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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 4 of 22

  1. The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patche...

    Authors: Melissa T. R. Hawkins, Ryan R. Culligan, Cynthia L. Frasier, Rebecca B. Dikow, Ryan Hagenson, Runhua Lei and Edward E. Louis Jr

    Citation: BMC Genomics 2018 19:445

    Content type: Research article

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  2. The role of PPARα in gene regulation in mouse liver is well characterized. However, less is known about the role of PPARα in human liver. The aim of the present study was to better characterize the impact of P...

    Authors: Montserrat A. de la Rosa Rodriguez, Go Sugahara, Guido J. E. J. Hooiveld, Yuji Ishida, Chise Tateno and Sander Kersten

    Citation: BMC Genomics 2018 19:443

    Content type: Research article

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  3. Lung cancer is a very heterogeneous disease that can be pathologically classified into different subtypes including small-cell lung carcinoma (SCLC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (L...

    Authors: Shu Zhang, Mingfa Li, Hongbin Ji and Zhaoyuan Fang

    Citation: BMC Genomics 2018 19:435

    Content type: Research article

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  4. Microdeletion of chromosome 22q11 is associated with significant developmental anomalies, including disruption of the cardiac outflow tract, thymic/parathyroid aplasia and cleft palate. Amongst the genes withi...

    Authors: Maria Zoupa, Guilherme Machado Xavier, Stephanie Bryan, Ioannis Theologidis, Matthew Arno and Martyn T. Cobourne

    Citation: BMC Genomics 2018 19:429

    Content type: Research article

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  5. Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are some...

    Authors: Guoliang Lyu, Chao Zhang, Te Ling, Rui Liu, Le Zong, Yiting Guan, Xiaoke Huang, Lei Sun, Lijun Zhang, Cheng Li, Yu Nie and Wei Tao

    Citation: BMC Genomics 2018 19:428

    Content type: Research article

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  6. The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could ...

    Authors: Noa Bossel Ben-Moshe, Shlomit Gilad, Gili Perry, Sima Benjamin, Nora Balint-Lahat, Anya Pavlovsky, Sharon Halperin, Barak Markus, Ady Yosepovich, Iris Barshack, Einav Nili Gal-Yam, Eytan Domany, Bella Kaufman and Maya Dadiani

    Citation: BMC Genomics 2018 19:419

    Content type: Research article

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  7. Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage...

    Authors: Luli S. Zou, Michael R. Erdos, D. Leland Taylor, Peter S. Chines, Arushi Varshney, Stephen C. J. Parker, Francis S. Collins and John P. Didion

    Citation: BMC Genomics 2018 19:390

    Content type: Methodology article

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  8. Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide associat...

    Authors: Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto and Jan Baumbach

    Citation: BMC Genomics 2018 19:369

    Content type: Software

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  9. Cell-type-specific genes exhibit heterogeneity in genomic contexts and may be subject to different epigenetic regulations through different gene transcriptional processes depending on the cell type involved. T...

    Authors: Mayumi Oda, Shunichi Wakabayashi, N. Ari Wijetunga, Shinsuke Yuasa, Hirokazu Enomoto, Ruri Kaneda, Sung Han Yoon, Nishant Mittal, Qiang Jing, Masako Suzuki, John M. Greally, Keiichi Fukuda and Shinji Makino

    Citation: BMC Genomics 2018 19:349

    Content type: Research article

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  10. Although sleep deprivation is associated with neurobehavioral impairment that may underlie significant risks to performance and safety, there is no reliable biomarker test to detect dangerous levels of impairm...

    Authors: Hilary A. Uyhelji, Doris M. Kupfer, Vicky L. White, Melinda L. Jackson, Hans P. A. Van Dongen and Dennis M. Burian

    Citation: BMC Genomics 2018 19:341

    Content type: Research article

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  11. Circular RNAs (circRNAs) are a novel class of endogenous, non-coding RNAs that form covalently closed continuous loops and that are both highly conserved and abundant in the mammalian brain. A role for circRNA...

    Authors: Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger and Winnie S. Liang

    Citation: BMC Genomics 2018 19:340

    Content type: Research article

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  12. The Jurkat cell line has an extensive history as a model of T cell signaling. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line p...

    Authors: Louis Gioia, Azeem Siddique, Steven R. Head, Daniel R. Salomon and Andrew I. Su

    Citation: BMC Genomics 2018 19:334

    Content type: Research article

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  13. Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells w...

    Authors: Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason, Gina Vicente, Michael Dasilva, Wendy Brodeur, Timothy DeSmet, Sheila Dodge, Niall J. Lennon…

    Citation: BMC Genomics 2018 19:332

    Content type: Research article

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  14. CRISPR/Cas9 enables the targeting of genes in zygotes; however, efficient approaches to create loxP-flanked (floxed) alleles remain elusive.

    Authors: Yoshiki Miyasaka, Yoshihiro Uno, Kazuto Yoshimi, Yayoi Kunihiro, Takuji Yoshimura, Tomohiro Tanaka, Harumi Ishikubo, Yuichi Hiraoka, Norihiko Takemoto, Takao Tanaka, Yoshihiro Ooguchi, Paul Skehel, Tomomi Aida, Junji Takeda and Tomoji Mashimo

    Citation: BMC Genomics 2018 19:318

    Content type: Research article

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  15. In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense o...

    Authors: Rahul Kumar Jangid, Ashwin Kelkar, Vijaykumar Yogesh Muley and Sanjeev Galande

    Citation: BMC Genomics 2018 19:313

    Content type: Research article

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  16. Identifying functional non-coding variation is critical for defining the genetic contributions to human disease. While single-nucleotide polymorphisms (SNPs) within cis-acting transcriptional regulatory elements ...

    Authors: William D. Law, Elizabeth A. Fogarty, Aimée Vester and Anthony Antonellis

    Citation: BMC Genomics 2018 19:311

    Content type: Research article

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  17. Salmonella is a Gram-negative bacterium causing a wide range of clinical syndromes ranging from typhoid fever to diarrheic disease. Non-typhoidal Salmonella (NTS) serovars infect humans and animals, causing impor...

    Authors: Jing Zhang, Danielle Malo, Richard Mott, Jean-Jacques Panthier, Xavier Montagutelli and Jean Jaubert

    Citation: BMC Genomics 2018 19:303

    Content type: Research article

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  18. Emissions from diesel vehicles and biomass burning are the principal sources of primary ultrafine particles (UFP). The exposure to UFP has been associated to cardiovascular and pulmonary diseases, including lu...

    Authors: Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia and Marina Camatini

    Citation: BMC Genomics 2018 19:302

    Content type: Research article

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  19. Considering the implication of gene expression in the susceptibility of chronic diseases and the familial clustering of chronic diseases, the study of familial resemblances in gene expression levels is then hi...

    Authors: Bénédicte L. Tremblay, Frédéric Guénard, Benoît Lamarche, Louis Pérusse and Marie-Claude Vohl

    Citation: BMC Genomics 2018 19:300

    Content type: Research article

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  20. Cigarette smoking has severe adverse health consequences in adults and in the offspring of mothers who smoke during pregnancy. One of the most widely reported effects of smoking during pregnancy is reduced bir...

    Authors: Stephanie H. Witt, Josef Frank, Maria Gilles, Maren Lang, Jens Treutlein, Fabian Streit, Isabell A. C. Wolf, Verena Peus, Barbara Scharnholz, Tabea S. Send, Stefanie Heilmann-Heimbach, Sugirthan Sivalingam, Helene Dukal, Jana Strohmaier, Marc Sütterlin, Janine Arloth…

    Citation: BMC Genomics 2018 19:290

    Content type: Research article

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  21. Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human dev...

    Authors: Osagie G. Izuogu, Abd A. Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K. Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David J. Elliott, Mauro Santibanez-Koref and Michael S. Jackson

    Citation: BMC Genomics 2018 19:276

    Content type: Research article

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  22. Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read de...

    Authors: Jeroen van den Akker, Gilad Mishne, Anjali D. Zimmer and Alicia Y. Zhou

    Citation: BMC Genomics 2018 19:263

    Content type: Methodology article

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  23. High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a spec...

    Authors: Zuguang Gu, Roland Eils, Matthias Schlesner and Naveed Ishaque

    Citation: BMC Genomics 2018 19:234

    Content type: Software

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  24. Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Nex...

    Authors: Georgia Giannoukos, Dawn M. Ciulla, Eugenio Marco, Hayat S. Abdulkerim, Luis A. Barrera, Anne Bothmer, Vidya Dhanapal, Sebastian W. Gloskowski, Hariharan Jayaram, Morgan L. Maeder, Maxwell N. Skor, Tongyao Wang, Vic E. Myer and Christopher J. Wilson

    Citation: BMC Genomics 2018 19:212

    Content type: Methodology article

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  25. Aneuploidy, or abnormal chromosome numbers, severely alters cell physiology and is widespread in cancers and other pathologies. Using model cell lines engineered to carry one or more extra chromosomes, it has ...

    Authors: Milena Dürrbaum, Christine Kruse, K. Julia Nieken, Bianca Habermann and Zuzana Storchová

    Citation: BMC Genomics 2018 19:197

    Content type: Research article

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  26. The murine discs large homolog 2 (DLG2; post synaptic density 93 (PSD-93); Chapsyn-110) is a member of the membrane-associated guanylate kinase (MAGUK) protein family involved in receptor assembly and associat...

    Authors: Shafaqat Ali, Alexander Hoven, Regine J. Dress, Heiner Schaal, Judith Alferink and Stefanie Scheu

    Citation: BMC Genomics 2018 19:194

    Content type: Research article

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  27. Noninvasive biomarkers are urgently needed for patients with nonalcoholic steatohepatitis (NASH) to assist in diagnosis, monitoring disease progression and assessing treatment response. Recently several explor...

    Authors: Jie Liu, Yue Xiao, Xikun Wu, Lichun Jiang, Shurong Yang, Zhiming Ding, Zhuo Fang, Haiqing Hua, Mark Stephen Kirby and Jianyong Shou

    Citation: BMC Genomics 2018 19:188

    Content type: Research article

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  28. The generation of induced pluripotent stem cells (iPSCs) has underdefined mechanisms. In addition, leukemia inhibitory factor (LIF) activated Janus kinase/signal transducer and activator of transcription 3 (JA...

    Authors: Ling Wang, Zongliang Jiang, Delun Huang, Jingyue Duan, Chang Huang, Shannon Sullivan, Kaneha Vali, Yexuan Yin, Ming Zhang, Jill Wegrzyn, Xiuchun ( Cindy) Tian and Young Tang

    Citation: BMC Genomics 2018 19:183

    Content type: Research article

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  29. The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of who...

    Authors: Casey L. Dagnall, Lindsay M. Morton, Belynda D. Hicks, Shengchao Li, Weiyin Zhou, Eric Karlins, Kedest Teshome, Salma Chowdhury, Kerrie S. Lashley, Joshua N. Sampson, Leslie L. Robison, Gregory T. Armstrong, Smita Bhatia, Gretchen A. Radloff, Stella M. Davies, Margaret A. Tucker…

    Citation: BMC Genomics 2018 19:182

    Content type: Methodology article

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  30. Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. H...

    Authors: Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Sougat Misra, Carsten O. Daub, Juha Kere and Peter Swoboda

    Citation: BMC Genomics 2018 19:181

    Content type: Research article

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  31. Gestational disorders such as intrauterine growth restriction (IUGR) and pre-eclampsia (PE) are main causes of poor perinatal outcomes worldwide. Both diseases are related with impaired materno-fetal nutrient ...

    Authors: Xiao Huang, Pascale Anderle, Lu Hostettler, Marc U. Baumann, Daniel V. Surbek, Edgar C. Ontsouka and Christiane Albrecht

    Citation: BMC Genomics 2018 19:173

    Content type: Research article

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  32. ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin...

    Authors: Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson and Lihua Julie Zhu

    Citation: BMC Genomics 2018 19:169

    Content type: Software

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  33. The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics an...

    Authors: Oluwatosin Oluwadare, Yuxiang Zhang and Jianlin Cheng

    Citation: BMC Genomics 2018 19:161

    Content type: Methodology article

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  34. Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have th...

    Authors: Gergely Ivády, László Madar, Erika Dzsudzsák, Katalin Koczok, János Kappelmayer, Veronika Krulisova, Milan Macek Jr, Attila Horváth and István Balogh

    Citation: BMC Genomics 2018 19:158

    Content type: Research article

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  35. Chromocenters are defined as a punctate condensed blocks of chromatin in the interphase cell nuclei of certain cell types with unknown biological significance. In recent years a progress in revealing of chromo...

    Authors: Dmitrii I. Ostromyshenskii, Ekaterina N. Chernyaeva, Inna S. Kuznetsova and Olga I. Podgornaya

    Citation: BMC Genomics 2018 19:151

    Content type: Research article

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  36. Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

    Authors: Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi…

    Citation: BMC Genomics 2018 19:150

    Content type: Research article

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  37. Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have ...

    Authors: Jian Wu, Wei Dai, Lin Wu and Jinke Wang

    Citation: BMC Genomics 2018 19:143

    Content type: Methodology article

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    The Correction to this article has been published in BMC Genomics 2018 19:327

  38. Comprehensive understanding of intratumor heterogeneity requires identification of molecular markers, which are capable of differentiating different subpopulations and which also have clinical significance. On...

    Authors: Fan Wang, Zachariah Dohogne, Jin Yang, Yu Liu and Benjamin Soibam

    Citation: BMC Genomics 2018 19:137

    Content type: Research article

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  39. Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A ...

    Authors: Qiuyan Li, Kexian Dong, Lidan Xu, Xueyuan Jia, Jie Wu, Wenjing Sun, Xuelong Zhang and Songbin Fu

    Citation: BMC Genomics 2018 19:134

    Content type: Research article

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  40. Transposable elements (TEs) are mobile genetic sequences that randomly propagate within their host’s genome. This mobility has the potential to affect gene transcription and cause disease. However, TEs are tec...

    Authors: Erika M. Kvikstad, Paolo Piazza, Jenny C. Taylor and Gerton Lunter

    Citation: BMC Genomics 2018 19:115

    Content type: Methodology article

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  41. Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under co...

    Authors: Qingzhou Guan, Haidan Yan, Yanhua Chen, Baotong Zheng, Hao Cai, Jun He, Kai Song, You Guo, Lu Ao, Huaping Liu, Wenyuan Zhao, Xianlong Wang and Zheng Guo

    Citation: BMC Genomics 2018 19:99

    Content type: Research article

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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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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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