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  1. The genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell’s protein composition. Since characterisation of the proteome remains technically laborious it is attractive ...

    Authors: Francois-Xavier Dieudonné, Patrick B. F. O’Connor, Pascale Gubler-Jaquier, Haleh Yasrebi, Beatrice Conne, Sergey Nikolaev, Stylianos Antonarakis, Pavel V. Baranov and Joseph Curran
    Citation: BMC Genomics 2015 16:986
    Content type: Research article Published on:

  2. Although extensive studies have investigated radiation-induced injuries in particular gastrointestinal (GI) segments, a systematic comparison among the different segments on the basis of mode, magnitude and me...

    Authors: Junying Zheng, Junru Wang, Mylene Pouliot, Simon Authier, Daohong Zhou, David S. Loose and Martin Hauer-Jensen
    Citation: BMC Genomics 2015 16:984
    Content type: Research article Published on:

  3. The trematode parasite, Schistosoma mansoni, has evolved to switch from oxidative phosphorylation to glycolysis in the presence of glucose immediately after invading the human host. This metabolic switch is depen...

    Authors: Alejandro Cabezas-Cruz, James J. Valdés, Julien Lancelot and Raymond J. Pierce
    Citation: BMC Genomics 2015 16:980
    Content type: Research article Published on:

  4. The liver possesses an ability of compensatory growth after removing three of five lobes in mammals or one of three lobes in zebrafish. The reenter of hepatocytes into the cell cycle is one of the hallmarks fo...

    Authors: Guohui Feng, Yong Long, Jinrong Peng, Qing Li and Zongbin Cui
    Citation: BMC Genomics 2015 16:979
    Content type: Research article Published on:

  5. Transcription start sites (TSSs) with pronounced and phased nucleosome arrays downstream and nucleosome-depleted regions upstream of TSSs are observed in various species.

    Authors: Yoichiro Nakatani, Cecilia C. Mello, Shin-ichi Hashimoto, Atsuko Shimada, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Jun Yoshimura, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Andrew Fire and Shinichi Morishita
    Citation: BMC Genomics 2015 16:978
    Content type: Research article Published on:

  6. RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there rem...

    Authors: Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kiyonari and Shigehiro Kuraku
    Citation: BMC Genomics 2015 16:977
    Content type: Research article Published on:

  7. Among the largest and most diverse transcription factor families in plants, basic leucine zipper (bZIP) family participate in regulating various processes, including floral induction and development, stress an...

    Authors: Xueyin Li, Shiqing Gao, Yimiao Tang, Lei Li, Fengjie Zhang, Biane Feng, Zhaofeng Fang, Lingjian Ma and Changping Zhao
    Citation: BMC Genomics 2015 16:976
    Content type: Research article Published on:

  8. The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf sp...

    Authors: Brice Roux, Stéphanie Bolot, Endrick Guy, Nicolas Denancé, Martine Lautier, Marie-Françoise Jardinaud, Marion Fischer-Le Saux, Perrine Portier, Marie-Agnès Jacques, Lionel Gagnevin, Olivier Pruvost, Emmanuelle Lauber, Matthieu Arlat, Sébastien Carrère, Ralf Koebnik and Laurent D. Noël
    Citation: BMC Genomics 2015 16:975
    Content type: Research article Published on:

  9. The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resista...

    Authors: Sabina Bajda, Wannes Dermauw, Robert Greenhalgh, Ralf Nauen, Luc Tirry, Richard M. Clark and Thomas Van Leeuwen
    Citation: BMC Genomics 2015 16:974
    Content type: Research article Published on:

  10. Controlling sex ratios is essential for the aquaculture industry, especially in those species with sex dimorphism for relevant productive traits, hence the importance of knowing how the sexual phenotype is est...

    Authors: Diego Robledo, Laia Ribas, Rosa Cal, Laura Sánchez, Francesc Piferrer, Paulino Martínez and Ana Viñas
    Citation: BMC Genomics 2015 16:973
    Content type: Research article Published on:

  11. Bacteriophage replication depends on bacterial proteins and inactivation of genes coding for such host factors should interfere with phage infection. To gain further insights into the interactions between S. pneu...

    Authors: Philippe Leprohon, Hélène Gingras, Siham Ouennane, Sylvain Moineau and Marc Ouellette
    Citation: BMC Genomics 2015 16:972
    Content type: Research article Published on:

  12. Gynogenesis is one of unisexual reproduction modes in vertebrates, and produces all-female individuals with identical genetic background. In sexual reproduction vertebrates, the roles of primordial germ cells ...

    Authors: Wei Liu, Shi-Zhu Li, Zhi Li, Yang Wang, Xi-Yin Li, Jian-Xiang Zhong, Xiao-Juan Zhang, Jun Zhang, Li Zhou and Jian-Fang Gui
    Citation: BMC Genomics 2015 16:971
    Content type: Research article Published on:

  13. The FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of...

    Authors: Christelle Robert, Ronan Kapetanovic, Dario Beraldi, Mick Watson, Alan L. Archibald and David A. Hume
    Citation: BMC Genomics 2015 16:970
    Content type: Research article Published on:

  14. The genetic architecture of complex traits in farmed animal populations is of interest from a scientific and practical perspective. The use of genetic markers to predict the genetic merit (breeding values) of ...

    Authors: Hsin-Yuan Tsai, Alastair Hamilton, Alan E. Tinch, Derrick R. Guy, Karim Gharbi, Michael J. Stear, Oswald Matika, Steve C. Bishop and Ross D. Houston
    Citation: BMC Genomics 2015 16:969
    Content type: Research article Published on:

  15. Phosphine is a valuable fumigant to control pest populations in stored grains and grain products. However, recent studies indicate a substantial increase in phosphine resistance in stored product pests worldwide.

    Authors: Brenda Oppert, Raul N. C. Guedes, Michael J. Aikins, Lindsey Perkin, Zhaorigetu Chen, Thomas W. Phillips, Kun Yan Zhu, George P. Opit, Kelly Hoon, Yongming Sun, Gavin Meredith, Kelli Bramlett, Natalie Supunpong Hernandez, Brian Sanderson, Madison W. Taylor, Dalia Dhingra…
    Citation: BMC Genomics 2015 16:968
    Content type: Research article Published on:

  16. Gene regulatory relationships can be inferred using matched array comparative genomics and transcriptomics data sets from cancer samples. The way in which copy numbers of genes in cancer samples are often grea...

    Authors: Richard Newton and Lorenz Wernisch
    Citation: BMC Genomics 2015 16:967
    Content type: Research Article Published on:

  17. Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive c...

    Authors: Chai Ling Chan, Su Mei Yew, Yun Fong Ngeow, Shiang Ling Na, Kok Wei Lee, Chee-Choong Hoh, Wai-Yan Yee and Kee Peng Ng
    Citation: BMC Genomics 2015 16:966
    Content type: Research article Published on:

  18. To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical ...

    Authors: Núria Casas-Vila, Marion Scheibe, Anja Freiwald, Dennis Kappei and Falk Butter
    Citation: BMC Genomics 2015 16:965
    Content type: Research article Published on:

  19. Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quan...

    Authors: Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson and D. G. Joakim Larsson
    Citation: BMC Genomics 2015 16:964
    Content type: Research article Published on:

  20. Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the sp...

    Authors: Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić and Boris Lenhard
    Citation: BMC Genomics 2015 16:963
    Content type: Software Published on:

  21. Forward genetic approaches have limited use for agronomic traits that can’t be reliably scored on a single plant basis. Thus, mutants in wheat and other crops are more useful for gene function studies by rever...

    Authors: Gaganjot Sidhu, Amita Mohan, Ping Zheng, Amandeep Kaur Dhaliwal, Dorrie Main and Kulvinder S Gill
    Citation: BMC Genomics 2015 16:962
    Content type: Research article Published on:

  22. HPA axis plays a major role in physiological homeostasis. It is also involved in stress and adaptive response to the environment. In farm animals in general and specifically in pigs, breeding strategies have h...

    Authors: Valérie Sautron, Elena Terenina, Laure Gress, Yannick Lippi, Yvon Billon, Catherine Larzul, Laurence Liaubet, Nathalie Villa-Vialaneix and Pierre Mormède
    Citation: BMC Genomics 2015 16:961
    Content type: Research Article Published on:

  23. Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into t...

    Authors: Kelley A. Gallagher and Paul R. Jensen
    Citation: BMC Genomics 2015 16:960
    Content type: Research article Published on:

  24. Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world’s population. However, grain yields are challenged by various abiotic stresses such as drought, fertil...

    Authors: Jun Yang, Xiaorong Chen, Changlan Zhu, Xiaosong Peng, Xiaopeng He, Junru Fu, Linjuan Ouyang, Jianmin Bian, Lifang Hu, Xiaotang Sun, Jie Xu and Haohua He
    Citation: BMC Genomics 2015 16:959
    Content type: Research article Published on:

  25. Dagginess (faecal soiling of the perineum region) and host nematode parasite resistance are important animal welfare traits in New Zealand sheep. Genomic prediction (GP) estimates the genetic merit, as a molec...

    Authors: Natalie K. Pickering, Benoit Auvray, Ken G. Dodds and John C. McEwan
    Citation: BMC Genomics 2015 16:958
    Content type: Research article Published on:

  26. It is generally accepted that gene duplication followed by functional divergence is one of the main sources of metabolic diversity. In this regard, there is an increasing interest in the development of methods...

    Authors: Augusto Cesar Poot-Hernandez, Katya Rodriguez-Vazquez and Ernesto Perez-Rueda
    Citation: BMC Genomics 2015 16:957
    Content type: Research article Published on:

  27. Alzheimer’s disease (AD) is the most common form of dementia. AD has a multifactorial disease etiology and is currently untreatable. Multiple genes and molecular mechanisms have been implicated in AD, includin...

    Authors: Arthur A. Bergen, Sovann Kaing, Jacoline B. ten Brink, Theo G. Gorgels and Sarah F. Janssen
    Citation: BMC Genomics 2015 16:956
    Content type: Research article Published on:

  28. Rice false smut caused by Ustilaginoidea virens has recently become one of the most devastating rice diseases worldwide. Breeding and deployment of resistant varieties is considered as the most effective strategy...

    Authors: Yanqing Han, Kang Zhang, Jun Yang, Nan Zhang, Anfei Fang, Yong Zhang, Yongfeng Liu, Zhiyi Chen, Tom Hsiang and Wenxian Sun
    Citation: BMC Genomics 2015 16:955
    Content type: Research article Published on:

  29. Dormant Mycobacterium tuberculosis bacilli are believed to play an important role in latent tuberculosis infection. Previously, we have demonstrated that cultivation of M. tuberculosis in K+-deficient medium resu...

    Authors: Dmitriy V. Ignatov, Elena G. Salina, Mikhail V. Fursov, Timofey A. Skvortsov, Tatyana L. Azhikina and Arseny S. Kaprelyants
    Citation: BMC Genomics 2015 16:954
    Content type: Research article Published on:

  30. Coxiella burnetii is the causative agent of the zoonotic disease Q fever. As it is an intracellular pathogen, infection by C. burnetii requires adaptation to its eukaryotic host and in...

    Authors: Runa Kuley, Ruth Bossers-deVries, Hilde E. Smith, Mari A. Smits, Hendrik I. J. Roest and Alex Bossers
    Citation: BMC Genomics 2015 16:953
    Content type: Research article Published on:

  31. Human erythrocytes are terminally differentiated, anucleate cells long thought to lack RNAs. However, previous studies have shown the persistence of many small-sized RNAs in erythrocytes. To comprehensively de...

    Authors: Jennifer F. Doss, David L. Corcoran, Dereje D. Jima, Marilyn J. Telen, Sandeep S. Dave and Jen-Tsan Chi
    Citation: BMC Genomics 2015 16:952
    Content type: Research article Published on:

  32. The plant phytohormone auxin controls many aspects of plant growth and development, which largely depends on its uneven distribution in plant tissues. Transmembrane proteins of the PIN family are auxin efflux ...

    Authors: Yongqin Wang, Chenglin Chai, Babu Valliyodan, Christine Maupin, Brad Annen and Henry T. Nguyen
    Citation: BMC Genomics 2015 16:951
    Content type: Research article Published on:

  33. The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human ...

    Authors: Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde and Sinnakaruppan Mathavan
    Citation: BMC Genomics 2015 16:950
    Content type: Research article Published on:

  34. Limited information is available on aluminum (Al)-toxicity-responsive proteins in woody plant roots. Seedlings of ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) were treated for 18 weeks with nutr...

    Authors: Huan-Xin Jiang, Lin-Tong Yang, Yi-Ping Qi, Yi-Bin Lu, Zeng-Rong Huang and Li-Song Chen
    Citation: BMC Genomics 2015 16:949
    Content type: Research article Published on:

  36. Shiga toxin (Stx)-producing E. coli (STEC) are responsible for foodborne outbreaks that can result in severe human disease. During an outbreak, differential disease outcomes are observed after infection with the ...

    Authors: Lisa M. Russo, Nourtan F. Abdeltawab, Alison D. O’Brien, Malak Kotb and Angela R. Melton-Celsa
    Citation: BMC Genomics 2015 16:947
    Content type: Research article Published on:

  37. Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biolog...

    Authors: Ryan Ghan, Steven C. Van Sluyter, Uri Hochberg, Asfaw Degu, Daniel W. Hopper, Richard L. Tillet, Karen A. Schlauch, Paul A. Haynes, Aaron Fait and Grant R. Cramer
    Citation: BMC Genomics 2015 16:946
    Content type: Research article Published on:

  38. MicroRNAs (miRNAs) have functions in diverse biological processes such as growth, signal transduction, disease resistance, and stress responses in plants. Thermotherapy is an effective approach for elimination...

    Authors: Juan Liu, XueJiao Zhang, FangPeng Zhang, Ni Hong, GuoPing Wang, Aiming Wang and LiPing Wang
    Citation: BMC Genomics 2015 16:945
    Content type: Research article Published on:

  39. Epithelial-mesenchymal transition (EMT) is an important process in embryonic development, especially during gastrulation and organ formation. Furthermore EMT is widely observed in pathological conditions, e.g....

    Authors: Priyank Shukla, Claus Vogl, Barbara Wallner, Doris Rigler, Mathias Müller and Sabine Macho-Maschler
    Citation: BMC Genomics 2015 16:944
    Content type: Research article Published on:

  40. Recent studies show that galling Hymenoptera and Diptera are able to synthesize the plant hormone indole-3-acetic acid (auxin) from tryptophan and that plant response to insect-produced auxin is implicated in ...

    Authors: Sebastian Bailey, Diana M. Percy, Charles A. Hefer and Quentin C. B. Cronk
    Citation: BMC Genomics 2015 16:943
    Content type: Research article Published on:

  41. Neural-endocrine-immune (NEI) system is a major modulation network among the nervous, endocrine and immune system and weights greatly in maintaining homeostasis of organisms during stress and infection. Some m...

    Authors: Hao Chen, Lingling Wang, Zhi Zhou, Zhanhui Hou, Zhaoqun Liu, Weilin Wang, Dahai Gao, Qiang Gao, Mengqiang Wang and Linsheng Song
    Citation: BMC Genomics 2015 16:942
    Content type: Research article Published on:

  42. The advent and democratization of next generation sequencing and genotyping technologies lead to a huge amount of data for the characterization of population genetic diversity in model and non model-species. H...

    Authors: Guilhem Sempéré, Katayoun Moazami-Goudarzi, André Eggen, Denis Laloë, Mathieu Gautier and Laurence Flori
    Citation: BMC Genomics 2015 16:940
    Content type: Database Published on:

  43. Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes (up to 11 Mb in size) appears to be the result of increased non-coding DNA, whic...

    Authors: Zhiqiang Wu, James D. Stone, Helena Štorchová and Daniel B. Sloan
    Citation: BMC Genomics 2015 16:938
    Content type: Research article Published on:

  44. The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expr...

    Authors: Christina D. Marth, Neil D. Young, Lisa Y. Glenton, Drew M. Noden, Glenn F. Browning and Natali Krekeler
    Citation: BMC Genomics 2015 16:934
    Content type: Research article Published on:

  45. A giant protein called BAP (biofilm-associated protein) plays a role in biofilm formation and adhesion to host cells in A. baumannii. Most of the protein is made by arrays of 80–110 aa modules featuring immunoglo...

    Authors: Eliana De Gregorio, Mariateresa Del Franco, Marianna Martinucci, Emanuela Roscetto, Raffaele Zarrilli and Pier Paolo Di Nocera
    Citation: BMC Genomics 2015 16:933
    Content type: Research article Published on:

  46. Next-generation sequencing (NGS) offers great opportunities for studying the biology of insect vectors of disease. Prerequisites for successful analyses include high quality annotated genome assemblies and tha...

    Authors: Gareth D. Weedall, Helen Irving, Margaret A. Hughes and Charles S. Wondji
    Citation: BMC Genomics 2015 16:931
    Content type: Research article Published on:

  47. Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unice...

    Authors: Shrikant Patil, Sara Moeys, Peter von Dassow, Marie J. J. Huysman, Daniel Mapleson, Lieven De Veylder, Remo Sanges, Wim Vyverman, Marina Montresor and Maria Immacolata Ferrante
    Citation: BMC Genomics 2015 16:930
    Content type: RESEARCH ARTICLE Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:544

  48. FUS (TLS) and EWS (EWSR1) belong to the FET-protein family of RNA and DNA binding proteins. FUS and EWS are structurally and functionally related and participate in transcriptional regulation and RNA processin...

    Authors: Yonglun Luo, Jenny Blechingberg, Ana Miguel Fernandes, Shengting Li, Tue Fryland, Anders D. Børglum, Lars Bolund and Anders Lade Nielsen
    Citation: BMC Genomics 2015 16:929
    Content type: Research article Published on:

  50. The MRL/MpJ mouse is a laboratory inbred strain known for regenerative abilities which are manifested by scarless closure of ear pinna punch holes. Enhanced healing responses have been reported in other organs...

    Authors: Justyna Podolak-Popinigis, Bartosz Górnikiewicz, Anna Ronowicz and Paweł Sachadyn
    Citation: BMC Genomics 2015 16:926
    Content type: Research article Published on:

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BMC Genomics

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