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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 4 of 22

  1. Content type: Research article

    Although sleep deprivation is associated with neurobehavioral impairment that may underlie significant risks to performance and safety, there is no reliable biomarker test to detect dangerous levels of impairm...

    Authors: Hilary A. Uyhelji, Doris M. Kupfer, Vicky L. White, Melinda L. Jackson, Hans P. A. Van Dongen and Dennis M. Burian

    Citation: BMC Genomics 2018 19:341

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  2. Content type: Research article

    Circular RNAs (circRNAs) are a novel class of endogenous, non-coding RNAs that form covalently closed continuous loops and that are both highly conserved and abundant in the mammalian brain. A role for circRNA...

    Authors: Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger and Winnie S. Liang

    Citation: BMC Genomics 2018 19:340

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  3. Content type: Research article

    The Jurkat cell line has an extensive history as a model of T cell signaling. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line p...

    Authors: Louis Gioia, Azeem Siddique, Steven R. Head, Daniel R. Salomon and Andrew I. Su

    Citation: BMC Genomics 2018 19:334

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  4. Content type: Research article

    Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells w...

    Authors: Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason, Gina Vicente, Michael Dasilva, Wendy Brodeur, Timothy DeSmet, Sheila Dodge, Niall J. Lennon…

    Citation: BMC Genomics 2018 19:332

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  5. Content type: Research article

    CRISPR/Cas9 enables the targeting of genes in zygotes; however, efficient approaches to create loxP-flanked (floxed) alleles remain elusive.

    Authors: Yoshiki Miyasaka, Yoshihiro Uno, Kazuto Yoshimi, Yayoi Kunihiro, Takuji Yoshimura, Tomohiro Tanaka, Harumi Ishikubo, Yuichi Hiraoka, Norihiko Takemoto, Takao Tanaka, Yoshihiro Ooguchi, Paul Skehel, Tomomi Aida, Junji Takeda and Tomoji Mashimo

    Citation: BMC Genomics 2018 19:318

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  6. Content type: Research article

    In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense o...

    Authors: Rahul Kumar Jangid, Ashwin Kelkar, Vijaykumar Yogesh Muley and Sanjeev Galande

    Citation: BMC Genomics 2018 19:313

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  7. Content type: Research article

    Identifying functional non-coding variation is critical for defining the genetic contributions to human disease. While single-nucleotide polymorphisms (SNPs) within cis-acting transcriptional regulatory elements ...

    Authors: William D. Law, Elizabeth A. Fogarty, Aimée Vester and Anthony Antonellis

    Citation: BMC Genomics 2018 19:311

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  8. Content type: Research article

    Salmonella is a Gram-negative bacterium causing a wide range of clinical syndromes ranging from typhoid fever to diarrheic disease. Non-typhoidal Salmonella (NTS) serovars infect humans and animals, causing impor...

    Authors: Jing Zhang, Danielle Malo, Richard Mott, Jean-Jacques Panthier, Xavier Montagutelli and Jean Jaubert

    Citation: BMC Genomics 2018 19:303

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  9. Content type: Research article

    Emissions from diesel vehicles and biomass burning are the principal sources of primary ultrafine particles (UFP). The exposure to UFP has been associated to cardiovascular and pulmonary diseases, including lu...

    Authors: Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia and Marina Camatini

    Citation: BMC Genomics 2018 19:302

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  10. Content type: Research article

    Considering the implication of gene expression in the susceptibility of chronic diseases and the familial clustering of chronic diseases, the study of familial resemblances in gene expression levels is then hi...

    Authors: Bénédicte L. Tremblay, Frédéric Guénard, Benoît Lamarche, Louis Pérusse and Marie-Claude Vohl

    Citation: BMC Genomics 2018 19:300

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  11. Content type: Research article

    Cigarette smoking has severe adverse health consequences in adults and in the offspring of mothers who smoke during pregnancy. One of the most widely reported effects of smoking during pregnancy is reduced bir...

    Authors: Stephanie H. Witt, Josef Frank, Maria Gilles, Maren Lang, Jens Treutlein, Fabian Streit, Isabell A. C. Wolf, Verena Peus, Barbara Scharnholz, Tabea S. Send, Stefanie Heilmann-Heimbach, Sugirthan Sivalingam, Helene Dukal, Jana Strohmaier, Marc Sütterlin, Janine Arloth…

    Citation: BMC Genomics 2018 19:290

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  12. Content type: Research article

    Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human dev...

    Authors: Osagie G. Izuogu, Abd A. Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K. Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David J. Elliott, Mauro Santibanez-Koref and Michael S. Jackson

    Citation: BMC Genomics 2018 19:276

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  13. Content type: Methodology article

    Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read de...

    Authors: Jeroen van den Akker, Gilad Mishne, Anjali D. Zimmer and Alicia Y. Zhou

    Citation: BMC Genomics 2018 19:263

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  14. Content type: Software

    High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a spec...

    Authors: Zuguang Gu, Roland Eils, Matthias Schlesner and Naveed Ishaque

    Citation: BMC Genomics 2018 19:234

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  15. Content type: Methodology article

    Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Nex...

    Authors: Georgia Giannoukos, Dawn M. Ciulla, Eugenio Marco, Hayat S. Abdulkerim, Luis A. Barrera, Anne Bothmer, Vidya Dhanapal, Sebastian W. Gloskowski, Hariharan Jayaram, Morgan L. Maeder, Maxwell N. Skor, Tongyao Wang, Vic E. Myer and Christopher J. Wilson

    Citation: BMC Genomics 2018 19:212

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  16. Content type: Research article

    Aneuploidy, or abnormal chromosome numbers, severely alters cell physiology and is widespread in cancers and other pathologies. Using model cell lines engineered to carry one or more extra chromosomes, it has ...

    Authors: Milena Dürrbaum, Christine Kruse, K. Julia Nieken, Bianca Habermann and Zuzana Storchová

    Citation: BMC Genomics 2018 19:197

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  17. Content type: Research article

    The murine discs large homolog 2 (DLG2; post synaptic density 93 (PSD-93); Chapsyn-110) is a member of the membrane-associated guanylate kinase (MAGUK) protein family involved in receptor assembly and associat...

    Authors: Shafaqat Ali, Alexander Hoven, Regine J. Dress, Heiner Schaal, Judith Alferink and Stefanie Scheu

    Citation: BMC Genomics 2018 19:194

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  18. Content type: Research article

    Noninvasive biomarkers are urgently needed for patients with nonalcoholic steatohepatitis (NASH) to assist in diagnosis, monitoring disease progression and assessing treatment response. Recently several explor...

    Authors: Jie Liu, Yue Xiao, Xikun Wu, Lichun Jiang, Shurong Yang, Zhiming Ding, Zhuo Fang, Haiqing Hua, Mark Stephen Kirby and Jianyong Shou

    Citation: BMC Genomics 2018 19:188

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  19. Content type: Research article

    The generation of induced pluripotent stem cells (iPSCs) has underdefined mechanisms. In addition, leukemia inhibitory factor (LIF) activated Janus kinase/signal transducer and activator of transcription 3 (JA...

    Authors: Ling Wang, Zongliang Jiang, Delun Huang, Jingyue Duan, Chang Huang, Shannon Sullivan, Kaneha Vali, Yexuan Yin, Ming Zhang, Jill Wegrzyn, Xiuchun ( Cindy) Tian and Young Tang

    Citation: BMC Genomics 2018 19:183

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  20. Content type: Methodology article

    The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of who...

    Authors: Casey L. Dagnall, Lindsay M. Morton, Belynda D. Hicks, Shengchao Li, Weiyin Zhou, Eric Karlins, Kedest Teshome, Salma Chowdhury, Kerrie S. Lashley, Joshua N. Sampson, Leslie L. Robison, Gregory T. Armstrong, Smita Bhatia, Gretchen A. Radloff, Stella M. Davies, Margaret A. Tucker…

    Citation: BMC Genomics 2018 19:182

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  21. Content type: Research article

    Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. H...

    Authors: Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Sougat Misra, Carsten O. Daub, Juha Kere and Peter Swoboda

    Citation: BMC Genomics 2018 19:181

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  22. Content type: Research article

    Gestational disorders such as intrauterine growth restriction (IUGR) and pre-eclampsia (PE) are main causes of poor perinatal outcomes worldwide. Both diseases are related with impaired materno-fetal nutrient ...

    Authors: Xiao Huang, Pascale Anderle, Lu Hostettler, Marc U. Baumann, Daniel V. Surbek, Edgar C. Ontsouka and Christiane Albrecht

    Citation: BMC Genomics 2018 19:173

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  23. Content type: Software

    ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin...

    Authors: Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson and Lihua Julie Zhu

    Citation: BMC Genomics 2018 19:169

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  24. Content type: Methodology article

    The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics an...

    Authors: Oluwatosin Oluwadare, Yuxiang Zhang and Jianlin Cheng

    Citation: BMC Genomics 2018 19:161

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  25. Content type: Research article

    Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have th...

    Authors: Gergely Ivády, László Madar, Erika Dzsudzsák, Katalin Koczok, János Kappelmayer, Veronika Krulisova, Milan Macek Jr, Attila Horváth and István Balogh

    Citation: BMC Genomics 2018 19:158

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  26. Content type: Research article

    Chromocenters are defined as a punctate condensed blocks of chromatin in the interphase cell nuclei of certain cell types with unknown biological significance. In recent years a progress in revealing of chromo...

    Authors: Dmitrii I. Ostromyshenskii, Ekaterina N. Chernyaeva, Inna S. Kuznetsova and Olga I. Podgornaya

    Citation: BMC Genomics 2018 19:151

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  27. Content type: Research article

    Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

    Authors: Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi…

    Citation: BMC Genomics 2018 19:150

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  28. Content type: Methodology article

    Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have ...

    Authors: Jian Wu, Wei Dai, Lin Wu and Jinke Wang

    Citation: BMC Genomics 2018 19:143

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    The Correction to this article has been published in BMC Genomics 2018 19:327

  29. Content type: Research article

    Comprehensive understanding of intratumor heterogeneity requires identification of molecular markers, which are capable of differentiating different subpopulations and which also have clinical significance. On...

    Authors: Fan Wang, Zachariah Dohogne, Jin Yang, Yu Liu and Benjamin Soibam

    Citation: BMC Genomics 2018 19:137

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  30. Content type: Research article

    Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A ...

    Authors: Qiuyan Li, Kexian Dong, Lidan Xu, Xueyuan Jia, Jie Wu, Wenjing Sun, Xuelong Zhang and Songbin Fu

    Citation: BMC Genomics 2018 19:134

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  31. Content type: Methodology article

    Transposable elements (TEs) are mobile genetic sequences that randomly propagate within their host’s genome. This mobility has the potential to affect gene transcription and cause disease. However, TEs are tec...

    Authors: Erika M. Kvikstad, Paolo Piazza, Jenny C. Taylor and Gerton Lunter

    Citation: BMC Genomics 2018 19:115

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  32. Content type: Research article

    Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under co...

    Authors: Qingzhou Guan, Haidan Yan, Yanhua Chen, Baotong Zheng, Hao Cai, Jun He, Kai Song, You Guo, Lu Ao, Huaping Liu, Wenyuan Zhao, Xianlong Wang and Zheng Guo

    Citation: BMC Genomics 2018 19:99

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  33. Content type: Research article

    SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing...

    Authors: Soheil Yousefi, Tooba Abbassi-Daloii, Thirsa Kraaijenbrink, Martijn Vermaat, Hailiang Mei, Peter van ‘t Hof, Maarten van Iterson, Daria V. Zhernakova, Annique Claringbould, Lude Franke, Leen M. ‘t Hart, Roderick C. Slieker, Amber van der Heijden, Peter de Knijff and Peter A. C. ’t Hoen

    Citation: BMC Genomics 2018 19:90

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  34. Content type: Research article

    Migraine is a common heritable neurovascular disorder typically characterised by episodic attacks of severe pulsating headache and nausea, often accompanied by visual, auditory or other sensory symptoms. Altho...

    Authors: Zachary F. Gerring, Allan F. McRae, Grant W. Montgomery and Dale R. Nyholt

    Citation: BMC Genomics 2018 19:69

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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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