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  1. The elucidation of novel transcripts and their expression in response to various stress conditions is necessary to understand the transcriptional network of plants as an adaptation to biotic and abiotic stress...

    Authors: Youko Oono, Takayuki Yazawa, Hiroyuki Kanamori, Harumi Sasaki, Satomi Mori and Takashi Matsumoto
    Citation: BMC Genomics 2017 18:761
    Content type: Research Article Published on:

  2. Alignment-free sequence comparison using counts of word patterns (grams, k-tuples) has become an active research topic due to the large amount of sequence data from the new sequencing technologies. Genome sequenc...

    Authors: Xin Bai, Kujin Tang, Jie Ren, Michael Waterman and Fengzhu Sun
    Citation: BMC Genomics 2017 18(Suppl 6):732
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  3. position weight matrix (PWM) and sequence logo are the most widely used representations of transcription factor binding site (TFBS) in biological sequences. Sequence logo - a graphical representation of PWM, h...

    Authors: Zhen Gao, Lu Liu and Jianhua Ruan
    Citation: BMC Genomics 2017 18(Suppl 6):709
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  4. In this editorial, we first summarize the 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) that was held on December 8–10, 2016 in Houston, Texas, USA, and then briefly introduce ...

    Authors: Zhongming Zhao, Zhandong Liu, Ken Chen, Yan Guo, Genevera I. Allen, Jiajie Zhang, W. Jim Zheng and Jianhua Ruan
    Citation: BMC Genomics 2017 18(Suppl 6):703
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  5. High-grade serous ovarian carcinoma (HG-SOC) is the dominant tumor histologic type in epithelial ovarian cancers, exhibiting highly aberrant microRNA expression profiles and diverse pathways that collectively ...

    Authors: Vladimir A. Kuznetsov, Zhiqun Tang and Anna V. Ivshina
    Citation: BMC Genomics 2017 18(Suppl 6):692
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  6. Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing. Reliance upon short DNA fragment paired end sequencing has yielded a...

    Authors: Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski and Richard A. Gibbs
    Citation: BMC Genomics 2017 18(Suppl 6):691
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  7. High throughput sequencing technology enables the both the human genome and transcriptome to be screened at the single nucleotide resolution. Tools have been developed to infer single nucleotide variants (SNVs...

    Authors: Yan Guo, Shilin Zhao, Quanhu Sheng, David C Samuels and Yu Shyr
    Citation: BMC Genomics 2017 18(Suppl 6):690
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  8. Research interests toward single cell analysis have greatly increased in basic, translational and clinical research areas recently, as advances in whole-transcriptome amplification technique allow scientists t...

    Authors: Lu Yang, Jiancheng Liu, Qiang Lu, Arthur D. Riggs and Xiwei Wu
    Citation: BMC Genomics 2017 18(Suppl 6):689
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  9. Circular RNA (circRNA) is one type of noncoding RNA that forms a covalently closed continuous loop. Similar to long noncoding RNA (lncRNA), circRNA can act as microRNA (miRNA) ‘sponges’ to regulate gene expres...

    Authors: Tianyi Xu, Jing Wu, Ping Han, Zhongming Zhao and Xiaofeng Song
    Citation: BMC Genomics 2017 18(Suppl 6):680
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  10. With the advances in high-throughput gene profiling technologies, a large volume of gene interaction maps has been constructed. A higher-level layer of gene-gene interaction, namely modulate gene interaction, ...

    Authors: Yu-Chiao Chiu, Li-Ju Wang, Tzu-Hung Hsiao, Eric Y. Chuang and Yidong Chen
    Citation: BMC Genomics 2017 18(Suppl 6):679
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  11. In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KI...

    Authors: Guangchun Han, Wei Zhao, Xiaofeng Song, Patrick Kwok-Shing Ng, Jose A. Karam, Eric Jonasch, Gordon B. Mills, Zhongming Zhao, Zhiyong Ding and Peilin Jia
    Citation: BMC Genomics 2017 18(Suppl 6):678
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  12. Flux Balance Analysis (FBA) based mathematical modeling enables in silico prediction of systems behavior for genome-scale metabolic networks. Computational methods have been derived in the FBA framework to solve ...

    Authors: Meltem Apaydin, Liang Xu, Bo Zeng and Xiaoning Qian
    Citation: BMC Genomics 2017 18(Suppl 6):677
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  13. The ability to predict epitopes plays an enormous role in vaccine development in terms of our ability to zero in on where to do a more thorough in-vivo analysis of the protein in question. Though for the past ...

    Authors: Gene Sher, Degui Zhi and Shaojie Zhang
    Citation: BMC Genomics 2017 18(Suppl 6):676
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 6

  14. Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide stu...

    Authors: Yanli Zhang, Fengzhe Li, Xu Feng, Hua Yang, Aoxiang Zhu, Jing Pang, Le Han, Tingting Zhang, Xiaolei Yao and Feng Wang
    Citation: BMC Genomics 2017 18:759
    Content type: Research article Published on:

  15. Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decrease...

    Authors: Stéphanie Durand, Killian Trillet, Arnaud Uguen, Aude Saint-Pierre, Catherine Le Jossic-Corcos and Laurent Corcos
    Citation: BMC Genomics 2017 18:758
    Content type: Research article Published on:

  16. In the domestic dog, corpora lutea (CL) are the only source of progesterone (P4), both in pregnant and non-pregnant cycles because there is no placental steroidogenesis. The absence of an endogenous luteolysin...

    Authors: Sophie Zatta, Hubert Rehrauer, Aykut Gram, Alois Boos and Mariusz Pawel Kowalewski
    Citation: BMC Genomics 2017 18:757
    Content type: Research article Published on:

  17. Authors: Timothy D. Read, Robert A. Petit III, Sandeep J. Joseph, Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan and Alistair D.M. Dove
    Citation: BMC Genomics 2017 18:755
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2017 18:532

  18. Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainl...

    Authors: Ming Li, Zhaoxu Liang, Shanshan He, Yuan Zeng, Yan Jing, Weikuan Fang, Kaichao Wu, Guanyu Wang, Xia Ning, Lunwang Wang, Song Li, Hongwei Tan and Fang Tan
    Citation: BMC Genomics 2017 18:754
    Content type: Research article Published on:

  19. Anopheles (An.) coluzzii, one of Africa’s primary malaria vectors, is highly anthropophilic. This human host preference contributes greatly to its ability to transmit malaria. In contr...

    Authors: G. Athrey, L. V. Cosme, Z. Popkin-Hall, S. Pathikonda, W. Takken and M. A. Slotman
    Citation: BMC Genomics 2017 18:751
    Content type: Research article Published on:

  20. 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 Published on:

  21. A genomic signal track is a set of genomic intervals associated with values of various types, such as measurements from high-throughput experiments. Analysis of signal tracks requires complex computational met...

    Authors: Xinjie Zhu, Qiang Zhang, Eric Dun Ho, Ken Hung-On Yu, Chris Liu, Tim H. Huang, Alfred Sze-Lok Cheng, Ben Kao, Eric Lo and Kevin Y. Yip
    Citation: BMC Genomics 2017 18:749
    Content type: Software Published on:

  22. We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.

    Authors: Alberto Magi, Tommaso Pippucci and Carlo Sidore
    Citation: BMC Genomics 2017 18:747
    Content type: Software Published on:

  23. This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck’s ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangoli...

    Authors: Zelda du Toit, Morné du Plessis, Desiré L. Dalton, Raymond Jansen, J. Paul Grobler and Antoinette Kotzé
    Citation: BMC Genomics 2017 18:746
    Content type: Research article Published on:

  24. RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression...

    Authors: Billy T. Lau and Hanlee P. Ji
    Citation: BMC Genomics 2017 18:745
    Content type: Methodology article Published on:

  25. The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well ...

    Authors: Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang and Yan Xu
    Citation: BMC Genomics 2017 18:744
    Content type: Research article Published on:

  26. The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to par...

    Authors: Gea Guerriero, Lauralie Mangeot-Peter, Sylvain Legay, Marc Behr, Stanley Lutts, Khawar Sohail Siddiqui and Jean-Francois Hausman
    Citation: BMC Genomics 2017 18:741
    Content type: Research article Published on:

  27. Nearly 6 million deaths and over a half trillion dollars in healthcare costs worldwide are attributed to tobacco smoking each year. Extensive research efforts have been pursued to elucidate the molecular under...

    Authors: David C. Qian, David L. Molfese, Jennifer L. Jin, Alexander J. Titus, Yixuan He, Yafang Li, Maxime Vaissié, Humsini Viswanath, Philip R. Baldwin, Ralf Krahe, Ramiro Salas and Christopher I. Amos
    Citation: BMC Genomics 2017 18:740
    Content type: Research article Published on:

  28. The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal gr...

    Authors: Lorenza Vitale, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Maria Chiara Pelleri and Maria Caracausi
    Citation: BMC Genomics 2017 18:739
    Content type: Research article Published on:

  29. Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occ...

    Authors: Helen Spiers, Eilis Hannon, Leonard C. Schalkwyk, Nicholas J. Bray and Jonathan Mill
    Citation: BMC Genomics 2017 18:738
    Content type: Research article Published on:

  30. Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in t...

    Authors: Y. Daguerre, E. Levati, J. Ruytinx, E. Tisserant, E. Morin, A. Kohler, B. Montanini, S. Ottonello, A. Brun, C. Veneault-Fourrey and F. Martin
    Citation: BMC Genomics 2017 18:737
    Content type: Research article Published on:

  31. Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A....

    Authors: Hariprasath Prakash, Shivaprakash Mandya Rudramurthy, Prasad S. Gandham, Anup Kumar Ghosh, Milner M. Kumar, Chandan Badapanda and Arunaloke Chakrabarti
    Citation: BMC Genomics 2017 18:736
    Content type: Research article Published on:

  32. The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative ...

    Authors: Balázs Brankovics, Peter van Dam, Martijn Rep, G. Sybren de Hoog, Theo A. J. van der Lee, Cees Waalwijk and Anne D. van Diepeningen
    Citation: BMC Genomics 2017 18:735
    Content type: Research article Published on:

  33. The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into se...

    Authors: Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Geoffrey I. McFadden and Stuart A. Ralph
    Citation: BMC Genomics 2017 18:734
    Content type: Research article Published on:

  34. The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) a...

    Authors: Jingyin Yu, Sadia Tehrim, Linhai Wang, Komivi Dossa, Xiurong Zhang, Tao Ke and Boshou Liao
    Citation: BMC Genomics 2017 18:733
    Content type: Research article Published on:

  35. During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. This is accompanied by dampened oscillations of circadian clock genes and disrup...

    Authors: Majken Pagter, Jessica Alpers, Alexander Erban, Joachim Kopka, Ellen Zuther and Dirk K. Hincha
    Citation: BMC Genomics 2017 18:731
    Content type: Research article Published on:

  36. Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome...

    Authors: X. Argout, G. Martin, G. Droc, O. Fouet, K. Labadie, E. Rivals, J.M. Aury and C. Lanaud
    Citation: BMC Genomics 2017 18:730
    Content type: Methodology article Published on:

  37. Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate ada...

    Authors: Bo Wang, Xiaofei Liang, Mark L. Gleason, Rong Zhang and Guangyu Sun
    Citation: BMC Genomics 2017 18:729
    Content type: Research article Published on:

  38. B-cell chronic lymphocytic leukemia (CLL) is a common type of adult leukemia. It often follows an indolent course and is preceded by monoclonal B-cell lymphocytosis, an asymptomatic condition, however it is no...

    Authors: Panagiotis Georgiadis, Irene Liampa, Dennie G. Hebels, Julian Krauskopf, Aristotelis Chatziioannou, Ioannis Valavanis, Theo M.C.M. de Kok, Jos C.S. Kleinjans, Ingvar A. Bergdahl, Beatrice Melin, Florentin Spaeth, Domenico Palli, R.C.H. Vermeulen, J. Vlaanderen, Marc Chadeau-Hyam, Paolo Vineis…
    Citation: BMC Genomics 2017 18:728
    Content type: Research article Published on:

  40. Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infect...

    Authors: Ana Cristina Ferreira, Rogério Tenreiro, Maria Inácia Corrêa de Sá and Ricardo Dias
    Citation: BMC Genomics 2017 18:726
    Content type: Research article Published on:

  41. In birds, blue-green eggshell color (BGEC) is caused by biliverdin, a bile pigment derived from the degradation of heme and secreted in the eggshell by the shell gland. Functionally, BGEC might promote the pat...

    Authors: Zhepeng Wang, Guohua Meng, Yun Bai, Ruifang Liu, Yu Du and Lihong Su
    Citation: BMC Genomics 2017 18:725
    Content type: Research Article Published on:

  42. Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic me...

    Authors: Jia Zhou, Renee L. Sears, Xiaoyun Xing, Bo Zhang, Daofeng Li, Nicole B. Rockweiler, Hyo Sik Jang, Mayank N.K. Choudhary, Hyung Joo Lee, Rebecca F. Lowdon, Jason Arand, Brianne Tabers, C. Charles Gu, Theodore J. Cicero and Ting Wang
    Citation: BMC Genomics 2017 18:724
    Content type: Research article Published on:

  43. Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tiss...

    Authors: Camila M. Lopes-Ramos, Joseph N. Paulson, Cho-Yi Chen, Marieke L. Kuijjer, Maud Fagny, John Platig, Abhijeet R. Sonawane, Dawn L. DeMeo, John Quackenbush and Kimberly Glass
    Citation: BMC Genomics 2017 18:723
    Content type: Research article Published on:

  45. Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights i...

    Authors: Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya and Sanghamitra Bandyopadhyay
    Citation: BMC Genomics 2017 18:721
    Content type: Research article Published on:

  46. We performed whole human genome expression analysis in placenta tissue (normal and T21) samples in order to investigate gene expression into the pathogenesis of trisomy 21 (T21) placenta. We profiled the whole...

    Authors: Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Dong Wook Kwak, So Yeon Park, Sun-Hee Chun and Hyun Mee Ryu
    Citation: BMC Genomics 2017 18:720
    Content type: Research article Published on:

  47. Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the Zrt- and Irt-like (ZIP; SLC39A) family of tran...

    Authors: Rebecca Lawson, Wolfgang Maret and Christer Hogstrand
    Citation: BMC Genomics 2017 18:719
    Content type: Research article Published on:

  48. Oogenesis in the domestic silkworm (Bombyx mori) is a complex process involving previtellogenesis, vitellogenesis and choriogenesis. During this process, follicles show drastic morphological and physiological cha...

    Authors: Qiang Zhang, Wei Sun, Bang-Yong Sun, Yang Xiao and Ze Zhang
    Citation: BMC Genomics 2017 18:714
    Content type: Research article Published on:

  49. MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evo...

    Authors: Showkat Ahmad Ganie, Ananda Bhusan Debnath, Abubakar Mohammad Gumi and Tapan Kumar Mondal
    Citation: BMC Genomics 2017 18:711
    Content type: Research article Published on:

  50. Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of cor...

    Authors: Monika Frazier, Martin Helmkampf, M. Renee Bellinger, Scott M. Geib and Misaki Takabayashi
    Citation: BMC Genomics 2017 18:710
    Content type: Research article Published on:

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BMC Genomics

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