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  1. The milk fat profile of the Danish Holstein (DH) and Danish Jersey (DJ) show clear differences. Identification of the genomic regions, genes and biological pathways underlying the milk fat biosynthesis will im...

    Authors: Bart Buitenhuis, Luc LG Janss, Nina A Poulsen, Lotte B Larsen, Mette K Larsen and Peter Sørensen
    Citation: BMC Genomics 2014 15:1112
    Content type: Research article Published on:

  2. Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no geno...

    Authors: Yan Long, Jingwen Zhang, Xinjie Tian, Shanshan Wu, Qiong Zhang, Jianping Zhang, Zhanhai Dang and Xin Wu Pei
    Citation: BMC Genomics 2014 15:1111
    Content type: Research article Published on:

  3. During the past two decades, avian influenza A H9N2 viruses have spread geographically and ecologically in China. Other than its current role in causing outbreaks in poultry and sporadic human infections by di...

    Authors: Yuan Jin, Dong Yu, Hongguang Ren, Zhiqiu Yin, Zhisong Huang, Mingda Hu, Beiping Li, Wei Zhou, Junjie Yue and Long Liang
    Citation: BMC Genomics 2014 15:1110
    Content type: Research article Published on:

  4. In invertebrates, genes belonging to dynamically regulated functional categories appear to be less methylated than “housekeeping” genes, suggesting that DNA methylation may modulate gene expression plasticity....

    Authors: Groves B Dixon, Line K Bay and Mikhail V Matz
    Citation: BMC Genomics 2014 15:1109
    Content type: Research article Published on:

  5. Human hepatoma HepG2 cells are used as an in vitro model of the human liver. High-throughput transcriptomic sequencing is an advanced approach for assessing the functional state of a tissue or cell type. However,...

    Authors: Alexander V Tyakht, Elena N Ilina, Dmitry G Alexeev, Dmitry S Ischenko, Alexey Y Gorbachev, Tatiana A Semashko, Andrei K Larin, Oksana V Selezneva, Elena S Kostryukova, Pavel A Karalkin, Igor V Vakhrushev, Leonid K Kurbatov, Alexander I Archakov and Vadim M Govorun
    Citation: BMC Genomics 2014 15:1108
    Content type: Research article Published on:

  6. Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (A...

    Authors: Nicholas B Justice, Anders Norman, Christopher T Brown, Andrea Singh, Brian C Thomas and Jillian F Banfield
    Citation: BMC Genomics 2014 15:1107
    Content type: Research article Published on:

  7. The peroxisome proliferator-activated receptor alpha (PPARα) is a ligand-activated transcription factor that regulates lipid catabolism and inflammation and is hepatocarcinogenic in rodents. It is presumed tha...

    Authors: Ewa Szalowska, Haftu A Tesfay, Sacha A F T van Hijum and Sander Kersten
    Citation: BMC Genomics 2014 15:1106
    Content type: Research article Published on:

  8. Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, diff...

    Authors: Poshen B Chen, Lihua J Zhu, Sarah J Hainer, Kurtis N McCannell and Thomas G Fazzio
    Citation: BMC Genomics 2014 15:1104
    Content type: Research article Published on:

  9. Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is ...

    Authors: Romain Blanc-Mathieu, Bram Verhelst, Evelyne Derelle, Stephane Rombauts, François-Yves Bouget, Isabelle Carré, Annie Château, Adam Eyre-Walker, Nigel Grimsley, Hervé Moreau, Benoit Piégu, Eric Rivals, Wendy Schackwitz, Yves Van de Peer and Gwenaël Piganeau
    Citation: BMC Genomics 2014 15:1103
    Content type: Research article Published on:

  10. Orange-spotted grouper (Epinephelus coioides) with protogynous hermaphroditic features are one of the most economically important aquaculture species in Taiwan. However, larvae stage grouper are susceptible to in...

    Authors: Yi-Da Wang, Shin-Jie Huang, Hong-Nong Chou, Wen-Liang Liao, Hong-Yi Gong and Jyh-Yih Chen
    Citation: BMC Genomics 2014 15:1102
    Content type: Research article Published on:

  11. Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. ...

    Authors: Mathieu Almeida, Agnès Hébert, Anne-Laure Abraham, Simon Rasmussen, Christophe Monnet, Nicolas Pons, Céline Delbès, Valentin Loux, Jean-Michel Batto, Pierre Leonard, Sean Kennedy, Stanislas Dusko Ehrlich, Mihai Pop, Marie-Christine Montel, Françoise Irlinger and Pierre Renault
    Citation: BMC Genomics 2014 15:1101
    Content type: Research article Published on:

  12. Proteins are composed of one or more amino acid chains and exhibit several structure levels. IDPs (intrinsically disordered proteins) represent a class of proteins that do not fold into any particular conforma...

    Authors: Patrícia de Cássia Ruy, Raul Torrieri, Juliano Simões Toledo, Viviane de Souza Alves, Angela Kaysel Cruz and Jeronimo Conceição Ruiz
    Citation: BMC Genomics 2014 15:1100
    Content type: Research article Published on:

  14. 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:

  15. The Hawaiian honeycreepers are an avian adaptive radiation containing many endangered and extinct species. They display a dramatic range of phenotypic variation and are a model system for studies of evolution,...

    Authors: Taylor Callicrate, Rebecca Dikow, James W Thomas, James C Mullikin, Erich D Jarvis and Robert C Fleischer
    Citation: BMC Genomics 2014 15:1098
    Content type: Research article Published on:

  16. 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:

  17. Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Never...

    Authors: Erin D Scully, Scott M Geib, John E Carlson, Ming Tien, Duane McKenna and Kelli Hoover
    Citation: BMC Genomics 2014 15:1096
    Content type: Research article Published on:

  18. 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:

  19. Cabbage Fusarium wilt is a major disease worldwide that can cause severe yield loss in cabbage (Brassica olerecea). Although markers linked to the resistance gene FOC1 have been identified, no candidate gene for ...

    Authors: Honghao Lv, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Qingbiao Wang, Yumei Liu, Mu Zhuang, Yuhong Yang, Bingyan Xie, Bo Liu, Jisheng Liu, Jungen Kang and Xiaowu Wang
    Citation: BMC Genomics 2014 15:1094
    Content type: Research article Published on:

  20. 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: Eglė Kudirkienė, Ragnhild J Bager, Timothy J Johnson and Anders M Bojesen
    Citation: BMC Genomics 2014 15:1093
    Content type: Research article Published on:

  22. 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

  23. Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obviou...

    Authors: Basir Shariat, Narjes Sadat Movahedi, Hamidreza Chitsaz and Christina Boucher
    Citation: BMC Genomics 2014 15(Suppl 10):S9
    Content type: Research Published on:

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

  24. Identification of genomic patterns in tumors is an important problem, which would enable the community to understand and extend effective therapies across the current tissue-based tumor boundaries. With this i...

    Authors: Alexandros Manolakos, Idoia Ochoa, Kartik Venkat, Andrea J Goldsmith and Olivier Gevaert
    Citation: BMC Genomics 2014 15(Suppl 10):S8
    Content type: Research Published on:

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

  25. With the advances in high-throughput DNA sequencing technologies, RNA-seq has rapidly emerged as a powerful tool for the quantitative analysis of gene expression and transcript variant discovery. In comparativ...

    Authors: Bingqing Lin, Li-Feng Zhang and Xin Chen
    Citation: BMC Genomics 2014 15(Suppl 10):S7
    Content type: Research Published on:

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

  26. Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, c...

    Authors: Ryota Mori, Michiaki Hamada and Kiyoshi Asai
    Citation: BMC Genomics 2014 15(Suppl 10):S6
    Content type: Research Published on:

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

  27. High-throughput RNA sequencing (RNA-Seq) enables quantification and identification of transcripts at single-base resolution. Recently, longer sequence reads become available thanks to the development of new ty...

    Authors: Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata and Masao Nagasaki
    Citation: BMC Genomics 2014 15(Suppl 10):S5
    Content type: Research Published on:

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

  28. Recent studies have underscored the role of enhancers in defining cell type-specific transcriptomes. Cell type-specific enhancers are bound by combinations of shared and cell type-specific transcription factor...

    Authors: Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki and Daron M Standley
    Citation: BMC Genomics 2014 15(Suppl 10):S4
    Content type: Research Published on:

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

  29. 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

  30. MicroRNAs are short RNA molecules that post-transcriptionally regulate gene expression. Today, microRNA target prediction remains challenging since very few have been experimentally validated and sequence-base...

    Authors: Daniel Tabas-Madrid, Ander Muniategui, Ignacio Sánchez-Caballero, Dannys Jorge Martínez-Herrera, Carlos Oscar S Sorzano, Angel Rubio and Alberto Pascual-Montano
    Citation: BMC Genomics 2014 15(Suppl 10):S2
    Content type: Research Published on:

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

  31. 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

  33. 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, Måns Magnusson, Rolf Wibom, Rolf H Zetterström, Valtteri Wirta…
    Citation: BMC Genomics 2014 15:1090
    Content type: Methodology article Published on:

  34. 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

  35. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

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BMC Genomics

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