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Transcriptomic methods

This section covers novel experimental and analytical approaches for transcriptomic, epigenetic, and related high-throughput genomic studies. Studies which use transcriptomic and high-throughput genomic methods, but which do not present a novel methodological approach, should be submitted to the section in the journal relating to the organism studied.

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  1. Content type: Research article

    Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide app...

    Authors: Clémentine Dressaire, Vânia Pobre, Sandrine Laguerre, Laurence Girbal, Cecilia Maria Arraiano and Muriel Cocaign-Bousquet

    Citation: BMC Genomics 2018 19:848

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  2. Content type: Methodology article

    Copy Number Alternations (CNAs) is defined as somatic gain or loss of DNA regions. The profiles of CNAs may provide a fingerprint specific to a tumor type or tumor grade. Low-coverage sequencing for reporting ...

    Authors: Sangdi Lin, Chen Wang, Shabnam Zarei, Debra A. Bell, Sarah E. Kerr, George C. Runger and Jean-Pierre A. Kocher

    Citation: BMC Genomics 2018 19:841

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  3. Content type: Research article

    Antimicrobial peptides (AMPs) are multifunctional effector molecules that often combine direct antimicrobial activities with signaling or immunomodulatory functions. The skin secretions of anurans contain a va...

    Authors: Tomislav Rončević, Marco Gerdol, Francesca Spazzali, Fiorella Florian, Stjepan Mekinić, Alessandro Tossi and Alberto Pallavicini

    Citation: BMC Genomics 2018 19:827

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  4. Content type: Software

    Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, ...

    Authors: Amanda W. Ernlund, Robert J. Schneider and Kelly V. Ruggles

    Citation: BMC Genomics 2018 19:809

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  5. Content type: Research article

    Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of th...

    Authors: Luyun Ning, Zhiwei Lin, Jianwei Gu, Lu Gan, Yonghong Li, Hao Wang, Liyun Miao, Libin Zhang, Baoshan Wang and Maoteng Li

    Citation: BMC Genomics 2018 19:806

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  6. Content type: Methodology article

    Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count dat...

    Authors: M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli and Héctor Corrada Bravo

    Citation: BMC Genomics 2018 19:799

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  7. Content type: Methodology article

    Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover...

    Authors: Trung Nghia Vu, Wenjiang Deng, Quang Thinh Trac, Stefano Calza, Woochang Hwang and Yudi Pawitan

    Citation: BMC Genomics 2018 19:786

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  8. Content type: Research article

    Transmissible gastroenteritis virus (TGEV) infection can activate NF-κB pathway in porcine intestinal epithelial cells and result in severe inflammation. Non-coding RNAs (ncRNAs) are not translated into protei...

    Authors: Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang and Dewen Tong

    Citation: BMC Genomics 2018 19:747

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  9. Content type: Research article

    Gray leaf spot (GLS), which is caused by the necrotrophic fungi Cercospora zeae-maydis and Cercospora zeina, is one of the most impactful diseases in maize worldwide. The aim of the present study is to identify t...

    Authors: Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Haichun Shi, Yongpei Ke and Qun Sun

    Citation: BMC Genomics 2018 19:742

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  10. Content type: Research article

    Transcription factors are essential regulators of gene expression and play critical roles in development, differentiation, and in many cancers. To carry out their regulatory programs, they must cooperate in ne...

    Authors: Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo and Kevin R. Coombes

    Citation: BMC Genomics 2018 19:738

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  11. Content type: Research article

    Capacitation, a prerequisite for oocyte fertilization, is a complex process involving series of structural and functional changes in sperms such as membrane modifications, modulation of enzyme activities, and ...

    Authors: Yuan Li, Rong-Hong Li, Ming-Xia Ran, Yan Zhang, Kai Liang, Ying-Nan Ren, Wen-Cheng He, Ming Zhang, Guang-Bin Zhou, Izhar Hyder Qazi and Chang-Jun Zeng

    Citation: BMC Genomics 2018 19:736

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  12. Content type: Research article

    RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to spl...

    Authors: Juan P. Romero, María Ortiz-Estévez, Ander Muniategui, Soraya Carrancio, Fernando J. de Miguel, Fernando Carazo, Luis M. Montuenga, Remco Loos, Rubén Pío, Matthew W. B. Trotter and Angel Rubio

    Citation: BMC Genomics 2018 19:703

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  13. Content type: Research article

    Cell type-specific ribosome-pulldown has become an increasingly popular method for analysis of gene expression. It allows for expression analysis from intact tissues and monitoring of protein synthesis in vivo...

    Authors: Yang Song, Beatrice Milon, Sandra Ott, Xuechu Zhao, Lisa Sadzewicz, Amol Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar and Ronna Hertzano

    Citation: BMC Genomics 2018 19:696

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  14. Content type: Research article

    The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during co...

    Authors: Maria Ballester, Marcel Amills, Olga González-Rodríguez, Tainã F. Cardoso, Mariam Pascual, Rayner González-Prendes, Núria Panella-Riera, Isabel Díaz, Joan Tibau and Raquel Quintanilla

    Citation: BMC Genomics 2018 19:682

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  15. Content type: Software

    The challenges when developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize a de Bruijn graph, with which complexity g...

    Authors: Seokhyun Yoon, Daeseung Kim, Keunsoo Kang and Woong June Park

    Citation: BMC Genomics 2018 19:653

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  16. Content type: Research article

    Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a widely cultivated medicinal and edible crop with excellent economic and nutritional value. The development of tartary buckwheat seeds is a very complex process...

    Authors: Moyang Liu, Zhaotang Ma, Tianrun Zheng, Wenjun Sun, Yanjun Zhang, Weiqiong Jin, Junyi Zhan, Yuntao Cai, Yujia Tang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2018 19:648

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  17. Content type: Database

    The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology w...

    Authors: Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A. Kuhlman and Stephan Q. Schneider

    Citation: BMC Genomics 2018 19:618

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  18. Content type: Research article

    Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to n...

    Authors: Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang and Ming Chen

    Citation: BMC Genomics 2018 19:607

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  19. Content type: Methodology article

    The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression ...

    Authors: Stephen J. Bush, Lucy Freem, Amanda J. MacCallum, Jenny O’Dell, Chunlei Wu, Cyrus Afrasiabi, Androniki Psifidi, Mark P. Stevens, Jacqueline Smith, Kim M. Summers and David A. Hume

    Citation: BMC Genomics 2018 19:594

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  20. Content type: Research article

    Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating an...

    Authors: C. Llorens, S. C. Arcos, L. Robertson, R. Ramos, R. Futami, B. Soriano, S. Ciordia, M. Careche, M. González-Muñoz, Y. Jiménez-Ruiz, N. Carballeda-Sangiao, I. Moneo, J. P. Albar, M. Blaxter and A. Navas

    Citation: BMC Genomics 2018 19:592

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  21. Content type: Research article

    The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflo...

    Authors: Jiang Chen, Xiaohui Tang, Chaoxiang Ren, Bin Wei, Yiyun Wu, Qinghua Wu and Jin Pei

    Citation: BMC Genomics 2018 19:548

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  22. Content type: Methodology article

    RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting materi...

    Authors: Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore and Zhiping Weng

    Citation: BMC Genomics 2018 19:531

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  23. Content type: Research article

    Infections with the West Nile virus (WNV) can attack neurological tissues in the host and alter gene expression levels therein. Several individual studies have analyzed these changes in the transcriptome based...

    Authors: Robin Kosch, Julien Delarocque, Peter Claus, Stefanie C. Becker and Klaus Jung

    Citation: BMC Genomics 2018 19:530

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  24. Content type: Research article

    Alternative polyadenylation (APA) results in messenger RNA molecules with different 3′ untranslated regions (3’ UTRs), affecting the molecules’ stability, localization, and translation. APA is pervasive and im...

    Authors: Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds and Inanc Birol

    Citation: BMC Genomics 2018 19:536

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  25. Content type: Research article

    The oriental armyworm, Mythimna separata, is an economically important and common Lepidopteran pest of cereal crops. Chemoreception plays a key role in insect life, such as foraging, oviposition site selection, a...

    Authors: Lixiao Du, Xincheng Zhao, Xiangzhi Liang, Xiwu Gao, Yang Liu and Guirong Wang

    Citation: BMC Genomics 2018 19:518

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  26. Content type: Research article

    Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify small RNAs as a...

    Authors: Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz and Claus O. Wilke

    Citation: BMC Genomics 2018 19:510

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  27. Content type: Methodology article

    Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipoten...

    Authors: Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom and Sandrine Dudoit

    Citation: BMC Genomics 2018 19:477

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  28. Content type: Research article

    Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynogloss...

    Authors: Yufeng Si, Haishen Wen, Yun Li, Feng He, Jifang Li, Siping Li and Huiwen He

    Citation: BMC Genomics 2018 19:464

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  29. Content type: Research article

    Iron (Fe) is an essential micronutrient for plants. Utilization of Fe deficiency-tolerant rootstock is an effective strategy to prevent Fe deficiency problems in fruit trees production. Malus halliana is an apple...

    Authors: Yan-xiu Wang, Ya Hu, Yan-fang Zhu, Abdul Wahid Baloch, Xu-mei Jia and Ai-xia Guo

    Citation: BMC Genomics 2018 19:461

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  30. Content type: Software

    Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling imprinted genes are associated with DNA methyla...

    Authors: Julien Richard Albert, Tasuku Koike, Hamid Younesy, Richard Thompson, Aaron B. Bogutz, Mohammad M. Karimi and Matthew C. Lorincz

    Citation: BMC Genomics 2018 19:463

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  31. Content type: Research article

    Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to iden...

    Authors: C. Peraldo-Neia, P. Ostano, G. Cavalloni, Y. Pignochino, D. Sangiolo, L. De Cecco, E. Marchesi, D. Ribero, A. Scarpa, A. M. De Rose, A. Giuliani, F. Calise, C. Raggi, P. Invernizzi, M. Aglietta, G. Chiorino…

    Citation: BMC Genomics 2018 19:440

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  32. Content type: Research article

    CCHCR1 (Coiled-Coil α-Helical Rod protein 1) is a putative psoriasis candidate gene with the risk alleles CCHCR1*WWCC and *Iso3, the latter inhibiting the translation of isoform 1. CCHCR1 was recently shown to be...

    Authors: Mari H. Tervaniemi, Shintaro Katayama, Tiina Skoog, H. Annika Siitonen, Jyrki Vuola, Kristo Nuutila, Kristiina Tammimies, Sari Suomela, Esko Kankuri, Juha Kere and Outi Elomaa

    Citation: BMC Genomics 2018 19:432

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  33. Content type: Research article

    Scylla paramamosain (Crustacea: Decapoda: Portunidae: Syclla De Hann) is a commercially important mud crab distributed along the coast of southern China and other Indo-Pacific countries (Lin Z, Hao M, Zhu D, et a...

    Authors: Huan Wang, Lei Tang, Hongling Wei, Junkai Lu, Changkao Mu and Chunlin Wang

    Citation: BMC Genomics 2018 19:421

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  34. Content type: Methodology article

    Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been ...

    Authors: Kuan Feng, Justin Costa and Jeremy S. Edwards

    Citation: BMC Genomics 2018 19:416

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  35. Content type: Research article

    Small RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next...

    Authors: Mohamed El-Mogy, Bernard Lam, Taha A. Haj-Ahmad, Shannon McGowan, Darrick Yu, Lucas Nosal, Nezar Rghei, Pam Roberts and Yousef Haj-Ahmad

    Citation: BMC Genomics 2018 19:408

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  36. Content type: Software

    Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular ch...

    Authors: Wenjie Sun, Ting Duan, Panmeng Ye, Kelie Chen, Guanling Zhang, Maode Lai and Honghe Zhang

    Citation: BMC Genomics 2018 19:405

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  37. Content type: Methodology article

    MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conv...

    Authors: Chung Wah Wu, Jared M. Evans, Shengbing Huang, Douglas W. Mahoney, Brian A. Dukek, William R. Taylor, Tracy C. Yab, Thomas C. Smyrk, Jin Jen, John B. Kisiel and David A. Ahlquist

    Citation: BMC Genomics 2018 19:401

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  38. Content type: Research article

    The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicti...

    Authors: Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée and Didier Mazel

    Citation: BMC Genomics 2018 19:373

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  39. Content type: Research article

    Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analy...

    Authors: Felix Seifert, Alexander Thiemann, Tobias A. Schrag, Dominika Rybka, Albrecht E. Melchinger, Matthias Frisch and Stefan Scholten

    Citation: BMC Genomics 2018 19:371

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  40. Content type: Research article

    Caponization results in reduced androgen levels, which leads to abdominal fat accumulation in capons. In this study, we sought to understand the molecular mechanisms behind this fat accumulation.

    Authors: Xiaoyan Cui, Huanxian Cui, Lu Liu, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng and Jie Wen

    Citation: BMC Genomics 2018 19:344

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  41. Content type: Research article

    337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory f...

    Authors: Longqing Sun, Genlou Sun, Chenxia Shi and Dongfa Sun

    Citation: BMC Genomics 2018 19:333

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  42. Content type: Methodology article

    Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA seque...

    Authors: Ashish Yeri, Amanda Courtright, Kirsty Danielson, Elizabeth Hutchins, Eric Alsop, Elizabeth Carlson, Michael Hsieh, Olivia Ziegler, Avash Das, Ravi V. Shah, Joel Rozowsky, Saumya Das and Kendall Van Keuren-Jensen

    Citation: BMC Genomics 2018 19:331

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  43. Content type: Methodology article

    Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable ...

    Authors: Wells W. Wu, Je-Nie Phue, Chun-Ting Lee, Changyi Lin, Lai Xu, Rong Wang, Yaqin Zhang and Rong-Fong Shen

    Citation: BMC Genomics 2018 19:326

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  44. Content type: Research article

    Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during panc...

    Authors: Zhihua Li and Rodney Rouse

    Citation: BMC Genomics 2018 19:297

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  45. Content type: Research article

    Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas ae...

    Authors: Erin E. Gill, Luisa S. Chan, Geoffrey L. Winsor, Neil Dobson, Raymond Lo, Shannan J. Ho Sui, Bhavjinder K. Dhillon, Patrick K. Taylor, Raunak Shrestha, Cory Spencer, Robert E. W. Hancock, Peter J. Unrau and Fiona S. L. Brinkman

    Citation: BMC Genomics 2018 19:223

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