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  1. Studies suggest that not only is insecticide resistance conferred via multiple gene up-regulation, but it is mediated through the interaction of regulatory factors. However, no regulatory factors in insecticid...

    Authors: Ming Li, William R Reid, Lee Zhang, Jeffery G Scott, Xiwu Gao, Michael Kristensen and Nannan Liu
    Citation: BMC Genomics 2013 14:803
    Content type: Research article Published on:

  2. Plant microRNAs are short (~21 nt) non-coding molecules that regulate gene expression by targeting the mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cel...

    Authors: Anna Lukasik, Halina Pietrykowska, Leszek Paczek, Zofia Szweykowska-Kulinska and Piotr Zielenkiewicz
    Citation: BMC Genomics 2013 14:801
    Content type: Research article Published on:

  3. Chronic infections can profoundly affect the physiology, behavior, fitness and longevity of individuals, and may alter the organization and demography of social groups. Nosema apis and Nosema ceranae are two micr...

    Authors: Holly L Holt, Katherine A Aronstein and Christina M Grozinger
    Citation: BMC Genomics 2013 14:799
    Content type: Research article Published on:

  4. Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic...

    Authors: Philipp Widmann, Antonio Reverter, Marina R S Fortes, Rosemarie Weikard, Karsten Suhre, Harald Hammon, Elke Albrecht and Christa Kuehn
    Citation: BMC Genomics 2013 14:798
    Content type: Research article Published on:

  6. Planarians can regenerate entire animals from a small fragment of the body. The regenerating fragment is able to create new tissues and remodel existing tissues to form a complete animal. Thus different fragme...

    Authors: Damian Kao, Daniel Felix and Aziz Aboobaker
    Citation: BMC Genomics 2013 14:797
    Content type: Research article Published on:

  7. Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contex...

    Authors: Shan Zhong, Xin He and Ziv Bar-Joseph
    Citation: BMC Genomics 2013 14:796
    Content type: Methodology article Published on:

  8. Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disor...

    Authors: Katherine A Bolton, Jason P Ross, Desma M Grice, Nikola A Bowden, Elizabeth G Holliday, Kelly A Avery-Kiejda and Rodney J Scott
    Citation: BMC Genomics 2013 14:795
    Content type: Research article Published on:

  9. Evidence in yeast indicates that gene expression is correlated with recombination activity and double-strand break (DSB) formation in some hotspots. Studies of nucleosome occupancy in yeast and mice also sugge...

    Authors: Andrew B Adrian and Josep M Comeron
    Citation: BMC Genomics 2013 14:794
    Content type: Research article Published on:

  10. Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme envir...

    Authors: Yang Ping Lee, Federico M Giorgi, Marc Lohse, Kotryna Kvederaviciute, Sven Klages, Björn Usadel, Irute Meskiene, Richard Reinhardt and Dirk K Hincha
    Citation: BMC Genomics 2013 14:793
    Content type: Research article Published on:

  11. Gene copy number variation plays a large role in the evolution of genomes. In Rattus norvegicus and other rodent species, the Y-chromosome has accumulated multiple copies of Sry loci. These copy number variations...

    Authors: Jeremy W Prokop, Adam C Underwood, Monte E Turner, Nic Miller, Dawn Pietrzak, Sarah Scott, Chris Smith and Amy Milsted
    Citation: BMC Genomics 2013 14:792
    Content type: Research article Published on:

  12. One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow ...

    Authors: Mathilde Causse, Nelly Desplat, Laura Pascual, Marie-Christine Le Paslier, Christopher Sauvage, Guillaume Bauchet, Aurélie Bérard, Rémi Bounon, Maria Tchoumakov, Dominique Brunel and Jean-Paul Bouchet
    Citation: BMC Genomics 2013 14:791
    Content type: Research article Published on:

  13. Advances in DNA sequencing and proteomics have facilitated quantitative comparisons of snake venom composition. Most studies have employed one approach or the other. Here, both Illumina cDNA sequencing and LC/...

    Authors: Steven D Aird, Yutaka Watanabe, Alejandro Villar-Briones, Michael C Roy, Kouki Terada and Alexander S Mikheyev
    Citation: BMC Genomics 2013 14:790
    Content type: Research article Published on:

  14. Deep RNA sequencing (RNAseq) has opened a new horizon for understanding global gene expression. The functional annotation of non-model mammalian genomes including bovines is still poor compared to that of huma...

    Authors: Rosemarie Weikard, Frieder Hadlich and Christa Kuehn
    Citation: BMC Genomics 2013 14:789
    Content type: Research article Published on:

  15. The intestinal microbiota is a complex and diverse ecosystem that plays a significant role in maintaining the health and well-being of the mammalian host. During the last decade focus has increased on the impo...

    Authors: Marie Louise Hermann-Bank, Kerstin Skovgaard, Anders Stockmarr, Niels Larsen and Lars Mølbak
    Citation: BMC Genomics 2013 14:788
    Content type: Methodology article Published on:

  16. Thalassosaline waters produced by the concentration of seawater are widespread and common extreme aquatic habitats. Their salinity varies from that of sea water (ca. 3.5%) to saturation for NaCl (ca. 37%). Obviou...

    Authors: Mario López-Pérez, Rohit Ghai, Maria Jose Leon, Ángel Rodríguez-Olmos, José Luis Copa-Patiño, Juan Soliveri, Cristina Sanchez-Porro, Antonio Ventosa and Francisco Rodriguez-Valera
    Citation: BMC Genomics 2013 14:787
    Content type: Research article Published on:

  17. In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutati...

    Authors: Miwa Kuroyanagi, Takashi Katayama, Tadashi Imai, Yoshihisa Yamamoto, Shin-ichi Chisada, Yasutoshi Yoshiura, Tomokazu Ushijima, Tomonao Matsushita, Masashi Fujita, Aoi Nozawa, Yuzuru Suzuki, Kiyoshi Kikuchi and Hiroyuki Okamoto
    Citation: BMC Genomics 2013 14:786
    Content type: Methodology article Published on:

  19. Obesity, excess fat tissue in the body, can underlie a variety of medical complaints including heart disease, stroke and cancer. The pig is an excellent model organism for the study of various human disorders,...

    Authors: Katie E Fowler, Ricardo Pong-Wong, Julien Bauer, Emily J Clemente, Christopher P Reitter, Nabeel A Affara, Stephen Waite, Grant A Walling and Darren K Griffin
    Citation: BMC Genomics 2013 14:784
    Content type: Research article Published on:

  20. Ribosomes are essential ribonucleoprotein complexes that are engaged in translation and thus indispensable for growth. Arabidopsis thaliana ribosomes are composed of 80 distinct ribosomal proteins (RPs), each of ...

    Authors: Jinyan Wang, Ping Lan, Huimin Gao, Lu Zheng, Wenfeng Li and Wolfgang Schmidt
    Citation: BMC Genomics 2013 14:783
    Content type: Research article Published on:

  21. Changes in the copy number of DNA sequences are one of the main mechanisms generating genome variability in eukaryotes. These changes are often related to phenotypic effects such as genetic disorders or novel ...

    Authors: Víctor M González, Núria Aventín, Emilio Centeno and Pere Puigdomènech
    Citation: BMC Genomics 2013 14:782
    Content type: Research article Published on:

  22. Many fruits, including watermelon, are proficient in carotenoid accumulation during ripening. While most genes encoding steps in the carotenoid biosynthetic pathway have been cloned, few transcriptional regula...

    Authors: Stefania Grassi, Gabriella Piro, Je Min Lee, Yi Zheng, Zhangjun Fei, Giuseppe Dalessandro, James J Giovannoni and Marcello S Lenucci
    Citation: BMC Genomics 2013 14:781
    Content type: Research article Published on:

  23. 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:

  24. Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explai...

    Authors: Goran Bozinovic, Tim L Sit, Richard Di Giulio, Lauren F Wills and Marjorie F Oleksiak
    Citation: BMC Genomics 2013 14:779
    Content type: Research article Published on:

  25. Early application of second-generation sequencing technologies to transcript quantitation (RNA-seq) has hinted at a vast mammalian transcriptome, including transcripts from nearly all known genes, which might ...

    Authors: Traver Hart, H Kiyomi Komori, Sarah LaMere, Katie Podshivalova and Daniel R Salomon
    Citation: BMC Genomics 2013 14:778
    Content type: Methodology article Published on:

  26. 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:

  27. The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and...

    Authors: Joseph I Said, Zhongxu Lin, Xianlong Zhang, Mingzhou Song and Jinfa Zhang
    Citation: BMC Genomics 2013 14:776
    Content type: Research article Published on:

  28. 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:

  29. 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:

  30. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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

  49. 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

  50. 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

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