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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 22

  1. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: methodology article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Methodology article

    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

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  7. Content type: Research Article

    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

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  8. Content type: Research Article

    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

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  9. Content type: Research Article

    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

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  10. Content type: Research article

    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

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  11. Content type: methodology article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Regular article

    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

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  15. Content type: Research Article

    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

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  16. Content type: Software

    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

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  17. Content type: Software

    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

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  18. Content type: Research Article

    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

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  19. Content type: Methodology Article

    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

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  20. Content type: Research Article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research Article

    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

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  23. Content type: Research article

    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

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  24. Content type: Methodology article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research Article

    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

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  29. Content type: Research article

    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

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  30. Content type: Methodology article

    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

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  31. Content type: Software

    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

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  32. Content type: Research article

    Diabetic nephropathy (DN) is a major complication of type1 and type 2 diabetes. Understanding how diabetes regulate transcriptome dynamics in DN is important for understanding the biology of the disease and fo...

    Authors: Ana Rubin, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli and Joyce Tombran-Tink

    Citation: BMC Genomics 2016 17:936

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  33. Content type: Research article

    Mouse models have served a valuable role in deciphering various facets of Salivary Gland (SG) biology, from normal developmental programs to diseased states. To facilitate such studies, gene expression profili...

    Authors: Christian Gluck, Sangwon Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha and Rose-Anne Romano

    Citation: BMC Genomics 2016 17:923

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  34. Content type: Software

    Next-generation sequencing (NGS) allows unbiased, in-depth interrogation of cancer genomes. Many somatic variant callers have been developed yet accurate ascertainment of somatic variants remains a considerabl...

    Authors: Jean-François Spinella, Pamela Mehanna, Ramon Vidal, Virginie Saillour, Pauline Cassart, Chantal Richer, Manon Ouimet, Jasmine Healy and Daniel Sinnett

    Citation: BMC Genomics 2016 17:912

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  35. Content type: Research article

    The TALLYHO/Jng (TH) mouse is a polygenic model for obesity and type 2 diabetes first described in the literature in 2001. The origin of the TH strain is an outbred colony of the Theiler Original strain and mi...

    Authors: James Denvir, Goran Boskovic, Jun Fan, Donald A. Primerano, Jacaline K. Parkman and Jung Han Kim

    Citation: BMC Genomics 2016 17:907

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  36. Content type: Research article

    We had previously identified Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), as a key factor regulating a massive ERα target gene expression and ERα-pos...

    Authors: Hao Zeng, Li Lu, Ngai Ting Chan, Mark Horswill, Paul Ahlquist, Xuehua Zhong and Wei Xu

    Citation: BMC Genomics 2016 17:902

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  37. Content type: Research article

    The transcription factor SOX10 is essential for all stages of Schwann cell development including myelination. SOX10 cooperates with other transcription factors to activate the expression of key myelin genes in...

    Authors: Chetna Gopinath, William D. Law, José F. Rodríguez-Molina, Arjun B. Prasad, Lingyun Song, Gregory E. Crawford, James C. Mullikin, John Svaren and Anthony Antonellis

    Citation: BMC Genomics 2016 17:887

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  38. Content type: Research article

    Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data b...

    Authors: Badri Adhikari, Tuan Trieu and Jianlin Cheng

    Citation: BMC Genomics 2016 17:886

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  39. Content type: Software

    Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into t...

    Authors: Christopher A. Miller, Joshua McMichael, Ha X. Dang, Christopher A. Maher, Li Ding, Timothy J. Ley, Elaine R. Mardis and Richard K. Wilson

    Citation: BMC Genomics 2016 17:880

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  40. Content type: Methodology article

    Complex diseases are characterized by multiple subtle perturbations to biological processes. New omics platforms can detect these perturbations, but translating the diverse molecular and statistical informatio...

    Authors: Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Mäkinen and Xia Yang

    Citation: BMC Genomics 2016 17:874

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  41. Content type: Research Article

    ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal us...

    Authors: Peter Hansen, Jochen Hecht, Jonas Ibn-Salem, Benjamin S. Menkuec, Sebastian Roskosch, Matthias Truss and Peter N. Robinson

    Citation: BMC Genomics 2016 17:873

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  42. Content type: Research article

    The differentiation of human bone marrow derived skeletal stem cells (known as human bone marrow stromal or mesenchymal stem cells, hMSCs) into osteoblasts involves the activation of a small number of well-des...

    Authors: Natalie A. Twine, Linda Harkness, Moustapha Kassem and Marc R. Wilkins

    Citation: BMC Genomics 2016 17:872

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  43. Content type: Research article

    Psoriasis is an immune-mediated, inflammatory disorder of the skin characterized by chronic inflammation and hyperproliferation of the epidermis. Differential expression analysis of microarray or RNA-seq data ...

    Authors: Richard Ahn, Rashmi Gupta, Kevin Lai, Nitin Chopra, Sarah T. Arron and Wilson Liao

    Citation: BMC Genomics 2016 17:841

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  44. Content type: Research article

    Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including...

    Authors: Yosuke Hirotsu, Yuichiro Kojima, Kenichiro Okimoto, Kenji Amemiya, Hitoshi Mochizuki and Masao Omata

    Citation: BMC Genomics 2016 17:833

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