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  1. Most semiconductor nanoparticles used in biomedical applications are made of heavy metals and involve synthetic methods that require organic solvents and high temperatures. This issue makes the development of ...

    Authors: Juan P Monrás, Bernardo Collao, Roberto C Molina-Quiroz, Gonzalo A Pradenas, Luis A Saona, Vicente Durán-Toro, Nicolás Órdenes-Aenishanslins, Felipe A Venegas, David E Loyola, Denisse Bravo, Paulina F Calderón, Iván L Calderón, Claudio C Vásquez, Thomas G Chasteen, Desiré A Lopez and José M Pérez-Donoso
    Citation: BMC Genomics 2014 15:1099
    Content type: Research article Published on:

  2. Lateral gene transfer (LGT) from bacterial Wolbachia endosymbionts has been detected in ~20% of arthropod and nematode genome sequencing projects. Many of these transfers are large and contain a substantial part ...

    Authors: Lisa Klasson, Nikhil Kumar, Robin Bromley, Karsten Sieber, Melissa Flowers, Sandra H Ott, Luke J Tallon, Siv G E Andersson and Julie C Dunning Hotopp
    Citation: BMC Genomics 2014 15:1097
    Content type: Research article Published on:

  3. Wild plants of Vitis closely related to the cultivated grapevine (V. v. vinifera) are believed to have been first domesticated 10,000 years BC around the Caspian Sea. V. v. vinifera is hermaphrodite whereas V. v....

    Authors: Miguel Jesus Nunes Ramos, João Lucas Coito, Helena Gomes Silva, Jorge Cunha, Maria Manuela Ribeiro Costa and Margarida Rocheta
    Citation: BMC Genomics 2014 15:1095
    Content type: Research article Published on:

  4. Fimbriae are bacterial cell surface organelles involved in the pathogenesis of many bacterial species, including Gallibacterium anatis, in which a F17-like fimbriae of the chaperone-usher (CU) family was recently...

    Authors: EglÄ— KudirkienÄ—, Ragnhild J Bager, Timothy J Johnson and Anders M Bojesen
    Citation: BMC Genomics 2014 15:1093
    Content type: Research article Published on:

  5. Development of drug resistance in bacteria causes antibiotic therapies to be less effective and more costly. Moreover, our understanding of the process remains incomplete. One promising approach to improve our...

    Authors: Michal Wozniak, Jerzy Tiuryn and Limsoon Wong
    Citation: BMC Genomics 2014 15(Suppl 10):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 10

  6. Short tandem repeats (STRs) are abundant in human genomes. Numerous STRs have been shown to be associated with genetic diseases and gene regulatory functions, and have been selected as genetic markers for evol...

    Authors: Chien-Ming Chen, Chi-Pong Sio, Yu-Lun Lu, Hao-Teng Chang, Chin-Hwa Hu and Tun-Wen Pai
    Citation: BMC Genomics 2014 15(Suppl 10):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 10

  7. It is common to get an optimal combination of markers for disease classification and prediction when multiple markers are available. Many approaches based on the area under the receiver operating characteristi...

    Authors: Wenbao Yu and Taesung Park
    Citation: BMC Genomics 2014 15(Suppl 10):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 10

  9. Massively parallel DNA sequencing (MPS) has the potential to revolutionize diagnostics, in particular for monogenic disorders. Inborn errors of metabolism (IEM) constitute a large group of monogenic disorders ...

    Authors: Henrik Stranneheim, Martin Engvall, Karin Naess, Nicole Lesko, Pontus Larsson, Mats Dahlberg, Robin Andeer, Anna Wredenberg, Chris Freyer, Michela Barbaro, Helene Bruhn, Tesfail Emahazion, MÃ¥ns Magnusson, Rolf Wibom, Rolf H Zetterström, Valtteri Wirta…
    Citation: BMC Genomics 2014 15:1090
    Content type: Methodology article Published on:

  10. The malaria mosquito Anopheles gambiae has a high preference for human hosts, a characteristic that contributes greatly to its capacity for transmitting human malaria. A sibling species, An. quadriannulatus, has ...

    Authors: Theresa K Hodges, Luciano V Cosme, Giridhar Athrey, Sharmila Pathikonda, Willem Takken and Michel A Slotman
    Citation: BMC Genomics 2014 15:1089
    Content type: Research article Published on:

    The Retraction Note to this article has been published in BMC Genomics 2015 16:572

  11. The phytoplasma-borne disease flavescence dorée is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of gra...

    Authors: Simona Abbà, Luciana Galetto, Patricia Carle, Sébastien Carrère, Massimo Delledonne, Xavier Foissac, Sabrina Palmano, Flavio Veratti and Cristina Marzachì
    Citation: BMC Genomics 2014 15:1088
    Content type: Research article Published on:

  13. The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded...

    Authors: Michael N Romanov, Marta Farré, Pamela E Lithgow, Katie E Fowler, Benjamin M Skinner, Rebecca O’Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D Jarvis, Hans Ellegren, David W Burt, Denis M Larkin and Darren K Griffin
    Citation: BMC Genomics 2014 15:1060
    Content type: Research article Published on:

  14. Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has li...

    Authors: Bin Li, Ling Tian, Jingying Zhang, Long Huang, Fenxia Han, Shurong Yan, Lianzheng Wang, Hongkun Zheng and Junming Sun
    Citation: BMC Genomics 2014 15:1086
    Content type: Research article Published on:

  15. Thiamine availability is involved in glycolytic flux and fermentation efficiency. A deficiency of this vitamin may be responsible for sluggish fermentations in wine making. Therefore, both thiamine uptake and de ...

    Authors: Christian Brion, Chloé Ambroset, Pierre Delobel, Isabelle Sanchez and Bruno Blondin
    Citation: BMC Genomics 2014 15:1085
    Content type: Research article Published on:

  16. In broilers, high ambient temperature can result in reduced feed consumption, digestive inefficiency, impaired metabolism, and even death. The broiler sector of the U.S. poultry industry incurs approximately $...

    Authors: Derrick J Coble, Damarius Fleming, Michael E Persia, Chris M Ashwell, Max F Rothschild, Carl J Schmidt and Susan J Lamont
    Citation: BMC Genomics 2014 15:1084
    Content type: Research article Published on:

  17. Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), have emerged as important regulators of eukaryotic gene expression. In plants, miRNAs play critical roles in development, n...

    Authors: Patricia Baldrich, Klementina Kakar, Christelle Siré, Ana Beatriz Moreno, Angélique Berger, Meritxell García-Chapa, Juan José López-Moya, José Luis Riechmann and Blanca San Segundo
    Citation: BMC Genomics 2014 15:1083
    Content type: Research article Published on:

  18. Powdery mildew, caused by the obligate biotrophic fungus Erysiphe necator, is an economically important disease of grapevines worldwide. Large quantities of fungicides are used for its control, accelerating the i...

    Authors: Laura Jones, Summaira Riaz, Abraham Morales-Cruz, Katherine CH Amrine, Brianna McGuire, W Douglas Gubler, M Andrew Walker and Dario Cantu
    Citation: BMC Genomics 2014 15:1081
    Content type: Research article Published on:

  19. The ~17 Gb hexaploid bread wheat genome is a high priority and a major technical challenge for genomic studies. In particular, the D sub-genome is relatively lacking in genetic diversity, making it both diffic...

    Authors: Stuart J Lucas, Bala Anı Akpınar, Hana Šimková, Marie Kubaláková, Jaroslav Doležel and Hikmet Budak
    Citation: BMC Genomics 2014 15:1080
    Content type: Research article Published on:

  20. DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biol...

    Authors: Steven H Lin, Jing Wang, Pierre Saintigny, Chia-Chin Wu, Uma Giri, Jing Zhang, Toshi Menju, Lixia Diao, Lauren Byers, John N Weinstein, Kevin R Coombes, Luc Girard, Ritsuko Komaki, Ignacio I Wistuba, Hiroshi Date, John D Minna…
    Citation: BMC Genomics 2014 15:1079
    Content type: Research article Published on:

  21. Non-small cell lung cancer (NSCLC) is a major cause of cancer-related death worldwide due to poor patient prognosis and clinical outcome. Here, we studied the genetic variations underlying NSCLC pathogenesis b...

    Authors: Tzia Liang Mah, Xin Ning Adeline Yap, Vachiranee Limviphuvadh, Nanpu Li, Srinath Sridharan, Vellaisemy Kuralmani, Mengling Feng, Natalia Liem, Sharmila Adhikari, Wei Peng Yong, Ross A Soo, Sebastian Maurer-Stroh, Frank Eisenhaber and Joo Chuan Tong
    Citation: BMC Genomics 2014 15(Suppl 9):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  22. Proteogenomics combines the cutting-edge methods from genomics and proteomics. While it has become cheap to sequence whole genomes, the correct annotation of protein coding regions in the genome is still tedio...

    Authors: Julian Uszkoreit, Nicole Plohnke, Sascha Rexroth, Katrin Marcus and Martin Eisenacher
    Citation: BMC Genomics 2014 15(Suppl 9):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  23. Sumoylation, which is a reversible and dynamic post-translational modification, is one of the vital processes in a cell. Before a protein matures to perform its function, sumoylation may alter its localization...

    Authors: Ahmet Sinan Yavuz and Osman Ugur Sezerman
    Citation: BMC Genomics 2014 15(Suppl 9):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  24. With the rapid accumulation of proteomic and genomic datasets in terms of genome-scale features and interaction networks through high-throughput experimental techniques, the process of manual predicting functi...

    Authors: Qingyao Wu, Yunming Ye, Shen-Shyang Ho and Shuigeng Zhou
    Citation: BMC Genomics 2014 15(Suppl 9):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  25. Altered expression profiles of microRNAs (miRNAs) are linked to many diseases including lung cancer. miRNA expression profiling is reproducible and miRNAs are very stable. These characteristics of miRNAs make ...

    Authors: Renhua Song, Qian Liu, Gyorgy Hutvagner, Hung Nguyen, Kotagiri Ramamohanarao, Limsoon Wong and Jinyan Li
    Citation: BMC Genomics 2014 15(Suppl 9):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  26. G-quadruplexes are four-stranded structures formed in guanine-rich nucleotide sequences. Several functional roles of DNA G-quadruplexes have so far been investigated, where their putative functional roles duri...

    Authors: Masato Yano and Yuki Kato
    Citation: BMC Genomics 2014 15(Suppl 9):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  27. RNA interference (RNAi) is involved in genome defense as well as diverse cellular, developmental, and physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA polymerase (RdR...

    Authors: Jaeyoung Choi, Ki-Tae Kim, Jongbum Jeon, Jiayao Wu, Hyeunjeong Song, Fred O Asiegbu and Yong-Hwan Lee
    Citation: BMC Genomics 2014 15(Suppl 9):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  28. Sequence data from the chloroplast genome have played a central role in elucidating the evolutionary history of flowering plants, Angiospermae. In the past decade, the number of complete chloroplast genomes has b...

    Authors: Catherine J Nock, Abdul Baten and Graham J King
    Citation: BMC Genomics 2014 15(Suppl 9):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  29. Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analys...

    Authors: Kuan-Bei Chen, Ross Hardison and Yu Zhang
    Citation: BMC Genomics 2014 15(Suppl 9):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  30. Editing and mutations in microRNAs (miRNAs) can change the stability of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles contain ...

    Authors: Yun Zheng, Ting Li, Ren Ren, Donghua Shi and Shengpeng Wang
    Citation: BMC Genomics 2014 15(Suppl 9):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  31. Recently, large bio-projects dealing with the release of different genomes have transpired. Most of these projects use next-generation sequencing platforms. As a consequence, many de novo assembly tools have evol...

    Authors: Mostafa M Abbas, Qutaibah M Malluhi and Ponnuraman Balakrishnan
    Citation: BMC Genomics 2014 15(Suppl 9):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  32. Computational prediction of major histocompatibility complex class II (MHC-II) binding peptides can assist researchers in understanding the mechanism of immune systems and developing peptide based vaccines. Al...

    Authors: Yichang Xu, Cheng Luo, Mingjie Qian, Xiaodi Huang and Shanfeng Zhu
    Citation: BMC Genomics 2014 15(Suppl 9):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  33. Drugs that simultaneously target multiple proteins often improve efficacy, particularly in the treatment of complex diseases such as cancers and central nervous system disorders. Many approaches have been prop...

    Authors: Yi-Yuan Chiu, Jen-Hu Tseng, Kuan-Hsiu Liu, Chih-Ta Lin, Kai-Cheng Hsu and Jinn-Moon Yang
    Citation: BMC Genomics 2014 15(Suppl 9):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  34. Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prog...

    Authors: Aliaksandr A Yarmishyn, Arsen O Batagov, Jovina Z Tan, Gopinath M Sundaram, Prabha Sampath, Vladimir A Kuznetsov and Igor V Kurochkin
    Citation: BMC Genomics 2014 15(Suppl 9):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  35. Transcriptome sequencing of brain samples provides detailed enrichment analysis of differential expression and genetic interactions for evaluation of mitochondrial and coagulation function of schizophrenia. It...

    Authors: Kuo-Chuan Huang, Ko-Chun Yang, Han Lin, Theresa Tsun-Hui Tsao and Sheng-An Lee
    Citation: BMC Genomics 2014 15(Suppl 9):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  36. Histone modification and remodeling play crucial roles in regulating gene transcription. These post-translational modifications of histones function in a combinatorial fashion and can be recognized by specific...

    Authors: Po-Cheng Hung, Tzu-Hsien Yang, Hung-Jiun Liaw and Wei-Sheng Wu
    Citation: BMC Genomics 2014 15(Suppl 9):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  37. The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the g...

    Authors: JeHoon Jun, Yun Sung Cho, Haejin Hu, Hak-Min Kim, Sungwoong Jho, Priyvrat Gadhvi, Kyung Mi Park, Jeongheui Lim, Woon Kee Paek, Kyudong Han, Andrea Manica, Jeremy S Edwards and Jong Bhak
    Citation: BMC Genomics 2014 15(Suppl 9):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  38. A number of microtubule disassembly blocking agents and inhibitors of tubulin polymerization have been elements of great interest in anti-cancer therapy, some of them even entering into the clinical trials. On...

    Authors: Chetna Tyagi, Ankita Gupta, Sukriti Goyal, Jaspreet Kaur Dhanjal and Abhinav Grover
    Citation: BMC Genomics 2014 15(Suppl 9):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  39. Non-small cell lung cancer (NSCLC) remains lethal despite the development of numerous drug therapy technologies. About 85% to 90% of lung cancers are NSCLC and the 5-year survival rate is at best still below 5...

    Authors: Hideaki Umeyama, Mitsuo Iwadate and Y-h Taguchi
    Citation: BMC Genomics 2014 15(Suppl 9):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  40. Proteomics research is enabled with the high-throughput technologies, but our ability to identify expressed proteome is limited in small samples. The coverage and consistency of proteome expression are critica...

    Authors: Jing Sun, Guang Lan Zhang, Siyang Li, Alexander R Ivanov, David Fenyo, Frederique Lisacek, Shashi K Murthy, Barry L Karger and Vladimir Brusic
    Citation: BMC Genomics 2014 15(Suppl 9):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  41. The 13th International Conference on Bioinformatics (InCoB2014) was held for the first time in Australia, at Sydney, July 31-2 August, 2014. InCoB is the annual scientific gathering of the Asia-Pacific Bioinfo...

    Authors: Christian Schönbach, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Genomics 2014 15(Suppl 9):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 15 Supplement 9

  42. Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resista...

    Authors: Yuning Chen, Xiaoping Ren, Xiaojing Zhou, Li Huang, Liying Yan, Yong Lei, Boshou Liao, Jinyong Huang, Shunmou Huang, Wenhui Wei and Huifang Jiang
    Citation: BMC Genomics 2014 15:1078
    Content type: Research article Published on:

  43. Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved i...

    Authors: Jérôme Grimplet, Anne-Françoise Adam-Blondon, Pierre-François Bert, Oliver Bitz, Dario Cantu, Christopher Davies, Serge Delrot, Mario Pezzotti, Stéphane Rombauts and Grant R Cramer
    Citation: BMC Genomics 2014 15:1077
    Content type: Methodology article Published on:

  44. Maintenance of metal homeostasis is crucial in bacterial pathogenicity as metal starvation is the most important mechanism in the nutritional immunity strategy of host cells. Thus, pathogenic bacteria have evo...

    Authors: Elke Eckelt, Michael Jarek, Cornelia Frömke, Jochen Meens and Ralph Goethe
    Citation: BMC Genomics 2014 15:1076
    Content type: Research article Published on:

  45. Strains of Escherichia coli cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylo...

    Authors: Robert J Goldstone, Roman Popat, Hans-Joachim Schuberth, Olivier Sandra, I Martin Sheldon and David GE Smith
    Citation: BMC Genomics 2014 15:1075
    Content type: Research article Published on:

  46. Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancie...

    Authors: John F Mulley, Adam D Hargreaves, Matthew J Hegarty, R Scott Heller and Martin T Swain
    Citation: BMC Genomics 2014 15:1074
    Content type: Research article Published on:

  48. Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their h...

    Authors: Raúl Castanera, Gúmer Pérez, Leticia López, Rubén Sancho, Francisco Santoyo, Manuel Alfaro, Toni Gabaldón, Antonio G Pisabarro, José A Oguiza and Lucía Ramírez
    Citation: BMC Genomics 2014 15:1071
    Content type: Research article Published on:

  49. Some species of fungi can cause serious human diseases, particularly to immuno-compromised individuals. Opportunistic fungal infections are a leading cause of mortality, and present an emerging challenge that ...

    Authors: Manish Datt and Amit Sharma
    Citation: BMC Genomics 2014 15:1069
    Content type: Research article Published on:

  50. Comparison of toxicogenomic data facilitates the identification of deregulated gene patterns and maximizes health risk prediction in human.

    Authors: Immacolata Porreca, Fulvio D’Angelo, Daniela Gentilcore, Emanuele Carchia, Angela Amoresano, Andrea Affuso, Michele Ceccarelli, Pasquale De Luca, Libera Esposito, Francesco M Guadagno, Massimo Mallardo, Antonio Nardone, Sergio Maccarone, Francesca Pane, Marzia Scarfò, Paolo Sordino…
    Citation: BMC Genomics 2014 15:1067
    Content type: Research article Published on:

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BMC Genomics

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