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  1. Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, thi...

    Authors: Isabelle Pieretti, Monique Royer, Valérie Barbe, Sébastien Carrere, Ralf Koebnik, Arnaud Couloux, Armelle Darrasse, Jérôme Gouzy, Marie-Agnès Jacques, Emmanuelle Lauber, Charles Manceau, Sophie Mangenot, Stéphane Poussier, Béatrice Segurens, Boris Szurek, Valérie Verdier…
    Citation: BMC Genomics 2012 13:658
    Content type: Research article Published on:

  2. Roses (Rosa sp.), which belong to the family Rosaceae, are the most economically important ornamental plants—making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs ...

    Authors: Jungeun Kim, June Hyun Park, Chan Ju Lim, Jae Yun Lim, Jee-Youn Ryu, Bong-Woo Lee, Jae-Pil Choi, Woong Bom Kim, Ha Yeon Lee, Yourim Choi, Donghyun Kim, Cheol-Goo Hur, Sukweon Kim, Yoo-Sun Noh, Chanseok Shin and Suk-Yoon Kwon
    Citation: BMC Genomics 2012 13:657
    Content type: Research article Published on:

  3. To study the role of microRNA (miRNA) in the regulation of Chinese hamster ovary (CHO) cell growth, qPCR, microarray and quantitative LC-MS/MS analysis were utilised for simultaneous expression profiling of mi...

    Authors: Colin Clarke, Michael Henry, Padraig Doolan, Shane Kelly, Sinead Aherne, Noelia Sanchez, Paul Kelly, Paula Kinsella, Laura Breen, Stephen F Madden, Lin Zhang, Mark Leonard, Martin Clynes, Paula Meleady and Niall Barron
    Citation: BMC Genomics 2012 13:656
    Content type: Research article Published on:

  4. MicroRNAs are small non-coding RNAs that regulate gene expression at the post-transcriptional level. While they have been implicated in various diseases, the profile changes in allergen inhalation challenge ar...

    Authors: Masatsugu Yamamoto, Amrit Singh, Jian Ruan, Gail M Gauvreau, Paul M O'Byrne, Christopher R Carlsten, J Mark FitzGerald, Louis-Philippe Boulet and Scott J Tebbutt
    Citation: BMC Genomics 2012 13:655
    Content type: Research article Published on:

  6. The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop imp...

    Authors: Mei Yang, Yanni Han, Robert VanBuren, Ray Ming, Liming Xu, Yuepeng Han and Yanling Liu
    Citation: BMC Genomics 2012 13:653
    Content type: Research article Published on:

  7. Elucidating the genomic basis of adaptation and speciation is a major challenge in natural systems with large quantities of environmental and phenotypic data, mostly because of the scarcity of genomic resource...

    Authors: Joanna L Kelley, Courtney N Passow, Martin Plath, Lenin Arias Rodriguez, Muh-Ching Yee and Michael Tobler
    Citation: BMC Genomics 2012 13:652
    Content type: Database Published on:

  8. Grouper (Epinephelus spp) is an economically important fish species worldwide. However, viral pathogens such as nervous necrosis virus (NNV) have been causing severe infections in the fish, resulting in great los...

    Authors: Ming-Wei Lu, Fang-Huar Ngou, Yung-Mei Chao, Yu-Shen Lai, Nai-Yu Chen, Fan-Yao Lee and Pinwen P Chiou
    Citation: BMC Genomics 2012 13:651
    Content type: Research article Published on:

  9. Bananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value. However, banana production has been devastated by fungal infestations caused by Fusariu...

    Authors: Zhuo Wang, JianBin Zhang, CaiHong Jia, JuHua Liu, YanQiang Li, XiaoMin Yin, BiYu Xu and ZhiQiang Jin
    Citation: BMC Genomics 2012 13:650
    Content type: Research article Published on:

  10. Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify t...

    Authors: Florencia del Viso, Dipankan Bhattacharya, Yong Kong, Michael J Gilchrist and Mustafa K Khokha
    Citation: BMC Genomics 2012 13:649
    Content type: Methodology article Published on:

  11. Chinese fir (Cunninghamia lanceolata) is an important timber species that accounts for 20–30% of the total commercial timber production in China. However, the available genomic information of Chinese fir is limit...

    Authors: Hua-Hong Huang, Li-Li Xu, Zai-Kang Tong, Er-Pei Lin, Qing-Po Liu, Long-Jun Cheng and Mu-Yuan Zhu
    Citation: BMC Genomics 2012 13:648
    Content type: Research article Published on:

  12. Cryptosporidium parvum is a globally distributed zoonotic parasite and an important opportunistic pathogen in immunocompromised patients. Little is known on the metabolic dynamics of the parasite, and study is ha...

    Authors: Haili Zhang, Fengguang Guo, Huaijun Zhou and Guan Zhu
    Citation: BMC Genomics 2012 13:647
    Content type: Research article Published on:

  13. Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant...

    Authors: Gregor D Gilfillan, Timothy Hughes, Ying Sheng, Hanne S Hjorthaug, Tobias Straub, Kristina Gervin, Jennifer R Harris, Dag E Undlien and Robert Lyle
    Citation: BMC Genomics 2012 13:645
    Content type: Methodology article Published on:

  14. We have previously shown that lipophilic components (LPC) of the brown seaweed Ascophyllum nodosum (ANE) improved freezing tolerance in Arabidopsis thaliana. However, the mechanism(s) of this induced freezing str...

    Authors: Prasanth Nair, Saveetha Kandasamy, Junzeng Zhang, Xiuhong Ji, Chris Kirby, Bernhard Benkel, Mark D Hodges, Alan T Critchley, David Hiltz and Balakrishnan Prithiviraj
    Citation: BMC Genomics 2012 13:643
    Content type: Research article Published on:

  15. Leaf rust, caused by the biotrophic fungal pathogen Puccinia hordei, is one of the most important foliar disease of barley (Hordeum vulgare) and represents a serious threat in many production regions of the world...

    Authors: Letizia Bernardo, Bhakti Prinsi, Alfredo Simone Negri, Luigi Cattivelli, Luca Espen and Giampiero Valè
    Citation: BMC Genomics 2012 13:642
    Content type: Research article Published on:

  17. Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and ...

    Authors: Arwa Shahin, Martijn van Kaauwen, Danny Esselink, Joachim W Bargsten, Jaap M van Tuyl, Richard GF Visser and Paul Arens
    Citation: BMC Genomics 2012 13:640
    Content type: Research article Published on:

  18. Heat shock transcriptional factors (Hsfs) play a crucial role in plant responses to biotic and abiotic stress conditions and in plant growth and development. Apple (Malus domestica Borkh) is an economically impor...

    Authors: Filomena Giorno, Gea Guerriero, Sanja Baric and Celestina Mariani
    Citation: BMC Genomics 2012 13:639
    Content type: Research article Published on:

  19. For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes ...

    Authors: Annick Dubois, Sebastien Carrere, Olivier Raymond, Benjamin Pouvreau, Ludovic Cottret, Aymeric Roccia, Jean-Paul Onesto, Soulaiman Sakr, Rossitza Atanassova, Sylvie Baudino, Fabrice Foucher, Manuel Le Bris, Jérôme Gouzy and Mohammed Bendahmane
    Citation: BMC Genomics 2012 13:638
    Content type: Research article Published on:

  20. Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, ...

    Authors: Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard Macknight and John A McCallum
    Citation: BMC Genomics 2012 13:637
    Content type: Research article Published on:

  21. The predominant model for regulation of gene expression through DNA methylation is an inverse association in which increased methylation results in decreased gene expression levels. However, recent studies sug...

    Authors: Kristel R van Eijk, Simone de Jong, Marco PM Boks, Terry Langeveld, Fabrice Colas, Jan H Veldink, Carolien GF de Kovel, Esther Janson, Eric Strengman, Peter Langfelder, René S Kahn, Leonard H van den Berg, Steve Horvath and Roel A Ophoff
    Citation: BMC Genomics 2012 13:636
    Content type: Research article Published on:

  22. LEF1/TCF transcription factors and their activator β-catenin are effectors of the canonical Wnt pathway. Although Wnt/β-catenin signaling has been implicated in neurodegenerative and psychiatric disorders, its...

    Authors: Marta B Wisniewska, Andrzej Nagalski, Michal Dabrowski, Katarzyna Misztal and Jacek Kuznicki
    Citation: BMC Genomics 2012 13:635
    Content type: Research article Published on:

  23. The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function an...

    Authors: Bhanu Rekapalli, Kristin Wuichet, Gregory D Peterson and Igor B Zhulin
    Citation: BMC Genomics 2012 13:634
    Content type: Research article Published on:

  24. The regulation and function of mammalian RNAs has been increasingly appreciated to operate via RNA-protein interactions. With the recent discovery of thousands of novel human RNA molecules by high-throughput R...

    Authors: Zurab Siprashvili, Dan E Webster, Markus Kretz, Danielle Johnston, John L Rinn, Howard Y Chang and Paul A Khavari
    Citation: BMC Genomics 2012 13:633
    Content type: Methodology article Published on:

  25. The Gram-negative bacterium Chlamydia pneumoniae (Cpn) is the leading intracellular human pathogen responsible for respiratory infections such as pneumonia and bronchitis. Basic and applied research in pathogen b...

    Authors: Christina J Maier, Richard H Maier, Dezso Peter Virok, Matthias Maass, Helmut Hintner, Johann W Bauer and Kamil Önder
    Citation: BMC Genomics 2012 13:632
    Content type: Research article Published on:

  26. The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified i...

    Authors: Feng-Jiau Lin, Yuan Liu, Zhongli Sha, Ling Ming Tsang, Ka Hou Chu, Tin-Yam Chan, Ruiyu Liu and Zhaoxia Cui
    Citation: BMC Genomics 2012 13:631
    Content type: Research article Published on:

  27. Applying supervised learning/classification techniques to epigenomic data may reveal properties that differentiate histone modifications. Previous analyses sought to classify nucleosomes containing histone H2A...

    Authors: Daniel Capurso, Hao Xiong and Mark R Segal
    Citation: BMC Genomics 2012 13:630
    Content type: Research article Published on:

  30. The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the l...

    Authors: Jennifer T Go, Sarah E Belisle, Nicolas Tchitchek, Terrence M Tumpey, Wenjun Ma, Juergen A Richt, David Safronetz, Heinz Feldmann and Michael G Katze
    Citation: BMC Genomics 2012 13:627
    Content type: Research article Published on:

  31. Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that mo...

    Authors: Iker Irisarri, Diego San Mauro, Federico Abascal, Annemarie Ohler, Miguel Vences and Rafael Zardoya
    Citation: BMC Genomics 2012 13:626
    Content type: Research article Published on:

  32. Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant ...

    Authors: Pieter De Maayer, Wai-Yin Chan, Jochen Blom, Stephanus N Venter, Brion Duffy, Theo H M Smits and Teresa A Coutinho
    Citation: BMC Genomics 2012 13:625
    Content type: Research article Published on:

  33. The availability of a high-density SNP genotyping chip and a reference genome sequence of the pig (Sus scrofa) enabled the construction of a high-density linkage map. A high-density linkage map is an essential to...

    Authors: Flavie Tortereau, Bertrand Servin, Laurent Frantz, Hendrik-Jan Megens, Denis Milan, Gary Rohrer, Ralph Wiedmann, Jonathan Beever, Alan L Archibald, Lawrence B Schook and Martien AM Groenen
    Citation: BMC Genomics 2012 13:586
    Content type: Research article Published on:

  34. The release of the porcine genome sequence offers great perspectives for Pig genetics and genomics, and more generally will contribute to the understanding of mammalian genome biology and evolution. The proces...

    Authors: Bertrand Servin, Thomas Faraut, Nathalie Iannuccelli, Diana Zelenika and Denis Milan
    Citation: BMC Genomics 2012 13:585
    Content type: Research article Published on:

  35. Insects and animals can recognize surrounding environments by detecting thousands of chemical odorants. Olfaction is a complicated process that begins in the olfactory epithelium with the specific binding of v...

    Authors: Dinh Truong Nguyen, Kyooyeol Lee, Hojun Choi, Min-kyeung Choi, Minh Thong Le, Ning Song, Jin-Hoi Kim, Han Geuk Seo, Jae-Wook Oh, Kyungtae Lee, Tae-Hun Kim and Chankyu Park
    Citation: BMC Genomics 2012 13:584
    Content type: Research article Published on:

  36. Carcass fatness is an important trait in most pig breeding programs. Following market requests, breeding plans for fresh pork consumption are usually designed to reduce carcass fat content and increase lean me...

    Authors: Luca Fontanesi, Giuseppina Schiavo, Giuliano Galimberti, Daniela Giovanna Calò, Emilio Scotti, Pier Luigi Martelli, Luca Buttazzoni, Rita Casadio and Vincenzo Russo
    Citation: BMC Genomics 2012 13:583
    Content type: Research article Published on:

  37. The pig is a biomedical model to study human and livestock traits. Many of these traits are controlled by neuropeptides that result from the cleavage of prohormones by prohormone convertases. Only 45 prohormon...

    Authors: Kenneth I Porter, Bruce R Southey, Jonathan V Sweedler and Sandra L Rodriguez-Zas
    Citation: BMC Genomics 2012 13:582
    Content type: Research article Published on:

  38. Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of ent...

    Authors: Hirohide Uenishi, Takeya Morozumi, Daisuke Toki, Tomoko Eguchi-Ogawa, Lauretta A Rund and Lawrence B Schook
    Citation: BMC Genomics 2012 13:581
    Content type: Research article Published on:

  39. The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incen...

    Authors: Samantha Wilkinson, Alan L Archibald, Chris S Haley, Hendrik-Jan Megens, Richard PMA Crooijmans, Martien AM Groenen, Pamela Wiener and Rob Ogden
    Citation: BMC Genomics 2012 13:580
    Content type: Research article Published on:

  40. Fuzzless-lintless cotton mutants are considered to be the ideal material to understand the molecular mechanisms involved in fibre cell development. Although there are few reports on transcriptome and proteome ...

    Authors: Kethireddy Venkata Padmalatha, Deepak P Patil, Krishan Kumar, Gurusamy Dhandapani, Mogilicherla Kanakachari, Mullapudi LV Phanindra, Saravanan Kumar, T C Mohan, Neha Jain, Arkalgud H Prakash, Hiremath Vamadevaiah, Ishwarappa S Katageri, Sadhu Leelavathi, Malireddy K Reddy, Polumetla Ananda Kumar and Vanga Siva Reddy
    Citation: BMC Genomics 2012 13:624
    Content type: Research article Published on:

  41. To balance the demand for uptake of essential elements with their potential toxicity living cells have complex regulatory mechanisms. Here, we describe a genome-wide screen to identify genes that impact the el...

    Authors: Danni Yu, John M C Danku, Ivan Baxter, Sungjin Kim, Olena K Vatamaniuk, Olga Vitek, Mourad Ouzzani and David E Salt
    Citation: BMC Genomics 2012 13:623
    Content type: Research article Published on:

  42. Mitochondrial (mt) genomes vary considerably in size, structure and gene content. The mt genomes of the phylum Apicomplexa, which includes important human pathogens such as the malaria parasite Plasmodium, also s...

    Authors: Kenji Hikosaka, Naotoshi Tsuji, Yoh-ichi Watanabe, Hiroe Kishine, Toshihiro Horii, Ikuo Igarashi, Kiyoshi Kita and Kazuyuki Tanabe
    Citation: BMC Genomics 2012 13:622
    Content type: Research article Published on:

  43. Leishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of resistance against the currently available anti-leishmanial drugs, there is a growing need for ...

    Authors: V S Gowri, Indira Ghosh, Amit Sharma and Rentala Madhubala
    Citation: BMC Genomics 2012 13:621
    Content type: Research article Published on:

  45. Triple-negative breast cancers (BC) represent a heterogeneous subtype of BCs, generally associated with an aggressive clinical course and where targeted therapies are currently limited. Target validation studi...

    Authors: Anita Grigoriadis, Alan Mackay, Elodie Noel, Pei Jun Wu, Rachel Natrajan, Jessica Frankum, Jorge S Reis-Filho and Andrew Tutt
    Citation: BMC Genomics 2012 13:619
    Content type: Research article Published on:

  46. Targeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and s...

    Authors: A Eliot Shearer, Michael S Hildebrand, Harini Ravi, Swati Joshi, Angelica C Guiffre, Barbara Novak, Scott Happe, Emily M LeProust and Richard JH Smith
    Citation: BMC Genomics 2012 13:618
    Content type: Research article Published on:

  47. Schistosoma mansoni is one of the causative agents of schistosomiasis, a neglected tropical disease that affects about 237 million people worldwide. Despite recent efforts, we still lack a general understanding o...

    Authors: Larissa Lopes Silva, Marina Marcet-Houben, Laila Alves Nahum, Adhemar Zerlotini, Toni Gabaldón and Guilherme Oliveira
    Citation: BMC Genomics 2012 13:617
    Content type: Research article Published on:

  48. The development of complex responses to hypoxia has played a key role in the evolution of mammals, as inadequate response to this condition is frequently associated with cardiovascular diseases, developmental ...

    Authors: Assaf Malik, Abraham Korol, Mathias Weber, Thomas Hankeln, Aaron Avivi and Mark Band
    Citation: BMC Genomics 2012 13:615
    Content type: Research article Published on:

  49. Cyanobacteria can form massive toxic blooms in fresh and brackish bodies of water and are frequently responsible for the poisoning of animals and pose a health risk for humans. Anabaena is a genus of filamentous ...

    Authors: Hao Wang, Kaarina Sivonen, Leo Rouhiainen, David P Fewer, Christina Lyra, Anne Rantala-Ylinen, Johanna Vestola, Jouni Jokela, Kaisa Rantasärkkä, Zhijie Li and Bin Liu
    Citation: BMC Genomics 2012 13:613
    Content type: Research article Published on:

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BMC Genomics

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