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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holo...

    Authors: Walter C Dunlap, Antonio Starcevic, Damir Baranasic, Janko Diminic, Jurica Zucko, Ranko Gacesa, Madeleine J H van Oppen, Daslav Hranueli, John Cullum and Paul F Long
    Citation: BMC Genomics 2013 14:509
    Content type: Database Published on:

  22. Epithelial ovarian cancer (EOC) is one of the most lethal gynecological cancers; the majority of EOC is the serous histotype and diagnosed at advanced stage. IL6 is the cytokine that has been found most freque...

    Authors: Patrizia Pinciroli, Chiara Alberti, Marialuisa Sensi, Silvana Canevari and Antonella Tomassetti
    Citation: BMC Genomics 2013 14:508
    Content type: Research article Published on:

  24. Genome-wide association studies (GWAS) using array-based genotyping technology are widely used to identify genetic loci associated with complex diseases or other phenotypes. The costs of GWAS projects based on...

    Authors: Alexander Teumer, Florian D Ernst, Anja Wiechert, Katharina Uhr, Matthias Nauck, Astrid Petersmann, Henry Völzke, Uwe Völker and Georg Homuth
    Citation: BMC Genomics 2013 14:506
    Content type: Research article Published on:

  25. 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:

  26. Genetic alterations of transcription factors (TFs) have been implicated in the tumorigenesis of cancers. In many cancers, alteration of TFs results in aberrant activity of them without changing their gene expr...

    Authors: Mingzhu Zhu, Chun-Chi Liu and Chao Cheng
    Citation: BMC Genomics 2013 14:504
    Content type: Methodology article Published on:

  27. The G protein-coupled receptor (GPCR) signaling pathway plays an essential role in signal transmission and response to external stimuli in mammalian cells. Protein components of this pathway have been characte...

    Authors: Jesse A Port, Micaela S Parker, Robin B Kodner, James C Wallace, E Virginia Armbrust and Elaine M Faustman
    Citation: BMC Genomics 2013 14:503
    Content type: Research article Published on:

  28. Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome siz...

    Authors: Saemundur Sveinsson, Navdeep Gill, Nolan C Kane and Quentin Cronk
    Citation: BMC Genomics 2013 14:502
    Content type: Research article Published on:

  29. Deep sequencing is a powerful tool for assessing viral genetic diversity. Such experiments harness the high coverage afforded by next generation sequencing protocols by treating sequencing reads as a populatio...

    Authors: Kerensa McElroy, Osvaldo Zagordi, Rowena Bull, Fabio Luciani and Niko Beerenwinkel
    Citation: BMC Genomics 2013 14:501
    Content type: Methodology article Published on:

  30. Antimicrobial resistance among pneumococci has greatly increased over the past two to three decades. Resistance to tetracycline (tet(M)), chloramphenicol (cat) and macrolides (erm(B) and/or mef(A/E)) is generally...

    Authors: Kelly L Wyres, Andries van Tonder, Lotte M Lambertsen, Regine Hakenbeck, Julian Parkhill, Stephen D Bentley and Angela B Brueggemann
    Citation: BMC Genomics 2013 14:500
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2023 24:664

  32. The moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usabilit...

    Authors: Andreas D Zimmer, Daniel Lang, Karol Buchta, Stephane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van de Peer, Stefan A Rensing and Ralf Reski
    Citation: BMC Genomics 2013 14:498
    Content type: Research article Published on:

  33. Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous invol...

    Authors: Ke-Shiuan Lynn, Chen-Hua Lu, Han-Ying Yang, Wen-Lian Hsu and Wen-Harn Pan
    Citation: BMC Genomics 2013 14:497
    Content type: Methodology article Published on:

  35. Regions of the genome that are under evolutionary constraint across multiple species have previously been used to identify functional sequences in the human genome. Furthermore, it is known that there is an in...

    Authors: Alan Hodgkinson, Ferran Casals, Youssef Idaghdour, Jean-Christophe Grenier, Ryan D Hernandez and Philip Awadalla
    Citation: BMC Genomics 2013 14:495
    Content type: Research article Published on:

  36. Funded by the National Institutes of Health (NIH), the aim of the Mod el Organism ENC yclopedia o f D NA E lements (modENCODE) project is to provide the biological research community with a comprehensive encyclop...

    Authors: Quang M Trinh, Fei-Yang Arthur Jen, Ziru Zhou, Kar Ming Chu, Marc D Perry, Ellen T Kephart, Sergio Contrino, Peter Ruzanov and Lincoln D Stein
    Citation: BMC Genomics 2013 14:494
    Content type: Software Published on:

  37. Homologous recombination is the key process that generates genetic diversity and drives evolution. SPO11 protein triggers recombination by introducing DNA double stranded breaks at discreet areas of the genome...

    Authors: Fatima Smagulova, Kevin Brick, Yongmei Pu, Uttara Sengupta, R Daniel Camerini-Otero and Galina V Petukhova
    Citation: BMC Genomics 2013 14:493
    Content type: Research article Published on:

  39. Termites are highly eusocial insects and show a division of labor whereby morphologically distinct individuals specialize in distinct tasks. In the lower termite Reticulitermes flavipes (Rhinotermitidae), non-rep...

    Authors: Ruchira Sen, Rhitoban Raychoudhury, Yunpeng Cai, Yijun Sun, Verena-Ulrike Lietze, Drion G Boucias and Michael E Scharf
    Citation: BMC Genomics 2013 14:491
    Content type: Research article Published on:

  40. Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long bee...

    Authors: Xingfei Zheng, Cheng Pan, Ying Diao, Yongning You, Chaozhu Yang and Zhongli Hu
    Citation: BMC Genomics 2013 14:490
    Content type: Research article Published on:

  41. Bacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete...

    Authors: Le Tang, Yang Li, Xia Deng, Randal N Johnston, Gui-Rong Liu and Shu-Lin Liu
    Citation: BMC Genomics 2013 14:489
    Content type: Research article Published on:

  42. Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., an evergreen broadleaf legume shrub, is distributed in Mid-Asia where the temperature can be as low as −30°C during the winter. Although A. mongolicus is an id...

    Authors: Tao Pang, Chu-Yu Ye, Xinli Xia and Weilun Yin
    Citation: BMC Genomics 2013 14:488
    Content type: Research article Published on:

  43. Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard c...

    Authors: Julia Metzger, Ute Philipp, Maria Susana Lopes, Artur da Camara Machado, Michela Felicetti, Maurizio Silvestrelli and Ottmar Distl
    Citation: BMC Genomics 2013 14:487
    Content type: Research article Published on:

  44. The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel,...

    Authors: Michael H Farkas, Gregory R Grant, Joseph A White, Maria E Sousa, Mark B Consugar and Eric A Pierce
    Citation: BMC Genomics 2013 14:486
    Content type: Research article Published on:

  45. Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microb...

    Authors: Alexis P Yelton, Luis R Comolli, Nicholas B Justice, Cindy Castelle, Vincent J Denef, Brian C Thomas and Jillian F Banfield
    Citation: BMC Genomics 2013 14:485
    Content type: Research article Published on:

  46. Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disea...

    Authors: Rory A Eutsey, N Luisa Hiller, Joshua P Earl, Benjamin A Janto, Margaret E Dahlgren, Azad Ahmed, Evan Powell, Matthew P Schultz, Janet R Gilsdorf, Lixin Zhang, Arnold Smith, Timothy F Murphy, Sanjay Sethi, Kai Shen, J Christopher Post, Fen Z Hu…
    Citation: BMC Genomics 2013 14:484
    Content type: Research article Published on:

  47. Associations between proteins are essential to understand cell biology. While this complex interplay between proteins has been studied in model organisms, it has not yet been described for the oomycete late bl...

    Authors: Michael F Seidl, Adrian Schneider, Francine Govers and Berend Snel
    Citation: BMC Genomics 2013 14:483
    Content type: Research article Published on:

  48. MicroRNAs (miRNAs) are an abundant class of endogenous small RNA molecules that downregulate gene expression at the posttranscriptional level. They play important roles in multiple biological processes by regu...

    Authors: Rune Andreassen, Merete Molton Worren and Bjørn Høyheim
    Citation: BMC Genomics 2013 14:482
    Content type: Research article Published on:

  49. Salmonella is a widely distributed foodborne pathogen that causes tens of millions of salmonellosis cases globally every year. While the genomic diversity of Salmonella is increasingly well studied, our knowledge...

    Authors: Andrea I Moreno Switt, Renato H Orsi, Henk C den Bakker, Kitiya Vongkamjan, Craig Altier and Martin Wiedmann
    Citation: BMC Genomics 2013 14:481
    Content type: Research article Published on:

  50. Two plant-specific transcription factors, NAC and YABBY, are involved in important plant developmental processes. However their molecular mechanisms, especially DNA binding sites and co-regulated genes, are la...

    Authors: Md Shamimuzzaman and Lila Vodkin
    Citation: BMC Genomics 2013 14:477
    Content type: Research article Published on:

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BMC Genomics

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