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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 1 of 20

  1. Content type: Research article

    The relationship between aging and epigenetic profiles has been highlighted in many recent studies. Models using somatic cell methylomes to predict age have been successfully constructed. However, gamete aging...

    Authors: Timothy G. Jenkins, Kenneth I. Aston, Bradley Cairns, Andrew Smith and Douglas T. Carrell

    Citation: BMC Genomics 2018 19:763

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  2. Content type: Research article

    Mitochondrial DNA (mtDNA) copy number has been found associated with multiple diseases, including cancers, diabetes and so on. Both environmental and genetic factors could affect the copy number of mtDNA. Howe...

    Authors: Zhihua Li, Meng Zhu, Jiangbo Du, Hongxia Ma, Guangfu Jin and Juncheng Dai

    Citation: BMC Genomics 2018 19:752

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  3. Content type: Research article

    Long noncoding RNAs (lncRNAs) are known to play important roles in different cell contexts, including cancers. However, little is known about lncRNAs in cholangiocarcinoma (CCA), a cholangiocyte malignancy wit...

    Authors: Bo-Wei Han, Hua Ye, Pan-Pan Wei, Bo He, Cai Han, Zhen-Hua Chen, Yue-Qin Chen and Wen-Tao Wang

    Citation: BMC Genomics 2018 19:735

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  4. Content type: Research article

    Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their gene transcription profile. This technology is widely used in medicine, animal husbandry and other industries. Ho...

    Authors: Yong Liu, Fengrui Wu, Ling Zhang, Xiaoqing Wu, Dengkun Li, Jing Xin, Juan Xie, Feng Kong, Wenying Wang, Qiaoqin Wu, Di Zhang, Rong Wang, Shaorong Gao and Wenyong Li

    Citation: BMC Genomics 2018 19:734

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  5. Content type: Research article

    The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early mouse development, SR-B1 is located in the maternal-fetal interf...

    Authors: Nicolás Santander, Carlos Lizama, Leandro Murgas, Sebastián Contreras, Alberto J. M. Martin, Paz Molina, Alonso Quiroz, Katherine Rivera, Francisca Salas-Pérez, Alejandro Godoy, Attilio Rigotti and Dolores Busso

    Citation: BMC Genomics 2018 19:731

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  6. Content type: Research article

    Transposome-based technologies have enabled the streamlined production of sequencer-ready DNA libraries; however, current methods are highly sensitive to the amount and quality of input nucleic acid.

    Authors: Stephen Bruinsma, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, Lee Brady, Anupama Khanna, Lindsay Freeberg, Rosamond G Jackson, Pascale Mathonet, Susan C Verity, Andrew F Slatter, Rooz Golshani, Haiying Grunenwald…

    Citation: BMC Genomics 2018 19:722

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  7. Content type: Software

    Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has great potential to illuminate our understanding of biology and medicine, but the ...

    Authors: Natalia Polouliakh, Paul Horton, Kazuhiro Shibanai, Kodai Takata, Vanessa Ludwig, Samik Ghosh and Hiroaki Kitano

    Citation: BMC Genomics 2018 19:715

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  8. Content type: Research article

    Human perception of bitter substances is partially genetically determined. Previously we discovered a single nucleotide polymorphism (SNP) within the cluster of bitter taste receptor genes on chromosome 12 tha...

    Authors: Liang-Dar Hwang, Puya Gharahkhani, Paul A. S. Breslin, Scott D. Gordon, Gu Zhu, Nicholas G. Martin, Danielle R. Reed and Margaret J. Wright

    Citation: BMC Genomics 2018 19:678

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  9. Content type: Research article

    The current literature on single cell genomic analyses on the DNA level is conflicting regarding requirements for cell quality, amplification success rates, allelic dropouts and resolution, lacking a systemati...

    Authors: Anita T. Simonsen, Marcus C. Hansen, Eigil Kjeldsen, Peter L. Møller, Johnny J. Hindkjær, Peter Hokland and Anni Aggerholm

    Citation: BMC Genomics 2018 19:681

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  10. Content type: Research article

    To explore long non-coding RNA (lncRNA), mRNA and circular RNA (circRNA) expression profiles and their biological functions in the pathogenesis of kidney stones in ethylene glycol-induced urolithiasis rats.

    Authors: Yanan Cao, Xiaowei Gao, Yue Yang, Zhi Ye, E. Wang and Zhitao Dong

    Citation: BMC Genomics 2018 19:660

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  11. Content type: Research article

    Intermittent fasting and time-restricted diets are associated with lower risk biomarkers for cardio-metabolic disease. The shared mechanisms underpinning the similar physiological response to these events is n...

    Authors: Alexessander Couto Alves, Craig A. Glastonbury, Julia S. El-Sayed Moustafa and Kerrin S. Small

    Citation: BMC Genomics 2018 19:659

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  12. Content type: Research article

    The transient middle cerebral artery occlusion (tMCAO) model is used for studying the molecular mechanisms of ischemic damage and neuroprotection. Numerous studies have demonstrated the role of individual gene...

    Authors: Lyudmila V. Dergunova, Ivan B. Filippenkov, Vasily V. Stavchansky, Alina E. Denisova, Vadim V. Yuzhakov, Sergey A. Mozerov, Leonid V. Gubsky and Svetlana A. Limborska

    Citation: BMC Genomics 2018 19:655

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  13. Content type: Research article

    MicroRNAs (miRNAs) are small non-coding RNAs that bind messenger RNAs and promote their degradation or repress their translation. There is increasing evidence of miRNAs playing an important role in alcohol rel...

    Authors: Pratyaydipta Rudra, Wen J. Shi, Pamela Russell, Brian Vestal, Boris Tabakoff, Paula Hoffman, Katerina Kechris and Laura Saba

    Citation: BMC Genomics 2018 19:639

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  14. Content type: Research article

    Mitochondria are organelles that fulfill a fundamental role in cell bioenergetics, as well as in other processes like cell signaling and death. Small non-coding RNAs (sncRNA) are now being considered as pivota...

    Authors: Eduardo Larriba, Eduardo Rial and Jesús del Mazo

    Citation: BMC Genomics 2018 19:634

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  15. Content type: Research article

    Although most genes in mammalian genomes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the functional repertoire of the gen...

    Authors: Shamsuddin A. Bhuiyan, Sophia Ly, Minh Phan, Brandon Huntington, Ellie Hogan, Chao Chun Liu, James Liu and Paul Pavlidis

    Citation: BMC Genomics 2018 19:637

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  16. Content type: Database

    Long non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modificati...

    Authors: Fengrui Wu, Yong Liu, Qingqing Wu, Dengkun Li, Ling Zhang, Xiaoqing Wu, Rong Wang, Di Zhang, Shaorong Gao and Wenyong Li

    Citation: BMC Genomics 2018 19:631

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  17. Content type: Research article

    Long-term exposure to elevated levels of free fatty acids (FFAs) is deleterious for beta-cell function and may contribute to development of type 2 diabetes mellitus (T2DM). Whereas mechanisms of impaired gluco...

    Authors: Ernest Sargsyan, Jing Cen, Kirsten Roomp, Reinhard Schneider and Peter Bergsten

    Citation: BMC Genomics 2018 19:629

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  18. Content type: Research article

    The emergence of fully antimicrobial resistant Neisseria gonorrhoeae has led global public health agencies to identify a critical need for next generation anti-gonococcal pharmaceuticals. The development and succ...

    Authors: Ian P. Francis, Epshita A. Islam, Adam C. Gower, Yazdani B. Shaik-Dasthagirisaheb, Scott D. Gray-Owen and Lee M. Wetzler

    Citation: BMC Genomics 2018 19:627

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  19. Content type: Review

    The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majori...

    Authors: K. Blighe, L. DeDionisio, K. A. Christie, B. Chawes, S. Shareef, T. Kakouli-Duarte, C. Chao-Shern, V. Harding, R. S. Kelly, L. Castellano, J. Stebbing, J. A. Lasky-Su, M. A. Nesbit and C. B. T. Moore

    Citation: BMC Genomics 2018 19:595

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  20. Content type: Research article

    Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4...

    Authors: Weijing Cai, Dapeng Zhou, Weibo Wu, Wen Ling Tan, Jiaqian Wang, Caicun Zhou and Yanyan Lou

    Citation: BMC Genomics 2018 19:582

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  21. Content type: Research article

    3,4-methylenedioxymethamphetamine (MDMA, “ecstasy”) is a widely used entactogenic drug known to impair cognitive functions on the long-run. Both hippocampal and frontal cortical regions have well established r...

    Authors: Peter Petschner, Viola Tamasi, Csaba Adori, Eszter Kirilly, Romeo D. Ando, Laszlo Tothfalusi and Gyorgy Bagdy

    Citation: BMC Genomics 2018 19:580

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  22. Content type: Research article

    N6-methyladenosine (m6A) is an important epigenetic modification which plays various roles in mRNA metabolism and embryogenesis directly related to human diseases. To identify m6A in a large scale, machine learni...

    Authors: Zhixun Zhao, Hui Peng, Chaowang Lan, Yi Zheng, Liang Fang and Jinyan Li

    Citation: BMC Genomics 2018 19:574

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  23. Content type: Research article

    Human neutrophils are central players in innate immunity, a major component of inflammatory responses, and a leading model for cell motility and chemotaxis. However, primary neutrophils are short-lived, limiti...

    Authors: Esther Rincón, Briana L. Rocha-Gregg and Sean R. Collins

    Citation: BMC Genomics 2018 19:573

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  24. Content type: Methodology article

    Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of mole...

    Authors: Thomas J. F. Pranzatelli, Drew G. Michael and John A. Chiorini

    Citation: BMC Genomics 2018 19:563

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  25. Content type: Research article

    Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify ...

    Authors: Jun Yasuda, Fumiki Katsuoka, Inaho Danjoh, Yosuke Kawai, Kaname Kojima, Masao Nagasaki, Sakae Saito, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N. Motoike, Kazuki Kumada, Mika Sakurai-Yageta, Osamu Tanabe, Nobuo Fuse, Gen Tamiya, Koichiro Higasa…

    Citation: BMC Genomics 2018 19:551

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  26. Content type: Research article

    Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberran...

    Authors: Yuhong Dou, Yong Zhu, Junmei Ai, Hankui Chen, Helu Liu, Jeffrey A. Borgia, Xiao Li, Fan Yang, Bin Jiang, Jun Wang and Youping Deng

    Citation: BMC Genomics 2018 19:545

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  27. Content type: Research article

    Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (lncRNAs) are ...

    Authors: Seong Hyeon Hong, Jun Tae Kwon, Jihye Kim, Juri Jeong, Jaehwan Kim, Seonhee Lee and Chunghee Cho

    Citation: BMC Genomics 2018 19:539

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  28. Content type: Research article

    Esophageal squamous cell carcinomas (ESCC) is the fourth most lethal cancer in China. Previous studies reveal several highly conserved mutational processes in ESCC. However, it remains unclear what are the tru...

    Authors: Jintao Guo, Jiankun Huang, Ying Zhou, Yulin Zhou, Liying Yu, Huili Li, Lingyun Hou, Liuwei Zhu, Dandan Ge, Yuanyuan Zeng, Bayasi Guleng and Qiyuan Li

    Citation: BMC Genomics 2018 19:538

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  29. Content type: Methodology article

    Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome...

    Authors: John Cologne, Lenora Loo, Yurii B. Shvetsov, Munechika Misumi, Philip Lin, Christopher A. Haiman, Lynne R. Wilkens and Loïc Le Marchand

    Citation: BMC Genomics 2018 19:524

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  30. Content type: Research article

    Human Endogenous Retroviruses (HERVs) and Mammalian apparent LTR-retrotransposons (MaLRs) represent the 8% of our genome and are distributed among our 46 chromosomes. These LTR-retrotransposons are thought to ...

    Authors: Marine Mommert, Olivier Tabone, Guy Oriol, Elisabeth Cerrato, Audrey Guichard, Magali Naville, Paola Fournier, Jean-Nicolas Volff, Alexandre Pachot, Guillaume Monneret, Fabienne Venet, Karen Brengel-Pesce, Julien Textoris and François Mallet

    Citation: BMC Genomics 2018 19:522

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  31. Content type: Research article

    Cis-regulatory elements control gene expression over large distances through the formation of chromatin loops, which allow contact between enhancers and gene promoters. Alterations in cis-acting regulatory system...

    Authors: Stéphanie Moisan, Stéphanie Levon, Emilie Cornec-Le Gall, Yannick Le Meur, Marie-Pierre Audrézet, Josée Dostie and Claude Férec

    Citation: BMC Genomics 2018 19:515

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  32. Content type: Research article

    Arylamine N-acetyltransferase 1 (NAT1) is a drug metabolizing enzyme that has been associated with cancer cell proliferation in vitro and with survival in vivo. NAT1 expression has been associated with the est...

    Authors: Rodney F. Minchin and Neville J. Butcher

    Citation: BMC Genomics 2018 19:513

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  33. Content type: Methodology article

    RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interd...

    Authors: Xiaoyong Pan, Peter Rijnbeek, Junchi Yan and Hong-Bin Shen

    Citation: BMC Genomics 2018 19:511

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  34. Content type: Methodology article

    To date, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants among a variety of traits/diseases, shedding light on the genetic architecture of complex dise...

    Authors: Yi Yang, Mingwei Dai, Jian Huang, Xinyi Lin, Can Yang, Min Chen and Jin Liu

    Citation: BMC Genomics 2018 19:503

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  35. Content type: Research article

    Radiation exposure due to the detonation of an improvised nuclear device remains a major security concern. Radiation from such a device involves a combination of photons and neutrons. Although photons will mak...

    Authors: Constantinos G. Broustas, Andrew D. Harken, Guy Garty and Sally A. Amundson

    Citation: BMC Genomics 2018 19:504

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  36. Content type: Research article

    The evolutionarily conserved Sonic Hedgehog (Shh) signaling pathway is essential for embryogenesis and orofacial development. SHH ligand secreted from the surface ectoderm activates pathway activity in the und...

    Authors: Joshua L. Everson, Dustin M. Fink, Hannah M. Chung, Miranda R. Sun and Robert J. Lipinski

    Citation: BMC Genomics 2018 19:497

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  37. Content type: Research article

    Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and su...

    Authors: Johannes Rainer, Viviana Meraviglia, Hagen Blankenburg, Chiara Piubelli, Peter P. Pramstaller, Adolfo Paolin, Elisa Cogliati, Giulio Pompilio, Elena Sommariva, Francisco S. Domingues and Alessandra Rossini

    Citation: BMC Genomics 2018 19:491

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  38. Content type: Methodology article

    There is considerable evidence that many complex traits have a partially shared genetic basis, termed pleiotropy. It is therefore useful to consider integrating genome-wide association study (GWAS) data across...

    Authors: Marissa LeBlanc, Verena Zuber, Wesley K. Thompson, Ole A. Andreassen, Arnoldo Frigessi and Bettina Kulle Andreassen

    Citation: BMC Genomics 2018 19:494

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  39. Content type: Methodology article

    The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and tes...

    Authors: Julie F. Foley, Dhiral P. Phadke, Owen Hardy, Sara Hardy, Victor Miller, Anup Madan, Kellie Howard, Kimberly Kruse, Cara Lord, Sreenivasa Ramaiahgari, Gregory G. Solomon, Ruchir R. Shah, Arun R. Pandiri, Ronald A. Herbert, Robert C. Sills and B. Alex Merrick

    Citation: BMC Genomics 2018 19:487

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  40. Content type: Research article

    Copy number variation (CNV) has been implicated in the genetics of multiple human diseases. Spinal muscular atrophy (SMA) and 22q11.2 deletion syndrome (22q11.2DS) are two of the most common diseases which are...

    Authors: Xiaoqing Zhang, Bo Wang, Lichen Zhang, Guoling You, Robert A. Palais, Luming Zhou and Qihua Fu

    Citation: BMC Genomics 2018 19:485

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  41. Content type: Research article

    Face morphology is strongly determined by genetic factors. However, only a small number of genes related to face morphology have been identified to date. Here, we performed a two-stage genome-wide association ...

    Authors: Seongwon Cha, Ji Eun Lim, Ah Yeon Park, Jun-Hyeong Do, Si Woo Lee, Chol Shin, Nam Han Cho, Ji-One Kang, Jeong Min Nam, Jong-Sik Kim, Kwang-Man Woo, Seung-Hwan Lee, Jong Yeol Kim and Bermseok Oh

    Citation: BMC Genomics 2018 19:481

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  42. Content type: Research article

    Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA meth...

    Authors: Elizabeth M. Kennedy, George N. Goehring, Michael H. Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K. Smith and Karen N. Conneely

    Citation: BMC Genomics 2018 19:476

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  43. Content type: Research article

    It is well known that development of prostate cancer (PC) can be attributed to somatic mutations of the genome, acquired within proto-oncogenes or tumor-suppressor genes. What is less well understood is how ge...

    Authors: Jean M. Winter, Natasha L. Curry, Derek M. Gildea, Kendra A. Williams, Minnkyong Lee, Ying Hu and Nigel P. S. Crawford

    Citation: BMC Genomics 2018 19:450

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  44. Content type: Research article

    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

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  45. Content type: Research article

    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

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  46. Content type: Research article

    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

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