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BMC Genomics

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.

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  1. Content type: Research article

    The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references. This hinders the correct identification of varian...

    Authors: Mahmoud Koko, Mohammed O. E. Abdallah, Mutaz Amin and Muntaser Ibrahim

    Citation: BMC Genomics 2018 19:46

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  2. Content type: Methodology article

    Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious disease...

    Authors: Yang Jiao, Ran Li, Chao Wu, Yibin Ding, Yanning Liu, Danmei Jia, Lifeng Wang, Xiang Xu, Jing Zhu, Min Zheng and Junling Jia

    Citation: BMC Genomics 2018 19:50

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  3. Content type: Methodology article

    Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that n...

    Authors: Eirini-Stavroula Komseli, Ioannis S. Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V. Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P. Zampetidis, Sentiljana Gumeni, Ioannis P. Trougakos, Dafni-Eleftheria Pefani, Eric O’Neill, Sarantis Gagos…

    Citation: BMC Genomics 2018 19:37

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  4. Content type: Research article

    Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigation...

    Authors: Laura E. MacConaill, Robert T. Burns, Anwesha Nag, Haley A. Coleman, Michael K. Slevin, Kristina Giorda, Madelyn Light, Kevin Lai, Mirna Jarosz, Matthew S. McNeill, Matthew D. Ducar, Matthew Meyerson and Aaron R. Thorner

    Citation: BMC Genomics 2018 19:30

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  5. Content type: Research article

    Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. We used the highly accurate microfluid...

    Authors: Hiba Zaidan, Gokul Ramaswami, Yaela N. Golumbic, Noa Sher, Assaf Malik, Michal Barak, Dalia Galiani, Nava Dekel, Jin B. Li and Inna Gaisler-Salomon

    Citation: BMC Genomics 2018 19:28

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  6. Content type: Methodology article

    Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumouri...

    Authors: Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi and Isabella Castiglioni

    Citation: BMC Genomics 2018 19:25

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  7. Content type: Methodology article

    Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using Hig...

    Authors: Maurizio Callari, Ankita Sati Batra, Rajbir Nath Batra, Stephen-John Sammut, Wendy Greenwood, Harry Clifford, Colin Hercus, Suet-Feung Chin, Alejandra Bruna, Oscar M. Rueda and Carlos Caldas

    Citation: BMC Genomics 2018 19:19

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  8. Content type: Research article

    Human induced pluripotent stem cells (hiPSCs) have been attempted for clinical application with diverse iPSCs sources derived from various cell types. This proposes that there would be a shared reprogramming r...

    Authors: Akihiro Kuno, Ken Nishimura and Satoru Takahashi

    Citation: BMC Genomics 2018 19:9

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  9. Content type: Research article

    Studies investigating associations between ACTN3 R577X and ACE I/D genotypes and endurance athletic status have been limited by small sample sizes from mixed sport disciplines and lack quantitative measures of pe...

    Authors: Ioannis D. Papadimitriou, Sarah J. Lockey, Sarah Voisin, Adam J. Herbert, Fleur Garton, Peter J. Houweling, Pawel Cieszczyk, Agnieszka Maciejewska-Skrendo, Marek Sawczuk, Myosotis Massidda, Carla Maria Calò, Irina V. Astratenkova, Anastasia Kouvatsi, Anastasiya M. Druzhevskaya, Macsue Jacques, Ildus I. Ahmetov…

    Citation: BMC Genomics 2018 19:13

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  10. Content type: Research Article

    The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key...

    Authors: David Martín-Gálvez, Denis Dunoyer de Segonzac, Man Chun John Ma, Anne E. Kwitek, David Thybert and Paul Flicek

    Citation: BMC Genomics 2017 18:986

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  11. Content type: Research article

    Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matri...

    Authors: Bing Li, Karthika Balasubramanian, Deborah Krakow and Daniel H. Cohn

    Citation: BMC Genomics 2017 18:983

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  12. Content type: Research article

    Previous studies have confirmed a family risk of nephrolithiasis (NL), but only 15% of all cases are associated with an identified monogenic factor. In clinical practice, our group encountered a patient with N...

    Authors: Zhenxing Yang, Tao Zhou, Bishao Sun, Qingqing Wang, Xingyou Dong, Xiaoyan Hu, Jiangfan Zhong, Bo Song and Longkun Li

    Citation: BMC Genomics 2017 18:982

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  13. Content type: Research article

    The transition from a high forage to a highly fermentable diet can induce digestive disorders in the rumen. To date, the host mechanisms that regulate the adaption to such dietary transition are largely unknow...

    Authors: K. Zhao, Y. H. Chen, G. B. Penner, M. Oba and L. L. Guan

    Citation: BMC Genomics 2017 18:976

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  14. Content type: Research Article

    Cytosine methylation is a stable epigenetic modification of DNA that plays an important role in both normal physiology and disease. Most diseases exhibit some degree of sexual dimorphism, but the extent to whi...

    Authors: Helen McCormick, Paul E. Young, Suzy S. J. Hur, Keith Booher, Hunter Chung, Jennifer E. Cropley, Eleni Giannoulatou and Catherine M. Suter

    Citation: BMC Genomics 2017 18:966

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  15. Content type: Research article

    The chemosensory system plays an important role in orchestrating sexual behaviors in mammals. Pheromones trigger sexually dimorphic behaviors and different mouse strains exhibit differential responses to phero...

    Authors: Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson and C. Ron Yu

    Citation: BMC Genomics 2017 18:965

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  16. Content type: Research Article

    DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is ex...

    Authors: Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand and Marcos J. Araúzo-Bravo

    Citation: BMC Genomics 2017 18:964

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  17. Content type: Research article

    The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict traj...

    Authors: Xianbin Su, Yi Shi, Xin Zou, Zhao-Ning Lu, Gangcai Xie, Jean Y. H. Yang, Chong-Chao Wu, Xiao-Fang Cui, Kun-Yan He, Qing Luo, Yu-Lan Qu, Na Wang, Lan Wang and Ze-Guang Han

    Citation: BMC Genomics 2017 18:946

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  18. Content type: Methodology article

    Significant human diseases/phenotypes exist which require both an environmental trigger event and a genetic predisposition before the disease/phenotype emerges, e.g. Carbamazepine with the rare SNP allele of r...

    Authors: Kaitlin Stouffer, Michael Nahorski, Pablo Moreno, Nivedita Sarveswaran, David Menon, Michael Lee and C. Geoffrey Woods

    Citation: BMC Genomics 2017 18:944

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  19. Content type: Methodology article

    Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic...

    Authors: Hidenobu Segawa, Yoji Kukita and Kikuya Kato

    Citation: BMC Genomics 2017 18:914

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  20. Content type: Methodology article

    Single-cell genome sequencing provides high-resolution details of the clonal genomic modifications that occur during cancer initiation, progression, and ongoing evolution as patients undergo treatment. One lim...

    Authors: John Easton, Veronica Gonzalez-Pena, Donald Yergeau, Xiaotu Ma and Charles Gawad

    Citation: BMC Genomics 2017 18:906

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