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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 1 of 20

  1. Content type: Review

    The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majori...

    Authors: K. Blighe, L. DeDionisio, K. A. Christie, B. Chawes, S. Shareef, T. Kakouli-Duarte, C. Chao-Shern, V. Harding, R. S. Kelly, L. Castellano, J. Stebbing, J. A. Lasky-Su, M. A. Nesbit and C. B. T. Moore

    Citation: BMC Genomics 2018 19:595

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  2. Content type: Research article

    Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4...

    Authors: Weijing Cai, Dapeng Zhou, Weibo Wu, Wen Ling Tan, Jiaqian Wang, Caicun Zhou and Yanyan Lou

    Citation: BMC Genomics 2018 19:582

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  3. Content type: Research article

    3,4-methylenedioxymethamphetamine (MDMA, “ecstasy”) is a widely used entactogenic drug known to impair cognitive functions on the long-run. Both hippocampal and frontal cortical regions have well established r...

    Authors: Peter Petschner, Viola Tamasi, Csaba Adori, Eszter Kirilly, Romeo D. Ando, Laszlo Tothfalusi and Gyorgy Bagdy

    Citation: BMC Genomics 2018 19:580

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  4. Content type: Research article

    N6-methyladenosine (m6A) is an important epigenetic modification which plays various roles in mRNA metabolism and embryogenesis directly related to human diseases. To identify m6A in a large scale, machine learni...

    Authors: Zhixun Zhao, Hui Peng, Chaowang Lan, Yi Zheng, Liang Fang and Jinyan Li

    Citation: BMC Genomics 2018 19:574

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  5. Content type: Research article

    Human neutrophils are central players in innate immunity, a major component of inflammatory responses, and a leading model for cell motility and chemotaxis. However, primary neutrophils are short-lived, limiti...

    Authors: Esther Rincón, Briana L. Rocha-Gregg and Sean R. Collins

    Citation: BMC Genomics 2018 19:573

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  6. Content type: Methodology article

    Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of mole...

    Authors: Thomas J. F. Pranzatelli, Drew G. Michael and John A. Chiorini

    Citation: BMC Genomics 2018 19:563

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  7. Content type: Research article

    Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify ...

    Authors: Jun Yasuda, Fumiki Katsuoka, Inaho Danjoh, Yosuke Kawai, Kaname Kojima, Masao Nagasaki, Sakae Saito, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N. Motoike, Kazuki Kumada, Mika Sakurai-Yageta, Osamu Tanabe, Nobuo Fuse, Gen Tamiya, Koichiro Higasa…

    Citation: BMC Genomics 2018 19:551

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  8. Content type: Research article

    Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberran...

    Authors: Yuhong Dou, Yong Zhu, Junmei Ai, Hankui Chen, Helu Liu, Jeffrey A. Borgia, Xiao Li, Fan Yang, Bin Jiang, Jun Wang and Youping Deng

    Citation: BMC Genomics 2018 19:545

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  9. Content type: Research article

    Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (lncRNAs) are ...

    Authors: Seong Hyeon Hong, Jun Tae Kwon, Jihye Kim, Juri Jeong, Jaehwan Kim, Seonhee Lee and Chunghee Cho

    Citation: BMC Genomics 2018 19:539

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  10. Content type: Research article

    Esophageal squamous cell carcinomas (ESCC) is the fourth most lethal cancer in China. Previous studies reveal several highly conserved mutational processes in ESCC. However, it remains unclear what are the tru...

    Authors: Jintao Guo, Jiankun Huang, Ying Zhou, Yulin Zhou, Liying Yu, Huili Li, Lingyun Hou, Liuwei Zhu, Dandan Ge, Yuanyuan Zeng, Bayasi Guleng and Qiyuan Li

    Citation: BMC Genomics 2018 19:538

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  11. Content type: Methodology article

    Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome...

    Authors: John Cologne, Lenora Loo, Yurii B. Shvetsov, Munechika Misumi, Philip Lin, Christopher A. Haiman, Lynne R. Wilkens and Loïc Le Marchand

    Citation: BMC Genomics 2018 19:524

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  12. Content type: Research article

    Human Endogenous Retroviruses (HERVs) and Mammalian apparent LTR-retrotransposons (MaLRs) represent the 8% of our genome and are distributed among our 46 chromosomes. These LTR-retrotransposons are thought to ...

    Authors: Marine Mommert, Olivier Tabone, Guy Oriol, Elisabeth Cerrato, Audrey Guichard, Magali Naville, Paola Fournier, Jean-Nicolas Volff, Alexandre Pachot, Guillaume Monneret, Fabienne Venet, Karen Brengel-Pesce, Julien Textoris and François Mallet

    Citation: BMC Genomics 2018 19:522

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  13. Content type: Research article

    Cis-regulatory elements control gene expression over large distances through the formation of chromatin loops, which allow contact between enhancers and gene promoters. Alterations in cis-acting regulatory system...

    Authors: Stéphanie Moisan, Stéphanie Levon, Emilie Cornec-Le Gall, Yannick Le Meur, Marie-Pierre Audrézet, Josée Dostie and Claude Férec

    Citation: BMC Genomics 2018 19:515

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  14. Content type: Research article

    Arylamine N-acetyltransferase 1 (NAT1) is a drug metabolizing enzyme that has been associated with cancer cell proliferation in vitro and with survival in vivo. NAT1 expression has been associated with the est...

    Authors: Rodney F. Minchin and Neville J. Butcher

    Citation: BMC Genomics 2018 19:513

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  15. Content type: Methodology article

    RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interd...

    Authors: Xiaoyong Pan, Peter Rijnbeek, Junchi Yan and Hong-Bin Shen

    Citation: BMC Genomics 2018 19:511

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  16. Content type: Methodology article

    To date, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants among a variety of traits/diseases, shedding light on the genetic architecture of complex dise...

    Authors: Yi Yang, Mingwei Dai, Jian Huang, Xinyi Lin, Can Yang, Min Chen and Jin Liu

    Citation: BMC Genomics 2018 19:503

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  17. Content type: Research article

    Radiation exposure due to the detonation of an improvised nuclear device remains a major security concern. Radiation from such a device involves a combination of photons and neutrons. Although photons will mak...

    Authors: Constantinos G. Broustas, Andrew D. Harken, Guy Garty and Sally A. Amundson

    Citation: BMC Genomics 2018 19:504

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  18. Content type: Research article

    The evolutionarily conserved Sonic Hedgehog (Shh) signaling pathway is essential for embryogenesis and orofacial development. SHH ligand secreted from the surface ectoderm activates pathway activity in the und...

    Authors: Joshua L. Everson, Dustin M. Fink, Hannah M. Chung, Miranda R. Sun and Robert J. Lipinski

    Citation: BMC Genomics 2018 19:497

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  19. Content type: Research article

    Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and su...

    Authors: Johannes Rainer, Viviana Meraviglia, Hagen Blankenburg, Chiara Piubelli, Peter P. Pramstaller, Adolfo Paolin, Elisa Cogliati, Giulio Pompilio, Elena Sommariva, Francisco S. Domingues and Alessandra Rossini

    Citation: BMC Genomics 2018 19:491

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  20. Content type: Methodology article

    There is considerable evidence that many complex traits have a partially shared genetic basis, termed pleiotropy. It is therefore useful to consider integrating genome-wide association study (GWAS) data across...

    Authors: Marissa LeBlanc, Verena Zuber, Wesley K. Thompson, Ole A. Andreassen, Arnoldo Frigessi and Bettina Kulle Andreassen

    Citation: BMC Genomics 2018 19:494

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  21. Content type: Methodology article

    The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and tes...

    Authors: Julie F. Foley, Dhiral P. Phadke, Owen Hardy, Sara Hardy, Victor Miller, Anup Madan, Kellie Howard, Kimberly Kruse, Cara Lord, Sreenivasa Ramaiahgari, Gregory G. Solomon, Ruchir R. Shah, Arun R. Pandiri, Ronald A. Herbert, Robert C. Sills and B. Alex Merrick

    Citation: BMC Genomics 2018 19:487

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  22. Content type: Research article

    Copy number variation (CNV) has been implicated in the genetics of multiple human diseases. Spinal muscular atrophy (SMA) and 22q11.2 deletion syndrome (22q11.2DS) are two of the most common diseases which are...

    Authors: Xiaoqing Zhang, Bo Wang, Lichen Zhang, Guoling You, Robert A. Palais, Luming Zhou and Qihua Fu

    Citation: BMC Genomics 2018 19:485

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  23. Content type: Research article

    Face morphology is strongly determined by genetic factors. However, only a small number of genes related to face morphology have been identified to date. Here, we performed a two-stage genome-wide association ...

    Authors: Seongwon Cha, Ji Eun Lim, Ah Yeon Park, Jun-Hyeong Do, Si Woo Lee, Chol Shin, Nam Han Cho, Ji-One Kang, Jeong Min Nam, Jong-Sik Kim, Kwang-Man Woo, Seung-Hwan Lee, Jong Yeol Kim and Bermseok Oh

    Citation: BMC Genomics 2018 19:481

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  24. Content type: Research article

    Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA meth...

    Authors: Elizabeth M. Kennedy, George N. Goehring, Michael H. Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K. Smith and Karen N. Conneely

    Citation: BMC Genomics 2018 19:476

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  25. Content type: Research article

    It is well known that development of prostate cancer (PC) can be attributed to somatic mutations of the genome, acquired within proto-oncogenes or tumor-suppressor genes. What is less well understood is how ge...

    Authors: Jean M. Winter, Natasha L. Curry, Derek M. Gildea, Kendra A. Williams, Minnkyong Lee, Ying Hu and Nigel P. S. Crawford

    Citation: BMC Genomics 2018 19:450

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  26. Content type: Research article

    The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patche...

    Authors: Melissa T. R. Hawkins, Ryan R. Culligan, Cynthia L. Frasier, Rebecca B. Dikow, Ryan Hagenson, Runhua Lei and Edward E. Louis Jr

    Citation: BMC Genomics 2018 19:445

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  27. Content type: Research article

    The role of PPARα in gene regulation in mouse liver is well characterized. However, less is known about the role of PPARα in human liver. The aim of the present study was to better characterize the impact of P...

    Authors: Montserrat A. de la Rosa Rodriguez, Go Sugahara, Guido J. E. J. Hooiveld, Yuji Ishida, Chise Tateno and Sander Kersten

    Citation: BMC Genomics 2018 19:443

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  28. Content type: Research article

    Lung cancer is a very heterogeneous disease that can be pathologically classified into different subtypes including small-cell lung carcinoma (SCLC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (L...

    Authors: Shu Zhang, Mingfa Li, Hongbin Ji and Zhaoyuan Fang

    Citation: BMC Genomics 2018 19:435

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  29. Content type: Research article

    Microdeletion of chromosome 22q11 is associated with significant developmental anomalies, including disruption of the cardiac outflow tract, thymic/parathyroid aplasia and cleft palate. Amongst the genes withi...

    Authors: Maria Zoupa, Guilherme Machado Xavier, Stephanie Bryan, Ioannis Theologidis, Matthew Arno and Martyn T. Cobourne

    Citation: BMC Genomics 2018 19:429

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  30. Content type: Research article

    Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are some...

    Authors: Guoliang Lyu, Chao Zhang, Te Ling, Rui Liu, Le Zong, Yiting Guan, Xiaoke Huang, Lei Sun, Lijun Zhang, Cheng Li, Yu Nie and Wei Tao

    Citation: BMC Genomics 2018 19:428

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  31. Content type: Research article

    The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could ...

    Authors: Noa Bossel Ben-Moshe, Shlomit Gilad, Gili Perry, Sima Benjamin, Nora Balint-Lahat, Anya Pavlovsky, Sharon Halperin, Barak Markus, Ady Yosepovich, Iris Barshack, Einav Nili Gal-Yam, Eytan Domany, Bella Kaufman and Maya Dadiani

    Citation: BMC Genomics 2018 19:419

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  32. Content type: Methodology article

    Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage...

    Authors: Luli S. Zou, Michael R. Erdos, D. Leland Taylor, Peter S. Chines, Arushi Varshney, Stephen C. J. Parker, Francis S. Collins and John P. Didion

    Citation: BMC Genomics 2018 19:390

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  33. Content type: Software

    Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide associat...

    Authors: Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto and Jan Baumbach

    Citation: BMC Genomics 2018 19:369

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  34. Content type: Research article

    Cell-type-specific genes exhibit heterogeneity in genomic contexts and may be subject to different epigenetic regulations through different gene transcriptional processes depending on the cell type involved. T...

    Authors: Mayumi Oda, Shunichi Wakabayashi, N. Ari Wijetunga, Shinsuke Yuasa, Hirokazu Enomoto, Ruri Kaneda, Sung Han Yoon, Nishant Mittal, Qiang Jing, Masako Suzuki, John M. Greally, Keiichi Fukuda and Shinji Makino

    Citation: BMC Genomics 2018 19:349

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