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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 23

  1. SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing...

    Authors: Soheil Yousefi, Tooba Abbassi-Daloii, Thirsa Kraaijenbrink, Martijn Vermaat, Hailiang Mei, Peter van ‘t Hof, Maarten van Iterson, Daria V. Zhernakova, Annique Claringbould, Lude Franke, Leen M. ‘t Hart, Roderick C. Slieker, Amber van der Heijden, Peter de Knijff and Peter A. C. ’t Hoen

    Citation: BMC Genomics 2018 19:90

    Content type: Research article

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  2. Migraine is a common heritable neurovascular disorder typically characterised by episodic attacks of severe pulsating headache and nausea, often accompanied by visual, auditory or other sensory symptoms. Altho...

    Authors: Zachary F. Gerring, Allan F. McRae, Grant W. Montgomery and Dale R. Nyholt

    Citation: BMC Genomics 2018 19:69

    Content type: Research article

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  3. Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious disease...

    Authors: Yang Jiao, Ran Li, Chao Wu, Yibin Ding, Yanning Liu, Danmei Jia, Lifeng Wang, Xiang Xu, Jing Zhu, Min Zheng and Junling Jia

    Citation: BMC Genomics 2018 19:50

    Content type: Methodology article

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  4. The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references. This hinders the correct identification of varian...

    Authors: Mahmoud Koko, Mohammed O. E. Abdallah, Mutaz Amin and Muntaser Ibrahim

    Citation: BMC Genomics 2018 19:46

    Content type: Research article

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  5. Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that n...

    Authors: Eirini-Stavroula Komseli, Ioannis S. Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V. Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P. Zampetidis, Sentiljana Gumeni, Ioannis P. Trougakos, Dafni-Eleftheria Pefani, Eric O’Neill, Sarantis Gagos…

    Citation: BMC Genomics 2018 19:37

    Content type: Methodology article

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  6. Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigation...

    Authors: Laura E. MacConaill, Robert T. Burns, Anwesha Nag, Haley A. Coleman, Michael K. Slevin, Kristina Giorda, Madelyn Light, Kevin Lai, Mirna Jarosz, Matthew S. McNeill, Matthew D. Ducar, Matthew Meyerson and Aaron R. Thorner

    Citation: BMC Genomics 2018 19:30

    Content type: Research article

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  7. Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. We used the highly accurate microfluid...

    Authors: Hiba Zaidan, Gokul Ramaswami, Yaela N. Golumbic, Noa Sher, Assaf Malik, Michal Barak, Dalia Galiani, Nava Dekel, Jin B. Li and Inna Gaisler-Salomon

    Citation: BMC Genomics 2018 19:28

    Content type: Research article

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  8. Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumouri...

    Authors: Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi and Isabella Castiglioni

    Citation: BMC Genomics 2018 19:25

    Content type: Methodology article

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  9. Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using Hig...

    Authors: Maurizio Callari, Ankita Sati Batra, Rajbir Nath Batra, Stephen-John Sammut, Wendy Greenwood, Harry Clifford, Colin Hercus, Suet-Feung Chin, Alejandra Bruna, Oscar M. Rueda and Carlos Caldas

    Citation: BMC Genomics 2018 19:19

    Content type: Methodology article

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  10. Studies investigating associations between ACTN3 R577X and ACE I/D genotypes and endurance athletic status have been limited by small sample sizes from mixed sport disciplines and lack quantitative measures of pe...

    Authors: Ioannis D. Papadimitriou, Sarah J. Lockey, Sarah Voisin, Adam J. Herbert, Fleur Garton, Peter J. Houweling, Pawel Cieszczyk, Agnieszka Maciejewska-Skrendo, Marek Sawczuk, Myosotis Massidda, Carla Maria Calò, Irina V. Astratenkova, Anastasia Kouvatsi, Anastasiya M. Druzhevskaya, Macsue Jacques, Ildus I. Ahmetov…

    Citation: BMC Genomics 2018 19:13

    Content type: Research article

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  11. Human induced pluripotent stem cells (hiPSCs) have been attempted for clinical application with diverse iPSCs sources derived from various cell types. This proposes that there would be a shared reprogramming r...

    Authors: Akihiro Kuno, Ken Nishimura and Satoru Takahashi

    Citation: BMC Genomics 2018 19:9

    Content type: Research article

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  12. The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key...

    Authors: David Martín-Gálvez, Denis Dunoyer de Segonzac, Man Chun John Ma, Anne E. Kwitek, David Thybert and Paul Flicek

    Citation: BMC Genomics 2017 18:986

    Content type: Research Article

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  13. Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matri...

    Authors: Bing Li, Karthika Balasubramanian, Deborah Krakow and Daniel H. Cohn

    Citation: BMC Genomics 2017 18:983

    Content type: Research article

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  14. Previous studies have confirmed a family risk of nephrolithiasis (NL), but only 15% of all cases are associated with an identified monogenic factor. In clinical practice, our group encountered a patient with N...

    Authors: Zhenxing Yang, Tao Zhou, Bishao Sun, Qingqing Wang, Xingyou Dong, Xiaoyan Hu, Jiangfan Zhong, Bo Song and Longkun Li

    Citation: BMC Genomics 2017 18:982

    Content type: Research article

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  15. Cytosine methylation is a stable epigenetic modification of DNA that plays an important role in both normal physiology and disease. Most diseases exhibit some degree of sexual dimorphism, but the extent to whi...

    Authors: Helen McCormick, Paul E. Young, Suzy S. J. Hur, Keith Booher, Hunter Chung, Jennifer E. Cropley, Eleni Giannoulatou and Catherine M. Suter

    Citation: BMC Genomics 2017 18:966

    Content type: Research Article

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  16. 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

    Content type: Research article

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  17. DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is ex...

    Authors: Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand and Marcos J. Araúzo-Bravo

    Citation: BMC Genomics 2017 18:964

    Content type: Research Article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Methodology article

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  20. 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

    Content type: Methodology article

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  21. 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

    Content type: Methodology article

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  22. 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

    Content type: Software

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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

  44. 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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  45. 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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  46. 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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  47. 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

    Published on:

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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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