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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 24

  1. Piwi interacting RNA, or piRNA, is a class of small RNA almost exclusively expressed in the germline where they serve essential roles in retrotransposon silencing. There are two types, primary and secondary pi...

    Authors: Harald M Oey, Neil A Youngson and Emma Whitelaw

    Citation: BMC Genomics 2011 12:315

    Content type: Research article

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  2. DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have develope...

    Authors: Srinivasan Yegnasubramanian, Zhijin Wu, Michael C Haffner, David Esopi, Martin J Aryee, Raghav Badrinath, Tony L He, James D Morgan, Benilton Carvalho, Qizhi Zheng, Angelo M De Marzo, Rafael A Irizarry and William G Nelson

    Citation: BMC Genomics 2011 12:313

    Content type: Research article

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  3. Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits o...

    Authors: Gloria L Fawcett, Muthuswamy Raveendran, David Rio Deiros, David Chen, Fuli Yu, Ronald Alan Harris, Yanru Ren, Donna M Muzny, Jeffrey G Reid, David A Wheeler, Kimberly C Worley, Steven E Shelton, Ned H Kalin, Aleksandar Milosavljevic, Richard Gibbs and Jeffrey Rogers

    Citation: BMC Genomics 2011 12:311

    Content type: Research article

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  4. The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the...

    Authors: Ulrich C Klostermeier, Matthias Barann, Michael Wittig, Robert Häsler, Andre Franke, Olga Gavrilova, Benjamin Kreck, Christian Sina, Markus B Schilhabel, Stefan Schreiber and Philip Rosenstiel

    Citation: BMC Genomics 2011 12:305

    Content type: Research article

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  5. Glucagon is an important hormone in the regulation of glucose homeostasis, particularly in the maintenance of euglycemia and prevention of hypoglycemia. In type 2 Diabetes Mellitus (T2DM), glucagon levels are ...

    Authors: Jianxin Yang, Margit L MacDougall, Michael T McDowell, Li Xi, Ru Wei, William J Zavadoski, Mark P Molloy, John D Baker, Max Kuhn, Over Cabrera and Judith L Treadway

    Citation: BMC Genomics 2011 12:281

    Content type: Research article

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  6. Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding ...

    Authors: Edith Hofer, Gerhard T Laschober, Matthias Hackl, Gerhard G Thallinger, Günter Lepperdinger, Johannes Grillari, Pidder Jansen-Dürr and Zlatko Trajanoski

    Citation: BMC Genomics 2011 12:262

    Content type: Database

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  7. In highly copy number variable (CNV) regions such as the human defensin gene locus, comprehensive assessment of sequence variations is challenging. PCR approaches are practically restricted to tiny fractions, ...

    Authors: Stefan Taudien, Karol Szafranski, Marius Felder, Marco Groth, Klaus Huse, Francesca Raffaelli, Andreas Petzold, Xinmin Zhang, Philip Rosenstiel, Jochen Hampe, Stefan Schreiber and Matthias Platzer

    Citation: BMC Genomics 2011 12:243

    Content type: Research article

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  8. Changes in DNA methylation in the mammalian genome during development are frequent events and play major roles regulating gene expression and other developmental processes. It is necessary to identify these ev...

    Authors: Ping Liang, Fei Song, Srimoyee Ghosh, Evan Morien, Maochun Qin, Saleh Mahmood, Kyoko Fujiwara, Jun Igarashi, Hiroki Nagase and William A Held

    Citation: BMC Genomics 2011 12:231

    Content type: Research article

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  9. While an increase in bone marrow adiposity is associated with age-related bone disease, the function of bone marrow adipocytes has not been studied. The aim of this study was to characterize and compare the ag...

    Authors: Li-Fen Liu, Wen-Jun Shen, Masami Ueno, Shailja Patel and Fredric B Kraemer

    Citation: BMC Genomics 2011 12:212

    Content type: Research article

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  10. Humans and mice with loss of function mutations in GPR54 (KISS1R) or kisspeptin do not progress through puberty, caused by a failure to release GnRH. The transcriptional networks regulated by these proteins in...

    Authors: Leah M Prentice, Xavier d'Anglemont de Tassigny, Steven McKinney, Teresa Ruiz de Algara, Damian Yap, Gulisa Turashvili, Steven Poon, Margaret Sutcliffe, Pat Allard, Angela Burleigh, John Fee, David G Huntsman, William H Colledge and Samuel AJ Aparicio

    Citation: BMC Genomics 2011 12:209

    Content type: Research article

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  11. The proximal region of murine Chr 2 has long been known to harbour one or more imprinted genes from classic genetic studies involving reciprocal translocations. No imprinted gene had been identified from this ...

    Authors: Qianwei Wang, Jacqueline Chow, Jenny Hong, Anne Ferguson Smith, Carol Moreno, Peter Seaby, Paul Vrana, Kamelia Miri, Joon Tak, Eu Ddeum Chung, Gabriela Mastromonaco, Isabella Caniggia and Susannah Varmuza

    Citation: BMC Genomics 2011 12:204

    Content type: Research article

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  12. Significant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well.

    Authors: Zakharia M Frenkel, Thomas Bettecken and Edward N Trifonov

    Citation: BMC Genomics 2011 12:203

    Content type: Research article

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  13. The decline noticed in several fertility traits of dairy cattle over the past few decades is of major concern. Understanding of the genomic factors underlying fertility, which could have potential applications...

    Authors: Arun Kommadath, Henri Woelders, Bonne Beerda, Herman A Mulder, Agnes AC de Wit, Roel F Veerkamp, Marinus FW te Pas and Mari A Smits

    Citation: BMC Genomics 2011 12:200

    Content type: Research article

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  14. Nerve growth factor (NGF) is a potent growth factor that plays a key role in neuronal cell differentiation and may also play a role in hematopoietic differentiation. It has been shown that NGF induced synergis...

    Authors: Priyanka Dutta, Alexandra Koch, Bjoern Breyer, Heike Schneider, Oliver Dittrich-Breiholz, Michael Kracht and Teruko Tamura

    Citation: BMC Genomics 2011 12:196

    Content type: Research article

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  15. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that elicits a broad spectrum of toxic effects in a species-specific manner. Current risk assessment practices routinely extrapolate resu...

    Authors: Edward Dere, Andrea W Lee, Lyle D Burgoon and Timothy R Zacharewski

    Citation: BMC Genomics 2011 12:193

    Content type: Research article

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  16. MicroRNAs (miRNAs) are important genetic elements that regulate the expression of thousands of human genes. Polymorphisms affecting miRNA biogenesis, dosage and target recognition may represent potentially fun...

    Authors: Malgorzata Marcinkowska, Maciej Szymanski, Wlodzimierz J Krzyzosiak and Piotr Kozlowski

    Citation: BMC Genomics 2011 12:183

    Content type: Research article

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  17. Diet plays a role on the development of the immune system, and polyunsaturated fatty acids can modulate the expression of a variety of genes. Human milk contains conjugated linoleic acid (CLA), a fatty acid th...

    Authors: Elisabet Selga, Francisco J Pérez-Cano, Àngels Franch, Carolina Ramírez-Santana, Montserrat Rivero, Carlos J Ciudad, Cristina Castellote and Véronique Noé

    Citation: BMC Genomics 2011 12:182

    Content type: Research article

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  18. MicroRNAs (miRNAs) are small non-coding RNAs that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. Characterisation of miRNAs in ad...

    Authors: King-Hwa Ling, Peter J Brautigan, Christopher N Hahn, Tasman Daish, John R Rayner, Pike-See Cheah, Joy M Raison, Sandra Piltz, Jeffrey R Mann, Deidre M Mattiske, Paul Q Thomas, David L Adelson and Hamish S Scott

    Citation: BMC Genomics 2011 12:176

    Content type: Research article

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  19. The typical objective of Genome-wide association (GWA) studies is to identify single-nucleotide polymorphisms (SNPs) and corresponding genes with the strongest evidence of association (the 'most-significant SN...

    Authors: Annarita D'Addabbo, Orazio Palmieri, Anna Latiano, Vito Annese, Sayan Mukherjee and Nicola Ancona

    Citation: BMC Genomics 2011 12:166

    Content type: Software

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  20. The sheep is an important model organism for many types of medically relevant research, but molecular genetic experiments in the sheep have been limited by the lack of knowledge about ovine gene sequences.

    Authors: Marten Jäger, Claus-Eric Ott, Johannes Grünhagen, Jochen Hecht, Hanna Schell, Stefan Mundlos, Georg N Duda, Peter N Robinson and Jasmin Lienau

    Citation: BMC Genomics 2011 12:158

    Content type: Research article

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  21. The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and...

    Authors: Søren F Schmidt, Mette Jørgensen, Yun Chen, Ronni Nielsen, Albin Sandelin and Susanne Mandrup

    Citation: BMC Genomics 2011 12:152

    Content type: Research article

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  22. Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human ...

    Authors: Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard and Curt P Van Tassell

    Citation: BMC Genomics 2011 12:127

    Content type: Research article

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  23. The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related...

    Authors: Vonick Sibut, Christelle Hennequet-Antier, Elisabeth Le Bihan-Duval, Sylvain Marthey, Michel J Duclos and Cécile Berri

    Citation: BMC Genomics 2011 12:112

    Content type: Research article

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  24. C57BL/6J mice possess a single intelectin (Itln) gene on chromosome 1. The function of intelectins is not well understood, but roles have been postulated in insulin sensitivity, bacterial recognition, intestinal ...

    Authors: Zen H Lu, Alex di Domenico, Steven H Wright, Pamela A Knight, C Bruce A Whitelaw and Alan D Pemberton

    Citation: BMC Genomics 2011 12:110

    Content type: Research article

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  25. Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The reso...

    Authors: Phuong Nguyen, Jing Ma, Deqing Pei, Caroline Obert, Cheng Cheng and Terrence L Geiger

    Citation: BMC Genomics 2011 12:106

    Content type: Research article

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  26. Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations ...

    Authors: Ryouka Kawahara-Miki, Kaoru Tsuda, Yuh Shiwa, Yuko Arai-Kichise, Takashi Matsumoto, Yu Kanesaki, Sen-ichi Oda, Shizufumi Ebihara, Shunsuke Yajima, Hirofumi Yoshikawa and Tomohiro Kono

    Citation: BMC Genomics 2011 12:103

    Content type: Research article

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  27. In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but al...

    Authors: Alexei A Sharov, Akira Nishiyama, Yulan Piao, Lina S Correa-Cerro, Tomokazu Amano, Marshall Thomas, Samir Mehta and Minoru SH Ko

    Citation: BMC Genomics 2011 12:102

    Content type: Research article

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  28. Several approaches have been developed for miRNA target prediction, including methods that incorporate expression profiling. However the methods are still in need of improvements due to a high false discovery ...

    Authors: Claus H Bang-Berthelsen, Lykke Pedersen, Tina Fløyel, Peter H Hagedorn, Titus Gylvin and Flemming Pociot

    Citation: BMC Genomics 2011 12:97

    Content type: Research article

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  29. Divergently selected Lean and Fat mouse lines represent unique models for a polygenic form of resistance and susceptibility to obesity development. Previous research on these lines focused mainly on obesity-su...

    Authors: Matjaž Simončič, Tadeja Režen, Peter Juvan, Damjana Rozman, Gregor Fazarinc, Catherine Fievet, Bart Staels and Simon Horvat

    Citation: BMC Genomics 2011 12:96

    Content type: Research article

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  30. Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more compl...

    Authors: Hindrik HD Kerstens, Richard PMA Crooijmans, Bert W Dibbits, Addie Vereijken, Ron Okimoto and Martien AM Groenen

    Citation: BMC Genomics 2011 12:94

    Content type: Methodology article

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  31. Chinese hamster ovary (CHO) cells are among the most widely used hosts for therapeutic protein production. Yet few genomic resources are available to aid in engineering high-producing cell lines.

    Authors: Stephanie Hammond, Jeffrey C Swanberg, Mihailo Kaplarevic and Kelvin H Lee

    Citation: BMC Genomics 2011 12:67

    Content type: Research article

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  32. Scanning the genome with high density SNP markers has become a standard approach for identifying regions of the genome showing substantial between-population genetic differentiation, and thus evidence of diver...

    Authors: Pamela Wiener, Mohammad A Edriss, John L Williams, David Waddington, Andrew Law, John A Woolliams and Beatriz Gutiérrez-Gil

    Citation: BMC Genomics 2011 12:65

    Content type: Research article

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  33. The bi-directional communication between the oocyte and its companion cumulus cells (CCs) is crucial for development and functions of both cell types. Transcripts that are exclusively expressed either in oocyt...

    Authors: A Regassa, F Rings, M Hoelker, U Cinar, E Tholen, C Looft, K Schellander and D Tesfaye

    Citation: BMC Genomics 2011 12:57

    Content type: Research article

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  34. Identifying the functional importance of the millions of single nucleotide polymorphisms (SNPs) in the human genome is a difficult challenge. Therefore, a reverse strategy, which identifies functionally import...

    Authors: Muna Affara, Benjamin J Dunmore, Deborah A Sanders, Nicola Johnson, Cristin G Print and D Stephen Charnock-Jones

    Citation: BMC Genomics 2011 12:43

    Content type: Research article

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  35. Comprehensive sequence characterization across the MHC is important for successful organ transplantation and genetic association studies. To this end, we have developed an automated sample preparation, molecul...

    Authors: Rachel L Erlich, Xiaoming Jia, Scott Anderson, Eric Banks, Xiaojiang Gao, Mary Carrington, Namrata Gupta, Mark A DePristo, Matthew R Henn, Niall J Lennon and Paul IW de Bakker

    Citation: BMC Genomics 2011 12:42

    Content type: Methodology article

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  36. Pathogen-associated molecular patterns (PAMPs) are structural components of pathogens such as lipopolysaccharide (LPS) and peptidoglycan (PGN) from bacterial cell walls. PAMP-recognition by the host results in...

    Authors: Sebastian Boltaña, Felipe Reyes-Lopez, Davinia Morera, Frederick Goetz and Simon A MacKenzie

    Citation: BMC Genomics 2011 12:34

    Content type: Research article

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  37. Stem cells and their niches are studied in many systems, but mammalian germ stem cells (GSC) and their niches are still poorly understood. In rat testis, spermatogonia and undifferentiated Sertoli cells prolif...

    Authors: Stephan Ryser, Dominique Glauser, Michelle Vigier, Yong Qiang Zhang, Philippe Tachini, Werner Schlegel, Philippe Durand and Irmgard Irminger-Finger

    Citation: BMC Genomics 2011 12:29

    Content type: Research article

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  38. The epigenetic regulator Histone Deacetylase 1 (Hdac1) is required for specification and patterning of neurones and myelinating glia during development of the vertebrate central nervous system (CNS). This co-o...

    Authors: Michael RM Harrison, Aristophanes S Georgiou, Herman P Spaink and Vincent T Cunliffe

    Citation: BMC Genomics 2011 12:24

    Content type: Research article

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  39. Gene regulation by transcription factors (TF) is species, tissue and time specific. To better understand how the genetic code controls gene expression in bovine muscle we associated gene expression data from d...

    Authors: Quan Gu, Shivashankar H Nagaraj, Nicholas J Hudson, Brian P Dalrymple and Antonio Reverter

    Citation: BMC Genomics 2011 12:23

    Content type: Research article

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  40. Recent progress in exploring the Y-chromosome gene content in humans, mice and cats have suggested that "autosome-to-Y" transposition of the male fertility genes is a recurrent theme during the mammalian Y-chr...

    Authors: Yang Yang, Ti-Cheng Chang, Hiroshi Yasue, Arvind K Bharti, Ernest F Retzel and Wan-Sheng Liu

    Citation: BMC Genomics 2011 12:13

    Content type: Research article

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  41. SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. SOX2 appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed res...

    Authors: Xuefeng Fang, Jae-Geun Yoon, Lisha Li, Wei Yu, Jiaofang Shao, Dasong Hua, Shu Zheng, Leroy Hood, David R Goodlett, Gregory Foltz and Biaoyang Lin

    Citation: BMC Genomics 2011 12:11

    Content type: Research article

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  42. Acute enteritis caused by Salmonella is a public health concern. Salmonella infection is also known to increase the risk of inflammatory bowel diseases and cancer. Therefore, it is important to understand how Sal...

    Authors: Xingyin Liu, Rong Lu, Yinglin Xia and Jun Sun

    Citation: BMC Genomics 2010 11:722

    Content type: Research article

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  43. Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest i...

    Authors: Rune Andreassen, Sigbjørn Lunner and Bjørn Høyheim

    Citation: BMC Genomics 2010 11:706

    Content type: Research article

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  44. 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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