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  1. Transcriptomic profiles can improve our understanding of the phenotypic molecular basis of biological research, and many statistical methods have been proposed to identify differentially expressed genes (DEGs)...

    Authors: Kyungtaek Park, Jaehoon An, Jungsoo Gim, Minseok Seo, Woojoo Lee, Taesung Park and Sungho Won
    Citation: BMC Genomics 2019 20:540
    Content type: Methodology article Published on:

  2. Long non-coding RNA (lncRNA) expression data have been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing do not effect...

    Authors: Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J. C. Slebos, Christine H. Chung and Xuefeng Wang
    Citation: BMC Genomics 2019 20:539
    Content type: Methodology article Published on:

  3. Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. T...

    Authors: Weixi Li, Dayong Zhang, Guozhong Zhu, Xinyue Mi and Wangzhen Guo
    Citation: BMC Genomics 2019 20:538
    Content type: Research article Published on:

  4. Usually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miR...

    Authors: Rui Wang, Zhongyi Yang, Yuhan Fei, Jiejie Feng, Hui Zhu, Fang Huang, Hongsheng Zhang and Ji Huang
    Citation: BMC Genomics 2019 20:534
    Content type: Methodology article Published on:

  5. Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and a...

    Authors: Yong Huang, Ling Jiang, Bo-Yu Liu, Cheng-Fang Tan, Dong-Hong Chen, Wen-Hui Shen and Ying Ruan
    Citation: BMC Genomics 2019 20:533
    Content type: Research article Published on:

  6. MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for...

    Authors: Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, Mohcen Benmounah and Hélène Touzet
    Citation: BMC Genomics 2019 20:532
    Content type: Software Published on:

  7. The Crustacea are an evolutionarily diverse taxon which underpins marine food webs and contributes significantly to the global economy. However, our knowledge of crustacean endocrinology and development is far...

    Authors: Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura
    Citation: BMC Genomics 2019 20:531
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:622

  8. Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicr...

    Authors: Nicholas Costa Barroso Lima, Arif M. Tanmoy, Emilie Westeel, Luiz Gonzaga Paula de Almeida, Alain Rajoharison, Maksuda Islam, Hubert P. Endtz, Samir K. Saha, Ana Tereza Ribeiro de Vasconcelos and Florence Komurian-Pradel
    Citation: BMC Genomics 2019 20:530
    Content type: Research article Published on:

  9. The Arctic charr (Salvelinus alpinus) has a highly seasonal feeding cycle that comprises long periods of voluntary fasting and a short but intense feeding period during summer. Therefore, the charr represents an ...

    Authors: Anja Striberny, Even H. Jørgensen, Christophe Klopp and Elodie Magnanou
    Citation: BMC Genomics 2019 20:529
    Content type: Research article Published on:

  11. Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. As...

    Authors: Teshale Assefa, Paul I. Otyama, Anne V. Brown, Scott R. Kalberer, Roshan S. Kulkarni and Steven B. Cannon
    Citation: BMC Genomics 2019 20:527
    Content type: Research article Published on:

  12. Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susc...

    Authors: Nadia Bertazzon, Paolo Bagnaresi, Vally Forte, Elisabetta Mazzucotelli, Luisa Filippin, Davide Guerra, Antonella Zechini, Luigi Cattivelli and Elisa Angelini
    Citation: BMC Genomics 2019 20:526
    Content type: Research article Published on:

  13. Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar prod...

    Authors: Marc G. Higgins, David A. Kenny, Claire Fitzsimons, Gordon Blackshields, Séan Coyle, Clare McKenna, Mark McGee, Derek W. Morris and Sinéad M. Waters
    Citation: BMC Genomics 2019 20:525
    Content type: Research article Published on:

  15. Following the publication of this article [1], the authors reported that the Fig. 2 described in the article had a mistake that two grey blocks in S. moellendorffii was not placed as background color, and in the ...

    Authors: Hong-Rui Zhang, Xian-Chun Zhang and Qiao-Ping Xiang
    Citation: BMC Genomics 2019 20:523
    Content type: Correction Published on:

    The original article was published in BMC Genomics 2019 20:484

  16. Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, ...

    Authors: Valeria Petrella, Serena Aceto, Vincenza Colonna, Giuseppe Saccone, Remo Sanges, Nikola Polanska, Petr Volf, Luigi Gradoni, Gioia Bongiorno and Marco Salvemini
    Citation: BMC Genomics 2019 20:522
    Content type: Research article Published on:

  17. Splicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related dise...

    Authors: Fernando Carazo, Marian Gimeno, Juan A. Ferrer-Bonsoms and Angel Rubio
    Citation: BMC Genomics 2019 20:521
    Content type: Research article Published on:

  18. The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed...

    Authors: Danielly Beraldo dos Santos Silva, Larissa Fernanda Simielli Fonseca, Daniel Guariz Pinheiro, Maria Malane Magalhães Muniz, Ana Fabrícia Braga Magalhães, Fernando Baldi, Jesus Aparecido Ferro, Luis Artur Loyola Chardulo and Lucia Galvão de Albuquerque
    Citation: BMC Genomics 2019 20:520
    Content type: Research article Published on:

  20. Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots...

    Authors: Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li and Ming Peng
    Citation: BMC Genomics 2019 20:519
    Content type: Research article Published on:

  21. The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we...

    Authors: Rayner González-Prendes, Emilio Mármol-Sánchez, Raquel Quintanilla, Anna Castelló, Ali Zidi, Yuliaxis Ramayo-Caldas, Tainã Figueiredo Cardoso, Arianna Manunza, Ángela Cánovas and Marcel Amills
    Citation: BMC Genomics 2019 20:518
    Content type: Research article Published on:

  22. Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen of domestic and wild ruminants. Apart from cattle, small ruminants (goats and sheep) are also the susceptible hosts for BVDV. BVDV...

    Authors: Wenliang Li, Li Mao, Xin Shu, Runxia Liu, Fei Hao, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Chunyan Zhong and Jieyuan Jiang
    Citation: BMC Genomics 2019 20:516
    Content type: Research article Published on:

  23. Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish s...

    Authors: Mingkun Luo, Lanmei Wang, Haoran Yin, Wenbin Zhu, Jianjun Fu and Zaijie Dong
    Citation: BMC Genomics 2019 20:515
    Content type: Research article Published on:

  24. Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are i...

    Authors: Liang Xiao, Xiao-Hong Shang, Sheng Cao, Xiang-Yu Xie, Wen-Dan Zeng, Liu-Ying Lu, Song-Bi Chen and Hua-Bing Yan
    Citation: BMC Genomics 2019 20:514
    Content type: Research article Published on:

  25. RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapt...

    Authors: Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger and Joo Heon Shin
    Citation: BMC Genomics 2019 20:513
    Content type: Methodology article Published on:

  26. Dermal papilla cells (DPCs), the “signaling center” of hair follicle (HF), delicately master continual growth of hair in mammals including cashmere, the fine fiber annually produced by secondary HF embedded in...

    Authors: Sen Ma, Ying Wang, Guangxian Zhou, Yi Ding, Yuxin Yang, Xiaolong Wang, Enping Zhang and Yulin Chen
    Citation: BMC Genomics 2019 20:512
    Content type: Research article Published on:

  27. Non-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational strategies have been developed to identify cis-regulatory enh...

    Authors: Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka and John A. Capra
    Citation: BMC Genomics 2019 20:511
    Content type: Research article Published on:

  28. In female mammals, the initiation of puberty, coupling with the dramatically morphological changes in ovaries, indicates the sexual and follicular maturation. Previous studies have suggested that the disrupted...

    Authors: Xiaolong Yuan, Shaopan Ye, Zitao Chen, Xiangchun Pan, Shuwen Huang, Zhonghui Li, Yuyi Zhong, Ning Gao, Hao Zhang, Jiaqi Li and Zhe Zhang
    Citation: BMC Genomics 2019 20:510
    Content type: Research article Published on:

  29. Livestock production aims to provide meats of high and consistent eating quality. Insufficient intramuscular (IM) fat and excessive subcutaneous (SC) fat are paramount pork quality challenges. IM fat and SC fa...

    Authors: Wenjing Wu, Dawei Zhang, Yajun Yin, Miao Ji, Ke Xu, Xin Huang, Yongjia Peng and Jin Zhang
    Citation: BMC Genomics 2019 20:509
    Content type: Research article Published on:

  30. DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modificatio...

    Authors: Mei-Wei Luan, Wei Chen, Jian-Feng Xing, Chuan-Le Xiao, Ying Chen and Shang-Qian Xie
    Citation: BMC Genomics 2019 20:508
    Content type: Research article Published on:

  31. Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad host range and ability to transmit viruses damage crop plants worldwide. B. tabaci are now known to be a complex of cryptic spe...

    Authors: Sonia Hussain, Muhammad Farooq, Hassan Jamil Malik, Imran Amin, Brian E. Scheffler, Jodi A. Scheffler, Shu-Sheng Liu and Shahid Mansoor
    Citation: BMC Genomics 2019 20:507
    Content type: Research article Published on:

  33. Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of C...

    Authors: Min Zhou, Shigang Zheng, Rong Liu, Jing Lu, Lu Lu, Chihong Zhang, Zehou Liu, Congpei Luo, Lei Zhang, Levi Yant and Yu Wu
    Citation: BMC Genomics 2019 20:505
    Content type: Research article Published on:

  34. Enterohemorrhagic Escherichia coli (E. coli) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid ph...

    Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka and Alexander Mellmann
    Citation: BMC Genomics 2019 20:504
    Content type: Research article Published on:

  35. Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognosticatio...

    Authors: Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao Saal, Åke Borg, Johan Vallon-Christerson and Carlos Rovira
    Citation: BMC Genomics 2019 20:503
    Content type: Research article Published on:

  36. We present results from a computational analysis developed to integrate transcriptome and metabolomic data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress i...

    Authors: Allen H. Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh and Carl Schmidt
    Citation: BMC Genomics 2019 20:502
    Content type: Research article Published on:

  37. Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information re...

    Authors: Elisa B. Carvalho, Mateus P. Gionbelli, Rafael T. S. Rodrigues, Sarah F. M. Bonilha, Charles J. Newbold, Simone E. F. Guimarães, Walmir Silva, Lucas L. Verardo, Fabyano F. Silva, Edenio Detmann and Marcio S. Duarte
    Citation: BMC Genomics 2019 20:501
    Content type: Research article Published on:

  38. The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity ...

    Authors: Mei Han, Guifeng Wei, Catherine E. McManus, LaDeana W. Hillier and Valerie Reinke
    Citation: BMC Genomics 2019 20:500
    Content type: Methodology article Published on:

  39. Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in see...

    Authors: Xi Zhang, Aiman Hina, Shiyu Song, Jiejie Kong, Javaid Akhter Bhat and Tuanjie Zhao
    Citation: BMC Genomics 2019 20:499
    Content type: Research article Published on:

  40. The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultiva...

    Authors: Yasmin A. Mohamoud, Lisa S. Mathew, Maria F. Torres, Shameem Younuskunju, Robert Krueger, Karsten Suhre and Joel A. Malek
    Citation: BMC Genomics 2019 20:498
    Content type: Research article Published on:

  41. The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gai...

    Authors: Charlotte R. Feddersen, Lexy S. Wadsworth, Eliot Y. Zhu, Hayley R. Vaughn, Andrew P. Voigt, Jesse D. Riordan and Adam J. Dupuy
    Citation: BMC Genomics 2019 20:497
    Content type: Methodology article Published on:

  42. Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. ...

    Authors: Matteo Soverini, Silvia Turroni, Elena Biagi, Patrizia Brigidi, Marco Candela and Simone Rampelli
    Citation: BMC Genomics 2019 20:496
    Content type: Software Published on:

  43. Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance l...

    Authors: Shyam Solanki, Jonathan Richards, Gazala Ameen, Xue Wang, Atiya Khan, Harris Ali, Alex Stangel, Prabin Tamang, Thomas Gross, Patrick Gross, Thomas G. Fetch and Robert S. Brueggeman
    Citation: BMC Genomics 2019 20:495
    Content type: Research article Published on:

  44. Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs.

    Authors: Lingyang Xu, Liu Yang, Bo Zhu, Wengang Zhang, Zezhao Wang, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, George E. Liu and Junya Li
    Citation: BMC Genomics 2019 20:494
    Content type: Research article Published on:

  45. Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in fi...

    Authors: Ashok Kumar Sharma, Barbora Pafčo, Klára Vlčková, Barbora Červená, Jakub Kreisinger, Samuel Davison, Karen Beeri, Terence Fuh, Steven R. Leigh, Michael B. Burns, Ran Blekhman, Klára J. Petrželková and Andres Gomez
    Citation: BMC Genomics 2019 20:493
    Content type: Research article Published on:

  46. With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post...

    Authors: Sridhar Ravichandran, Raja Ragupathy, Tara Edwards, Michael Domaratzki and Sylvie Cloutier
    Citation: BMC Genomics 2019 20:488
    Content type: Research article Published on:

  47. Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested t...

    Authors: Juan Pablo A. Ortiz, Olivier Leblanc, Cristian Rohr, Mauricio Grisolia, Lorena A. Siena, Maricel Podio, Carolina Colono, Celeste Azzaro and Silvina C. Pessino
    Citation: BMC Genomics 2019 20:487
    Content type: Research article Published on:

  48. Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading en...

    Authors: Lei Li, Lifang Yuan, Yanxia Shi, Xuewen Xie, Ali Chai, Qi Wang and Baoju Li
    Citation: BMC Genomics 2019 20:486
    Content type: Research article Published on:

  49. Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regu...

    Authors: Ehsan Hajiramezanali, Mahdi Imani, Ulisses Braga-Neto, Xiaoning Qian and Edward R. Dougherty
    Citation: BMC Genomics 2019 20(Suppl 6):435
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  50. Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost im...

    Authors: Rasha Elhesha, Aisharjya Sarkar, Christina Boucher and Tamer Kahveci
    Citation: BMC Genomics 2019 20(Suppl 6):434
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

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BMC Genomics

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