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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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

  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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