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.

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  1. Research article

    The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

    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 ...

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

    BMC Genomics 2017 18:805

    Published on: 18 October 2017

  2. Methodology article

    Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure

    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...

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

    BMC Genomics 2017 18:789

    Published on: 16 October 2017

  3. Research article

    A transcriptome-based protein network that identifies new therapeutic targets in colorectal cancer

    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...

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

    BMC Genomics 2017 18:758

    Published on: 30 September 2017

  4. Software

    START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries

    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...

    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

    BMC Genomics 2017 18:749

    Published on: 22 September 2017

  5. Research article

    Genome-wide imaging association study implicates functional activity and glial homeostasis of the caudate in smoking addiction

    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...

    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

    BMC Genomics 2017 18:740

    Published on: 19 September 2017

  6. Research article

    A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map

    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...

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

    BMC Genomics 2017 18:739

    Published on: 18 September 2017

  7. Research article

    5-hydroxymethylcytosine is highly dynamic across human fetal brain development

    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...

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

    BMC Genomics 2017 18:738

    Published on: 18 September 2017

  8. Research article

    Evolving DNA methylation and gene expression markers of B-cell chronic lymphocytic leukemia are present in pre-diagnostic blood samples more than 10 years prior to diagnosis

    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...

    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…

    BMC Genomics 2017 18:728

    Published on: 13 September 2017

  9. Research article

    Biological networks in Parkinson’s disease: an insight into the epigenetic mechanisms associated with this disease

    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...

    Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya and Sanghamitra Bandyopadhyay

    BMC Genomics 2017 18:721

    Published on: 12 September 2017

  10. Research article

    Regulatory network changes between cell lines and their tissues of origin

    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...

    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

    BMC Genomics 2017 18:723

    Published on: 12 September 2017

  11. Research article

    Genome-wide gene expression analysis in the placenta from fetus with trisomy 21

    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...

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

    BMC Genomics 2017 18:720

    Published on: 12 September 2017

  12. Research

    Dual transcriptome of the immediate neutrophil and Candida albicans interplay

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

    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

    BMC Genomics 2017 18:696

    Published on: 6 September 2017

  13. Research article

    Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes

    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...

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

    BMC Genomics 2017 18:666

    Published on: 29 August 2017

  14. Research article

    Expression profiling of genes regulated by sphingosine kinase1 signaling in a murine model of hyperoxia induced neonatal bronchopulmonary dysplasia

    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

    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

    BMC Genomics 2017 18:664

    Published on: 29 August 2017

  15. Research article

    Genetic influences on the human oral microbiome

    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...

    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

    BMC Genomics 2017 18:659

    Published on: 24 August 2017

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Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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