    Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Id...

    Authors: Melissa S. Monson, Angelica G. Van Goor, Christopher M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt and Susan J. Lamont

    Citation: BMC Genomics 2018 19:643

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  35. Content type: Research article

    Hair follicles (HFs), upon development, undergo repetitive cycles of growth (anagen), regression (catagen), and rest (telogen). The transition between the stages is determined by multiple molecular signals, in...

    Authors: Chao Li, Yan Li, Guangxian Zhou, Ye Gao, Sen Ma, Yulin Chen, Jiuzhou Song and Xiaolong Wang

    Citation: BMC Genomics 2018 19:638

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  36. Content type: Research article

    Delivery of colostrum within the first several hours after birth is vital for establishing successful passive immunity in neonatal dairy calves. However, it is unclear whether a difference in colostrum feeding...

    Authors: Zhixiong He, Amanda Fischer, Yang Song, Michael Steele and Le Luo Guan

    Citation: BMC Genomics 2018 19:635

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  37. Content type: Research article

    During hair growth, cortical cells emerging from the proliferative follicle bulb rapidly undergo a differentiation program and synthesize large amounts of hair keratin proteins. In this process, HOXC13 is one ...

    Authors: Shanhe Wang, Zhixin Luo, Yuelang Zhang, Dan Yuan, Wei Ge and Xin Wang

    Citation: BMC Genomics 2018 19:630

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  38. Content type: Research article

    The success of early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as n...

    Authors: C. Almiñana, G. Tsikis, V. Labas, R. Uzbekov, J. C. da Silveira, S. Bauersachs and P. Mermillod

    Citation: BMC Genomics 2018 19:622

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  39. Content type: Research article

    In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; h...

    Authors: Laiza Helena de Souza Iung, Herman Arend Mulder, Haroldo Henrique de Rezende Neves and Roberto Carvalheiro

    Citation: BMC Genomics 2018 19:619

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  40. Content type: Research article

    The expression of microRNAs (miRNAs) is essential for the proper development of the mammalian embryo. A maternal exposure to endocrine disrupting chemicals during preimplantation bears the potential for transg...

    Authors: Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs and Susanne E. Ulbrich

    Citation: BMC Genomics 2018 19:590

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  41. Content type: Research article

    The Mediterranean diet is considered one of the healthier food habits and olive oil is one of its key components. Olive oil polyphenols are known to induce beneficial effects in several pathological conditions...

    Authors: Marcella Sabino, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Ilaria Biasato, Andrea Verini-Supplizi, Andrea Valiani and Massimo Trabalza-Marinucci

    Citation: BMC Genomics 2018 19:576

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  42. Content type: Research article

    Severe equine asthma, also known as recurrent airway obstruction (RAO), is a debilitating, performance limiting, obstructive respiratory condition in horses that is phenotypically similar to human asthma. Past...

    Authors: Victor C. Mason, Robert J. Schaefer, Molly E. McCue, Tosso Leeb and Vinzenz Gerber

    Citation: BMC Genomics 2018 19:581

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  43. Content type: Research article

    Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and disco...

    Authors: Romolo Caniglia, Elena Fabbri, Pavel Hulva, Barbora Černá Bolfíková, Milena Jindřichová, Astrid Vik Stronen, Ihor Dykyy, Alessio Camatta, Paolo Carnier, Ettore Randi and Marco Galaverni

    Citation: BMC Genomics 2018 19:533

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  44. Content type: Research article

    Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and m...

    Authors: Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, Phil J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett A. Mason, Josie B. Garner, Leah C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain…

    Citation: BMC Genomics 2018 19:521

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  45. Content type: Research article

    Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs...

    Authors: Hao Bai, Yanyan Sun, Nian Liu, Fuguang Xue, Yunlei Li, Songshan Xu, Jianhua Ye, Lei Zhang, Yu Chen and Jilan Chen

    Citation: BMC Genomics 2018 19:501

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  46. Content type: Research article

    Anuran metamorphosis, which is obligatorily initiated and sustained by thyroid hormone (TH), is a dramatic example of extensive morphological, biochemical and cellular changes occurring during post-embryonic d...

    Authors: Lusha Liu, Wei Zhu, Jiongyu Liu, Shouhong Wang and Jianping Jiang

    Citation: BMC Genomics 2018 19:507

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  47. Content type: Research article

    The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding...

    Authors: Shengru Wu, Yanli Liu, Wei Guo, Xi Cheng, Xiaochun Ren, Si Chen, Xueyuan Li, Yongle Duan, Qingzhu Sun and Xiaojun Yang

    Citation: BMC Genomics 2018 19:498

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  48. Content type: Research article

    Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a who...

    Authors: Aline S. M. Cesar, Luciana C. A. Regitano, James M. Reecy, Mirele D. Poleti, Priscila S. N. Oliveira, Gabriella B. de Oliveira, Gabriel C. M. Moreira, Maurício A. Mudadu, Polyana C. Tizioto, James E. Koltes, Elyn Fritz-Waters, Luke Kramer, Dorian Garrick, Hamid Beiki, Ludwig Geistlinger, Gerson B. Mourão…

    Citation: BMC Genomics 2018 19:499

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