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  2. Antibody responses against Anopheles salivary proteins can indicate individual exposure to bites of malaria vectors. The extent to which these salivary proteins are species-specific is not entirely resolved. Thus...

    Authors: Albin Fontaine, Thierry Fusaï, Sébastien Briolant, Sylvain Buffet, Claude Villard, Emilie Baudelet, Mathieu Pophillat, Samuel Granjeaud, Christophe Rogier and Lionel Almeras
    Citation: BMC Genomics 2012 13:614
    Content type: Research article Published on:

  3. Transitions from cross- to self-fertilization are associated with increased genetic drift rendering weakly selected mutations effectively neutral. The effect of drift is predicted to reduce selective constrain...

    Authors: Rob W Ness, Mathieu Siol and Spencer C H Barrett
    Citation: BMC Genomics 2012 13:611
    Content type: Research article Published on:

  4. Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Popula...

    Authors: Alexandre Kuhn, Azad Kumar, Alexandra Beilina, Allissa Dillman, Mark R Cookson and Andrew B Singleton
    Citation: BMC Genomics 2012 13:610
    Content type: Research article Published on:

  5. The genomes of three major mosquito vectors of human diseases, Anopheles gambiae, Aedes aegypti, and Culex pipiens quinquefasciatus, have been previously sequenced. C. p. quinquefasciatus has the largest number o...

    Authors: Liangzhen Yan, Pengcheng Yang, Feng Jiang, Na Cui, Enbo Ma, Chuanling Qiao and Feng Cui
    Citation: BMC Genomics 2012 13:609
    Content type: Research article Published on:

  6. Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and it...

    Authors: Yufang Guo, Sameer Khanal, Shunxue Tang, John E Bowers, Adam F Heesacker, Nelly Khalilian, Ervin D Nagy, Dong Zhang, Christopher A Taylor, H Thomas Stalker, Peggy Ozias-Akins and Steven J Knapp
    Citation: BMC Genomics 2012 13:608
    Content type: Research article Published on:

  7. Empirical evaluations of sexually dimorphic expression of genes on the mammalian X-chromosome are needed to understand the evolutionary forces and the gene-regulatory mechanisms controlling this chromosome. We...

    Authors: Björn Reinius, Martin M Johansson, Katarzyna J Radomska, Edward H Morrow, Gaurav K Pandey, Chandrasekhar Kanduri, Rickard Sandberg, Robert W Williams and Elena Jazin
    Citation: BMC Genomics 2012 13:607
    Content type: Research article Published on:

  8. Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are requ...

    Authors: Jared E Decker, Daniel A Vasco, Stephanie D McKay, Matthew C McClure, Megan M Rolf, JaeWoo Kim, Sally L Northcutt, Stewart Bauck, Brent W Woodward, Robert D Schnabel and Jeremy F Taylor
    Citation: BMC Genomics 2012 13:606
    Content type: Research article Published on:

  9. Oomycetes are fungal-like microorganisms evolutionary distinct from true fungi, belonging to the Stramenopile lineage and comprising major plant pathogens. Both oomycetes and fungi express proteins able to int...

    Authors: Mathieu Larroque, Roland Barriot, Arnaud Bottin, Annick Barre, Pierre Rougé, Bernard Dumas and Elodie Gaulin
    Citation: BMC Genomics 2012 13:605
    Content type: Research article Published on:

  10. Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm ...

    Authors: Kazumi Matsubara, Shigehiro Kuraku, Hiroshi Tarui, Osamu Nishimura, Chizuko Nishida, Kiyokazu Agata, Yoshinori Kumazawa and Yoichi Matsuda
    Citation: BMC Genomics 2012 13:604
    Content type: Research article Published on:

  11. Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Pir...

    Authors: Lowell S Kappmeyer, Mathangi Thiagarajan, David R Herndon, Joshua D Ramsay, Elisabet Caler, Appolinaire Djikeng, Joseph J Gillespie, Audrey OT Lau, Eric H Roalson, Joana C Silva, Marta G Silva, Carlos E Suarez, Massaro W Ueti, Vishvanath M Nene, Robert H Mealey, Donald P Knowles…
    Citation: BMC Genomics 2012 13:603
    Content type: Research article Published on:

  12. Faba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection ...

    Authors: Tao Yang, Shi-ying Bao, Rebecca Ford, Teng-jiao Jia, Jian-ping Guan, Yu-hua He, Xue-lian Sun, Jun-ye Jiang, Jun-jie Hao, Xiao-yan Zhang and Xu-xiao Zong
    Citation: BMC Genomics 2012 13:602
    Content type: Research article Published on:

  13. Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evalu...

    Authors: Cristina Roig, Ana Fita, Gabino Ríos, John P Hammond, Fernando Nuez and Belén Picó
    Citation: BMC Genomics 2012 13:601
    Content type: Research article Published on:

  14. The yak (Bos grunniens) is a long-haired bovine that lives at high altitudes and is an important source of milk, meat, fiber and fuel. The recent sequencing, assembly and annotation of its genome are expected to ...

    Authors: Quanjun Hu, Tao Ma, Kun Wang, Ting Xu, Jianquan Liu and Qiang Qiu
    Citation: BMC Genomics 2012 13:600
    Content type: Database Published on:

  15. Pine wilt disease (PWD), caused by the pinewood nematode (PWN; Bursaphelenchus xylophilus), damages and kills pine trees and is causing serious economic damage worldwide. Although the ecological mechanism of infe...

    Authors: Carla S Santos, Miguel Pinheiro, Ana I Silva, Conceição Egas and Marta W Vasconcelos
    Citation: BMC Genomics 2012 13:599
    Content type: Research article Published on:

  16. Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cau...

    Authors: Settu Sridhar, Animesh Sharma, Heidi Kongshaug, Frank Nilsen and Inge Jonassen
    Citation: BMC Genomics 2012 13:598
    Content type: Research article Published on:

  17. Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes,...

    Authors: Ajay Kumar, Kristin Simons, Muhammad J Iqbal, Monika Michalak de Jiménez, Filippo M Bassi, Farhad Ghavami, Omar Al-Azzam, Thomas Drader, Yi Wang, Ming-Cheng Luo, Yong Q Gu, Anne Denton, Gerard R Lazo, Steven S Xu, Jan Dvorak, Penny MA Kianian…
    Citation: BMC Genomics 2012 13:597
    Content type: Research article Published on:

  18. Malignant cells in tumours of B-cell origin account for 0.1% to 98% of the total cell content, depending on disease entity. Recently, gene expression profiles (GEPs) of B-cell lymphomas based on microarray tec...

    Authors: Maria Bro Kloster, Anders Ellern Bilgrau, Maria Rodrigo-Domingo, Kim Steve Bergkvist, Alexander Schmitz, Mads Sønderkær, Julie Støve Bødker, Steffen Falgreen, Mette Nyegaard, Hans Erik Johnsen, Kåre Lehmann Nielsen, Karen Dybkaer and Martin Bøgsted
    Citation: BMC Genomics 2012 13:596
    Content type: Methodology article Published on:

  19. Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript in...

    Authors: Shikai Liu, Yu Zhang, Zunchun Zhou, Geoff Waldbieser, Fanyue Sun, Jianguo Lu, Jiaren Zhang, Yanliang Jiang, Hao Zhang, Xiuli Wang, KV Rajendran, Lester Khoo, Huseyin Kucuktas, Eric Peatman and Zhanjiang Liu
    Citation: BMC Genomics 2012 13:595
    Content type: Research article Published on:

  20. Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected one NET and the corresponding lymph node and ...

    Authors: Beate Rinner, Birgit Gallè, Slave Trajanoski, Carina Fischer, Martina Hatz, Theresa Maierhofer, Gabriele Michelitsch, Farid Moinfar, Ingeborg Stelzer, Roswitha Pfragner and Christian Guelly
    Citation: BMC Genomics 2012 13:594
    Content type: Research article Published on:

  21. Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Ci...

    Authors: Patrick Ollitrault, Javier Terol, Chunxian Chen, Claire T Federici, Samia Lotfy, Isabelle Hippolyte, Frédérique Ollitrault, Aurélie Bérard, Aurélie Chauveau, Jose Cuenca, Gilles Costantino, Yildiz Kacar, Lisa Mu, Andres Garcia-Lor, Yann Froelicher, Pablo Aleza…
    Citation: BMC Genomics 2012 13:593
    Content type: Research article Published on:

  22. We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To faci...

    Authors: Arimantas Lionikas, Caroline Meharg, Jonathan MJ Derry, Aivaras Ratkevicius, Andrew M Carroll, David J Vandenbergh and David A Blizard
    Citation: BMC Genomics 2012 13:592
    Content type: Research article Published on:

  23. Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, ...

    Authors: Gro Nilsen, Knut Liestøl, Peter Van Loo, Hans Kristian Moen Vollan, Marianne B Eide, Oscar M Rueda, Suet-Feung Chin, Roslin Russell, Lars O Baumbusch, Carlos Caldas, Anne-Lise Børresen-Dale and Ole Christian Lingjærde
    Citation: BMC Genomics 2012 13:591
    Content type: Software Published on:

  24. We previously localized a quantitative trait locus (QTL) on bovine chromosome 6 affecting milk production traits to a 1.5-Mb region between BMS483 and MNB-209 via genome scanning followed by fine mapping.

    Authors: Qing Xu, Gui Mei, Dongxiao Sun, Qin Zhang, Yuan Zhang, Cengceng Yin, Huiyong Chen, Xiangdong Ding and Jianfeng Liu
    Citation: BMC Genomics 2012 13:590
    Content type: Research article Published on:

  25. A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely...

    Authors: Jun Chen, Severin Uebbing, Niclas Gyllenstrand, Ulf Lagercrantz, Martin Lascoux and Thomas Källman
    Citation: BMC Genomics 2012 13:589
    Content type: Research article Published on:

  26. Understanding how organisms adapt to high-elevation environments at a genome scale provides novel insights into the process of adaptive evolution. Previous studies have mainly focused on endothermic organisms,...

    Authors: Weizhao Yang, Yin Qi, Ke Bi and Jinzhong Fu
    Citation: BMC Genomics 2012 13:588
    Content type: Research article Published on:

  27. The primary plant cell wall is a complex mixture of polysaccharides and proteins encasing living plant cells. Among these polysaccharides, cellulose is the most abundant and useful biopolymer present on earth....

    Authors: Roy Kirsch, Natalie Wielsch, Heiko Vogel, Aleš Svatoš, David G Heckel and Yannick Pauchet
    Citation: BMC Genomics 2012 13:587
    Content type: Research article Published on:

  28. The hypothalamic-pituitary-adrenal (HPA) axis is essential to control physiological stress responses in mammals. Its dysfunction is related to several mental disorders, including anxiety and depression. The ai...

    Authors: Mariya Gonik, Elisabeth Frank, Melanie S Keßler, Darina Czamara, Mirjam Bunck, Yi-Chun Yen, Benno Pütz, Florian Holsboer, Thomas Bettecken, Rainer Landgraf, Bertram Müller-Myhsok, Chadi Touma and Ludwig Czibere
    Citation: BMC Genomics 2012 13:579
    Content type: Research article Published on:

  29. Porphyromonas gingivalis is a Gram-negative anaerobic bacterium associated with periodontal disease onset and progression. Genetic tools for the manipulation of bacterial genomes allow for in-depth mechanistic st...

    Authors: Brian A Klein, Elizabeth L Tenorio, David W Lazinski, Andrew Camilli, Margaret J Duncan and Linden T Hu
    Citation: BMC Genomics 2012 13:578
    Content type: Research article Published on:

  30. Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the numbe...

    Authors: Rolf S Kaas, Carsten Friis, David W Ussery and Frank M Aarestrup
    Citation: BMC Genomics 2012 13:577
    Content type: Research article Published on:

  31. Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst ...

    Authors: István Molnár, David Lopez, Jennifer H Wisecaver, Timothy P Devarenne, Taylor L Weiss, Matteo Pellegrini and Jeremiah D Hackett
    Citation: BMC Genomics 2012 13:576
    Content type: Research article Published on:

  32. Lichens are symbiotic organisms that have a remarkable ability to survive in some of the most extreme terrestrial climates on earth. Lichens can endure frequent desiccation and wetting cycles and are able to s...

    Authors: Sini Junttila and Stephen Rudd
    Citation: BMC Genomics 2012 13:575
    Content type: Research article Published on:

  33. The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions fro...

    Authors: Beata Werne Solnestam, Henrik Stranneheim, Jimmie Hällman, Max Käller, Emma Lundberg, Joakim Lundeberg and Pelin Akan
    Citation: BMC Genomics 2012 13:574
    Content type: Research article Published on:

  34. Wine aroma results from the combination of numerous volatile compounds, some produced by yeast and others produced in the grapes and further metabolized by yeast. However, little is known about the consequence...

    Authors: Damien Steyer, Chloe Ambroset, Christian Brion, Patricia Claudel, Pierre Delobel, Isabelle Sanchez, Claude Erny, Bruno Blondin, Francis Karst and Jean-Luc Legras
    Citation: BMC Genomics 2012 13:573
    Content type: Research article Published on:

  35. A proper balance between different T helper (Th) cell subsets is necessary for normal functioning of the adaptive immune system. Revealing key genes and pathways driving the differentiation to distinct Th cell...

    Authors: Tarmo Äijö, Sanna M Edelman, Tapio Lönnberg, Antti Larjo, Henna Kallionpää, Soile Tuomela, Emilia Engström, Riitta Lahesmaa and Harri Lähdesmäki
    Citation: BMC Genomics 2012 13:572
    Content type: Research article Published on:

  36. Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, ...

    Authors: Hamid Ashrafi, Theresa Hill, Kevin Stoffel, Alexander Kozik, JiQiang Yao, Sebastian Reyes Chin-Wo and Allen Van Deynze
    Citation: BMC Genomics 2012 13:571
    Content type: Research article Published on:

  37. The significant mortality associated with breast cancer (BCa) suggests a need to improve current research strategies to identify new genes that predispose women to breast cancer. Differential allele-specific e...

    Authors: Chuan Gao, Karthik Devarajan, Yan Zhou, Carolyn M Slater, Mary B Daly and Xiaowei Chen
    Citation: BMC Genomics 2012 13:570
    Content type: Research article Published on:

  38. We applied comparative phylogenomics (whole genome comparisons of microbes using DNA microarrays combined with Bayesian-based phylogenies) to investigate S. pneumoniae isolates from West Africa, with the aim of p...

    Authors: Eric S Donkor, Richard A Stabler, Jason Hinds, Richard A Adegbola, Martin Antonio and Brendan W Wren
    Citation: BMC Genomics 2012 13:569
    Content type: Research article Published on:

  39. Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. M...

    Authors: Xuehui Li, Ananta Acharya, Andrew D Farmer, John A Crow, Arvind K Bharti, Robin S Kramer, Yanling Wei, Yuanhong Han, Jiqing Gou, Gregory D May, Maria J Monteros and E Charles Brummer
    Citation: BMC Genomics 2012 13:568
    Content type: Research article Published on:

  40. The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the toxR mutant TW30 by massively parallel cDN...

    Authors: Stefano Campanaro, Fabio De Pascale, Andrea Telatin, Riccardo Schiavon, Douglas H Bartlett and Giorgio Valle
    Citation: BMC Genomics 2012 13:567
    Content type: Research article Published on:

  41. About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macro...

    Authors: Yunji Wang, Tianyi Yang, Yonggang Ma, Ganesh V Halade, Jianqiu Zhang, Merry L Lindsey and Yu-Fang Jin
    Citation: BMC Genomics 2012 13(Suppl 6):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  42. DNA methylation occurs in the context of a CpG dinucleotide. It is an important epigenetic modification, which can be inherited through cell division. The two major types of methylation include hypomethylation...

    Authors: Lin Zhang, Jia Meng, Hui Liu and Yufei Huang
    Citation: BMC Genomics 2012 13(Suppl 6):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  43. Until recently, sequencing has primarily been carried out in large genome centers which have invested heavily in developing the computational infrastructure that enables genomic sequence analysis. The recent a...

    Authors: Uday S Evani, Danny Challis, Jin Yu, Andrew R Jackson, Sameer Paithankar, Matthew N Bainbridge, Adinarayana Jakkamsetti, Peter Pham, Cristian Coarfa, Aleksandar Milosavljevic and Fuli Yu
    Citation: BMC Genomics 2012 13(Suppl 6):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  44. Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storag...

    Authors: Benjamin AT Rodriguez, David Frankhouser, Mark Murphy, Michael Trimarchi, Hok-Hei Tam, John Curfman, Rita Huang, Michael WY Chan, Hung-Cheng Lai, Deval Parikh, Bryan Ball, Sebastian Schwind, William Blum, Guido Marcucci, Pearlly Yan and Ralf Bundschuh
    Citation: BMC Genomics 2012 13(Suppl 6):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  45. Metastatic breast cancer is a leading cause of cancer-related deaths in women worldwide. DNA microarray has become an important tool to help identify biomarker genes for improving the prognosis of breast cance...

    Authors: Md Jamiul Jahid and Jianhua Ruan
    Citation: BMC Genomics 2012 13(Suppl 6):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  46. A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approa...

    Authors: Fábio FR Vicente, Fabrício M Lopes, Ronaldo F Hashimoto and Roberto M Cesar Jr
    Citation: BMC Genomics 2012 13(Suppl 6):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  47. Estrogens control multiple functions of hormone-responsive breast cancer cells. They regulate diverse physiological processes in various tissues through genomic and non-genomic mechanisms that result in activa...

    Authors: Heng-Yi Wu, Pengyue Zheng, Guanglong Jiang, Yunlong Liu, Kenneth P Nephew, Tim HM Huang and Lang Li
    Citation: BMC Genomics 2012 13(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  48. Cancer and other gene related diseases are usually caused by a failure in the signaling pathway between genes and cells. These failures can occur in different areas of the gene regulatory network, but can be a...

    Authors: Pey-Chang Kent Lin and Sunil P Khatri
    Citation: BMC Genomics 2012 13(Suppl 6):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

  49. Regulation of gene expression has been shown to involve not only the binding of transcription factor at target gene promoters but also the characterization of histone around which DNA is wrapped around. Some h...

    Authors: Cenny Taslim, Shili Lin, Kun Huang and Tim Hui-Ming Huang
    Citation: BMC Genomics 2012 13(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 6

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