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Proteomics

This section covers all aspects of high-throughput proteomics, experimental and analytical approaches to proteome analysis, mass spectrometry, and also metabolomics.

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  1. Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers a...

    Authors: Héctor Cordero, Monica F. Brinchmann, Alberto Cuesta and María A. Esteban

    Citation: BMC Genomics 2017 18:939

    Content type: Research article

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  2. Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns durin...

    Authors: Hui-Zeng Sun, Kai Shi, Xue-Hui Wu, Ming-Yuan Xue, Zi-Hai Wei, Jian-Xin Liu and Hong-Yun Liu

    Citation: BMC Genomics 2017 18:936

    Content type: Research article

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  3. Parthenocarpy is an excellent agronomic trait that enables crops to set fruit in the absence of pollination and fertilization, and therefore to produce seedless fruit. Although parthenocarpy is widely recogniz...

    Authors: Ji Li, Jian Xu, Qin-Wei Guo, Zhe Wu, Ting Zhang, Kai-Jing Zhang, Chun-yan Cheng, Pin-yu Zhu, Qun-Feng Lou and Jin-Feng Chen

    Citation: BMC Genomics 2017 18:896

    Content type: Research article

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  4. Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics resu...

    Authors: J. Michael Proffitt, Jeremy Glenn, Anthony J. Cesnik, Avinash Jadhav, Michael R. Shortreed, Lloyd M. Smith, Kylie Kavanagh, Laura A. Cox and Michael Olivier

    Citation: BMC Genomics 2017 18:877

    Content type: Research article

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  5. Skeletal muscle development is closely linked to meat production and its quality. This study is the first to quantify the proteomes and metabolomes of breast muscle in two distinct chicken breeds at embryonic ...

    Authors: Ranran Liu, Hongyang Wang, Jie Liu, Jie Wang, Maiqing Zheng, Xiaodong Tan, Siyuan Xing, Huanxian Cui, Qinghe Li, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2017 18:816

    Content type: Research article

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  6. Haliotis diversicolor is commercially important species. The trochophore and veliger are distinct larval stages in gastropod development. Their development involves complex morphologic...

    Authors: Guilan Di, Xianghui Kong, Xiulian Miao, Yifang Zhang, Miaoqin Huang, Yuting Gu, Weiwei You, Jianxin Zhang and Caihuan Ke

    Citation: BMC Genomics 2017 18:809

    Content type: Research article

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  7. Nanobodies are single-domain antibodies that contain the unique structural and functional properties of naturally-occurring heavy chain in camelidae. As a novel class of antibody, they show many advantages com...

    Authors: Jing Zuo, Jian Li, Rongxin Zhang, Longsheng Xu, Hanhan Chen, Xiaohuan Jia, Zhipeng Su, Linhong Zhao, Xing Huang and Wei Xie

    Citation: BMC Genomics 2017 18:797

    Content type: Database

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  8. Salamanders regenerate their limbs after amputation. However, the molecular mechanism of this unique regeneration remains unclear. In this study, isobaric tags for relative and absolute quantification (iTRAQ) ...

    Authors: Jie Tang, Yuan Yu, Hanxue Zheng, Lu Yin, Mei Sun, Wenjun Wang, Jihong Cui, Wenguang Liu, Xin Xie and Fulin Chen

    Citation: BMC Genomics 2017 18:750

    Content type: Research article

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  9. Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia ...

    Authors: Qiuxiang Luo, Mu Peng, Xiuli Zhang, Pei Lei, Ximei Ji, Wahsoon Chow, Fanjuan Meng and Guanyu Sun

    Citation: BMC Genomics 2017 18:648

    Content type: Research article

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  10. Human hepatitis B virus (HBV) infection is an important public health issue in the Asia-Pacific region and is associated with chronic hepatitis, liver fibrosis, cirrhosis and even liver cancer. However, the un...

    Authors: Fangming Kan, Lei Ye, Tao Yan, Jiaqi Cao, Jianhua Zheng and Wuping Li

    Citation: BMC Genomics 2017 18:641

    Content type: Research article

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  11. Aedes albopictus is a vector of arboviruses that cause severe diseases in humans such as Chikungunya, Dengue and Zika fevers. The vector competence of Ae. albopictus varies depending o...

    Authors: Yoann Saucereau, Claire Valiente Moro, Cindy Dieryckx, Jean-William Dupuy, Florence-Hélène Tran, Vincent Girard, Patrick Potier and Patrick Mavingui

    Citation: BMC Genomics 2017 18:635

    Content type: Research article

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  12. Nelson Bay orthoreovirus (NBV) is a fusogenic bat borne virus with an unknown zoonotic potential. Previous studies have shown that NBV can infect and replicate in a wide variety of cell types derived from thei...

    Authors: Lawrence Mok, James W. Wynne, Mary Tachedjian, Brian Shiell, Kris Ford, David A. Matthews, Antony Bacic and Wojtek P. Michalski

    Citation: BMC Genomics 2017 18:615

    Content type: Research article

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  13. Spiders are predaceous arthropods that are capable of subduing and consuming relatively large prey items compared to their own body size. For this purpose, spiders have evolved potent venoms to immobilise prey...

    Authors: André Walter, Jesper Bechsgaard, Carsten Scavenius, Thomas S. Dyrlund, Kristian W. Sanggaard, Jan J. Enghild and Trine Bilde

    Citation: BMC Genomics 2017 18:600

    Content type: Research article

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  14. Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Ch...

    Authors: Shangguo Feng, Kaili Jiao, Hong Guo, Mengyi Jiang, Juan Hao, Huizhong Wang and Chenjia Shen

    Citation: BMC Genomics 2017 18:598

    Content type: Research article

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  15. Dermatophytes, the most common cause of fungal infections, affect millions of individuals worldwide. They pose a major threat to public health because of the severity and longevity of infections caused by derm...

    Authors: Xingye Xu, Tao Liu, Jian Yang, Lihong Chen, Bo Liu, Candong Wei, Lingling Wang and Qi Jin

    Citation: BMC Genomics 2017 18:577

    Content type: Research article

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  16. The monovalent anions formate, nitrite and hydrosulphide are main metabolites of bacterial respiration during anaerobic mixed-acid fermentation. When accumulated in the cytoplasm, these anions become cytotoxic...

    Authors: Mishtu Mukherjee, Manu Vajpai and Ramasubbu Sankararamakrishnan

    Citation: BMC Genomics 2017 18:560

    Content type: Research article

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  17. Corynebacterium pseudotuberculosis is a pathogen classified into two biovars: C. pseudotuberculosis biovar ovis, the etiologic agent of caseous lymphadenitis and C. pseudotuberculosis ...

    Authors: Wanderson M. Silva, Edson L. Folador, Siomar C. Soares, Gustavo H. M. F. Souza, Agenor V. Santos, Cassiana S. Sousa, Henrique Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur Silva and Vasco Azevedo

    Citation: BMC Genomics 2017 18:451

    Content type: Research article

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  18. Recombinant peptide chips could constitute a versatile complementation to state-of-the-art in situ (chemical on-chip) synthesis, particle-based printing, or pre-manufactured peptide spotting. Bottlenecks still im...

    Authors: Harald Hundsberger, Kamil Önder, Peter Schuller-Götzburg, Dezso P. Virok, Julia Herzog and Raphaela Rid

    Citation: BMC Genomics 2017 18:450

    Content type: Methodology article

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  19. Lamprosema indicate is a major leaf feeding insect pest to soybean, which has caused serious yield losses in central and southern China. To explore the defense mechanisms of soybean resistance to Lamprosema indic...

    Authors: Weiying Zeng, Zudong Sun, Zhaoyan Cai, Huaizhu Chen, Zhenguang Lai, Shouzhen Yang and Xiangmin Tang

    Citation: BMC Genomics 2017 18:444

    Content type: Research article

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  20. This study characterises the molecular processes altered by both elevated CO2 and increasing temperature in oysters. Differences in resilience of marine organisms against the environmental stressors associated wi...

    Authors: Priscila Goncalves, Emma L. Thompson and David A. Raftos

    Citation: BMC Genomics 2017 18:431

    Content type: Research article

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  21. Brucella spp. are Gram-negative, facultative intracellular pathogens that cause brucellosis in both humans and animals. The B. abortus vaccine strain 104 M is the only vaccine availabl...

    Authors: Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu and Wei Chen

    Citation: BMC Genomics 2017 18:402

    Content type: Research article

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  22. The function of the prion protein, involved in the so-called prion diseases, remains a subject of intense debate and the possibility that it works as a pleiotropic protein through the interaction with multiple...

    Authors: J. A. Macedo, D. Schrama, I. Duarte, E. Tavares, J. Renaut, M. E. Futschik, P. M. Rodrigues and E. P. Melo

    Citation: BMC Genomics 2017 18:319

    Content type: Research article

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  23. Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological functi...

    Authors: Colin W. Brown, Viswanadham Sridhara, Daniel R. Boutz, Maria D. Person, Edward M. Marcotte, Jeffrey E. Barrick and Claus O. Wilke

    Citation: BMC Genomics 2017 18:301

    Content type: Research Article

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  24. Intra-uterine growth restriction (IUGR) and fetal overgrowth increase risks to postnatal health. Maternal nutrition is the major intrauterine environmental factor that alters fetal weight. However, the mechani...

    Authors: Long Che, ZhenGuo Yang, MengMeng Xu, ShengYu Xu, LianQiang Che, Yan Lin, ZhengFeng Fang, Bin Feng, Jian Li, DaiWen Chen and De Wu

    Citation: BMC Genomics 2017 18:213

    Content type: Research article

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  25. Intermuscular bones (IBs) and ribs both are a part of skeletal system in teleosts, but with different developing process. The chemical composition of fish IBs and ribs as well as the underlying mechanism about...

    Authors: Chun-Hong Nie, Shi-Ming Wan, Tea Tomljanovic, Tomislav Treer, Chung-Der Hsiao, Wei-Min Wang and Ze-Xia Gao

    Citation: BMC Genomics 2017 18:147

    Content type: Research article

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  26. Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable e...

    Authors: Kevin Maringer, Amjad Yousuf, Kate J. Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A. Matthews and Andrew D. Davidson

    Citation: BMC Genomics 2017 18:101

    Content type: Research Article

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  27. Barley seed proteins are of prime importance to the brewing industry, human and animal nutrition and in plant breeding for cultivar identification. To obtain comprehensive proteomic data from seeds, total prot...

    Authors: Ramamurthy Mahalingam

    Citation: BMC Genomics 2017 18:44

    Content type: Research Article

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  28. Lysine acetylation in proteins is a ubiquitous and conserved post-translational modification, playing a critical regulatory role in almost every aspect of living cells. Although known for many years, its funct...

    Authors: Shanyue Zhou, Qianqian Yang, Changfa Yin, Lin Liu and Wenxing Liang

    Citation: BMC Genomics 2016 17:1019

    Content type: Research article

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  29. Diatoms are able to acclimate to frequent and large light fluctuations in the surface ocean waters. However, the molecular mechanisms underlying these acclimation responses of diaotms remain elusive.

    Authors: Hong-Po Dong, Yue-Lei Dong, Lei Cui, Srinivasan Balamurugan, Jian Gao, Song-Hui Lu and Tao Jiang

    Citation: BMC Genomics 2016 17:994

    Content type: Research article

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  30. The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been ...

    Authors: Juliane Wippler, Manuel Kleiner, Christian Lott, Alexander Gruhl, Paul E. Abraham, Richard J. Giannone, Jacque C. Young, Robert L. Hettich and Nicole Dubilier

    Citation: BMC Genomics 2016 17:942

    Content type: Research article

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  31. Tibetan wild barley (Hordeum spontaneum L.) has been confirmed to contain elite accessions in tolerance to abiotic stresses, including salinity. However, molecular mechanisms underlying genotypic difference of sa...

    Authors: Qiufang Shen, Liangbo Fu, Fei Dai, Lixi Jiang, Guoping Zhang and Dezhi Wu

    Citation: BMC Genomics 2016 17:889

    Content type: Research article

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  32. NR2E1 (Tlx) is an orphan nuclear receptor that regulates the maintenance and self-renewal of neural stem cells, and promotes tumourigenesis. Nr2e1-null mice exhibit reduced cortical and limbic structures and pron...

    Authors: Ximena Corso-Díaz, Charles N. de Leeuw, Vivian Alonso, Diana Melchers, Bibiana K. Y. Wong, René Houtman and Elizabeth M. Simpson

    Citation: BMC Genomics 2016 17:832

    Content type: Research article

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  33. Alzheimer’s disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this ...

    Authors: Salma Jamal, Sukriti Goyal, Asheesh Shanker and Abhinav Grover

    Citation: BMC Genomics 2016 17:807

    Content type: Research article

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  34. Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of control...

    Authors: Yachun Su, Liping Xu, Zhuqing Wang, Qiong Peng, Yuting Yang, Yun Chen and Youxiong Que

    Citation: BMC Genomics 2016 17:800

    Content type: Research article

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  35. Spiders are known for their predatory efficiency and for their high capacity of digesting relatively large prey. They do this by combining both extracorporeal and intracellular digestion. Whereas many high thr...

    Authors: Felipe J. Fuzita, Martijn W. H. Pinkse, José S. L. Patane, Peter D. E. M. Verhaert and Adriana R. Lopes

    Citation: BMC Genomics 2016 17:716

    Content type: Research article

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  36. Major depressive disorder (MDD) is a heterogeneous disease at the level of clinical symptoms, and this heterogeneity is likely reflected at the level of biology. Two clinical subtypes within MDD that have garn...

    Authors: Yashu Liu, Lynn Yieh, Tao Yang, Wilhelmus Drinkenburg, Pieter Peeters, Thomas Steckler, Vaibhav A. Narayan, Gayle Wittenberg and Jieping Ye

    Citation: BMC Genomics 2016 17:669

    Content type: Methodology article

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  37. Cichlid fishes have evolved remarkably diverse reproductive, social, and feeding behaviors. Cell-to-cell signaling molecules, notably neuropeptides and peptide hormones, are known to regulate these behaviors a...

    Authors: Caroline K. Hu, Bruce R. Southey, Elena V. Romanova, Karen P. Maruska, Jonathan V. Sweedler and Russell D. Fernald

    Citation: BMC Genomics 2016 17:660

    Content type: Research article

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  38. Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size...

    Authors: Sandip Chatterjee, Gregory S. Stupp, Sung Kyu Robin Park, Jean-Christophe Ducom, John R. Yates III, Andrew I. Su and Dennis W. Wolan

    Citation: BMC Genomics 2016 17:642

    Content type: Methodology article

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  39. High throughput protein expression studies can be performed using bead-based protein immunoassays, such as the Luminex® xMAP® technology. Technical variability is inherent to these experiments and may lead to ...

    Authors: Tanja K. Rausch, Arne Schillert, Andreas Ziegler, Angelika Lüking, Hans-Dieter Zucht and Peter Schulz-Knappe

    Citation: BMC Genomics 2016 17:601

    Content type: Research article

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  40. Although the toxicological impacts of the xenoestrogen bisphenol-A (BPA) have been studied extensively, but the mechanism of action is poorly understood. Eventually, no standard method exists for evaluating th...

    Authors: Md Saidur Rahman, Woo-Sung Kwon, Sung-Jae Yoon, Yoo-Jin Park, Buom-Yong Ryu and Myung-Geol Pang

    Citation: BMC Genomics 2016 17:577

    Content type: Research article

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  41. Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of MeHg-mediated toxicity, we...

    Authors: Fekadu Yadetie, Silje Bjørneklett, Hilde Kristin Garberg, Eystein Oveland, Frode Berven, Anders Goksøyr and Odd André Karlsen

    Citation: BMC Genomics 2016 17:554

    Content type: Research article

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  42. The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identi...

    Authors: Zeeshan Khaliq, Mikael Leijon, Sándor Belák and Jan Komorowski

    Citation: BMC Genomics 2016 17:529

    Content type: Research Article

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  43. Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation ...

    Authors: Kyle R. Pomraning, Young-Mo Kim, Carrie D. Nicora, Rosalie K. Chu, Erin L. Bredeweg, Samuel O. Purvine, Dehong Hu, Thomas O. Metz and Scott E. Baker

    Citation: BMC Genomics 2016 17:138

    Content type: Research article

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  44. Pig (Sus scrofa) is a major source of dietary proteins for human consumption and is becoming a valuable model in agricultural and biomedical research. The recently developed isobaric tag for relative and absol...

    Authors: Xumeng Zhang, Yaosheng Chen, Jinchun Pan, Xiaohong Liu, Hu Chen, Xingyu Zhou, Zhuning Yuan, Xilong Wang and Delin Mo

    Citation: BMC Genomics 2016 17:137

    Content type: Research article

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  45. Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numero...

    Authors: Ogonna Obudulu, Joakim Bygdell, Björn Sundberg, Thomas Moritz, Torgeir R. Hvidsten, Johan Trygg and Gunnar Wingsle

    Citation: BMC Genomics 2016 17:119

    Content type: Research article

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  46. Pluripotent cells can be differentiated into many different cell types in vitro. Successful differentiation is guided in large part by epigenetic reprogramming and regulation of critical gene expression patter...

    Authors: Michelle Gonzales-Cope, Simone Sidoli, Natarajan V. Bhanu, Kyoung-Jae Won and Benjamin A. Garcia

    Citation: BMC Genomics 2016 17:95

    Content type: Research article

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  47. The liver plays important roles in nutrient metabolism, detoxification and immunity. Enterococcus faecium (E. faecium) is a probiotic that has been shown to have positive effects on broiler production. However, i...

    Authors: Aijuan Zheng, Jianjie Luo, Kun Meng, Jianke Li, Wayne L. Bryden, Wenhuan Chang, Shu Zhang, L. X. N. Wang, Guohua Liu and Bin Yao

    Citation: BMC Genomics 2016 17:89

    Content type: Research article

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