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  1. The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the matur...

    Authors: Ling Li, Manhoi Hur, Joon-Yong Lee, Wenxu Zhou, Zhihong Song, Nick Ransom, Cumhur Yusuf Demirkale, Dan Nettleton, Mark Westgate, Zebulun Arendsee, Vidya Iyer, Jackie Shanks, Basil Nikolau and Eve Syrkin Wurtele
    Citation: BMC Genomics 2015 16(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 3

  2. By comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stim...

    Authors: Benjamin B Green, Stephanie D McKay and David E Kerr
    Citation: BMC Genomics 2015 16:30
    Content type: Research article Published on:

  3. Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produc...

    Authors: Omar Darwish, Rachel Shahan, Zhongchi Liu, Janet P Slovin and Nadim W Alkharouf
    Citation: BMC Genomics 2015 16:29
    Content type: Research article Published on:

  4. In recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of b...

    Authors: Xiuna Wang, Xiaoling Zhang, Ling Liu, Meichun Xiang, Wenzhao Wang, Xiang Sun, Yongsheng Che, Liangdong Guo, Gang Liu, Liyun Guo, Chengshu Wang, Wen-Bing Yin, Marc Stadler, Xinyu Zhang and Xingzhong Liu
    Citation: BMC Genomics 2015 16:28
    Content type: Research article Published on:

  5. Unicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent ph...

    Authors: Jan M Meyer, Christian Rödelsperger, Karsten Eichholz, Urban Tillmann, Allan Cembella, Angela McGaughran and Uwe John
    Citation: BMC Genomics 2015 16:27
    Content type: Research article Published on:

  6. Our purpose was to obtain genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myr...

    Authors: Vincent Jacquier, Jordi Estellé, Barbara Schmaltz-Panneau, Jérôme Lecardonnel, Marco Moroldo, Gaëtan Lemonnier, Jason Turner-Maier, Véronique Duranthon, Isabelle P Oswald, Thierry Gidenne and Claire Rogel-Gaillard
    Citation: BMC Genomics 2015 16:26
    Content type: Research article Published on:

  7. Genetic variants may predispose humans to elevated risk of common metabolic morbidities such as obesity and Type 2 Diabetes (T2D). Some of these variants have also been shown to influence elite athletic perfor...

    Authors: Lauren K Banting, Vladimir P Pushkarev, Pawel Cieszczyk, Aleksandra Zarebska, Agnieszka Maciejewska-Karlowska, M-arek Sawczuk, Agata Leońska-Duniec, Dmitry A Dyatlov, Evgeniy F Orekhov, Aleksandr V Degtyarev, Yuliya E Pushkareva, Xu Yan, Ruth Birk and Nir Eynon
    Citation: BMC Genomics 2015 16:25
    Content type: Research article Published on:

  8. QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed ...

    Authors: Wellington Muchero, Jianjun Guo, Stephen P DiFazio, Jin-Gui Chen, Priya Ranjan, Gancho T Slavov, Lee E Gunter, Sara Jawdy, Anthony C Bryan, Robert Sykes, Angela Ziebell, Jaroslav Klápště, Ilga Porth, Oleksandr Skyba, Faride Unda, Yousry A El-Kassaby…
    Citation: BMC Genomics 2015 16:24
    Content type: Research article Published on:

  9. 2,2′,4,4′-Tetrabromodiphenyl ether (BDE47) is a prevalent environmental pollutant and has been demonstrated to be a serious toxicant in both humans and animals, but little is known about the molecular mechanis...

    Authors: Ting Xu, Jing Zhao, Daqiang Yin, Qingshun Zhao and Bingzhi Dong
    Citation: BMC Genomics 2015 16:23
    Content type: Research article Published on:

  10. Regional specificity allows different skin regions to exhibit different characteristics, enabling complementary functions to make effective use of the integumentary surface. Chickens exhibit a high degree of r...

    Authors: Kai-Wei Chang, Nancy A Huang, I-Hsuan Liu, Yi-Hui Wang, Ping Wu, Yen-Tzu Tseng, Michael W Hughes, Ting Xin Jiang, Mong-Hsun Tsai, Chien-Yu Chen, Yen-Jen Oyang, En-Chung Lin, Cheng-Ming Chuong and Shau-Ping Lin
    Citation: BMC Genomics 2015 16:22
    Content type: Research article Published on:

  11. Epigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation.

    Authors: Pengfei Wang, Han Xia, Ye Zhang, Shuzhen Zhao, Chuanzhi Zhao, Lei Hou, Changsheng Li, Aiqin Li, Chuanxi Ma and Xingjun Wang
    Citation: BMC Genomics 2015 16:21
    Content type: Research article Published on:

  14. Rice yield and quality are adversely affected by high temperatures, especially at night; high nighttime temperatures are more harmful to grain weight than high daytime temperatures. Unfortunately, global tempe...

    Authors: Jiang-Lin Liao, Hui-Wen Zhou, Qi Peng, Ping-An Zhong, Hong-Yu Zhang, Chao He and Ying-Jin Huang
    Citation: BMC Genomics 2015 16:18
    Content type: Research article Published on:

  15. The MYB superfamily is one of the most abundant transcription factor (TF) families in plants. MYB proteins include highly conserved N-terminal MYB repeats (1R, R2R3, 3R, and atypical) and various C-terminal se...

    Authors: Zhen Wang, Jun Tang, Rong Hu, Peng Wu, Xi-Lin Hou, Xiao-Ming Song and Ai-Sheng Xiong
    Citation: BMC Genomics 2015 16:17
    Content type: Research article Published on:

  16. Mouse chromosome 2 is linked to growth and body fat phenotypes in many mouse crosses. With the goal to identify the underlying genes regulating growth and body fat on mouse chromosome 2, we developed five over...

    Authors: Rodrigo Gularte-Mérida, Charles R Farber, Ricardo A Verdugo, Alma Islas–Trejo, Thomas R Famula, Craig H Warden and Juan F Medrano
    Citation: BMC Genomics 2015 16:16
    Content type: Research article Published on:

  17. Although feeding behavior and food habit are ecologically and economically important properties, little is known about formation and evolution of herbivory. Grass carp (Ctenopharyngodon idella) is an ecologically...

    Authors: Shan He, Xu-Fang Liang, Ling Li, Jian Sun, Zheng-Yong Wen, Xiao-Yan Cheng, Ai-Xuan Li, Wen-Jing Cai, Yu-Hui He, Ya-Ping Wang, Ya-Xiong Tao and Xiao-Chen Yuan
    Citation: BMC Genomics 2015 16:15
    Content type: Research article Published on:

  18. The production of metabolites via in vitro culture is promoted by the availability of fully defined metabolic pathways. Withanolides, the major bioactive phytochemicals of Withania somnifera, have been well studi...

    Authors: Kalaiselvi Senthil, Murukarthick Jayakodi, Pankajavalli Thirugnanasambantham, Sang Choon Lee, Pradeepa Duraisamy, Preethi M Purushotham, Kalaiselvi Rajasekaran, Shobana Nancy Charles, Irene Mariam Roy, Arul Kumar Nagappan, Gon Sup Kim, Yun Sun Lee, Senthil Natesan, Tae-Sun Min and Tae Jin Yang
    Citation: BMC Genomics 2015 16:14
    Content type: Research article Published on:

  19. Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools aro...

    Authors: Jung Youn Park, Yong-Rock An, Naohisa Kanda, Chul-Min An, Hye Suck An, Jung-Ha Kang, Eun Mi Kim, Du-Hae An, Hojin Jung, Myunghee Joung, Myung Hum Park, Sook Hee Yoon, Bo-Young Lee, Taeheon Lee, Kyu-Won Kim, Won Cheoul Park…
    Citation: BMC Genomics 2015 16:13
    Content type: Research article Published on:

  20. Garlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not bee...

    Authors: Rina Kamenetsky, Adi Faigenboim, Einat Shemesh Mayer, Tomer Ben Michael, Chen Gershberg, Sagie Kimhi, Itzhak Esquira, Sarit Rohkin Shalom, Dani Eshel, Haim D Rabinowitch and Amir Sherman
    Citation: BMC Genomics 2015 16:12
    Content type: Research article Published on:

  21. Expression quantitative trait loci (eQTL) play an important role in the regulation of gene expression. Gene expression levels and eQTLs are expected to vary from tissue to tissue, and therefore multi-tissue an...

    Authors: Eric F Lock, Karen L Soldano, Melanie E Garrett, Heidi Cope, Christina A Markunas, Herbert Fuchs, Gerald Grant, David B Dunson, Simon G Gregory and Allison E Ashley-Koch
    Citation: BMC Genomics 2015 16:11
    Content type: Research article Published on:

  22. Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well...

    Authors: Julien Recoquillay, Frédérique Pitel, Cécile Arnould, Sophie Leroux, Patrice Dehais, Carole Moréno, Ludovic Calandreau, Aline Bertin, David Gourichon, Olivier Bouchez, Alain Vignal, Maria Ines Fariello, Francis Minvielle, Catherine Beaumont, Christine Leterrier and Elisabeth Le Bihan-Duval
    Citation: BMC Genomics 2015 16:10
    Content type: Research article Published on:

  24. Members of the fungal genus Trichoderma directly antagonize soil-borne fungal pathogens, and an increasing number of species are studied for their potential in biocontrol of plant pathogens in agriculture. Some s...

    Authors: Maria E Morán-Diez, Naomi Trushina, Netta Li Lamdan, Lea Rosenfelder, Prasun K Mukherjee, Charles M Kenerley and Benjamin A Horwitz
    Citation: BMC Genomics 2015 16:8
    Content type: Research article Published on:

  26. Prokaryotic plasmids have played significant roles in the evolution of bacterial genomes and have a great impact on the metabolic functions of the host cell. Many bacterial strains contain multiple plasmids, b...

    Authors: Jinshui Zheng, Ziyu Guan, Shiyun Cao, Donghai Peng, Lifang Ruan, Daohong Jiang and Ming Sun
    Citation: BMC Genomics 2015 16:6
    Content type: Research article Published on:

  27. There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are a...

    Authors: Daniel Garcia-Seco, Yang Zhang, Francisco J Gutierrez-Mañero, Cathie Martin and Beatriz Ramos-Solano
    Citation: BMC Genomics 2015 16:5
    Content type: Research article Published on:

  28. The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insu...

    Authors: Jason M Argyris, Aurora Ruiz-Herrera, Pablo Madriz-Masis, Walter Sanseverino, Jordi Morata, Marta Pujol, Sebastián E Ramos-Onsins and Jordi Garcia-Mas
    Citation: BMC Genomics 2015 16:4
    Content type: Research article Published on:

  29. RNA-Seq based transcriptome assembly has become a fundamental technique for studying expressed mRNAs (i.e., transcripts or isoforms) in a cell using high-throughput sequencing technologies, and is serving as a ba...

    Authors: Masruba Tasnim, Shining Ma, Ei-Wen Yang, Tao Jiang and Wei Li
    Citation: BMC Genomics 2015 16(Suppl 2):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  31. Next generation sequencing (NGS) technologies have made it possible to exhaustively detect structural variations (SVs) in genomes. Although various methods for detecting SVs have been developed, the global str...

    Authors: Tomohiro Yasuda and Satoru Miyano
    Citation: BMC Genomics 2015 16(Suppl 2):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

    The Erratum to this article has been published in BMC Genomics 2015 16:276

  32. MicroRNAs (miRNAs) simultaneously target many transcripts through partial complementarity binding, and have emerged as a key type of post-transcriptional regulator for gene expression. How miRNA accomplishes i...

    Authors: Sheng-Da Hsu, Hsi-Yuan Huang, Chih-Hung Chou, Yi-Ming Sun, Ming-Ta Hsu and Ann-Ping Tsou
    Citation: BMC Genomics 2015 16(Suppl 2):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  33. Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chro...

    Authors: Renhua Song, Qian Liu, Tao Liu and Jinyan Li
    Citation: BMC Genomics 2015 16(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  34. Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "...

    Authors: Yu-Ting Tseng, Wenyuan Li, Ching-Hsien Chen, Shihua Zhang, Jeremy JW Chen, Xianghong Jasmine Zhou and Chun-Chi Liu
    Citation: BMC Genomics 2015 16(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  35. The emergence of next-generation RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate detection of intron retenti...

    Authors: Yang Bai, Shufan Ji and Yadong Wang
    Citation: BMC Genomics 2015 16(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  36. Epigenetic modifications are essential for controlling gene expression. Recent studies have shown that not only single epigenetic modifications but also combinations of multiple epigenetic modifications play v...

    Authors: Kazuki Ichikawa and Shinichi Morishita
    Citation: BMC Genomics 2015 16(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  37. Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA...

    Authors: Naoki Nariai, Kaname Kojima, Sakae Saito, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Jun Yasuda and Masao Nagasaki
    Citation: BMC Genomics 2015 16(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  38. In general, the expression of gene alters conditionally to catalyze a specific metabolic pathway. Microarray-based datasets have been massively produced to monitor gene expression levels in parallel with numer...

    Authors: Chia-Hung Chien, Chi-Nga Chow, Nai-Yun Wu, Yi-Fan Chiang-Hsieh, Ping-Fu Hou and Wen-Chi Chang
    Citation: BMC Genomics 2015 16(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  39. Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis. The problem is difficult because genome-wide association data is very ...

    Authors: Thanh-Tung Nguyen, Joshua Zhexue Huang, Qingyao Wu, Thuy Thi Nguyen and Mark Junjie Li
    Citation: BMC Genomics 2015 16(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  40. Accurate determination of protein complexes is crucial for understanding cellular organization and function. High-throughput experimental techniques have generated a large amount of protein-protein interaction...

    Authors: Yijia Zhang, Hongfei Lin, Zhihao Yang and Jian Wang
    Citation: BMC Genomics 2015 16(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  41. Pinpointing genes involved in inherited human diseases remains a great challenge in the post-genomics era. Although approaches have been proposed either based on the guilt-by-association principle or making us...

    Authors: Rui Jiang, Mengmeng Wu and Lianshuo Li
    Citation: BMC Genomics 2015 16(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  42. Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Mon...

    Authors: Hsei-Wei Wang, Hsing-Jen Sun, Ting-Yu Chang, Hung-Hao Lo, Wei-Chung Cheng, George C Tseng, Chin-Teng Lin, Shing-Jyh Chang, Nikhil Ranjan Pal and I-Fang Chung
    Citation: BMC Genomics 2015 16(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 2

  44. A central problem of computational metagenomics is determining the correct placement into an existing phylogenetic tree of individual reads (nucleotide sequences of varying lengths, ranging from hundreds to th...

    Authors: Alan Filipski, Koichiro Tamura, Paul Billing-Ross, Oscar Murillo and Sudhir Kumar
    Citation: BMC Genomics 2015 16(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  45. We report a consanguineous couple that has experienced three consecutive pregnancy losses following the foetal ultrasound finding of short limbs. Post-termination examination revealed no skeletal dysplasia, bu...

    Authors: Christian R Marshall, Sandra A Farrell, Donna Cushing, Tara Paton, Tracy L Stockley, Dimitri J Stavropoulos, Peter N Ray, Michael Szego, Lynette Lau, Sergio L Pereira, Ronald D Cohn, Richard F Wintle, Adel M Abuzenadah, Muhammad Abu-Elmagd and Stephen W Scherer
    Citation: BMC Genomics 2015 16(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  46. Epilepsy is genetically complex neurological disorder affecting millions of people of different age groups varying in its type and severity. Copy number variants (CNVs) are key players in the genetic etiology ...

    Authors: Muhammad Imran Naseer, Muhammad Faheem, Adeel G Chaudhary, Taha A Kumosani, Maha Mohsin Al-Quaiti, Mohammed M Jan, Hasan Saleh Jamal and Mohammad H Al-Qahtani
    Citation: BMC Genomics 2015 16(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  47. Follicular variant of papillary thyroid carcinoma (FVPTC) and follicular adenoma (FA) are histologically closely related tumors and differential diagnosis remains challenging. RNA expression profiling is an es...

    Authors: Hans-Juergen Schulten, Zuhoor Al-Mansouri, Ibtisam Baghallab, Nadia Bagatian, Ohoud Subhi, Sajjad Karim, Hosam Al-Aradati, Abdulmonem Al-Mutawa, Adel Johary, Abdulrahman A Meccawy, Khalid Al-Ghamdi, Osman Abdel Al-Hamour, Mohammad Hussain Al-Qahtani and Jaudah Al-Maghrabi
    Citation: BMC Genomics 2015 16(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  48. Acute myeloid leukemia (AML) is a clonal disorder of the blood forming cells characterized by accumulation of immature blast cells in the bone marrow and peripheral blood. Being a heterogeneous disease, AML ha...

    Authors: Asad Muhammad Ilyas, Sultan Ahmad, Muhammad Faheem, Muhammad Imran Naseer, Taha A Kumosani, Muhammad Hussain Al-Qahtani, Mamdooh Gari and Farid Ahmed
    Citation: BMC Genomics 2015 16(Suppl 1):S5
    Content type: Review Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  49. The contribution of genetic factors to the development of breast cancer in the admixed and consanguineous population of the western region of Saudi Arabia is thought to be significant as the disease is early o...

    Authors: Adnan Merdad, Mamdooh A Gari, Shireen Hussein, Shadi Al-Khayat, Hana Tashkandi, Jaudah Al-Maghrabi, Fatma Al-Thubaiti, Ibtessam R Hussein, Taha Koumosani, Nehad Shaer, Adeel G Chaudhary, Adel M Abuzenadah, Mohammed H Al-Qahtani and Ashraf Dallol
    Citation: BMC Genomics 2015 16(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  50. Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer deaths worldwide with less than a 6% 5-year survival rate. PDAC is associated with poor prognosis based on the late stage diagnosis...

    Authors: Joseph J LaConti, Evagelia C Laiakis, Anne Deslattes Mays, Ivana Peran, Sung Eun Kim, Jerry W Shay, Anna T Riegel, Albert J Fornace Jr and Anton Wellstein
    Citation: BMC Genomics 2015 16(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

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BMC Genomics

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