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  1. Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aqu...

    Authors: Yanliang Jiang, Xiaoyu Gao, Shikai Liu, Yu Zhang, Hong Liu, Fanyue Sun, Lisui Bao, Geoff Waldbieser and Zhanjiang Liu
    Citation: BMC Genomics 2013 14:780
    Content type: Research article Published on:

  2. Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of bio...

    Authors: Jianhua Zheng, Liguo Liu, Jin Wang and Qi Jin
    Citation: BMC Genomics 2013 14:777
    Content type: Research article Published on:

  3. Streptococcus agalactiae, also referred to as Group B Streptococcus (GBS), is a frequent resident of the rectovaginal tract in humans, and a major cause of neonatal infection. In addition, S. agalactiae is a know...

    Authors: Guangjin Liu, Wei Zhang and Chengping Lu
    Citation: BMC Genomics 2013 14:775
    Content type: Research article Published on:

  4. DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wid...

    Authors: Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen and Matteo Pellegrini
    Citation: BMC Genomics 2013 14:774
    Content type: Software Published on:

  5. Transcription activator-like effector nucleases (TALENs) have emerged as a tool for enabling targeted gene editing and disruption in difficult systems, such as human pluripotent stem cells (hPSCs). The modular...

    Authors: Stefan Frank, Boris V Skryabin and Boris Greber
    Citation: BMC Genomics 2013 14:773
    Content type: Methodology article Published on:

  7. Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengt...

    Authors: Murat A Abdurashitov, Danila A Gonchar, Valery A Chernukhin, Victor N Tomilov, Julia E Tomilova, Natalia G Schostak, Olga G Zatsepina, Elena S Zelentsova, Michael B Evgen’ev and Sergey Kh Degtyarev
    Citation: BMC Genomics 2013 14:771
    Content type: Research article Published on:

  8. Porphyromonas gingivalis is a gram-negative bacterium that causes destructive chronic periodontitis. In addition, this bacterium is also involved in the development of cardiovascular disease. The aim of this stud...

    Authors: Boxi Zhang, Ali Ateia Elmabsout, Hazem Khalaf, Vladimir T Basic, Kartheyaene Jayaprakash, Robert Kruse, Torbjörn Bengtsson and Allan Sirsjö
    Citation: BMC Genomics 2013 14:770
    Content type: Research article Published on:

  9. Essential genes are indispensable for the survival of living entities. They are the cornerstones of synthetic biology, and are potential candidate targets for antimicrobial and vaccine design.

    Authors: Yuan-Nong Ye, Zhi-Gang Hua, Jian Huang, Nini Rao and Feng-Biao Guo
    Citation: BMC Genomics 2013 14:769
    Content type: Database Published on:

  10. Formation of compression (CW) and opposite wood (OW) in branches and bent trunks is an adaptive feature of conifer trees in response to various displacement forces, such as gravity, wind, snow and artificial b...

    Authors: Xinguo Li, Xiaohui Yang and Harry X Wu
    Citation: BMC Genomics 2013 14:768
    Content type: Research article Published on:

  11. Honeybee venom is a complicated defensive toxin that has a wide range of pharmacologically active compounds. Some of these compounds are useful for human therapeutics. There are two major forms of honeybee ven...

    Authors: Rongli Li, Lan Zhang, Yu Fang, Bin Han, Xiaoshan Lu, Tiane Zhou, Mao Feng and Jianke Li
    Citation: BMC Genomics 2013 14:766
    Content type: Research article Published on:

  13. The transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloe...

    Authors: James A Anstead, Steven D Hartson and Gary A Thompson
    Citation: BMC Genomics 2013 14:764
    Content type: Research article Published on:

  14. Loss of virulence is a phenotypic adaptation commonly seen in prokaryotic and eukaryotic pathogens. This mechanism is not well studied, especially in organisms with multiple host and life cycle stages such as Bab...

    Authors: Monica J Pedroni, Kerry S Sondgeroth, Gina M Gallego-Lopez, Ignacio Echaide and Audrey OT Lau
    Citation: BMC Genomics 2013 14:763
    Content type: Research article Published on:

  15. Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In thi...

    Authors: Armelle Darrasse, Sébastien Carrère, Valérie Barbe, Tristan Boureau, Mario L Arrieta-Ortiz, Sophie Bonneau, Martial Briand, Chrystelle Brin, Stéphane Cociancich, Karine Durand, Stéphanie Fouteau, Lionel Gagnevin, Fabien Guérin, Endrick Guy, Arnaud Indiana, Ralf Koebnik…
    Citation: BMC Genomics 2013 14:761
    Content type: Research article Published on:

  16. Plant calcium (Ca2+) signals are involved in a wide array of intracellular signalling pathways following pathogen invasion. Ca2+-binding sensory proteins such as Ca2+-dependent protein kinases (CPKs) have been pr...

    Authors: Chidananda Nagamangala Kanchiswamy, Tapan Kumar Mohanta, Andrea Capuzzo, Andrea Occhipinti, Francesca Verrillo, Massimo E Maffei and Mickael Malnoy
    Citation: BMC Genomics 2013 14:760
    Content type: Research article Published on:

  17. When the filamentous cyanobacterium Anabaena variabilis grows aerobically without combined nitrogen, some vegetative cells differentiate into N2-fixing heterocysts, while the other vegetative cells perform photos...

    Authors: Jeong-Jin Park, Sigal Lechno-Yossef, Coleman Peter Wolk and Claire Vieille
    Citation: BMC Genomics 2013 14:759
    Content type: Research article Published on:

  18. Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a...

    Authors: Michael Schupp, Fang Chen, Erika R Briggs, Shilpa Rao, Helmut J Pelzmann, Ariane R Pessentheiner, Juliane G Bogner-Strauss, Mitchell A Lazar, Don Baldwin and Andreas Prokesch
    Citation: BMC Genomics 2013 14:758
    Content type: Research article Published on:

  19. Our recent study showed the global physiological function of the differentially expressed genes of prostate cancer in Chinese patients was different from that of other non-Chinese populations. microRNA are est...

    Authors: Hui-chan He, Zhao-dong Han, Qi-shan Dai, Xiao-hui Ling, Xin Fu, Zhuo-yuan Lin, Ye-han Deng, Guo-qiang Qin, Chao Cai, Jia-hong Chen, Fu-neng Jiang, Xingyin Liu and Wei-de Zhong
    Citation: BMC Genomics 2013 14:757
    Content type: Research article Published on:

  20. Comparative genomics approaches help to shed light on evolutionary processes that shape differentiation between lineages. The nine-spined stickleback (Pungitius pungitius) is a closely related species of the ecol...

    Authors: Baocheng Guo, Frédéric JJ Chain, Erich Bornberg-Bauer, Erica H Leder and Juha Merilä
    Citation: BMC Genomics 2013 14:756
    Content type: Research article Published on:

  21. The genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average...

    Authors: Maria Costantini, Fernando Alvarez-Valin, Susan Costantini, Rosalia Cammarano and Giorgio Bernardi
    Citation: BMC Genomics 2013 14:755
    Content type: Research article Published on:

  22. Blunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important role...

    Authors: Shaokui Yi, Ze-Xia Gao, Honghao Zhao, Cong Zeng, Wei Luo, Boxiang Chen and Wei-Min Wang
    Citation: BMC Genomics 2013 14:754
    Content type: Research article Published on:

  23. A hexaploidization event over 125 Mya underlies the evolutionary lineage of the majority of flowering plants, including very many species of agricultural importance. Half of these belong to the rosid subgroupi...

    Authors: Chunfang Zheng, Eric Chen, Victor A Albert, Eric Lyons and David Sankoff
    Citation: BMC Genomics 2013 14(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  24. The identification of proteins based on analysis of tandem mass spectrometry (MS/MS) data is a valuable tool that is not fully realized because of the difficulty in carrying out automated analysis of large num...

    Authors: Jason Gallia, Katelyn Lavrich, Anna Tan-Wilson and Patrick H Madden
    Citation: BMC Genomics 2013 14(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  25. Flow cytometry has been widely used for the diagnosis of various hematopoietic diseases. Although there have been advances in the number of biomarkers that can be analyzed simultaneously and technologies that ...

    Authors: Ming-Chih Shih, Shou-Hsuan Stephen Huang, Rachel Donohue, Chung-Che Chang and Youli Zu
    Citation: BMC Genomics 2013 14(Suppl 7):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  27. AtPAP2 is a purple acid phosphatase that is targeted to both chloroplasts and mitochondria. Over-expression (OE) lines of AtPAP2 grew faster, produced more seeds, and contained higher leaf sucrose and glucose ...

    Authors: Feng Sun, Chao Liang, James Whelan, Jun Yang, Peng Zhang and Boon Leong Lim
    Citation: BMC Genomics 2013 14:752
    Content type: Research article Published on:

  28. Diapause is programmed developmental arrest coupled with the depression of metabolic activity and the enhancement of stress resistance. Pupal diapause is induced by environmental signals and is prepared during...

    Authors: Qi Zhang, Yu-Xuan Lu and Wei-Hua Xu
    Citation: BMC Genomics 2013 14:751
    Content type: Research article Published on:

  29. Peach [Prunus persica (L.) Batsch] is an economically important fruit crop that has become a genetic-genomic model for all Prunus species in the family Rosaceae. A doubled haploid reference genome sequence length...

    Authors: Jonathan Fresnedo-Ramírez, Pedro J Martínez-García, Dan E Parfitt, Carlos H Crisosto and Thomas M Gradziel
    Citation: BMC Genomics 2013 14:750
    Content type: Research article Published on:

  30. Two sibling members of the Anopheles gambiae species complex display notable differences in female blood meal preferences. An. gambiae s.s. has a well-documented preference for feeding upon human hosts, whereas A...

    Authors: David C Rinker, Xiaofan Zhou, Ronald Jason Pitts, Antonis Rokas and Laurence J Zwiebel
    Citation: BMC Genomics 2013 14:749
    Content type: Research article Published on:

  31. The Himalayan or Indian Mayapple (Podophyllum hexandrum Royle) produces podophyllotoxin, which is used in the production of semisynthetic anticancer drugs. High throughput transcriptome sequences or genomic seque...

    Authors: Dipto Bhattacharyya, Ragini Sinha, Saptarshi Hazra, Riddhi Datta and Sharmila Chattopadhyay
    Citation: BMC Genomics 2013 14:748
    Content type: Research article Published on:

  32. The relationship between fish health and muscle growth is critical for continued expansion of the aquaculture industry. The effect of immune stimulation on the expression of genes related to the energy balance...

    Authors: Nicholas J Pooley, Luca Tacchi, Christopher J Secombes and Samuel AM Martin
    Citation: BMC Genomics 2013 14:747
    Content type: Research article Published on:

  34. Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, wh...

    Authors: Pavel S Novichkov, Alexey E Kazakov, Dmitry A Ravcheev, Semen A Leyn, Galina Y Kovaleva, Roman A Sutormin, Marat D Kazanov, William Riehl, Adam P Arkin, Inna Dubchak and Dmitry A Rodionov
    Citation: BMC Genomics 2013 14:745
    Content type: Database Published on:

  35. In the model eukaryote, Saccharomyces cerevisiae, previous experiments have identified those genes that exert the most significant control over cell growth rate. These genes are termed HFC for high flux control. ...

    Authors: Annette A Alcasabas, Michaela de Clare, Pınar Pir and Stephen G Oliver
    Citation: BMC Genomics 2013 14:744
    Content type: Research article Published on:

  36. Infectious bronchitis virus (IBV), a prototype of the Coronaviridae family, is an economically important causative agent of infectious bronchitis in chickens and causes an acute and highly contagious upper respir...

    Authors: Feng Cong, Xiaoli Liu, Zongxi Han, Yuhao Shao, Xiangang Kong and Shengwang Liu
    Citation: BMC Genomics 2013 14:743
    Content type: Research article Published on:

  37. Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonans in the cell wall; their activity is regulated in part by pectin methylesterase inhibitors (PMEIs). PME activity may result...

    Authors: David Pinzón-Latorre and Michael K Deyholos
    Citation: BMC Genomics 2013 14:742
    Content type: Research article Published on:

  38. The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors su...

    Authors: Ricardo B Leite, Massimo Milan, Alessandro Coppe, Stefania Bortoluzzi, António dos Anjos, Richard Reinhardt, Carlos Saavedra, Tomaso Patarnello, M Leonor Cancela and Luca Bargelloni
    Citation: BMC Genomics 2013 14:741
    Content type: Research article Published on:

  39. Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a ...

    Authors: Ashley E Culver-Cochran and Brian P Chadwick
    Citation: BMC Genomics 2013 14:740
    Content type: Research article Published on:

  40. Dengue is the most prevalent arboviral disease world-wide and its primary vector is the mosquito Aedes aegypti. The current lack of commercially-available vaccines makes control of vector populations the only eff...

    Authors: Mariangela Bonizzoni, Monica Britton, Osvaldo Marinotti, William Augustine Dunn, Joseph Fass and Anthony A James
    Citation: BMC Genomics 2013 14:739
    Content type: Research article Published on:

  41. The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants...

    Authors: Lifen Gao, Yinghao Cao, Zhihui Xia, Guanghuai Jiang, Guozhen Liu, Weixiong Zhang and Wenxue Zhai
    Citation: BMC Genomics 2013 14:738
    Content type: Research article Published on:

  42. The interaction between insect pests and their host plants is a never-ending race of evolutionary adaption. Plants have developed an armament against insect herbivore attacks, and attackers continuously learn ...

    Authors: Birgit Kersten, Andrea Ghirardo, Jörg-Peter Schnitzler, Basem Kanawati, Philippe Schmitt-Kopplin, Matthias Fladung and Hilke Schroeder
    Citation: BMC Genomics 2013 14:737
    Content type: Research article Published on:

  43. Hepatocellular carcinoma (HCC) in young subjects is rare but more devastating. We hypothesize that genes and etiological pathways are unique to young HCC (yHCC; ≤40 years old at diagnosis) patients. We therefo...

    Authors: Hsei-Wei Wang, Tsung-Han Hsieh, SSu-Yi Huang, Gar-Yang Chau, Chien-Yi Tung, Chien-Wei Su and Jaw-Ching Wu
    Citation: BMC Genomics 2013 14:736
    Content type: Research article Published on:

  44. The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Fu...

    Authors: Patricia Severino, Liliane Santana Oliveira, Natalia Torres, Flavia Maziero Andreghetto, Maria de Fatima Guarizo Klingbeil, Raquel Moyses, Victor Wünsch-Filho, Fabio Daumas Nunes, Monica Beatriz Mathor, Alexandre Rossi Paschoal and Alan Mitchell Durham
    Citation: BMC Genomics 2013 14:735
    Content type: Research article Published on:

  45. Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Diant...

    Authors: Masafumi Yagi, Toshiya Yamamoto, Sachiko Isobe, Hideki Hirakawa, Satoshi Tabata, Koji Tanase, Hiroyasu Yamaguchi and Takashi Onozaki
    Citation: BMC Genomics 2013 14:734
    Content type: Research article Published on:

  46. Hypodontia, the congenital absence of one or a few teeth is one of the most common alterations of the human dentition. Familial hypodontia is caused by mutations in PAX9, Msx1 and Axin2 genes. Limited numbers of ...

    Authors: Eren Isman, Suleyman Nergiz, Hasan Acar and Zafer Sari
    Citation: BMC Genomics 2013 14:733
    Content type: Research article Published on:

  47. 4-Hydroxy-tamoxifen (4OHT) triggers Cre-mediated K-Ras removal in [H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert] fibroblasts, generating growth-arrested “Rasless” MEFs which are able to recover their proliferative ...

    Authors: Sami S Azrak, Alicia Ginel-Picardo, Matthias Drosten, Mariano Barbacid and Eugenio Santos
    Citation: BMC Genomics 2013 14:731
    Content type: Research article Published on:

  48. It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms ...

    Authors: Jipei Yue, Guiling Sun, Xiangyang Hu and Jinling Huang
    Citation: BMC Genomics 2013 14:729
    Content type: Research article Published on:

  49. Current immunological bioinformatic approaches focus on the prediction of allele-specific epitopes capable of triggering immunogenic activity. The prediction of major histocompatibility complex (MHC) class I e...

    Authors: Anderson R Santos, Vanessa Bastos Pereira, Eudes Barbosa, Jan Baumbach, Josch Pauling, Richard Röttger, Meritxell Zurita Turk, Artur Silva, Anderson Miyoshi and Vasco Azevedo
    Citation: BMC Genomics 2013 14(Suppl 6):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  50. The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associate...

    Authors: Flávia A Miyazaki, Gabriela DA Guardia, Ricardo ZN Vêncio and Cléver RG de Farias
    Citation: BMC Genomics 2013 14(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

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