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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 6 of 23

  1. Monoallelic expression of autosomal genes has been implicated in human psychiatric disorders. However, there is a paucity of allelic expression studies in human brain cells at the single cell and genome wide l...

    Authors: Dejian Zhao, Mingyan Lin, Erika Pedrosa, Herbert M. Lachman and Deyou Zheng

    Citation: BMC Genomics 2017 18:860

    Content type: Research article

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  2. A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wound...

    Authors: Piotr Andrzej Sass, Michał Dąbrowski, Agata Charzyńska and Paweł Sachadyn

    Citation: BMC Genomics 2017 18:850

    Content type: Research article

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  3. Higher fasting Growth Hormone (GH) has been associated with increased cardiovascular morbidity and mortality. Our objective was to find genetic determinants of fasting GH in order to facilitate future efforts ...

    Authors: Erik Hallengren, Peter Almgren, Malin Svensson, Widet Gallo, Gunnar Engström, Margaretha Persson and Olle Melander

    Citation: BMC Genomics 2017 18:822

    Content type: Research article

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  4. The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using ...

    Authors: Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K. Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger and Melanie Waldenberger

    Citation: BMC Genomics 2017 18:805

    Content type: Research article

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  5. Genotypes not directly measured in genetic studies are often imputed to improve statistical power and to increase mapping resolution. The accuracy of standard imputation techniques strongly depends on the simi...

    Authors: Maria Kabisch, Ute Hamann and Justo Lorenzo Bermejo

    Citation: BMC Genomics 2017 18:798

    Content type: Methodology article

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  6. Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome...

    Authors: Jinyoung Byun, Younghun Han, Ivan P. Gorlov, Jonathan A. Busam, Michael F. Seldin and Christopher I. Amos

    Citation: BMC Genomics 2017 18:789

    Content type: Methodology article

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  7. Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decrease...

    Authors: Stéphanie Durand, Killian Trillet, Arnaud Uguen, Aude Saint-Pierre, Catherine Le Jossic-Corcos and Laurent Corcos

    Citation: BMC Genomics 2017 18:758

    Content type: Research article

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  8. A genomic signal track is a set of genomic intervals associated with values of various types, such as measurements from high-throughput experiments. Analysis of signal tracks requires complex computational met...

    Authors: Xinjie Zhu, Qiang Zhang, Eric Dun Ho, Ken Hung-On Yu, Chris Liu, Tim H. Huang, Alfred Sze-Lok Cheng, Ben Kao, Eric Lo and Kevin Y. Yip

    Citation: BMC Genomics 2017 18:749

    Content type: Software

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  9. We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.

    Authors: Alberto Magi, Tommaso Pippucci and Carlo Sidore

    Citation: BMC Genomics 2017 18:747

    Content type: Software

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  10. Nearly 6 million deaths and over a half trillion dollars in healthcare costs worldwide are attributed to tobacco smoking each year. Extensive research efforts have been pursued to elucidate the molecular under...

    Authors: David C. Qian, David L. Molfese, Jennifer L. Jin, Alexander J. Titus, Yixuan He, Yafang Li, Maxime Vaissié, Humsini Viswanath, Philip R. Baldwin, Ralf Krahe, Ramiro Salas and Christopher I. Amos

    Citation: BMC Genomics 2017 18:740

    Content type: Research article

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  11. The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal gr...

    Authors: Lorenza Vitale, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Maria Chiara Pelleri and Maria Caracausi

    Citation: BMC Genomics 2017 18:739

    Content type: Research article

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  12. Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occ...

    Authors: Helen Spiers, Eilis Hannon, Leonard C. Schalkwyk, Nicholas J. Bray and Jonathan Mill

    Citation: BMC Genomics 2017 18:738

    Content type: Research article

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  13. B-cell chronic lymphocytic leukemia (CLL) is a common type of adult leukemia. It often follows an indolent course and is preceded by monoclonal B-cell lymphocytosis, an asymptomatic condition, however it is no...

    Authors: Panagiotis Georgiadis, Irene Liampa, Dennie G. Hebels, Julian Krauskopf, Aristotelis Chatziioannou, Ioannis Valavanis, Theo M.C.M. de Kok, Jos C.S. Kleinjans, Ingvar A. Bergdahl, Beatrice Melin, Florentin Spaeth, Domenico Palli, R.C.H. Vermeulen, J. Vlaanderen, Marc Chadeau-Hyam, Paolo Vineis…

    Citation: BMC Genomics 2017 18:728

    Content type: Research article

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  14. Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tiss...

    Authors: Camila M. Lopes-Ramos, Joseph N. Paulson, Cho-Yi Chen, Marieke L. Kuijjer, Maud Fagny, John Platig, Abhijeet R. Sonawane, Dawn L. DeMeo, John Quackenbush and Kimberly Glass

    Citation: BMC Genomics 2017 18:723

    Content type: Research article

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  15. Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights i...

    Authors: Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya and Sanghamitra Bandyopadhyay

    Citation: BMC Genomics 2017 18:721

    Content type: Research article

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  16. We performed whole human genome expression analysis in placenta tissue (normal and T21) samples in order to investigate gene expression into the pathogenesis of trisomy 21 (T21) placenta. We profiled the whole...

    Authors: Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Dong Wook Kwak, So Yeon Park, Sun-Hee Chun and Hyun Mee Ryu

    Citation: BMC Genomics 2017 18:720

    Content type: Research article

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  17. Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the Zrt- and Irt-like (ZIP; SLC39A) family of tran...

    Authors: Rebecca Lawson, Wolfgang Maret and Christer Hogstrand

    Citation: BMC Genomics 2017 18:719

    Content type: Research article

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  18. Neutrophils are traditionally considered transcriptionally inactive. Compared to other immune cells, little is known about their transcriptional profile during interaction with pathogens.

    Authors: Maria J. Niemiec, Christian Grumaz, David Ermert, Christiane Desel, Madhu Shankar, José Pedro Lopes, Ian G. Mills, Philip Stevens, Kai Sohn and Constantin F. Urban

    Citation: BMC Genomics 2017 18:696

    Content type: Research

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    The Correction to this article has been published in BMC Genomics 2017 18:863

  19. TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes...

    Authors: Yongcheng Dong, Ziyan Huang, Qifan Kuang, Zhining Wen, Zhibin Liu, Yizhou Li, Yi Yang and Menglong Li

    Citation: BMC Genomics 2017 18:666

    Content type: Research article

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  20. Sphingosine- 1-Phosphate (S1P) is a bioactive lipid and an intracellular as well as an extracellular signaling molecule. S1P ligand specifically binds to five related cell surface G-protein-coupled receptors (S1P

    Authors: Viswanathan Natarajan, Alison W. Ha, Yangbasai Dong, Narsa M. Reddy, David L. Ebenezer, Prasad Kanteti, Sekhar P. Reddy, J. Usha Raj, Zhengdeng Lei, Mark Maienschein-Cline, Zarema Arbieva and Anantha Harijith

    Citation: BMC Genomics 2017 18:664

    Content type: Research article

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  21. The human oral microbiome is formed early in development. Its composition is influenced by environmental factors including diet, substance use, oral health, and overall health and disease. The influence of hum...

    Authors: Brittany A. Demmitt, Robin P. Corley, Brooke M. Huibregtse, Matthew C. Keller, John K. Hewitt, Matthew B. McQueen, Rob Knight, Ivy McDermott and Kenneth S. Krauter

    Citation: BMC Genomics 2017 18:659

    Content type: Research article

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  22. Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of ...

    Authors: Zhiwen Jiang, Jiaqi Yang, Aimei Dai, Yuming Wang, Wei Li and Zhi Xie

    Citation: BMC Genomics 2017 18:638

    Content type: Research article

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  23. DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid c...

    Authors: David P. Astling, Ilea E. Heft, Kenneth L. Jones and James M. Sikela

    Citation: BMC Genomics 2017 18:614

    Content type: Methodology article

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  24. Fasting glucose and fasting insulin are glycemic traits closely related to diabetes, and understanding the role of genetic factors in these traits can help reveal the etiology of type 2 diabetes. Although sing...

    Authors: Ren-Hua Chung, Yen-Feng Chiu, Yi-Jen Hung, Wen-Jane Lee, Kwan-Dun Wu, Hui-Ling Chen, Ming-Wei Lin, Yii-Der I. Chen, Thomas Quertermous and Chao A. Hsiung

    Citation: BMC Genomics 2017 18:591

    Content type: Research article

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  25. Human polymorphisms with derived alleles that are protective against disease may provide powerful translational opportunities. Here we report a method to identify such candidate polymorphisms and apply it to c...

    Authors: Joe M. Butler, Neil Hall, Niro Narendran, Yit C. Yang and Luminita Paraoan

    Citation: BMC Genomics 2017 18:575

    Content type: Research Article

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  26. The association studies on human complex traits are admittedly propitious to identify deleterious genetic markers. Compared to single-trait analyses, multiple-trait analyses can arguably make better use of the...

    Authors: Wei Zhang, Liu Yang, Larry L. Tang, Aiyi Liu, James L. Mills, Yuanchang Sun and Qizhai Li

    Citation: BMC Genomics 2017 18:552

    Content type: Methodology Article

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  27. An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks ...

    Authors: Mahesh Iddawela, Oscar Rueda, Jenny Eremin, Oleg Eremin, Jed Cowley, Helena M. Earl and Carlos Caldas

    Citation: BMC Genomics 2017 18:526

    Content type: Research article

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  28. The placenta is the principal organ regulating intrauterine growth and development, performing critical functions on behalf of the developing fetus. The delineation of functional networks and pathways driving ...

    Authors: Maya A. Deyssenroth, Shouneng Peng, Ke Hao, Luca Lambertini, Carmen J. Marsit and Jia Chen

    Citation: BMC Genomics 2017 18:520

    Content type: Research article

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  29. Gastric cancer is the fourth most common cancer and the second leading cause of cancer death worldwide. In order to understand the genetic background, we sequenced the whole exome and the whole genome of one m...

    Authors: Daniela Esser, Niklas Holze, Jochen Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel and Christoph Röcken

    Citation: BMC Genomics 2017 18:517

    Content type: Research article

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  30. Nuclear Factor Erythroid-derived 2-like 2 (Nrf2) senses oxidative environments and/or stress and initiates a cytoprotective response through transcriptional activation of antioxidant and detoxification genes. ...

    Authors: Justin M. Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John R. Hoidal and Namakkal S. Rajasekaran

    Citation: BMC Genomics 2017 18:509

    Content type: Research article

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  31. Human endogenous retroviruses (HERVs) belong to the LTR-retrotransposon family, where the complete HERV sequence contains two long terminal repeats (LTRs) located at each end. Intact LTRs possess highly conser...

    Authors: Tomoaki Kahyo, Hidetaka Yamada, Hong Tao, Nobuya Kurabe and Haruhiko Sugimura

    Citation: BMC Genomics 2017 18:487

    Content type: Research article

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  32. The understanding of genomic and physiological mechanisms related to how organisms living in extreme environments survive and reproduce is an outstanding question facing evolutionary and organismal biologists....

    Authors: Lauren Kordonowy and Matthew MacManes

    Citation: BMC Genomics 2017 18:473

    Content type: Research article

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  33. Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibl...

    Authors: Alexandra R. Buckley, Kristopher A. Standish, Kunal Bhutani, Trey Ideker, Roger S. Lasken, Hannah Carter, Olivier Harismendy and Nicholas J. Schork

    Citation: BMC Genomics 2017 18:458

    Content type: Research article

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  34. Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleoti...

    Authors: Dmitriy A. Shagin, Maria A. Turchaninova, Irina A. Shagina, Mikhail Shugay, Andrew R. Zaretsky, Olga I. Zueva, Dmitriy A. Bolotin, Sergey Lukyanov and Dmitriy M. Chudakov

    Citation: BMC Genomics 2017 18:440

    Content type: Methodology article

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  35. Nicotinic acetylcholine receptors (nAChRs) play an important role in cellular physiology and human nicotine dependence, and are closely associated with many human diseases including cancer. For example, previo...

    Authors: Bo Zhang, Pamela Madden, Junchen Gu, Xiaoyun Xing, Savita Sankar, Jennifer Flynn, Kristen Kroll and Ting Wang

    Citation: BMC Genomics 2017 18:439

    Content type: Research Article

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  36. Long non-coding RNAs (lncRNAs) have emerged as a class of factors that are important for regulating development and cancer. Computational prediction of lncRNAs from ultra-deep RNA sequencing has been successfu...

    Authors: Yixiao Gong, Hsuan-Ting Huang, Yu Liang, Thomas Trimarchi, Iannis Aifantis and Aristotelis Tsirigos

    Citation: BMC Genomics 2017 18:434

    Content type: Software

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  37. The cerebrospinal fluid (CSF) levels of total tau (t-tau) and Aβ1–42 are potential early diagnostic markers for probable Alzheimer’s disease (AD). The influence of genetic variation on these CSF biomarkers has be...

    Authors: Wang Cong, Xianglian Meng, Jin Li, Qiushi Zhang, Feng Chen, Wenjie Liu, Ying Wang, Sipu Cheng, Xiaohui Yao, Jingwen Yan, Sungeun Kim, Andrew J. Saykin, Hong Liang and Li Shen

    Citation: BMC Genomics 2017 18:421

    Content type: Research article

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  38. MicroRNAs (miRNAs) play multiple roles in tumor biology. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration. Specifically, co...

    Authors: Hua-Sheng Chiu, María Rodríguez Martínez, Mukesh Bansal, Aravind Subramanian, Todd R. Golub, Xuerui Yang, Pavel Sumazin and Andrea Califano

    Citation: BMC Genomics 2017 18:418

    Content type: Research article

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  39. One problem that plagues epigenome-wide association studies is the potential confounding due to cell mixtures when purified target cells are not available. Reference-free adjustment of cell mixtures has become...

    Authors: Jun Chen, Ehsan Behnam, Jinyan Huang, Miriam F. Moffatt, Daniel J. Schaid, Liming Liang and Xihong Lin

    Citation: BMC Genomics 2017 18:413

    Content type: Methodology article

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  40. Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire ...

    Authors: Farah R. Zahir, Jill C. Mwenifumbo, Hye-Jung E. Chun, Emilia L. Lim, Clara D. M. Van Karnebeek, Madeline Couse, Karen L. Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F. Boerkoel, Sylvie L. Langlois, Barbara M. McGillivray, Steven J. M. Jones, Jan M. Friedman and Marco A. Marra

    Citation: BMC Genomics 2017 18:403

    Content type: Research Article

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  41. The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studie...

    Authors: Navin Rustagi, Anbo Zhou, W. Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A. Gibbs, Lynn B. Jorde, Fuli Yu and Jinchuan Xing

    Citation: BMC Genomics 2017 18:396

    Content type: Research article

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  42. Transversions (Tv’s) are more likely to alter the amino acid sequence of proteins than transitions (Ts’s), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the...

    Authors: Cong Guo, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe and Timothy E. Reddy

    Citation: BMC Genomics 2017 18:394

    Content type: Research article

    Published on:

  43. Development of primary open-angle glaucoma (POAG) is associated with the malfunctioning trabecular meshwork (TM). Cell therapy offers great potential for the treatment of POAG, but requires the generation of f...

    Authors: Padmapriya Sathiyanathan, Cheryl Y. Tay and Lawrence W. Stanton

    Citation: BMC Genomics 2017 18:383

    Content type: Research article

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  44. Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the...

    Authors: Qi Liu, Russell Bonneville, Tianbao Li and Victor X. Jin

    Citation: BMC Genomics 2017 18:375

    Content type: Methodology article

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