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  1. Replication-independent endogenous double-strand breaks (RIND-EDSBs) occur in both humans and yeast in the absence of inductive agents and DNA replication. In human cells, RIND-EDSBs are hypermethylated, prefe...

    Authors: Monnat Pongpanich, Maturada Patchsung, Jirapan Thongsroy and Apiwat Mutirangura
    Citation: BMC Genomics 2014 15:750
    Content type: Research article Published on:

  2. Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant s...

    Authors: Johan Bengtsson-Palme, Magnus Alm Rosenblad, Mikael Molin and Anders Blomberg
    Citation: BMC Genomics 2014 15:749
    Content type: Research article Published on:

  4. The Orchidaceae is one of the largest families in the plant kingdom and orchid mycorrhizae (OM) are indispensable in the life cycle of all orchids under natural conditions. In spite of this, little is known co...

    Authors: Xiaolan Zhao, Jianxia Zhang, Chunli Chen, Jingze Yang, Haiyan Zhu, Min Liu and Fubing Lv
    Citation: BMC Genomics 2014 15:747
    Content type: Research article Published on:

  5. Saponins are mainly amphipathic glycosides that posses many biological activities and confer potential health benefits to humans. Inspite of its medicinal attributes most of the triterpenes and enzymes involve...

    Authors: Swati Upadhyay, Ujjal J Phukan, Sonal Mishra and Rakesh Kumar Shukla
    Citation: BMC Genomics 2014 15:746
    Content type: Research article Published on:

  6. Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 20...

    Authors: Bryan D Merrill, Julianne H Grose, Donald P Breakwell and Sandra H Burnett
    Citation: BMC Genomics 2014 15:745
    Content type: Research article Published on:

  7. Apis mellifera and Apis cerana are two sibling species of Apidae. Apis cerana is adept at collecting sporadic nectar in mountain and forest region and exhibits stiffer hardiness and acarid resistance as a result ...

    Authors: Hao Liu, Zi-Long Wang, Liu-Qing Tian, Qiu-Hong Qin, Xiao-Bo Wu, Wei-Yu Yan and Zhi-Jiang Zeng
    Citation: BMC Genomics 2014 15:744
    Content type: Research article Published on:

  8. Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly under...

    Authors: Chunhua Wei, Hanhui Kuang, Feng Li and Jiongjiong Chen
    Citation: BMC Genomics 2014 15:743
    Content type: Research article Published on:

  9. Shigella flexneri is the major cause of bacillary dysentery in the developing countries. The lipopolysaccharide (LPS) O-antigen of S. flexneri plays an important role in its pathogenesis and also divides S. flexn...

    Authors: Richa Jakhetia, Aruna Marri, Jonas Ståhle, Göran Widmalm and Naresh K Verma
    Citation: BMC Genomics 2014 15:742
    Content type: Research article Published on:

  10. Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding ...

    Authors: Nina Opitz, Anja Paschold, Caroline Marcon, Waqas Ahmed Malik, Christa Lanz, Hans-Peter Piepho and Frank Hochholdinger
    Citation: BMC Genomics 2014 15:741
    Content type: Research article Published on:

  11. Advances in genotyping technology, such as genotyping by sequencing (GBS), are making genomic prediction more attractive to reduce breeding cycle times and costs associated with phenotyping. Genomic prediction...

    Authors: Diego Jarquín, Kyle Kocak, Luis Posadas, Katie Hyma, Joseph Jedlicka, George Graef and Aaron Lorenz
    Citation: BMC Genomics 2014 15:740
    Content type: Research article Published on:

  13. Halyomorpha halys (Stål) (Insecta:Hemiptera;Pentatomidae), commonly known as the Brown Marmorated Stink Bug (BMSB), is an invasive pest of the mid-Atlantic region of the United States, causing economically import...

    Authors: Panagiotis Ioannidis, Yong Lu, Nikhil Kumar, Todd Creasy, Sean Daugherty, Marcus C Chibucos, Joshua Orvis, Amol Shetty, Sandra Ott, Melissa Flowers, Naomi Sengamalay, Luke J Tallon, Leslie Pick and Julie C Dunning Hotopp
    Citation: BMC Genomics 2014 15:738
    Content type: Research article Published on:

  14. Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genom...

    Authors: Egon A Ozer, Jonathan P Allen and Alan R Hauser
    Citation: BMC Genomics 2014 15:737
    Content type: Research article Published on:

  15. MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development st...

    Authors: Yun Bai, Zhuangzhi Zhang, Lei Jin, Hui Kang, Yongqiang Zhu, Lu Zhang, Xia Li, Fengshou Ma, Li Zhao, Baoxin Shi, Jun Li, Donald P McManus, Wenbao Zhang and Shengyue Wang
    Citation: BMC Genomics 2014 15:736
    Content type: Research article Published on:

  17. Intracellular zinc concentration needs to be maintained within strict limits due to its toxicity at high levels, and this is achieved by a finely regulated balance between uptake and efflux. Many bacteria use ...

    Authors: Ricardo Ruiz Mazzon, Vânia Santos Braz, José Freire da Silva Neto and Marilis do Valle Marques
    Citation: BMC Genomics 2014 15:734
    Content type: Research article Published on:

  19. Using whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequencing, however is predominantly used for variant detection and infrequently utilised for dete...

    Authors: Kaushalya C Amarasinghe, Jason Li, Sally M Hunter, Georgina L Ryland, Prue A Cowin, Ian G Campbell and Saman K Halgamuge
    Citation: BMC Genomics 2014 15:732
    Content type: Methodology article Published on:

  20. Shrimp culture is a fast growing aquaculture sector, but in recent years there has been a shift away from tiger shrimp Penaeus monodon to other species. This is largely due to the susceptibility of P. monodon to ...

    Authors: Nicholas A Robinson, Gopalapillay Gopikrishna, Matthew Baranski, Vinaya Kumar Katneni, Mudagandur S Shekhar, Jayakani Shanmugakarthik, Sarangapani Jothivel, Chavali Gopal, Pitchaiyappan Ravichandran, Thomas Gitterle and Alphis G Ponniah
    Citation: BMC Genomics 2014 15:731
    Content type: Research article Published on:

  21. The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully ...

    Authors: Lourdes Peña-Castillo, Ryan G Mercer, Anastasia Gurinovich, Stephen J Callister, Aaron T Wright, Alexander B Westbye, J Thomas Beatty and Andrew S Lang
    Citation: BMC Genomics 2014 15:730
    Content type: Research article Published on:

  22. The mesencephalic dopaminergic (mDA) cell system is composed of two major groups of projecting cells in the Substantia Nigra (SN) (A9 neurons) and the Ventral Tegmental Area (VTA) (A10 cells). Selective degene...

    Authors: Alice Grison, Silvia Zucchelli, Alice Urzì, Ilaria Zamparo, Dejan Lazarevic, Giovanni Pascarella, Paola Roncaglia, Alejandro Giorgetti, Paula Garcia-Esparcia, Christina Vlachouli, Roberto Simone, Francesca Persichetti, Alistair RR Forrest, Yoshihide Hayashizaki, Paolo Carloni, Isidro Ferrer…
    Citation: BMC Genomics 2014 15:729
    Content type: Research article Published on:

  23. The advent of low cost next generation sequencing has made it possible to sequence a large number of dairy and beef bulls which can be used as a reference for imputation of whole genome sequence data. The aim ...

    Authors: Rasmus Froberg Brøndum, Bernt Guldbrandtsen, Goutam Sahana, Mogens Sandø Lund and Guosheng Su
    Citation: BMC Genomics 2014 15:728
    Content type: Research article Published on:

  24. The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversi...

    Authors: Gabriel Luz Wallau, Pierre Capy, Elgion Loreto and Aurélie Hua-Van
    Citation: BMC Genomics 2014 15:727
    Content type: Research article Published on:

  25. Large scale transcript analysis of human glomerular microvascular endothelial cells (HGMEC) has never been accomplished. We designed this study to define the transcriptome of HGMEC and facilitate a better char...

    Authors: Guerkan Sengoelge, Wolfgang Winnicki, Anne Kupczok, Arndt von Haeseler, Michael Schuster, Walter Pfaller, Paul Jennings, Ansgar Weltermann, Sophia Blake and Gere Sunder-Plassmann
    Citation: BMC Genomics 2014 15:725
    Content type: Research article Published on:

  26. Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understand...

    Authors: Sally Yoo and Mark C Bieda
    Citation: BMC Genomics 2014 15:724
    Content type: Research article Published on:

  27. Most biological nitrogen fixation is catalyzed by the molybdenum nitrogenase. This enzyme is a complex which contains the MoFe protein encoded by nifDK and the Fe protein encoded by nifH. In addition to nifHDK, n...

    Authors: Xinxin Li, Zhiping Deng, Zhanzhi Liu, Yongliang Yan, Tianshu Wang, Jianbo Xie, Min Lin, Qi Cheng and Sanfeng Chen
    Citation: BMC Genomics 2014 15:723
    Content type: Research article Published on:

  28. Since the first fungal genome sequences became available, investigators have been employing comparative genomics to understand how fungi have evolved to occupy diverse ecological niches. The secretome, i.e. th...

    Authors: Jorrit-Jan Krijger, Michael R Thon, Holger B Deising and Stefan GR Wirsel
    Citation: BMC Genomics 2014 15:722
    Content type: Research article Published on:

  29. The forces underlying genome architecture and organization are still only poorly understood in detail. Overlapping genes (genes partially or entirely overlapping) represent a genomic feature that is shared wid...

    Authors: Maxime Huvet and Michael PH Stumpf
    Citation: BMC Genomics 2014 15:721
    Content type: Research article Published on:

  30. Molecular characterization of highly diverse gene families can be time consuming, expensive, and difficult, especially when considering the potential for relatively large numbers of paralogs and/or pseudogenes...

    Authors: Peter A Larsen, Amy M Heilman and Anne D Yoder
    Citation: BMC Genomics 2014 15:720
    Content type: Research article Published on:

  31. Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insight...

    Authors: Christopher G Jacob, John C Tan, Becky A Miller, Asako Tan, Shannon Takala-Harrison, Michael T Ferdig and Christopher V Plowe
    Citation: BMC Genomics 2014 15:719
    Content type: Methodology article Published on:

  32. The complex societies of ants and other social insects rely on sophisticated chemical communication. Two families of small soluble proteins, the odorant binding and chemosensory proteins (OBPs and CSPs), are b...

    Authors: Sean K McKenzie, Peter R Oxley and Daniel JC Kronauer
    Citation: BMC Genomics 2014 15:718
    Content type: Research article Published on:

  34. The serious feeding- and microbiota-associated intestinal disease, necrotizing enterocolitis (NEC), occurs mainly in infants born prematurely (5-10% of all newborns) and most frequently after formula-feeding. ...

    Authors: Fei Gao, Juyong Zhang, Pingping Jiang, Desheng Gong, Jun-Wen Wang, Yudong Xia, Mette Viberg Østergaard, Jun Wang and Per Torp Sangild
    Citation: BMC Genomics 2014 15:716
    Content type: Research article Published on:

  35. Schistosoma japonicum is a pathogen of the phylum Platyhelminthes that causes zoonotic schistosomiasis in China and Southeast Asian countries where a lack of efficient measures has hampered disease control. The d...

    Authors: Xianyu Piao, Nan Hou, Pengfei Cai, Shuai Liu, Chuang Wu and Qijun Chen
    Citation: BMC Genomics 2014 15:715
    Content type: Research article Published on:

  36. The olive fly, Bactrocera oleae, is the most devastating pest of cultivated olives. Its control has been traditionally based on insecticides, mainly organophosphates and pyrethroids. In recent years, the naturaly...

    Authors: Efthimia Sagri, Martin Reczko, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Nikolaos E Zygouridis, Klelia D Salpea, Frank G Zalom, Jiannis Ragoussis and Kostas D Mathiopoulos
    Citation: BMC Genomics 2014 15:714
    Content type: Research article Published on:

  37. There is a need to characterize genomes of the foodborne pathogen, Salmonella enterica serovar Enteritidis (SE) and identify genetic information that could be ultimately deployed for differentiating strains of th...

    Authors: Dele Ogunremi, John Devenish, Kingsley Amoako, Hilary Kelly, Andrée Ann Dupras, Sebastien Belanger and Lin Ru Wang
    Citation: BMC Genomics 2014 15:713
    Content type: Research article Published on:

  38. Legumes form root nodules to house nitrogen fixing bacteria of the rhizobium family. The rhizobia are located intracellularly in the symbiotic nodule cells. In the legume Medicago truncatula these cells produce h...

    Authors: Ibtissem Guefrachi, Marianna Nagymihaly, Catalina I Pislariu, Willem Van de Velde, Pascal Ratet, Mohamed Mars, Michael K Udvardi, Eva Kondorosi, Peter Mergaert and Benoît Alunni
    Citation: BMC Genomics 2014 15:712
    Content type: Research article Published on:

  39. SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic tran...

    Authors: Sebastian F Vencken, Praveen Sethupathy, Gordon Blackshields, Cathy Spillane, Salah Elbaruni, Orla Sheils, Michael F Gallagher and John J O’Leary
    Citation: BMC Genomics 2014 15:711
    Content type: Research article Published on:

  40. Fusarium verticillioides causes ear rot in maize (Zea mays L.) and accumulation of mycotoxins, that affect human and animal health. Currently, chemical and agronomic measures to control Fusarium ear rot are not v...

    Authors: Alessandra Lanubile, Alberto Ferrarini, Valentina Maschietto, Massimo Delledonne, Adriano Marocco and Diana Bellin
    Citation: BMC Genomics 2014 15:710
    Content type: Research article Published on:

  41. The laying hen model of spontaneous epithelial ovarian cancer (EOC) is unique in that it is the only model that enables observations of early events in disease progression and is therefore also uniquely suited...

    Authors: Karen H Hales, Sheree C Speckman, Nawneet K Kurrey and Dale B Hales
    Citation: BMC Genomics 2014 15:709
    Content type: Research article Published on:

  42. In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic m...

    Authors: Amit A Deokar, Larissa Ramsay, Andrew G Sharpe, Marwan Diapari, Anoop Sindhu, Kirstin Bett, Thomas D Warkentin and Bunyamin Tar’an
    Citation: BMC Genomics 2014 15:708
    Content type: Research article Published on:

  43. The Smyth line (SL) chicken is the only animal model for autoimmune vitiligo that spontaneously displays all clinical and biological manifestations of the human disorder. To understand the genetic components u...

    Authors: Hyeon-Min Jang, Gisela F Erf, Kaylee C Rowland and Byung-Whi Kong
    Citation: BMC Genomics 2014 15:707
    Content type: Research article Published on:

  44. Magnolia sprengeri Pamp is one of the most highly valuable medicinal and ornamental plants of the Magnolia Family. The natural color of M. sprengeri is variable. The complete genome sequence of M. sprengeri is no...

    Authors: Shou-Guo Shi, Mei Yang, Min Zhang, Ping Wang, Yong-Xiang Kang and Jian-Jun Liu
    Citation: BMC Genomics 2014 15:706
    Content type: Research article Published on:

  46. Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and gra...

    Authors: Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin Grenet, Florence Blanc, François Cousserans, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempes, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro…
    Citation: BMC Genomics 2014 15:704
    Content type: Research article Published on:

  47. Current practice in mass spectrometry (MS)-based proteomics is to identify peptides by comparison of experimental mass spectra with theoretical mass spectra derived from a reference protein database; however, ...

    Authors: Gloria M Sheynkman, James E Johnson, Pratik D Jagtap, Michael R Shortreed, Getiria Onsongo, Brian L Frey, Timothy J Griffin and Lloyd M Smith
    Citation: BMC Genomics 2014 15:703
    Content type: Methodology article Published on:

  48. Iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. A lack of bioavailable iron in soil leads to iron deficiency chlorosis (IDC), causin...

    Authors: Adrienne N Moran Lauter, Gregory A Peiffer, Tengfei Yin, Steven A Whitham, Dianne Cook, Randy C Shoemaker and Michelle A Graham
    Citation: BMC Genomics 2014 15:702
    Content type: Research article Published on:

  49. Hybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. In particular, gene loss and gene silencing are ...

    Authors: Tina Sehrish, V Vaughan Symonds, Douglas E Soltis, Pamela S Soltis and Jennifer A Tate
    Citation: BMC Genomics 2014 15:701
    Content type: Research article Published on:

  50. Engineered nanomaterials may release nanosized residues, by degradation, throughout their life cycle. These residues may be a threat for living organisms. They may be ingested by humans through food and water....

    Authors: Matthieu Fisichella, Frederic Berenguer, Gerard Steinmetz, Melanie Auffan, Jerome Rose and Odette Prat
    Citation: BMC Genomics 2014 15:700
    Content type: Research article Published on:

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BMC Genomics

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