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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 18 of 19

  1. The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD) event between 25 and100 million years ago. Existing data on the proportion of para...

    Authors: Sigbjørn Lien, Lars Gidskehaug, Thomas Moen, Ben J Hayes, Paul R Berg, William S Davidson, Stig W Omholt and Matthew P Kent

    Citation: BMC Genomics 2011 12:615

    Content type: Research article

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  2. In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this...

    Authors: Lisette JA Kogelman, Keren Byrne, Tony Vuocolo, Nathan S Watson-Haigh, Haja N Kadarmideen, James W Kijas, Hutton V Oddy, Graham E Gardner, Cedric Gondro and Ross L Tellam

    Citation: BMC Genomics 2011 12:607

    Content type: Research article

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  3. MicroRNAs (miRNAs) play important roles in regulating the expression of protein-coding genes by directing the degradation and/or repression of the translation of gene transcripts. Growing evidence shows that m...

    Authors: Ruolin Yang, Zhonghua Dai, Shue Chen and Liangbiao Chen

    Citation: BMC Genomics 2011 12:605

    Content type: Research article

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  4. Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific e...

    Authors: Anu Sironen, Pekka Uimari, Heli Venhoranta, Magnus Andersson and Johanna Vilkki

    Citation: BMC Genomics 2011 12:591

    Content type: Research article

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  5. When compared to primary chicken embryo fibroblast (CEF) cells, the immortal DF-1 CEF line exhibits enhanced growth rates and susceptibility to oxidative stress. Although genes responsible for cell cycle regul...

    Authors: Byung-Whi Kong, Jeong Yoon Lee, Walter G Bottje, Kentu Lassiter, Jonghyuk Lee and Douglas N Foster

    Citation: BMC Genomics 2011 12:571

    Content type: Research article

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  6. Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose...

    Authors: Yuna Blum, Guillaume Le Mignon, David Causeur, Olivier Filangi, Colette Désert, Olivier Demeure, Pascale Le Roy and Sandrine Lagarrigue

    Citation: BMC Genomics 2011 12:567

    Content type: Research article

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  7. One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic vari...

    Authors: Paul Stothard, Jung-Woo Choi, Urmila Basu, Jennifer M Sumner-Thomson, Yan Meng, Xiaoping Liao and Stephen S Moore

    Citation: BMC Genomics 2011 12:559

    Content type: Research article

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  8. Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variatio...

    Authors: Bujie Zhan, João Fadista, Bo Thomsen, Jakob Hedegaard, Frank Panitz and Christian Bendixen

    Citation: BMC Genomics 2011 12:557

    Content type: Research article

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  9. Orange-spotted grouper (Epinephelus coioides) is an economically important marine fish cultured in China and Southeast Asian countries. The emergence of infectious viral diseases, including iridovirus and betanod...

    Authors: Youhua Huang, Xiaohong Huang, Yang Yan, Jia Cai, Zhengliang Ouyang, Huachun Cui, Peiran Wang and Qiwei Qin

    Citation: BMC Genomics 2011 12:556

    Content type: Research article

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  10. Although RNA-seq greatly advances our understanding of complex transcriptome landscapes, such as those found in mammals, complete RNA-seq studies in livestock and in particular in the pig are still lacking. He...

    Authors: Anna Esteve-Codina, Robert Kofler, Nicola Palmieri, Giovanni Bussotti, Cedric Notredame and Miguel Pérez-Enciso

    Citation: BMC Genomics 2011 12:552

    Content type: Research article

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  11. The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from ...

    Authors: Laurence Liaubet, Valérie Lobjois, Thomas Faraut, Aurélie Tircazes, Francis Benne, Nathalie Iannuccelli, José Pires, Jérome Glénisson, Annie Robic, Pascale Le Roy, Magali SanCristobal and Pierre Cherel

    Citation: BMC Genomics 2011 12:548

    Content type: Research article

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  12. Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains us...

    Authors: Silvia T Rodríguez-Ramilo, Miguel A Toro, Carmen Bouza, Miguel Hermida, Belén G Pardo, Santiago Cabaleiro, Paulino Martínez and Jesús Fernández

    Citation: BMC Genomics 2011 12:541

    Content type: Research article

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  13. Common carp (Cyprinus carpio), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the al...

    Authors: Peng Xu, Jian Wang, Jintu Wang, Runzi Cui, Yan Li, Zixia Zhao, Peifeng Ji, Yan Zhang, Jiongtang Li and Xiaowen Sun

    Citation: BMC Genomics 2011 12:537

    Content type: Research article

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  14. Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have ...

    Authors: Florian Geay, Serena Ferraresso, Jose L Zambonino-Infante, Luca Bargelloni, Claire Quentel, Marc Vandeputte, Sachi Kaushik, Chantal L Cahu and David Mazurais

    Citation: BMC Genomics 2011 12:522

    Content type: Research article

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  15. Although an adverse early-life environment has been linked to an increased risk of developing the metabolic syndrome, the molecular mechanisms underlying altered disease susceptibility as well as their relevan...

    Authors: Bright Starling Emerald, Keefe Chng, Shinya Masuda, Deborah M Sloboda, Mark H Vickers, Ravi Kambadur and Peter D Gluckman

    Citation: BMC Genomics 2011 12:509

    Content type: Research article

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  16. Two strains of the silver fox (Vulpes vulpes), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards ...

    Authors: Anna V Kukekova, Jennifer L Johnson, Clotilde Teiling, Lewyn Li, Irina N Oskina, Anastasiya V Kharlamova, Rimma G Gulevich, Ravee Padte, Michael M Dubreuil, Anastasiya V Vladimirova, Darya V Shepeleva, Svetlana G Shikhevich, Qi Sun, Lalit Ponnala, Svetlana V Temnykh, Lyudmila N Trut…

    Citation: BMC Genomics 2011 12:482

    Content type: Research article

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  17. Studies of closely related species with different sex chromosome systems can provide insights into the processes of sex chromosome differentiation and evolution. To investigate the potential utility of molecul...

    Authors: Takahito Shikano, Heini M Natri, Yukinori Shimada and Juha Merilä

    Citation: BMC Genomics 2011 12:474

    Content type: Research article

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  18. The turbot (Scophthalmus maximus) is a highly appreciated European aquaculture species. Growth related traits constitute the main goal of the ongoing genetic breeding programs of this species. The recent construc...

    Authors: Enrique Sánchez-Molano, Alex Cerna, Miguel A Toro, Carmen Bouza, Miguel Hermida, Belén G Pardo, Santiago Cabaleiro, Jesús Fernández and Paulino Martínez

    Citation: BMC Genomics 2011 12:473

    Content type: Research article

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  19. Avian pathogenic Escherichia coli (APEC) is detrimental to poultry health and its zoonotic potential is a food safety concern. Regulation of antimicrobials in food-production animals has put greater focus on enha...

    Authors: Erin E Sandford, Megan Orr, Emma Balfanz, Nate Bowerman, Xianyao Li, Huaijun Zhou, Timothy J Johnson, Subhashinie Kariyawasam, Peng Liu, Lisa K Nolan and Susan J Lamont

    Citation: BMC Genomics 2011 12:469

    Content type: Research article

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  20. Cardiomyopathy syndrome (CMS) is a disease associated with severe myocarditis primarily in adult farmed Atlantic salmon (Salmo salar L.), caused by a double-stranded RNA virus named piscine myocarditis virus (PMC...

    Authors: Gerrit Timmerhaus, Aleksei Krasnov, Pål Nilsen, Marta Alarcon, Sergey Afanasyev, Marit Rode, Harald Takle and Sven Martin Jørgensen

    Citation: BMC Genomics 2011 12:459

    Content type: Research article

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  21. Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution has been likened to lactation in mammals, ...

    Authors: Meagan J Gillespie, Volker R Haring, Kenneth A McColl, Paul Monaghan, John A Donald, Kevin R Nicholas, Robert J Moore and Tamsyn M Crowley

    Citation: BMC Genomics 2011 12:452

    Content type: Research article

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  22. Elucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth.

    Authors: Congying Chen, Huashui Ai, Jun Ren, Wanbo Li, Pinghua Li, Ruimin Qiao, Jing Ouyang, Ming Yang, Junwu Ma and Lusheng Huang

    Citation: BMC Genomics 2011 12:448

    Content type: Research article

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  23. A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-...

    Authors: Yang Zhang, Xiaojun Zhang, Thomas H O'Hare, William S Payne, Jennifer J Dong, Chantel F Scheuring, Meiping Zhang, James J Huang, Mi-Kyung Lee, Mary E Delany, Hong-Bin Zhang and Jerry B Dodgson

    Citation: BMC Genomics 2011 12:447

    Content type: Research article

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  24. Successful achievement of early folliculogenesis is crucial for female reproductive function. The process is finely regulated by cell-cell interactions and by the coordinated expression of genes in both the oo...

    Authors: Agnes Bonnet, Claudia Bevilacqua, Francis Benne, Loys Bodin, Corinne Cotinot, Laurence Liaubet, Magali Sancristobal, Julien Sarry, Elena Terenina, Patrice Martin, Gwenola Tosser-Klopp and Beatrice Mandon-Pepin

    Citation: BMC Genomics 2011 12:417

    Content type: Research article

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  25. Structural variation contributes to the rich genetic and phenotypic diversity of the modern domestic dog, Canis lupus familiaris, although compared to other organisms, catalogs of canine copy number variants (CNV...

    Authors: Thomas J Nicholas, Carl Baker, Evan E Eichler and Joshua M Akey

    Citation: BMC Genomics 2011 12:414

    Content type: Research article

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  26. Genome-wide association analysis is a powerful tool for annotating phenotypic effects on the genome and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene...

    Authors: John B Cole, George R Wiggans, Li Ma, Tad S Sonstegard, Thomas J Lawlor Jr, Brian A Crooker, Curtis P Van Tassell, Jing Yang, Shengwen Wang, Lakshmi K Matukumalli and Yang Da

    Citation: BMC Genomics 2011 12:408

    Content type: Research article

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  27. The Australian sheep blowfly Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) is a destructive pest of the sheep, a model organism for insecticide resistance research, and a valuable tool for medical and fore...

    Authors: Siu F Lee, Zhenzhong Chen, Annette McGrath, Robert T Good and Philip Batterham

    Citation: BMC Genomics 2011 12:406

    Content type: Research article

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  28. There are large differences between the sexes at the genetic level; these differences include heterogametic sex chromosomes and/or differences in expression of genes between the sexes. In rainbow trout (Oncorhync...

    Authors: Matthew C Hale, Peng Xu, Julie Scardina, Paul A Wheeler, Gary H Thorgaard and Krista M Nichols

    Citation: BMC Genomics 2011 12:404

    Content type: Research article

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  29. As a mild, highly contagious, respiratory disease, swine influenza always damages the innate immune systems, and increases susceptibility to secondary infections which results in considerable morbidity and mor...

    Authors: Yongtao Li, Hongbo Zhou, Zhibin Wen, Shujuan Wu, Canhui Huang, Guangmin Jia, Huanchun Chen and Meilin Jin

    Citation: BMC Genomics 2011 12:398

    Content type: Research article

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  30. Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androsten...

    Authors: Eli Grindflek, Sigbjørn Lien, Hanne Hamland, Marianne HS Hansen, Matthew Kent, Maren van Son and Theo HE Meuwissen

    Citation: BMC Genomics 2011 12:362

    Content type: Research article

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  31. Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they prov...

    Authors: Razvan Anistoroaei, Boudewijn ten Hallers, Michael Nefedov, Knud Christensen and Pieter de Jong

    Citation: BMC Genomics 2011 12:354

    Content type: Research article

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  32. Bacterial Artificial Chromosomes (BACs) have been widely used as transgenes in vertebrate model systems such as mice and zebrafish, for a variety of studies. BAC transgenesis has been a powerful tool to study ...

    Authors: Leighcraft A Shakes, Gembu Abe, Mugtaba A Eltayeb, Hope M Wolf, Koichi Kawakami and Pradeep K Chatterjee

    Citation: BMC Genomics 2011 12:351

    Content type: Methodology article

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  33. Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speci...

    Authors: Ted Cosart, Albano Beja-Pereira, Shanyuan Chen, Sarah B Ng, Jay Shendure and Gordon Luikart

    Citation: BMC Genomics 2011 12:347

    Content type: Methodology article

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  34. Modern dog breeds display traits that are either breed-specific or shared by a few breeds as a result of genetic bottlenecks during the breed creation process and artificial selection for breed standards. Sele...

    Authors: Javier Quilez, Andrea D Short, Verónica Martínez, Lorna J Kennedy, William Ollier, Armand Sanchez, Laura Altet and Olga Francino

    Citation: BMC Genomics 2011 12:339

    Content type: Research article

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  35. Human killer immunoglobulin-like receptors (KIRs) play a critical role in governing the immune response to neoplastic and infectious disease. Rhesus macaques serve as important animal models for many human dis...

    Authors: Anna J Moreland, Lisbeth A Guethlein, R Keith Reeves, Karl W Broman, R Paul Johnson, Peter Parham, David H O'Connor and Benjamin N Bimber

    Citation: BMC Genomics 2011 12:295

    Content type: Research article

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  36. In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referre...

    Authors: Martien AM Groenen, Hendrik-Jan Megens, Yalda Zare, Wesley C Warren, LaDeana W Hillier, Richard PMA Crooijmans, Addie Vereijken, Ron Okimoto, William M Muir and Hans H Cheng

    Citation: BMC Genomics 2011 12:274

    Content type: Research article

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  37. Populations of Atlantic killifish (Fundulus heteroclitus) have evolved resistance to the embryotoxic effects of polychlorinated biphenyls (PCBs) and other halogenated and nonhalogenated aromatic hydrocarbons that...

    Authors: Marjorie F Oleksiak, Sibel I Karchner, Matthew J Jenny, Diana G Franks, David B Mark Welch and Mark E Hahn

    Citation: BMC Genomics 2011 12:263

    Content type: Research article

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  38. A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or comb...

    Authors: Jordi Durban, Paula Juárez, Yamileth Angulo, Bruno Lomonte, Marietta Flores-Diaz, Alberto Alape-Girón, Mahmood Sasa, Libia Sanz, José M Gutiérrez, Joaquín Dopazo, Ana Conesa and Juan J Calvete

    Citation: BMC Genomics 2011 12:259

    Content type: Research article

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  39. Expansion of aquaculture is seriously limited by reductions in fish oil (FO) supply for aquafeeds. Terrestrial alternatives such as vegetable oils (VO) have been investigated and recently a strategy combining ...

    Authors: Sofia Morais, Jarunan Pratoomyot, John B Taggart, James E Bron, Derrick R Guy, J Gordon Bell and Douglas R Tocher

    Citation: BMC Genomics 2011 12:255

    Content type: Research article

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  40. Streptococcus suis serotype 2 (S. suis 2) is an important pathogen of pigs. S suis 2 infections have high mortality rates and are characterized by meningitis, septicemia and pneumonia. S. suis 2 is also an emergi...

    Authors: Manli Liu, Liurong Fang, Chen Tan, Tiansi Long, Huanchun Chen and Shaobo Xiao

    Citation: BMC Genomics 2011 12:253

    Content type: Research article

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  41. Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies vi...

    Authors: Sem Genini, Bouabid Badaoui, Gert Sclep, Stephen C Bishop, Dave Waddington, Marie-Hélène Pinard van der Laan, Christophe Klopp, Cédric Cabau, Hans-Martin Seyfert, Wolfram Petzl, Kirsty Jensen, Elizabeth J Glass, Astrid de Greeff, Hilde E Smith, Mari A Smits, Ingrid Olsaker…

    Citation: BMC Genomics 2011 12:225

    Content type: Research article

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  42. Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we presen...

    Authors: Bonnie A Fraser, Cameron J Weadick, Ilana Janowitz, F Helen Rodd and Kimberly A Hughes

    Citation: BMC Genomics 2011 12:202

    Content type: Research article

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  43. Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combinatio...

    Authors: Olafur Fridjonsson, Kristinn Olafsson, Scott Tompsett, Snaedis Bjornsdottir, Sonia Consuegra, David Knox, Carlos Garcia de Leaniz, Steinunn Magnusdottir, Gudbjorg Olafsdottir, Eric Verspoor and Sigridur Hjorleifsdottir

    Citation: BMC Genomics 2011 12:179

    Content type: Methodology article

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  44. High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in ...

    Authors: Chun Ming Wang, Zhi Yi Bai, Xiao Ping He, Grace Lin, Jun Hong Xia, Fei Sun, Loong Chueng Lo, Felicia Feng, Ze Yuan Zhu and Gen Hua Yue

    Citation: BMC Genomics 2011 12:174

    Content type: Research article

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  45. Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competen...

    Authors: Solomon Mamo, Fiona Carter, Patrick Lonergan, Cláudia LV Leal, Abdullah Al Naib, Paul McGettigan, Jai P Mehta, Alexander CO Evans and Trudee Fair

    Citation: BMC Genomics 2011 12:151

    Content type: Research article

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  46. Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species...

    Authors: Kelly RB Sporer, Robert J Tempelman, Catherine W Ernst, Kent M Reed, Sandra G Velleman and Gale M Strasburg

    Citation: BMC Genomics 2011 12:143

    Content type: Research article

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  47. The salmon louse (Lepeophtheirus salmonis Krøyer), an ectoparasitic copepod with a complex life cycle causes significant losses in salmon aquaculture. Pesticide treatments against the parasite raise environmental...

    Authors: Tariku Markos Tadiso, Aleksei Krasnov, Stanko Skugor, Sergey Afanasyev, Ivar Hordvik and Frank Nilsen

    Citation: BMC Genomics 2011 12:141

    Content type: Research article

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  48. Mucins are large glycoproteins implicated in protection of all mucosal surfaces. In humans and rodents, the mucin gene family has been well described and previous studies have investigated the distribution and...

    Authors: Prisca R Hoorens, Manuela Rinaldi, Robert W Li, Bruno Goddeeris, Edwin Claerebout, Jozef Vercruysse and Peter Geldhof

    Citation: BMC Genomics 2011 12:140

    Content type: Research article

    Published on:

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