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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 7 of 23

  1. Spinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord...

    Authors: Ling-Ling Shi, Nan Zhang, Xiu-Mei Xie, Yue-Juan Chen, Rui Wang, Lin Shen, Jian-Sheng Zhou, Jian-Guo Hu and He-Zuo Lü

    Citation: BMC Genomics 2017 18:173

    Content type: Research article

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  2. Aging human skin undergoes significant morphological and functional changes such as wrinkle formation, reduced wound healing capacity, and altered epidermal barrier function. Besides known age-related alterati...

    Authors: Andreas Kuehne, Janosch Hildebrand, Joern Soehle, Horst Wenck, Lara Terstegen, Stefan Gallinat, Anja Knott, Marc Winnefeld and Nicola Zamboni

    Citation: BMC Genomics 2017 18:169

    Content type: Research article

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  3. At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences...

    Authors: Gerhard Schöfl, Kathrin Lang, Philipp Quenzel, Irina Böhme, Jürgen Sauter, Jan A. Hofmann, Julia Pingel, Alexander H. Schmidt and Vinzenz Lange

    Citation: BMC Genomics 2017 18:161

    Content type: Research article

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  4. Among the different tobacco products that are available on the US market, cigarette smoking is shown to be the most harmful and the effects of cigarette smoking have been well studied. US epidemiological studi...

    Authors: Subhashini Arimilli, Behrouz Madahian, Peter Chen, Kristin Marano and G. L. Prasad

    Citation: BMC Genomics 2017 18:156

    Content type: Research article

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  5. Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family...

    Authors: Alessia Visconti, Mashael Al-Shafai, Wadha A. Al Muftah, Shaza B. Zaghlool, Massimo Mangino, Karsten Suhre and Mario Falchi

    Citation: BMC Genomics 2017 18:150

    Content type: Software

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  6. Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab...

    Authors: Andreas R. Gschwind, Anjali Singh, Ulrich Certa, Alexandre Reymond and Tobias Heckel

    Citation: BMC Genomics 2017 18:144

    Content type: Research article

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  7. Cardiometabolic (CM) risk factors are heritable and cluster in individuals. We hypothesized that CM risk factors are associated with multiple shared and unique mRNA and microRNA (miRNA) signatures. We examined...

    Authors: David D. McManus, Jian Rong, Tianxiao Huan, Sean Lacey, Kahraman Tanriverdi, Peter J. Munson, Martin G. Larson, Roby Joehanes, Venkatesh Murthy, Ravi Shah, Jane E. Freedman and Daniel Levy

    Citation: BMC Genomics 2017 18:139

    Content type: Research article

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  8. We have identified molecules that exhibit synthetic lethality in cells with loss of the neurofibromin 1 (NF1) tumor suppressor gene. However, recognizing tumors that have inactivation of the NF1 tumor suppressor ...

    Authors: Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez and Casey S. Greene

    Citation: BMC Genomics 2017 18:127

    Content type: Research article

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  9. Alternative mRNA isoform usage is an important source of protein diversity in mammalian cells. This phenomenon has been extensively studied in bulk tissues, however, it remains unclear how this diversity is re...

    Authors: Kasper Karlsson and Sten Linnarsson

    Citation: BMC Genomics 2017 18:126

    Content type: Research article

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  10. Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these changes are in need of further elucidation. I...

    Authors: Elizabeth L. Johnson, David G. Robinson and Hilary A. Coller

    Citation: BMC Genomics 2017 18:123

    Content type: Research article

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  11. High-protein diets (HPD) alter the large intestine microbiota composition in association with a metabolic shift towards protein degradation. Some amino acid-derived metabolites produced by the colon bacteria a...

    Authors: Martin Beaumont, Mireille Andriamihaja, Lucie Armand, Marta Grauso, Florence Jaffrézic, Denis Laloë, Marco Moroldo, Anne-Marie Davila, Daniel Tomé, François Blachier and Annaïg Lan

    Citation: BMC Genomics 2017 18:116

    Content type: Research article

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  12. Significant gaps remain regarding the pathomechanisms underlying the autoimmune response in vitiligo (VL), where the loss of self-tolerance leads to the targeted killing of melanocytes. Specifically, there is ...

    Authors: Rama Dey-Rao and Animesh A. Sinha

    Citation: BMC Genomics 2017 18:109

    Content type: Research article

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  13. We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their gen...

    Authors: Amy M. Cole, Sean Cox, Choongwon Jeong, Nayia Petousi, Dhana R. Aryal, Yunden Droma, Masayuki Hanaoka, Masao Ota, Nobumitsu Kobayashi, Paolo Gasparini, Hugh Montgomery, Peter Robbins, Anna Di Rienzo and Gianpiero L. Cavalleri

    Citation: BMC Genomics 2017 18:102

    Content type: Research article

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  14. Epigenetic modifications of DNA, such as 5-methylcytosine and 5-hydroxymethycytosine, play important roles in development and disease. Here, we present a cost-effective and versatile methodology for the analys...

    Authors: Gary G. Chen, Jeffrey A. Gross, Pierre-Eric Lutz, Kathryn Vaillancourt, Gilles Maussion, Alexandre Bramoulle, Jean-François Théroux, Elena S. Gardini, Ulrike Ehlert, Geneviève Bourret, Aurélie Masurel, Pierre Lepage, Naguib Mechawar, Gustavo Turecki and Carl Ernst

    Citation: BMC Genomics 2017 18:96

    Content type: methodology article

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  15. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adi...

    Authors: Jenny C. Link, Yehudit Hasin-Brumshtein, Rita M. Cantor, Xuqi Chen, Arthur P. Arnold, Aldons J. Lusis and Karen Reue

    Citation: BMC Genomics 2017 18:89

    Content type: Research article

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  16. Bone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the trans...

    Authors: M. Ampuja, T. Rantapero, A. Rodriguez-Martinez, M. Palmroth, E. L. Alarmo, M. Nykter and A. Kallioniemi

    Citation: BMC Genomics 2017 18:68

    Content type: Research article

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  17. Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly du...

    Authors: Marzieh Eslami Rasekh, Giorgia Chiatante, Mattia Miroballo, Joyce Tang, Mario Ventura, Chris T. Amemiya, Evan E. Eichler, Francesca Antonacci and Can Alkan

    Citation: BMC Genomics 2017 18:65

    Content type: Methodology article

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  18. The study of epigenetic processes and mechanisms present a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool...

    Authors: Kathryn Tully Oelsner, Yan Guo, Sophie Bao-Chieu To, Amy L. Non and Shari L. Barkin

    Citation: BMC Genomics 2017 18:57

    Content type: Research Article

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  19. Mouse fetuses up to 16 day of embryonic development and nude (Foxn1- deficient) mice are examples of animals that undergo regenerative (scar-free) skin healing. The expression of transcription factor Foxn1 in ...

    Authors: Anna Kur-Piotrowska, Marta Kopcewicz, Leslie P. Kozak, Pawel Sachadyn, Anna Grabowska and Barbara Gawronska-Kozak

    Citation: BMC Genomics 2017 18:56

    Content type: Research Article

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  20. MiRNAs are essential regulators of skeletal muscle development and homeostasis. To date, the role and regulation of miRNAs in myogenesis have been mostly studied in tissue culture and during embryogenesis. How...

    Authors: Séverine Lamon, Evelyn Zacharewicz, Lauren C. Butchart, Liliana Orellana, Jasmine Mikovic, Miranda D. Grounds and Aaron P. Russell

    Citation: BMC Genomics 2017 18:52

    Content type: Research Article

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  21. DNA and RNA fractions from whole blood, serum and plasma are increasingly popular analytes that are currently under investigation for their utility in the diagnosis and staging of disease. Small non-coding rib...

    Authors: Yan Guo, Kasey Vickers, Yanhua Xiong, Shilin Zhao, Quanhu Sheng, Pan Zhang, Wanding Zhou and Charles R. Flynn

    Citation: BMC Genomics 2017 18:50

    Content type: Research article

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  22. Measuring genome-wide changes in transcript abundance in circulating peripheral whole blood is a useful way to study disease pathobiology and may help elucidate the molecular mechanisms of disease, or discover...

    Authors: Casey P. Shannon, Robert Balshaw, Virginia Chen, Zsuzsanna Hollander, Mustafa Toma, Bruce M. McManus, J. Mark FitzGerald, Don D. Sin, Raymond T. Ng and Scott J. Tebbutt

    Citation: BMC Genomics 2017 18:43

    Content type: methodology article

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  23. Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-b...

    Authors: Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Katsuhiko Hayashi, Mitinori Saitou, Mikita Suyama, Takashi Ito and Hiroyuki Sasaki

    Citation: BMC Genomics 2017 18:31

    Content type: Research article

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  24. Endurance exercise training, especially the high-intensity training, exhibits a strong influence on the immune system. However, the mechanisms underpinning the immune-regulatory effect of exercise remain uncle...

    Authors: Dongmei Liu, Ru Wang, Ana R. Grant, Jinming Zhang, Paul M. Gordon, Yuqin Wei and Peijie Chen

    Citation: BMC Genomics 2017 18:29

    Content type: Research article

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  25. UK Biobank is a large prospective cohort study in the UK established by the Medical Research Council (MRC) and the Wellcome Trust to enable approved researchers to investigate the role of genetic factors, envi...

    Authors: Samantha Welsh, Tim Peakman, Simon Sheard and Rachael Almond

    Citation: BMC Genomics 2017 18:26

    Content type: Regular article

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  26. DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood.

    Authors: Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Ulrike Gehring, Soesma A. Jankipersadsing, Pieter van der Vlies, Cleo C. van Diemen, Bianca van Rijkom, Jocelyne Just, Inger Kull, Juha Kere, Josep Maria Antó, Jean Bousquet, Alexandra Zhernakova…

    Citation: BMC Genomics 2017 18:25

    Content type: Research Article

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  27. Chromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex a...

    Authors: Charalampos Lazaris, Stephen Kelly, Panagiotis Ntziachristos, Iannis Aifantis and Aristotelis Tsirigos

    Citation: BMC Genomics 2017 18:22

    Content type: Software

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  28. Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somati...

    Authors: Chun Hang Au, Anskar Y. H. Leung, Ava Kwong, Tsun Leung Chan and Edmond S. K. Ma

    Citation: BMC Genomics 2017 18:16

    Content type: Software

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  29. Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exp...

    Authors: Sam Buckberry, Tina Bianco-Miotto, Stephen J. Bent, Vicki Clifton, Cheryl Shoubridge, Kartik Shankar and Claire T. Roberts

    Citation: BMC Genomics 2017 18:10

    Content type: Research Article

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  30. Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation s...

    Authors: Chang Xu, Mohammad R. Nezami Ranjbar, Zhong Wu, John DiCarlo and Yexun Wang

    Citation: BMC Genomics 2017 18:5

    Content type: Methodology Article

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  31. In the event of an improvised nuclear device detonation, the prompt radiation exposure would consist of photons plus a neutron component that would contribute to the total dose. As neutrons cause more complex ...

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

    Citation: BMC Genomics 2017 18:2

    Content type: Research Article

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  32. Low-abundance mutations in mitochondrial populations (mutations with minor allele frequency ≤ 1%), are associated with cancer, aging, and neurodegenerative disorders. While recent progress in high-throughput s...

    Authors: Levent Albayrak, Kamil Khanipov, Maria Pimenova, George Golovko, Mark Rojas, Ioannis Pavlidis, Sergei Chumakov, Gerardo Aguilar, Arturo Chávez, William R. Widger and Yuriy Fofanov

    Citation: BMC Genomics 2016 17:1017

    Content type: Research article

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  33. In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included i...

    Authors: Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori and Masao Nagasaki

    Citation: BMC Genomics 2016 17:991

    Content type: Research Article

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  34. The COP9 signalosome, composed of eight subunits, is implicated in cancer genetics with its deneddylase activity to modulate cellular concentration of oncogenic proteins such as IkB and TGFβ. However, its func...

    Authors: Christina A. Wicker and Tadahide Izumi

    Citation: BMC Genomics 2016 17:983

    Content type: Research article

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  35. Although CRISPR/Cas enables one-step gene cassette knock-in, assembling targeting vectors containing long homology arms is a laborious process for high-throughput knock-in. We recently developed the CRISPR/Cas...

    Authors: Tomomi Aida, Shota Nakade, Tetsushi Sakuma, Yayoi Izu, Ayu Oishi, Keiji Mochida, Harumi Ishikubo, Takako Usami, Hidenori Aizawa, Takashi Yamamoto and Kohichi Tanaka

    Citation: BMC Genomics 2016 17:979

    Content type: Methodology article

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  36. Children exposed to maternal smoking during pregnancy exhibit increased risk for many adverse health effects. Maternal smoking influences methylation in newborns at specific CpG sites (CpGs). Here, we extend e...

    Authors: Daniel M. Rotroff, Bonnie R. Joubert, Skylar W. Marvel, Siri E. Håberg, Michael C. Wu, Roy M. Nilsen, Per M. Ueland, Wenche Nystad, Stephanie J. London and Alison Motsinger-Reif

    Citation: BMC Genomics 2016 17:976

    Content type: Research article

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  37. Visfatin is an adipokine associated with glucose and lipid metabolism. We previously reported two visfatin upstream single nucleotide polymorphisms (SNPs), c.-3187G > A (rs11977021) and c.-1537C > T (rs6133008...

    Authors: Delicia Shu Qin Ooi, Siong Gim Ong, Chew Kiat Heng, Kah Yin Loke and Yung Seng Lee

    Citation: BMC Genomics 2016 17:974

    Content type: Research article

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  38. Human central memory CD4 T cells are characterized by their capacity of proliferation and differentiation into effector memory CD4 T cells. Homeostasis of central memory CD4 T cells is considered a key factor ...

    Authors: Gustavo Olvera-García, Tania Aguilar-García, Fany Gutiérrez-Jasso, Iván Imaz-Rosshandler, Claudia Rangel-Escareño, Lorena Orozco, Irma Aguilar-Delfín, Joel A. Vázquez-Pérez, Joaquín Zúñiga, Santiago Pérez-Patrigeon and Enrique Espinosa

    Citation: BMC Genomics 2016 17:956

    Content type: Research article

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  39. Mesenchymal Stromal/Stem Cells (MSCs), isolated under the criteria established by the ISCT, still have a poorly characterized phenotype that is difficult to distinguish from similar cell populations. Although ...

    Authors: Beatriz Roson-Burgo, Fermin Sanchez-Guijo, Consuelo Del Cañizo and Javier De Las Rivas

    Citation: BMC Genomics 2016 17:944

    Content type: Research Article

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  40. Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in ho...

    Authors: Emily R. Davenport, Julia K. Goodrich, Jordana T. Bell, Tim D. Spector, Ruth E. Ley and Andrew G. Clark

    Citation: BMC Genomics 2016 17:941

    Content type: Research article

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  41. Graves’ disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves’ disease and it is therefore likely that these can be identifi...

    Authors: Jwu Jin Khong, Kathryn P. Burdon, Yi Lu, Kate Laurie, Lefta Leonardos, Paul N. Baird, Srujana Sahebjada, John P. Walsh, Adam Gajdatsy, Peter R. Ebeling, Peter Shane Hamblin, Rosemary Wong, Simon P. Forehan, Spiros Fourlanos, Anthony P. Roberts, Matthew Doogue…

    Citation: BMC Genomics 2016 17:939

    Content type: Methodology article

    Published on:

  42. ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friend...

    Authors: Giovanna Ambrosini, René Dreos, Sunil Kumar and Philipp Bucher

    Citation: BMC Genomics 2016 17:938

    Content type: Software

    Published on:

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