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  1. We introduce Iterative Feature Removal (IFR) as an unbiased approach for selecting features with diagnostic capacity from large data sets. The algorithm is based on recently developed tools in machine learning...

    Authors: Stephen O’Hara, Kun Wang, Richard A Slayden, Alan R Schenkel, Greg Huber, Corey S O’Hern, Mark D Shattuck and Michael Kirby
    Citation: BMC Genomics 2013 14:832
  2. Cell-specific gene expression is controlled by epigenetic modifications and transcription factor binding. While genome-wide maps for these protein-DNA interactions have become widely available, quantitative co...

    Authors: Gabriele Schweikert, Botond Cseke, Thomas Clouaire, Adrian Bird and Guido Sanguinetti
    Citation: BMC Genomics 2013 14:826
  3. Psoriasis is a chronic autoimmune disease in which T cells have a predominant role in initiating and perpetuating the chronic inflammation in skin. However, the mechanisms that regulate T cell activation in ps...

    Authors: Nuria Palau, Antonio Julià, Carlos Ferrándiz, Lluís Puig, Eduardo Fonseca, Emilia Fernández, María López-Lasanta, Raül Tortosa and Sara Marsal
    Citation: BMC Genomics 2013 14:825
  4. SUMOylation, as part of the epigenetic regulation of transcription, has been intensively studied in lower eukaryotes that contain only a single SUMO protein; however, the functions of SUMOylation during mammal...

    Authors: Pei-Ching Chang, Chia-Yang Cheng, Mel Campbell, Yi-Cheng Yang, Hung-Wei Hsu, Ting-Yu Chang, Chia-Han Chu, Yi-Wei Lee, Chiu-Lien Hung, Shi-Mei Lai, Clifford G Tepper, Wen-Ping Hsieh, Hsei-Wei Wang, Chuan-Yi Tang, Wen-Ching Wang and Hsing-Jien Kung
    Citation: BMC Genomics 2013 14:824
  5. Pear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Combining the Solexa/Illumina RNA-seq high-throughput sequencing approach (RNA-seq) with Digital...

    Authors: Min Xie, Ying Huang, Yanping Zhang, Xin Wang, Hua Yang, Oliver Yu, Wenhao Dai and Congbing Fang
    Citation: BMC Genomics 2013 14:823
  6. Serratia sp. ATCC 39006 (S39006) is a Gram-negative enterobacterium that is virulent in plant and animal models. It produces a red-pigmented trypyrrole secondary metabolite, prodigiosin (Pig), and a carbapenem an...

    Authors: Nabil M Wilf, Adam J Reid, Joshua P Ramsay, Neil R Williamson, Nicholas J Croucher, Laurent Gatto, Svenja S Hester, David Goulding, Lars Barquist, Kathryn S Lilley, Robert A Kingsley, Gordon Dougan and George PC Salmond
    Citation: BMC Genomics 2013 14:822
  7. Durum wheat often faces water scarcity and high temperatures, two events that usually occur simultaneously in the fields. Here we report on the stress responsive strategy of two durum wheat cultivars, characte...

    Authors: Alessio Aprile, Lenka Havlickova, Riccardo Panna, Caterina Marè, Grazia M Borrelli, Daniela Marone, Carla Perrotta, Patrizia Rampino, Luigi De Bellis, Vladislav Curn, Anna M Mastrangelo, Fulvia Rizza and Luigi Cattivelli
    Citation: BMC Genomics 2013 14:821
  8. As the largest low-latitude permafrost region, the Tibetan Plateau (TP) is an important part of the earth’s terrestrial ecosystem and one of the most vulnerable areas to climate change and human activities. Ho...

    Authors: Xiangyu Guan, Jinfeng Wang, Hui Zhao, Jianjun Wang, Ximing Luo, Fei Liu and Fangqing Zhao
    Citation: BMC Genomics 2013 14:820
  9. Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNA...

    Authors: Thomas Bruun Rasmussen, Peter Christian Risager, Ulrik Fahnøe, Martin Barfred Friis, Graham J Belsham, Dirk Höper, Ilona Reimann and Martin Beer
    Citation: BMC Genomics 2013 14:819
  10. RNA-seq has spurred important gene fusion discoveries in a number of different cancers, including lung, prostate, breast, brain, thyroid and bladder carcinomas. Gene fusion discovery can potentially lead to th...

    Authors: Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder and Greg Foltz
    Citation: BMC Genomics 2013 14:818
  11. Warmer seawater as a result of climate change may impose environmental challenges for Atlantic salmon aquaculture in its southernmost geographic range. Seawater temperatures above optimal level for growth may ...

    Authors: Pål A Olsvik, Vibeke Vikeså, Kai K Lie and Ernst M Hevrøy
    Citation: BMC Genomics 2013 14:817
  12. The genetic make-up of humans and other mammals (such as mice) affects their resistance to influenza virus infection. Considering the complexity and moral issues associated with experiments on human subjects, ...

    Authors: Suying Bao, Xueya Zhou, Liangcai Zhang, Jie Zhou, Kelvin Kai-Wang To, Binbin Wang, Liqiu Wang, Xuegong Zhang and You-Qiang Song
    Citation: BMC Genomics 2013 14:816
  13. Diapause or developmental arrest, is one of the major adaptations that allows mites and insects to survive unfavorable conditions. Diapause evokes a number of physiological, morphological and molecular modific...

    Authors: Astrid Bryon, Nicky Wybouw, Wannes Dermauw, Luc Tirry and Thomas Van Leeuwen
    Citation: BMC Genomics 2013 14:815
  14. Freezing provokes severe yield losses to different fall-sown annual legumes. Understanding the molecular bases of freezing tolerance is of great interest for breeding programs. Medicago truncatula Gaertn. is an a...

    Authors: Nadim Tayeh, Nasser Bahrman, Hélène Sellier, Aurélie Bluteau, Christelle Blassiau, Joëlle Fourment, Arnaud Bellec, Frédéric Debellé, Isabelle Lejeune-Hénaut and Bruno Delbreil
    Citation: BMC Genomics 2013 14:814
  15. Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is ...

    Authors: Ignacio Soriano, Luis Quintales and Francisco Antequera
    Citation: BMC Genomics 2013 14:813
  16. It is generally accepted that gene order in eukaryotes is nonrandom, with adjacent genes often sharing expression patterns across tissues, and that this organization may be important for gene regulation. Here ...

    Authors: Alan F Rubin and Phil Green
    Citation: BMC Genomics 2013 14:812
  17. The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for thi...

    Authors: David B Jones, Dean R Jerry, Mehar S Khatkar, Herman W Raadsma and Kyall R Zenger
    Citation: BMC Genomics 2013 14:810
  18. Stem cells located in the centre of the shoot apical meristem are required for the repetitive formation of new organs such as leaves, branches and flowers. In Arabidopsis thaliana, the ZWILLE/PINHEAD/AGO10 (ZLL) ...

    Authors: Matthew R Tucker, Farshad Roodbarkelari, Elisabeth Truernit, Nikolai M Adamski, Annika Hinze, Barbara Lohmüller, Tobias Würschum and Thomas Laux
    Citation: BMC Genomics 2013 14:809
  19. Cell growth rate reflects an organism’s physiological state and largely relies on the ability of gene expression to respond to the environment. The relationship between cellular growth rate and gene expression...

    Authors: Yuki Matsumoto, Yoshie Murakami, Saburo Tsuru, Bei-Wen Ying and Tetsuya Yomo
    Citation: BMC Genomics 2013 14:808
  20. Fungal pathogens cause devastating losses in economically important cereal crops by utilising pathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus far ...

    Authors: Jana Sperschneider, Donald M Gardiner, Jennifer M Taylor, James K Hane, Karam B Singh and John M Manners
    Citation: BMC Genomics 2013 14:807
  21. The phytohormone auxin mediates a stunning array of plant development through the functions of AUXIN RESPONSE FACTORs (ARFs), which belong to transcription factors and are present as a protein family comprisin...

    Authors: Qian Zhu, Baoyan Li, Shuyuan Mu, Bing Han, Runzhi Cui, Manyu Xu, Zhenzhen You and Hansong Dong
    Citation: BMC Genomics 2013 14:806
  22. We conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, u...

    Authors: Haiyan Lei, Tianwei Li, Guo-Chiuan Hung, Bingjie Li, Shien Tsai and Shyh-Ching Lo
    Citation: BMC Genomics 2013 14:804
  23. 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
  24. Lycium chinense is well known in traditional Chinese herbal medicine for its medicinal value and composition, which have been widely studied for decades. However, further research on Lycium chinense is limited du...

    Authors: Shicheng Zhao, Pham Anh Tuan, Xiaohua Li, Yeon Bok Kim, HyeRan Kim, Chun Geon Park, Jingli Yang, Cheng Hao Li and Sang Un Park
    Citation: BMC Genomics 2013 14:802
  25. 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
  26. The bacterium Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the most frequent causes of foodborne outbreaks of gastroenteritis. Between 2005–2008 a series of S. Typhimurium outbreaks occurred...

    Authors: Jane Hawkey, David J Edwards, Karolina Dimovski, Lester Hiley, Helen Billman-Jacobe, Geoff Hogg and Kathryn E Holt
    Citation: BMC Genomics 2013 14:800
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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

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