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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 5 of 22

  1. Content type: Research article

    The chemosensory system plays an important role in orchestrating sexual behaviors in mammals. Pheromones trigger sexually dimorphic behaviors and different mouse strains exhibit differential responses to phero...

    Authors: Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson and C. Ron Yu

    Citation: BMC Genomics 2017 18:965

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  2. Content type: Research article

    The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict traj...

    Authors: Xianbin Su, Yi Shi, Xin Zou, Zhao-Ning Lu, Gangcai Xie, Jean Y. H. Yang, Chong-Chao Wu, Xiao-Fang Cui, Kun-Yan He, Qing Luo, Yu-Lan Qu, Na Wang, Lan Wang and Ze-Guang Han

    Citation: BMC Genomics 2017 18:946

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  3. Content type: Methodology article

    Significant human diseases/phenotypes exist which require both an environmental trigger event and a genetic predisposition before the disease/phenotype emerges, e.g. Carbamazepine with the rare SNP allele of r...

    Authors: Kaitlin Stouffer, Michael Nahorski, Pablo Moreno, Nivedita Sarveswaran, David Menon, Michael Lee and C. Geoffrey Woods

    Citation: BMC Genomics 2017 18:944

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  4. Content type: Methodology article

    Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic...

    Authors: Hidenobu Segawa, Yoji Kukita and Kikuya Kato

    Citation: BMC Genomics 2017 18:914

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  5. Content type: Methodology article

    Single-cell genome sequencing provides high-resolution details of the clonal genomic modifications that occur during cancer initiation, progression, and ongoing evolution as patients undergo treatment. One lim...

    Authors: John Easton, Veronica Gonzalez-Pena, Donald Yergeau, Xiaotu Ma and Charles Gawad

    Citation: BMC Genomics 2017 18:906

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  6. Content type: Software

    As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a l...

    Authors: Dietrich Trümbach, Susanne Pfeiffer, Manuel Poppe, Hagen Scherb, Sebastian Doll, Wolfgang Wurst and Joel A. Schick

    Citation: BMC Genomics 2017 18:905

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  7. Content type: Research article

    Epigenetic alterations are strongly associated with the development of cancer. The aim of this study was to identify epigenetic pattern in squamous cell lung cancer (LUSC) on a genome-wide scale.

    Authors: Yuan-Xiang Shi, Ying Wang, Xi Li, Wei Zhang, Hong-Hao Zhou, Ji-Ye Yin and Zhao-Qian Liu

    Citation: BMC Genomics 2017 18:901

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  8. Content type: Research article

    Many genes important for reproductive performance are shared by both sexes. However, fecundity indices are primarily based on female parameters such as litter size. We examined a fertility mouse line (FL2), wh...

    Authors: Marten Michaelis, Alexander Sobczak, Dirk Koczan, Martina Langhammer, Norbert Reinsch, Jennifer Schoen and Joachim M. Weitzel

    Citation: BMC Genomics 2017 18:889

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  9. Content type: Research article

    The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and...

    Authors: Weijing Wang, Wenjie Jiang, Lin Hou, Haiping Duan, Yili Wu, Chunsheng Xu, Qihua Tan, Shuxia Li and Dongfeng Zhang

    Citation: BMC Genomics 2017 18:872

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Methodology article

    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

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  15. Content type: Methodology article

    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

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  16. Content type: Research article

    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

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  17. Content type: Software

    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

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  18. Content type: Software

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research

    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

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

  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Methodology article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research Article

    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

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  35. Content type: Methodology Article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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  42. Content type: Research article

    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

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  43. Content type: Methodology article

    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

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  44. Content type: Research Article

    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

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