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  1. Content type: Research article

    Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of whe...

    Authors: Chengwei Wang, Yu Wang, Qi Pan, Shoukun Chen, Cuizhu Feng, Jiangbo Hai and Haifeng Li

    Citation: BMC Genomics 2019 20:142

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  2. Content type: Research article

    Heat illness remains a significant cause of morbidity in susceptible populations. Recent research elucidating the cellular mechanism of heat stress leading to heat illness may provide information to develop be...

    Authors: Matthew G. Permenter, Bonna C. McDyre, Danielle L. Ippolito and Jonathan D. Stallings

    Citation: BMC Genomics 2019 20:141

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  3. Content type: Research article

    Hair fibre length is an important economic trait of rabbits in fur production. However, molecular mechanisms regulating rabbit hair growth have remained elusive.

    Authors: Haisheng Ding, Huiling Zhao, Guanglong Cheng, Yongxin Yang, Xiaofei Wang, Xiaowei Zhao, Yunxia Qi and Dongwei Huang

    Citation: BMC Genomics 2019 20:140

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  4. Content type: Research article

    A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, ear...

    Authors: Amin R. Mohamed, Klara L. Verbyla, Hawlader A. Al-Mamun, Sean McWilliam, Bradley Evans, Harry King, Peter Kube and James W. Kijas

    Citation: BMC Genomics 2019 20:139

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  5. Content type: Research article

    Carbonic anhydrase (CA) catalyzes the hydration of CO2 in the first biochemical step of C4 photosynthesis, and has been considered a potentially rate-limiting step when CO2 availability within a leaf is low. Prev...

    Authors: Allison R. Kolbe, Anthony J. Studer, Omar E. Cornejo and Asaph B. Cousins

    Citation: BMC Genomics 2019 20:138

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  6. Content type: Methodology article

    Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA’s functional versatility includes epigenetic modification, nuclear domain organization, transcriptional c...

    Authors: Sarah C. Pyfrom, Hong Luo and Jacqueline E. Payton

    Citation: BMC Genomics 2019 20:137

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  7. Content type: Research article

    Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to...

    Authors: Xinyou Cao, Liqin Hu, Xueyan Chen, Rongzhi Zhang, Dungong Cheng, Haosheng Li, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Aifeng Liu, Jianming Song, Cheng Liu, Jianjun Liu, Zhendong Zhao, Ming Chen and Youzhi Ma

    Citation: BMC Genomics 2019 20:136

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  8. Content type: Research article

    Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.

    Authors: Kathleen DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Ling-Ling Gao, Karen Frick and Karam B. Singh

    Citation: BMC Genomics 2019 20:135

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  9. Content type: Research article

    The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression me...

    Authors: Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang and Zheng Guo

    Citation: BMC Genomics 2019 20:134

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  10. Content type: Software

    MicroRNAs (miRNAs) constitute a well-known small RNA (sRNA) species with important regulatory roles. To date, several bioinformatics tools have been developed for large-scale prediction of miRNAs based on high...

    Authors: Dongliang Yu, Ying Wan, Hidetaka Ito, Xiaoxia Ma, Tian Xie, Tingzhang Wang, Chaogang Shao and Yijun Meng

    Citation: BMC Genomics 2019 20:133

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  11. Content type: Research article

    Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolution...

    Authors: Desre Pinard, Alexander A. Myburg and Eshchar Mizrachi

    Citation: BMC Genomics 2019 20:132

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  12. Content type: Research article

    Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Historically, gene targeting was first done in embryonic stem cells (ESCs) derived from the 129 famil...

    Authors: C. Farkas, F. Fuentes-Villalobos, B. Rebolledo-Jaramillo, F. Benavides, A. F. Castro and R. Pincheira

    Citation: BMC Genomics 2019 20:131

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  13. Content type: Research article

    Methanotrophs play an important role in biotechnological applications, with their ability to utilize single carbon (C1) feedstock such as methane and methanol to produce a range of high-value compounds. A newl...

    Authors: Anh Duc Nguyen, Donghyuk Kim and Eun Yeol Lee

    Citation: BMC Genomics 2019 20:130

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  14. Content type: Research article

    A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intrig...

    Authors: Shyamasree De Majumdar, Kriti Sikri, Payel Ghosh, Neetika Jaisinghani, Malobi Nandi, Sheetal Gandotra, Shekhar Mande and Jaya Sivaswami Tyagi

    Citation: BMC Genomics 2019 20:129

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  15. Content type: Research article

    The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical ...

    Authors: Li Ma, Tad S. Sonstegard, John B. Cole, Curtis P. VanTassell, George R. Wiggans, Brian A. Crooker, Cheng Tan, Dzianis Prakapenka, George E. Liu and Yang Da

    Citation: BMC Genomics 2019 20:128

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  16. Content type: Research article

    Warm winter and hot spring attributed to global warming affected floral development and may induce floral abortion, resulted in poor flowering in litchi. To identify genes potentially involved in litchi floral...

    Authors: Hao Liu, Congcong Wang, Houbin Chen and Biyan Zhou

    Citation: BMC Genomics 2019 20:127

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  17. Content type: Research article

    Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. longan fruit yield, the difficulty and instability of blossom...

    Authors: Dengwei Jue, Xuelian Sang, Liqin Liu, Bo Shu, Yicheng Wang, Chengming Liu, Yi Wang, Jianghui Xie and Shengyou Shi

    Citation: BMC Genomics 2019 20:126

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  18. Content type: Research article

    Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to t...

    Authors: Qi Xu, Songtai Wang, Huazhu Hong and Yin Zhou

    Citation: BMC Genomics 2019 20:125

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  19. Content type: Research article

    We describe the virulence factors of a methicillin-sensitive Staphylococcus aureus sequence type (ST) 45 strain, MCRF184, (spa type t917), that caused severe necrotizing fasciitis in a 72-year-old diabetic male. ...

    Authors: Vijay Aswani, Fares Najar, Madhulatha Pantrangi, Bob Mau, William R. Schwan and Sanjay K. Shukla

    Citation: BMC Genomics 2019 20:123

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  20. Content type: Research article

    Marine bivalves undergo complex development processes, such as shell morphology conversion and changes of anatomy and life habits. In this study, the transcriptomes of pearl oyster Pinctada fucata martensii and P...

    Authors: Zhe Zheng, Ruijuan Hao, Xinwei Xiong, Yu Jiao, Yuewen Deng and Xiaodong Du

    Citation: BMC Genomics 2019 20:122

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  21. Content type: Research article

    Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial ti...

    Authors: Seung-il Yoo, Hwa-Yong Lee, Kesavan Markkandan, Suyun Moon, Yong Ju Ahn, Sumin Ji, Junsu Ko, Seong-Jin Kim, Hojin Ryu and Chang Pyo Hong

    Citation: BMC Genomics 2019 20:121

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  22. Content type: Research article

    Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. Even strains of the same species may exhibit differences in metabolite production, a finding that has important i...

    Authors: Rodrigo A. Olarte, Jon Menke, Ying Zhang, Shawn Sullivan, Jason C. Slot, Yinyin Huang, Jonathan P. Badalamenti, Alisha C. Quandt, Joseph W. Spatafora and Kathryn E. Bushley

    Citation: BMC Genomics 2019 20:120

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  23. Content type: Research article

    Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although th...

    Authors: Rick Masonbrink, Tom R. Maier, Usha Muppirala, Arun S. Seetharam, Etienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nathan T. Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves-van den Akker, Matthew Hudson, Andrew J. Severin and Thomas J. Baum

    Citation: BMC Genomics 2019 20:119

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  24. Content type: Research article

    The leishmaniasis are parasitic diseases caused by protozoans of the genus Leishmania, highly divergent eukaryotes, characterized by unique biological features. To survive in both the mammalian hosts and insect v...

    Authors: Artur L. Castro Neto, Adriana N. A. L. M. Brito, Antonio M. Rezende, Franklin B. Magalhães and Osvaldo P. de Melo Neto

    Citation: BMC Genomics 2019 20:118

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  25. Content type: Research article

    Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect ...

    Authors: Sheng-Hui Jiang, Qing-Guo Sun, Min Chen, Nan Wang, Hai-Feng Xu, Hong-Cheng Fang, Yi-Cheng Wang, Zong-Ying Zhang and Xue-Sen Chen

    Citation: BMC Genomics 2019 20:117

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  26. Content type: Research article

    Cytochrome P450 (P450) is a functionally diverse and multifamily class of enzymes which catalyses vast variety of biochemical reactions. P450 genes play regulatory role in growth, development and secondary met...

    Authors: A. P. Vasav and V. T. Barvkar

    Citation: BMC Genomics 2019 20:116

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  27. Content type: Research article

    Pokkah boeng is one of the most serious and devastating diseases of sugarcane and causes significant loss in cane yield and sugar content. Although carbendazim is widely used to prevent fungal diseases, the mo...

    Authors: Shiqiang Xu, Jihua Wang, Haixuan Wang, Yixue Bao, Yisha Li, Muralidharan Govindaraju, Wei Yao, Baoshan Chen and Muqing Zhang

    Citation: BMC Genomics 2019 20:115

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  28. Content type: Research article

    Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation,...

    Authors: Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny and Krzysztof Fujarewicz

    Citation: BMC Genomics 2019 20:114

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  29. Content type: Research article

    The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, the...

    Authors: Moyang Liu, Zhaotang Ma, Wenjun Sun, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2019 20:113

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  30. Content type: Research article

    Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic...

    Authors: Marina Naoumkina, Gregory N. Thyssen, David D. Fang, Johnie N. Jenkins, Jack C. McCarty and Christopher B. Florane

    Citation: BMC Genomics 2019 20:112

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  31. Content type: Research article

    Cultured pearls are unique gems produced by living organisms, mainly molluscs of the Pinctada genus, through the biomineralization properties of pearl sac tissue. Improvement of P. margaritifera pearl quality is ...

    Authors: J. Le Luyer, P. Auffret, V. Quillien, N. Leclerc, C. Reisser, J. Vidal-Dupiol and C.-L. Ky

    Citation: BMC Genomics 2019 20:111

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  32. Content type: Research article

    Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available fo...

    Authors: Luana P. Gonçalves, Raquel L. Boscariol Camargo, Marco Aurélio Takita, Marcos A. Machado, Walter S. dos Soares Filho and Marcio G. C. Costa

    Citation: BMC Genomics 2019 20:110

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  33. Content type: Research article

    Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. A...

    Authors: Camille Détrée, Iman Haddad, Emmanuelle Demey-Thomas, Joëlle Vinh, François H. Lallier, Arnaud Tanguy and Jean Mary

    Citation: BMC Genomics 2019 20:109

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  34. Content type: Research article

    Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The fl...

    Authors: Cristian Vergara-Pulgar, Karin Rothkegel, Mauricio González-Agüero, Romina Pedreschi, Reinaldo Campos-Vargas, Bruno G. Defilippi and Claudio Meneses

    Citation: BMC Genomics 2019 20:108

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  35. Content type: Research article

    While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investig...

    Authors: Michael Boettcher, Sergio Covarrubias, Anne Biton, James Blau, Haopeng Wang, Noah Zaitlen and Michael T. McManus

    Citation: BMC Genomics 2019 20:107

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  36. Content type: Research article

    Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associate...

    Authors: A. A. Kampfraath, L. Klasson, S. Y. Anvar, R. H. A. M. Vossen, D. Roelofs, K. Kraaijeveld and J. Ellers

    Citation: BMC Genomics 2019 20:106

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  37. Content type: Research article

    Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus preda...

    Authors: Nathan D. McDonald, Abish Regmi, Daniel P. Morreale, Joseph D. Borowski and E. Fidelma Boyd

    Citation: BMC Genomics 2019 20:105

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  38. Content type: Research article

    Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds...

    Authors: Brandon D. Velie, Mette Lillie, Kim Jäderkvist Fegraeus, Maria K. Rosengren, Marina Solé, Maja Wiklund, Carl-Fredrik Ihler, Eric Strand and Gabriella Lindgren

    Citation: BMC Genomics 2019 20:104

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  39. Content type: Research

    Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of...

    Authors: Jingcheng Du, Peilin Jia, Yulin Dai, Cui Tao, Zhongming Zhao and Degui Zhi

    Citation: BMC Genomics 2019 20(Suppl 1):82

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    This article is part of a Supplement: Volume 20 Supplement 1

  40. Content type: Research

    Cell lines form the cornerstone of cell-based experimentation studies into understanding the underlying mechanisms of normal and disease biology including cancer. However, it is commonly acknowledged that cont...

    Authors: Tabrez A. Mohammad, Yun S. Tsai, Safwa Ameer, Hung-I Harry Chen, Yu-Chiao Chiu and Yidong Chen

    Citation: BMC Genomics 2019 20(Suppl 1):81

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    This article is part of a Supplement: Volume 20 Supplement 1

  41. Content type: Introduction

    The sixth International Conference on Intelligent Biology and Medicine (ICIBM) took place in Los Angeles, California, USA on June 10–12, 2018. This conference featured eleven regular scientific sessions, four ...

    Authors: Zhijin Wu, Jingwen Yan, Kai Wang, Xiaoming Liu, Yan Guo, Degui Zhi, Jianhua Ruan and Zhongming Zhao

    Citation: BMC Genomics 2019 20(Suppl 1):80

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    This article is part of a Supplement: Volume 20 Supplement 1

  42. Content type: Research

    Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. Recently, an increasing number of GWAS summary statistics have been made available to the researc...

    Authors: Guangsheng Pei, Hua Sun, Yulin Dai, Xiaoming Liu, Zhongming Zhao and Peilin Jia

    Citation: BMC Genomics 2019 20(Suppl 1):79

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    This article is part of a Supplement: Volume 20 Supplement 1

  43. Content type: Research

    Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analy...

    Authors: Qian Liu, Daniela C. Georgieva, Dieter Egli and Kai Wang

    Citation: BMC Genomics 2019 20(Suppl 1):78

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    This article is part of a Supplement: Volume 20 Supplement 1

  44. Content type: Methodology article

    In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conse...

    Authors: Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier and Laurent Bréhélin

    Citation: BMC Genomics 2019 20:103

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  45. Content type: Research article

    DNA methylation is involved in the regulation of gene expression. Although bisulfite-sequencing based methods profile DNA methylation at a single CpG resolution, methylation levels are usually averaged over ge...

    Authors: Anna V. Lioznova, Abdullah M. Khamis, Artem V. Artemov, Elizaveta Besedina, Vasily Ramensky, Vladimir B. Bajic, Ivan V. Kulakovskiy and Yulia A. Medvedeva

    Citation: BMC Genomics 2019 20:102

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  46. Content type: Research article

    Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXL...

    Authors: Zhisheng Han, Yanlin Liu, Xiong Deng, Dongmiao Liu, Yue Liu, Yingkao Hu and Yueming Yan

    Citation: BMC Genomics 2019 20:101

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  47. Content type: Research article

    Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific trans...

    Authors: Alexander Kanitz, Afzal Pasha Syed, Keisuke Kaji and Mihaela Zavolan

    Citation: BMC Genomics 2019 20:100

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  48. Content type: Research article

    Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasiv...

    Authors: Joaquín Giner-Lamia, Pablo Vinuesa, Laura Betancor, Claudia Silva, Julieta Bisio, Lorena Soleto, José A. Chabalgoity, José Luis Puente and Francisco García-del Portillo

    Citation: BMC Genomics 2019 20:99

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  49. Content type: Research article

    Protein secretion is an essential process in all eukaryotes including organisms belonging to the phylum Apicomplexa, which includes many intracellular parasites. The apicomplexan parasites possess a specialize...

    Authors: K. M. Kaderi Kibria, Jannatul Ferdous, Rahila Sardar, Ashutosh Panda, Dinesh Gupta, Asif Mohmmed and Pawan Malhotra

    Citation: BMC Genomics 2019 20:98

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