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Human and rodent genomics

Section edited by Leonid Bystrykh, Leonard Schalkwyck and Stefan Wiemann

This section covers the genome structure and function in humans, primates and rodents.

Page 22 of 23

  1. Changes in promoter DNA methylation pattern of genes involved in key biological pathways have been reported in glioblastoma. Genome-wide assessments of DNA methylation levels are now required to decipher the e...

    Authors: Amandine Etcheverry, Marc Aubry, Marie de Tayrac, Elodie Vauleon, Rachel Boniface, Frederique Guenot, Stephan Saikali, Abderrahmane Hamlat, Laurent Riffaud, Philippe Menei, Veronique Quillien and Jean Mosser

    Citation: BMC Genomics 2010 11:701

    Content type: Research article

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  2. Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in the salmonid species rainbow trout (Oncorhynchus mykiss) contain either one or two extracellular Ig domains of the V-...

    Authors: Anders E Østergaard, Krzysztof P Lubieniecki, Samuel AM Martin, René JM Stet, William S Davidson and Christopher J Secombes

    Citation: BMC Genomics 2010 11:697

    Content type: Research article

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  3. Pax3 is a key upstream regulator of the onset of myogenesis, controlling progenitor cell survival and behaviour as well as entry into the myogenic programme. It functions in the dermomyotome of the somite from...

    Authors: Mounia Lagha, Takahiko Sato, Béatrice Regnault, Ana Cumano, Aimée Zuniga, Jonathan Licht, Frédéric Relaix and Margaret Buckingham

    Citation: BMC Genomics 2010 11:696

    Content type: Research article

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  4. The reptiles, characterized by both diversity and unique evolutionary adaptations, provide a comprehensive system for comparative studies of metabolism, physiology, and development. However, molecular resource...

    Authors: Tonia S Schwartz, Hongseok Tae, Youngik Yang, Keithanne Mockaitis, John L Van Hemert, Stephen R Proulx, Jeong-Hyeon Choi and Anne M Bronikowski

    Citation: BMC Genomics 2010 11:694

    Content type: Research article

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  5. An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome sc...

    Authors: Daniel Klevebring, Linn Fagerberg, Emma Lundberg, Olof Emanuelsson, Mathias Uhlén and Joakim Lundeberg

    Citation: BMC Genomics 2010 11:684

    Content type: Research article

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  6. The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still...

    Authors: David G Dineen, Markus Schröder, Desmond G Higgins and Pádraig Cunningham

    Citation: BMC Genomics 2010 11:677

    Content type: Research article

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  7. Age- and sex-related susceptibility to adverse drug reactions and disease is a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of hepatic genes expres...

    Authors: Joshua C Kwekel, Varsha G Desai, Carrie L Moland, William S Branham and James C Fuscoe

    Citation: BMC Genomics 2010 11:675

    Content type: Research article

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  8. Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. G...

    Authors: Eyal Seroussi, Giora Glick, Andrey Shirak, Emanuel Yakobson, Joel I Weller, Ephraim Ezra and Yoel Zeron

    Citation: BMC Genomics 2010 11:673

    Content type: Research article

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  9. The molecular mechanisms underlying the sex differences in human muscle morphology and function remain to be elucidated. The sex differences in the skeletal muscle transcriptome in both the resting state and f...

    Authors: Dongmei Liu, Maureen A Sartor, Gustavo A Nader, Laurie Gutmann, Mary K Treutelaar, Emidio E Pistilli, Heidi B IglayReger, Charles F Burant, Eric P Hoffman and Paul M Gordon

    Citation: BMC Genomics 2010 11:659

    Content type: Research article

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  10. About forty human diseases are caused by repeat instability mutations. A distinct subset of these diseases is the result of extreme expansions of polymorphic trinucleotide repeats; typically CAG repeats encodi...

    Authors: Vicki Whan, Matthew Hobbs, Sean McWilliam, David J Lynn, Ylva Strandberg Lutzow, Mehar Khatkar, William Barendse, Herman Raadsma and Ross L Tellam

    Citation: BMC Genomics 2010 11:654

    Content type: Research article

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  11. mRNA polyadenylation is an essential step of pre-mRNA processing in eukaryotes. Accurate prediction of the pre-mRNA 3'-end cleavage/polyadenylation sites is important for defining the gene boundaries and under...

    Authors: Malik Nadeem Akhtar, Syed Abbas Bukhari, Zeeshan Fazal, Raheel Qamar and Ilham A Shahmuradov

    Citation: BMC Genomics 2010 11:646

    Content type: Methodology article

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  12. A goal of the Bovine Genome Database (BGD; http://​BovineGenome.​org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in...

    Authors: Justin T Reese, Christopher P Childers, Jaideep P Sundaram, C Michael Dickens, Kevin L Childs, Donald C Vile and Christine G Elsik

    Citation: BMC Genomics 2010 11:645

    Content type: Database

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  13. Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activa...

    Authors: Jared V Goldstone, Andrew G McArthur, Akira Kubota, Juliano Zanette, Thiago Parente, Maria E Jönsson, David R Nelson and John J Stegeman

    Citation: BMC Genomics 2010 11:643

    Content type: Research article

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  14. Monocyte-derived macrophages and dendritic cells (DCs) are important in inflammatory processes and are often used for immunotherapeutic approaches. Blood monocytes can be differentiated into macrophages and DC...

    Authors: Liina Tserel, Raivo Kolde, Ana Rebane, Kai Kisand, Tõnis Org, Hedi Peterson, Jaak Vilo and Pärt Peterson

    Citation: BMC Genomics 2010 11:642

    Content type: Research article

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  15. The primary goal of genetic linkage analysis is to identify genes affecting a phenotypic trait. After localisation of the linkage region, efficient genetic dissection of the disease linked loci requires that f...

    Authors: Nik Cummings, Rob King, Andre Rickers, Antony Kaspi, Sebastian Lunke, Izhak Haviv and Jeremy BM Jowett

    Citation: BMC Genomics 2010 11:641

    Content type: Methodology article

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  16. The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite o...

    Authors: Lucile Soler, Matthew A Conte, Takayuki Katagiri, Aimee E Howe, Bo-Young Lee, Chris Amemiya, Andrew Stuart, Carole Dossat, Julie Poulain, Jeremy Johnson, Federica Di Palma, Kerstin Lindblad-Toh, Jean-Francois Baroiller, Helena D'Cotta, Catherine Ozouf-Costaz and Thomas D Kocher

    Citation: BMC Genomics 2010 11:636

    Content type: Research article

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  17. Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by...

    Authors: Deanna C Tremblay, Graham Alexander Jr, Shawn Moseley and Brian P Chadwick

    Citation: BMC Genomics 2010 11:632

    Content type: Research article

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  18. When selecting mates, many vertebrate species seek partners with major histocompatibility complex (MHC) genes different from their own, presumably in response to selective pressure against inbreeding and towar...

    Authors: Pouya Khankhanian, Pierre-Antoine Gourraud, Stacy J Caillier, Adam Santaniello, Stephen L Hauser, Sergio E Baranzini and Jorge R Oksenberg

    Citation: BMC Genomics 2010 11:626

    Content type: Research article

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  19. Infestation of ovine skin with the ectoparasitic mite Psoroptes ovis results in a rapid cutaneous immune response, leading to the crusted skin lesions characteristic of sheep scab. Little is known regarding the m...

    Authors: Stewart TG Burgess, David Frew, Francesca Nunn, Craig A Watkins, Tom N McNeilly, Alasdair J Nisbet and John F Huntley

    Citation: BMC Genomics 2010 11:624

    Content type: Research article

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  20. Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling marke...

    Authors: Seung-Hwan Lee, Cedric Gondro, Julius van der Werf, Nam-Kuk Kim, Da-jeong Lim, Eung-Woo Park, Sung-Jong Oh, John P Gibson and John M Thompson

    Citation: BMC Genomics 2010 11:623

    Content type: Research article

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  21. The chicken karyotype is composed of 39 chromosome pairs, of which 9 still remain totally absent from the current genome sequence assembly, despite international efforts towards complete coverage. Some others ...

    Authors: Romain Solinhac, Sophie Leroux, Svetlana Galkina, Olympe Chazara, Katia Feve, Florence Vignoles, Mireille Morisson, Svetlana Derjusheva, Bertrand Bed'hom, Alain Vignal, Valérie Fillon and Frédérique Pitel

    Citation: BMC Genomics 2010 11:616

    Content type: Research article

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  22. Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression...

    Authors: Björn Reinius, Chengxi Shi, Liu Hengshuo, Kuljeet Singh Sandhu, Katarzyna J Radomska, Glenn D Rosen, Lu Lu, Klas Kullander, Robert W Williams and Elena Jazin

    Citation: BMC Genomics 2010 11:614

    Content type: Research article

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  23. Dysregulated expression of microRNAs (miRNAs) has been previously observed in human cancer tissues and shown promise in defining tumor status. However, there is little information as to if or when expression c...

    Authors: Zhiguang Li, William S Branham, Stacey L Dial, Yexun Wang, Lei Guo, Leming Shi and Tao Chen

    Citation: BMC Genomics 2010 11:609

    Content type: Research article

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  24. Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consisten...

    Authors: Shoshana Greenberger, Erez Y Levanon, Nurit Paz-Yaacov, Aviv Barzilai, Michal Safran, Sivan Osenberg, Ninette Amariglio, Gideon Rechavi and Eli Eisenberg

    Citation: BMC Genomics 2010 11:608

    Content type: Research article

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  25. Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to id...

    Authors: Yuliaxis Ramayo-Caldas, Anna Castelló, Romi N Pena, Estefania Alves, Anna Mercadé, Carla A Souza, Ana I Fernández, Miguel Perez-Enciso and Josep M Folch

    Citation: BMC Genomics 2010 11:593

    Content type: Research article

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  26. The current study focused on the extent genetic diversity within a species (Mus musculus) affects gene co-expression network structure. To examine this issue, we have created a new mouse resource, a heterogeneous...

    Authors: Ovidiu D Iancu, Priscila Darakjian, Nicole AR Walter, Barry Malmanger, Denesa Oberbeck, John Belknap, Shannon McWeeney and Robert Hitzemann

    Citation: BMC Genomics 2010 11:585

    Content type: Research article

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  27. Two year cancer bioassays conducted by the National Toxicology Program have shown chronic exposure to dioxin-like compounds (DLCs) to lead to the development of both neoplastic and non-neoplastic lesions in th...

    Authors: Bladimir J Ovando, Corie A Ellison, Chad M Vezina and James R Olson

    Citation: BMC Genomics 2010 11:583

    Content type: Research article

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  28. Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray a...

    Authors: Siriluck Ponsuksili, Eduard Murani, Manfred Schwerin, Karl Schellander and Klaus Wimmers

    Citation: BMC Genomics 2010 11:572

    Content type: Research article

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  29. Rainbow trout are important fish for aquaculture and recreational fisheries and serves as a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and evol...

    Authors: Mohamed Salem, Caird E Rexroad III, Jiannan Wang, Gary H Thorgaard and Jianbo Yao

    Citation: BMC Genomics 2010 11:564

    Content type: Research article

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  30. Streptococcus suis serotype 2 (SS2), a major swine pathogen and an emerging zoonotic agent, has greatly challenged global public health. Systematical information about host immune response to the infection is imp...

    Authors: Ran Li, Anding Zhang, Bo Chen, Liu Teng, Ya Wang, Huanchun Chen and Meilin Jin

    Citation: BMC Genomics 2010 11:556

    Content type: Research article

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  31. Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in b...

    Authors: Cecilia Castaño-Sánchez, Kanako Fuji, Akiyuki Ozaki, Osamu Hasegawa, Takashi Sakamoto, Kagayaki Morishima, Ichiro Nakayama, Atsushi Fujiwara, Tetsuji Masaoka, Hiroyuki Okamoto, Kengo Hayashida, Michihira Tagami, Jun Kawai, Yoshihide Hayashizaki and Nobuaki Okamoto

    Citation: BMC Genomics 2010 11:554

    Content type: Research article

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  32. Thoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible ...

    Authors: Emmeline W Hill, Beatrice A McGivney, Jingjing Gu, Ronan Whiston and David E MacHugh

    Citation: BMC Genomics 2010 11:552

    Content type: Research article

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  33. The pivotal role of stress in the precipitation of psychiatric diseases such as depression is generally accepted. This study aims at the identification of genes that are directly or indirectly responding to st...

    Authors: Amalia Tsolakidou, Ludwig Czibere, Benno Pütz, Dietrich Trümbach, Markus Panhuysen, Jan M Deussing, Wolfgang Wurst, Inge Sillaber, Rainer Landgraf, Florian Holsboer and Theo Rein

    Citation: BMC Genomics 2010 11:546

    Content type: Research article

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  34. Macrophages play essential roles in both innate and adaptive immune responses. Bacteria require endotoxin, a complex lipopolysaccharide, for outer membrane permeability and the host interprets endotoxin as a s...

    Authors: Ceren Ciraci, Christopher K Tuggle, Michael J Wannemuehler, Dan Nettleton and Susan J Lamont

    Citation: BMC Genomics 2010 11:545

    Content type: Research article

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  35. There was a large scale outbreak of the highly pathogenic porcine reproductive and respiratory syndrome (PRRS) in China and Vietnam during 2006 and 2007 that resulted in unusually high morbidity and mortality ...

    Authors: Shuqi Xiao, Delin Mo, Qiwei Wang, Jianyu Jia, Limei Qin, Xiangchun Yu, Yuna Niu, Xiao Zhao, Xiaohong Liu and Yaosheng Chen

    Citation: BMC Genomics 2010 11:544

    Content type: Research article

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  36. The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent ...

    Authors: Nicole L Quinn, Keith A Boroevich, Krzysztof P Lubieniecki, William Chow, Evelyn A Davidson, Ruth B Phillips, Ben F Koop and William S Davidson

    Citation: BMC Genomics 2010 11:539

    Content type: Research article

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  37. In the past, molecular mechanisms that drive the initiation of an inflammatory response have been studied intensively. However, corresponding mechanisms that sustain the expression of inflammatory response gen...

    Authors: Astrid Riehl, Tobias Bauer, Benedikt Brors, Hauke Busch, Regina Mark, Julia Németh, Christoffer Gebhardt, Angelika Bierhaus, Peter Nawroth, Roland Eils, Rainer König, Peter Angel and Jochen Hess

    Citation: BMC Genomics 2010 11:537

    Content type: Research article

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  38. miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including mal...

    Authors: Ludwig Christian G Hinske, Pedro AF Galante, Winston P Kuo and Lucila Ohno-Machado

    Citation: BMC Genomics 2010 11:533

    Content type: Research article

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  39. Cellular senescence is a major barrier to tumour progression, though its role in pathogenesis of cancer and other diseases is poorly understood in vivo. Improved understanding of the degree to which latent sen...

    Authors: Kyle Lafferty-Whyte, Alan Bilsland, Claire J Cairney, Lorna Hanley, Nigel B Jamieson, Nadia Zaffaroni, Karin A Oien, Sharon Burns, Jon Roffey, Susan M Boyd and W Nicol Keith

    Citation: BMC Genomics 2010 11:532

    Content type: Research article

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  40. The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corres...

    Authors: Jocelyn Poissant, John T Hogg, Corey S Davis, Joshua M Miller, Jillian F Maddox and David W Coltman

    Citation: BMC Genomics 2010 11:524

    Content type: Research article

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  41. DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription fact...

    Authors: Mun-Kit Choy, Mehregan Movassagh, Hock-Guan Goh, Martin R Bennett, Thomas A Down and Roger SY Foo

    Citation: BMC Genomics 2010 11:519

    Content type: Research article

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  42. Despite rhabdoviral infections being one of the best known fish diseases, the gene expression changes induced at the surface tissues after the natural route of infection (infection-by-immersion) have not been ...

    Authors: Paloma Encinas, Miguel A Rodriguez-Milla, Beatriz Novoa, Amparo Estepa, Antonio Figueras and Julio Coll

    Citation: BMC Genomics 2010 11:518

    Content type: Research article

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  43. MicroRNAs (miRs or miRNAs) regulate several biological processes in the cell. However, evidence for miRNAs that control the differentiation program of specific neural cell types has been elusive. Recently, we ...

    Authors: Márcia M Aranha, Daniela M Santos, Joana M Xavier, Walter C Low, Clifford J Steer, Susana Solá and Cecília MP Rodrigues

    Citation: BMC Genomics 2010 11:514

    Content type: Research article

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  44. The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China suffering from severe outbreaks of infectious disease caused by marine bacteria such as Aeromonas hydrophila (A. h...

    Authors: Yinnan Mu, Feng Ding, Peng Cui, Jingqun Ao, Songnian Hu and Xinhua Chen

    Citation: BMC Genomics 2010 11:506

    Content type: Research article

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  45. The analysis of expression quantitative trait loci (eQTL) is a potentially powerful way to detect transcriptional regulatory relationships at the genomic scale. However, eQTL data sets often go underexploited ...

    Authors: Jacob J Michaelson, Rudi Alberts, Klaus Schughart and Andreas Beyer

    Citation: BMC Genomics 2010 11:502

    Content type: Methodology article

    Published on:

  46. A large proportion of pregnancy losses occur during the pre-implantation period, when the developing embryo is elongating rapidly and signalling its presence to the maternal system. The molecular mechanisms th...

    Authors: Caroline G Walker, Susanne Meier, Mathew D Littlejohn, Klaus Lehnert, John R Roche and Murray D Mitchell

    Citation: BMC Genomics 2010 11:474

    Content type: Research article

    Published on:

  47. Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing t...

    Authors: Li-xin Xiang, Ding He, Wei-ren Dong, Yi-wen Zhang and Jian-zhong Shao

    Citation: BMC Genomics 2010 11:472

    Content type: Research article

    Published on:

  48. The ovine Major Histocompatibility Complex (MHC) harbors clusters of genes involved in overall resistance/susceptibility of an animal to infectious pathogens. However, only a limited number of ovine MHC genes ...

    Authors: Jianfeng Gao, Ka Liu, Haibo Liu, Hugh T Blair, Gang Li, Chuangfu Chen, Pingping Tan and Runlin Z Ma

    Citation: BMC Genomics 2010 11:466

    Content type: Research article

    Published on:

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