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  1. Aging-related kidney diseases are a major health concern. Currently, models to study renal aging are lacking. Due to a reduced life-span progeroid models hold the promise to facilitate aging studies and allow ...

    Authors: Bernhard Schermer, Valerie Bartels, Peter Frommolt, Bianca Habermann, Fabian Braun, Joachim L Schultze, Marianne Roodbergen, Jan HJ Hoeijmakers, Björn Schumacher, Peter Nürnberg, Martijn ET Dollé, Thomas Benzing, Roman-Ulrich Müller and Christine E Kurschat
    Citation: BMC Genomics 2013 14:559
    Content type: Research article Published on:

  2. This descriptive study of the abdominal fat transcriptome takes advantage of two experimental lines of meat-type chickens (Gallus domesticus), which were selected over seven generations for a large difference in ...

    Authors: Christopher W Resnyk, Wilfrid Carré, Xiaofei Wang, Tom E Porter, Jean Simon, Elisabeth Le Bihan-Duval, Michael J Duclos, Sam E Aggrey and Larry A Cogburn
    Citation: BMC Genomics 2013 14:557
    Content type: Research article Published on:

  3. Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflowe...

    Authors: Venkatramana Pegadaraju, Rick Nipper, Brent Hulke, Lili Qi and Quentin Schultz
    Citation: BMC Genomics 2013 14:556
    Content type: Research article Published on:

  5. Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cel...

    Authors: Rongrong Guo, Xiaozhao Xu, Bassett Carole, Xiaoqin Li, Min Gao, Yi Zheng and Xiping Wang
    Citation: BMC Genomics 2013 14:554
    Content type: Research article Published on:

  6. Recent studies suggested that human/mammalian genomes are divided into large, discrete domains that are units of chromosome organization. CTCF, a CCCTC binding factor, has a diverse role in genome regulation i...

    Authors: Yuanyuan Li, Weichun Huang, Liang Niu, David M Umbach, Shay Covo and Leping Li
    Citation: BMC Genomics 2013 14:553
    Content type: Research article Published on:

  7. Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the mo...

    Authors: Caiqin Li, Yan Wang, Xuming Huang, Jiang Li, Huicong Wang and Jianguo Li
    Citation: BMC Genomics 2013 14:552
    Content type: Research article Published on:

  8. Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a ty...

    Authors: Neha Jalan, Dibyendu Kumar, Maxuel O Andrade, Fahong Yu, Jeffrey B Jones, James H Graham, Frank F White, João C Setubal and Nian Wang
    Citation: BMC Genomics 2013 14:551
    Content type: Research article Published on:

  9. Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.

    Authors: Lucas Swanson, Gordon Robertson, Karen L Mungall, Yaron S Butterfield, Readman Chiu, Richard D Corbett, T Roderick Docking, Donna Hogge, Shaun D Jackman, Richard A Moore, Andrew J Mungall, Ka Ming Nip, Jeremy DK Parker, Jenny Qing Qian, Anthony Raymond, Sandy Sung…
    Citation: BMC Genomics 2013 14:550
    Content type: Methodology article Published on:

  11. Larix gmelinii is a dominant tree species in China’s boreal forests and plays an important role in the coniferous ecosystem. It is also one of the most economically important tree species in the Chinese timber in...

    Authors: Lina Men, Shanchun Yan and Guanjun Liu
    Citation: BMC Genomics 2013 14:548
    Content type: Research article Published on:

  12. A co-ordinated tissue-independent gene expression profile associated with growth is present in rodent models and this is hypothesised to extend to all mammals. Growth in humans has similarities to other mammal...

    Authors: Adam Stevens, Daniel Hanson, Andrew Whatmore, Benoit Destenaves, Pierre Chatelain and Peter Clayton
    Citation: BMC Genomics 2013 14:547
    Content type: Research article Published on:

  13. Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synth...

    Authors: Shaadi F Pooyaei Mehr, Rob DeSalle, Hung-Teh Kao, Apurva Narechania, Zhou Han, Dan Tchernov, Vincent Pieribone and David F Gruber
    Citation: BMC Genomics 2013 14:546
    Content type: Research article Published on:

  14. METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription.

    Authors: Jean Lud Cadet, Subramaniam Jayanthi, Michael T McCoy, Bruce Ladenheim, Fabienne Saint-Preux, Elin Lehrmann, Supriyo De, Kevin G Becker and Christie Brannock
    Citation: BMC Genomics 2013 14:545
    Content type: Research article Published on:

  15. MicroRNAs (miRNAs) are a family of short, non-coding RNAs modulating expression of human protein coding genes (miRNA target genes). Their dysfunction is associated with many human diseases, including neurodeve...

    Authors: Ying Qiao, Chansonette Badduke, Eloi Mercier, Suzanne ME Lewis, Paul Pavlidis and Evica Rajcan-Separovic
    Citation: BMC Genomics 2013 14:544
    Content type: Research article Published on:

  17. The Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used...

    Authors: Simone Sommer, Alexandre Courtiol and Camila J Mazzoni
    Citation: BMC Genomics 2013 14:542
    Content type: Research article Published on:

  18. A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cockt...

    Authors: Laure Ries, Steven T Pullan, Stéphane Delmas, Sunir Malla, Martin J Blythe and David B Archer
    Citation: BMC Genomics 2013 14:541
    Content type: Research article Published on:

  19. Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nemato...

    Authors: Paolo Bagnaresi, Tea Sala, Tiziana Irdani, Cristina Scotto, Antonella Lamontanara, Massimiliano Beretta, Giuseppe Leonardo Rotino, Sara Sestili, Luigi Cattivelli and Emidio Sabatini
    Citation: BMC Genomics 2013 14:540
    Content type: Research article Published on:

  21. Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecu...

    Authors: Alberto Pallavicini, Adriana Canapa, Marco Barucca, Jessica Alfőldi, Maria Assunta Biscotti, Francesco Buonocore, Gianluca De Moro, Federica Di Palma, Anna Maria Fausto, Mariko Forconi, Marco Gerdol, Daisy Monica Makapedua, Jason Turner-Meier, Ettore Olmo and Giuseppe Scapigliati
    Citation: BMC Genomics 2013 14:538
    Content type: Research article Published on:

  22. The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat struc...

    Authors: David Williams, William L Trimble, Meghan Shilts, Folker Meyer and Howard Ochman
    Citation: BMC Genomics 2013 14:537
    Content type: Methodology article Published on:

  23. RNA-seq can be used to measure allele-specific expression (ASE) by assigning sequence reads to individual alleles; however, relative ASE is systematically biased when sequence reads are aligned to a single ref...

    Authors: Kraig R Stevenson, Joseph D Coolon and Patricia J Wittkopp
    Citation: BMC Genomics 2013 14:536
    Content type: Methodology article Published on:

  24. As the error rate is high and the distribution of errors across sites is non-uniform in next generation sequencing (NGS) data, it has been a challenge to estimate DNA polymorphism (θ) accurately from NGS data.

    Authors: Ziwen He, Xinnian Li, Shaoping Ling, Yun-Xin Fu, Eric Hungate, Suhua Shi and Chung-I Wu
    Citation: BMC Genomics 2013 14:535
    Content type: Methodology article Published on:

  25. Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hin...

    Authors: Li Wei, Yi Xin, Dongmei Wang, Xiaoyan Jing, Qian Zhou, Xiaoquan Su, Jing Jia, Kang Ning, Feng Chen, Qiang Hu and Jian Xu
    Citation: BMC Genomics 2013 14:534
    Content type: Research article Published on:

  26. Physiological processes aiding the conversion of muscle to meat involve many genes associated with muscle structure and metabolic processes. MicroRNAs regulate networks of genes to orchestrate cellular functio...

    Authors: Siriluck Ponsuksili, Yang Du, Frieder Hadlich, Puntita Siengdee, Eduard Murani, Manfred Schwerin and Klaus Wimmers
    Citation: BMC Genomics 2013 14:533
    Content type: Research article Published on:

  27. Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in m...

    Authors: Jin Zhang, Jianbo Li, Bobin Liu, Li Zhang, Jun Chen and Mengzhu Lu
    Citation: BMC Genomics 2013 14:532
    Content type: Research article Published on:

  28. Snake venom is shaped by the ecology and evolution of venomous species, and signals of positive selection in toxins have been consistently documented, reflecting the role of venoms as an ecologically critical ...

    Authors: Mark J Margres, Karalyn Aronow, Jacob Loyacano and Darin R Rokyta
    Citation: BMC Genomics 2013 14:531
    Content type: Research article Published on:

  29. Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-...

    Authors: Milkha M Leimena, Javier Ramiro-Garcia, Mark Davids, Bartholomeus van den Bogert, Hauke Smidt, Eddy J Smid, Jos Boekhorst, Erwin G Zoetendal, Peter J Schaap and Michiel Kleerebezem
    Citation: BMC Genomics 2013 14:530
    Content type: Research article Published on:

  30. ‘Candidatus Phytoplasma australiense’ is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a...

    Authors: Mark T Andersen, Lia W Liefting, Ilkka Havukkala and Ross E Beever
    Citation: BMC Genomics 2013 14:529
    Content type: Research article Published on:

  31. Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression stud...

    Authors: Armando Caballero, María Jesús García-Pereira and Humberto Quesada
    Citation: BMC Genomics 2013 14:528
    Content type: Research article Published on:

  32. Psoriasis lesions are characterized by large-scale shifts in gene expression. Mechanisms that underlie differentially expressed genes (DEGs), however, are not completely understood. We analyzed existing datase...

    Authors: William R Swindell, Andrew Johnston, John J Voorhees, James T Elder and Johann E Gudjonsson
    Citation: BMC Genomics 2013 14:527
    Content type: Research article Published on:

  33. Acetobacter pasteurianus 386B, an acetic acid bacterium originating from a spontaneous cocoa bean heap fermentation, proved to be an ideal functional starter culture for coca bean fermentations. It is able to dom...

    Authors: Koen Illeghems, Luc De Vuyst and Stefan Weckx
    Citation: BMC Genomics 2013 14:526
    Content type: Research article Published on:

  34. CCN2/CTGF is an established effector of TGFβ driven responses in diabetic nephropathy. We have identified an interaction between CCN2 and TGFβ leading to altered phenotypic differentiation and inhibited cellul...

    Authors: Noel Faherty, Helen O’Donovan, David Kavanagh, Stephen Madden, Gareth J McKay, Alexander P Maxwell, Finian Martin, Catherine Godson and John Crean
    Citation: BMC Genomics 2013 14:525
    Content type: Research article Published on:

  35. The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the s...

    Authors: Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M Eskridge, Etsuko N Moriyama and Greg A Somerville
    Citation: BMC Genomics 2013 14:524
    Content type: Research article Published on:

  36. S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-produci...

    Authors: Yuan-Yuan Li, Xiao Chang, Wen-Bang Yu, Hao Li, Zhi-Qiang Ye, Hui Yu, Bao-Hong Liu, Yan Zhang, Si-Liang Zhang, Bang-Ce Ye and Yi-Xue Li
    Citation: BMC Genomics 2013 14:523
    Content type: Research article Published on:

  37. REPs (Repetitive Extragenic Palindromes) are small (20–40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, m...

    Authors: Pier Paolo Di Nocera, Eliana De Gregorio and Francesco Rocco
    Citation: BMC Genomics 2013 14:522
    Content type: Research article Published on:

  38. Segmental duplications (SDs) or low-copy repeats play important roles in both gene and genome evolution. SDs have been extensively investigated in many organisms, however, there is no information about SDs in ...

    Authors: Qian Zhao, Zhenglin Zhu, Masahiro Kasahara, Shinichi Morishita and Ze Zhang
    Citation: BMC Genomics 2013 14:521
    Content type: Research article Published on:

  39. Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes a...

    Authors: Shan Li, Xia Dong and Zhengchang Su
    Citation: BMC Genomics 2013 14:520
    Content type: Research article Published on:

  40. Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s wi...

    Authors: Kyung-Tai Lee, Won-Hyong Chung, Sung-Yeoun Lee, Jung-Woo Choi, Jiwoong Kim, Dajeong Lim, Seunghwan Lee, Gul-Won Jang, Bumsoo Kim, Yun Ho Choy, Xiaoping Liao, Paul Stothard, Stephen S Moore, Sang-Heon Lee, Sungmin Ahn, Namshin Kim…
    Citation: BMC Genomics 2013 14:519
    Content type: Research article Published on:

  41. Comparative analysis of tissue-specific transcriptomes is a powerful technique to uncover tissue functions. Our FlyAtlas.org provides authoritative gene expression levels for multiple tissues of Drosophila melano...

    Authors: Venkateswara R Chintapalli, Jing Wang, Pawel Herzyk, Shireen A Davies and Julian AT Dow
    Citation: BMC Genomics 2013 14:518
    Content type: Review Published on:

  42. After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried...

    Authors: Han Xia, Chuanzhi Zhao, Lei Hou, Aiqin Li, Shuzhen Zhao, Yuping Bi, Jing An, Yanxiu Zhao, Shubo Wan and Xingjun Wang
    Citation: BMC Genomics 2013 14:517
    Content type: Research article Published on:

  43. There are very few molecular genetic tools available to study the apicomplexan parasite Cryptosporidium parvum. The organism is not amenable to continuous in vitro cultivation or transfection, and purification of...

    Authors: Jenna Oberstaller, Sandeep J Joseph and Jessica C Kissinger
    Citation: BMC Genomics 2013 14:516
    Content type: Research article Published on:

  44. Aphids are among the most destructive pests in temperate climates, causing significant damage on several crops including tomato. We carried out a transcriptomic and proteomic study to get insights into the mol...

    Authors: Valentina Coppola, Mariangela Coppola, Mariapina Rocco, Maria Cristina Digilio, Chiara D’Ambrosio, Giovanni Renzone, Rosanna Martinelli, Andrea Scaloni, Francesco Pennacchio, Rosa Rao and Giandomenico Corrado
    Citation: BMC Genomics 2013 14:515
    Content type: Research article Published on:

  45. High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics...

    Authors: Leandro Hermida, Carine Poussin, Michael B Stadler, Sylvain Gubian, Alain Sewer, Dimos Gaidatzis, Hans-Rudolf Hotz, Florian Martin, Vincenzo Belcastro, Stéphane Cano, Manuel C Peitsch and Julia Hoeng
    Citation: BMC Genomics 2013 14:514
    Content type: Software Published on:

  46. The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accur...

    Authors: David P Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale, Paula de Matos, Christopher J Mungall, Gareth Owen, Paola Roncaglia…
    Citation: BMC Genomics 2013 14:513
    Content type: Methodology article Published on:

  47. Argonaute (AGO) is the core component of RNA-induced silencing complex. The AGO gene family has been analyzed in various plant species; however, there is no report about AGOs in the well-known Traditional Chinese...

    Authors: Fenjuan Shao and Shanfa Lu
    Citation: BMC Genomics 2013 14:512
    Content type: Research article Published on:

  48. MicroRNAs (miRNAs) are a large family of endogenous, non-coding RNAs, about 22 nucleotides long, which regulate gene expression through sequence-specific base pairing with target mRNAs. Extensive studies have ...

    Authors: Chao Yuan, Xiaolong Wang, Rongqing Geng, Xiaolin He, Lei Qu and Yulin Chen
    Citation: BMC Genomics 2013 14:511
    Content type: Research article Published on:

  49. The root systems play essential roles for plants to anchorage to the soil, and to exploit the mineral and water resources. The molecular mechanisms underlying root development have been extensively studied to ...

    Authors: Xiaoxia Ma, Chaogang Shao, Huizhong Wang, Yongfeng Jin and Yijun Meng
    Citation: BMC Genomics 2013 14:510
    Content type: Research article Published on:

  50. Solid tumors present a panoply of genomic alterations, from single base changes to the gain or loss of entire chromosomes. Although aberrations at the two extremes of this spectrum are readily defined, compreh...

    Authors: Mohana Ray, Steve Goldstein, Shiguo Zhou, Konstantinos Potamousis, Deepayan Sarkar, Michael A Newton, Elizabeth Esterberg, Christina Kendziorski, Oliver Bogler and David C Schwartz
    Citation: BMC Genomics 2013 14:505
    Content type: Research article Published on:

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BMC Genomics

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