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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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

  21. 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:

  22. 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:

  24. 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:

  25. 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:

  26. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. Cancer cells frequently adopt cellular and molecular alterations and acquire resistance to cytostatic drugs. Chemotherapy with oxaliplatin is among the leading treatments for colorectal cancer with a response ...

    Authors: Piroska Virag, Eva Fischer-Fodor, Maria Perde-Schrepler, Ioana Brie, Corina Tatomir, Loredana Balacescu, Ioana Berindan-Neagoe, Bogdan Victor and Ovidiu Balacescu
    Citation: BMC Genomics 2013 14:480
    Content type: Research article Published on:

  40. Gcn5 belongs to a family of histone acetyltransferases (HATs) that regulate protein function by acetylation. Gcn5 plays several different roles in gene transcription throughout the genome but their characteris...

    Authors: Yongtao Xue-Franzén, Johan Henriksson, Thomas R Bürglin and Anthony PH Wright
    Citation: BMC Genomics 2013 14:479
    Content type: Research article Published on:

  41. Nonsense-Mediated decay (NMD) selectively degrades mRNA transcripts that carry premature stop codons. NMD is often triggered by alternative splicing (AS) modifications introducing such codons. NMD plays an imp...

    Authors: Lilach Soreq, Hagai Bergman, Zvi Israel and Hermona Soreq
    Citation: BMC Genomics 2013 14:478
    Content type: Research article Published on:

  42. 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:

  43. Genlisea aurea (Lentibulariaceae) is a carnivorous plant with unusually small genome size - 63.6 Mb – one of the smallest known among higher plants. Data on the genome sizes and the phylogeny of Genlisea suggest ...

    Authors: Evgeny V Leushkin, Roman A Sutormin, Elena R Nabieva, Aleksey A Penin, Alexey S Kondrashov and Maria D Logacheva
    Citation: BMC Genomics 2013 14:476
    Content type: Research article Published on:

  44. The endothelial compartment, comprising arterial, venous and lymphatic cell types, is established prenatally in association with rapid phenotypic and functional changes. The molecular mechanisms underpinning t...

    Authors: Jihoon E Joo, Ursula Hiden, Luciana Lassance, Lavinia Gordon, David J Martino, Gernot Desoye and Richard Saffery
    Citation: BMC Genomics 2013 14:475
    Content type: Research article Published on:

  45. Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of...

    Authors: Subarna Thakur, Philippe Normand, Vincent Daubin, Louis S Tisa and Arnab Sen
    Citation: BMC Genomics 2013 14:474
    Content type: Research article Published on:

  46. Neurofibromatosis type 1 (NF1) is a common dominant tumor predisposition syndrome affecting 1 in 3,500 individuals. The hallmarks of NF1 are the development of peripheral nerve sheath tumors either benign (der...

    Authors: Julien Masliah-Planchon, Eric Pasmant, Armelle Luscan, Ingrid Laurendeau, Nicolas Ortonne, Mikael Hivelin, Jennifer Varin, Laurence Valeyrie-Allanore, Valérie Dumaine, Laurent Lantieri, Karen Leroy, Béatrice Parfait, Pierre Wolkenstein, Michel Vidaud, Dominique Vidaud and Ivan Bièche
    Citation: BMC Genomics 2013 14:473
    Content type: Research article Published on:

  47. Offspring of pregnancy complicated with preeclampsia are at high risk for hypertension, stroke and possibly obesity. The mechanisms behind the association of intrauterine exposure to preeclampsia and high risk...

    Authors: Jing He, Aiping Zhang, Min Fang, Rong Fang, Jiamei Ge, Yuan Jiang, Hong Zhang, Cong Han, Xiaoqun Ye, Danqing Yu, Hefeng Huang, Yun Liu and Minyue Dong
    Citation: BMC Genomics 2013 14:472
    Content type: Research article Published on:

  48. Next generation sequencing provides new opportunities to explore transcriptomes. However, challenges remain for accurate differentiation of homoeoalleles and paralogs, particularly in polyploid organisms with ...

    Authors: Juan J Gutierrez-Gonzalez, Zheng Jin Tu and David F Garvin
    Citation: BMC Genomics 2013 14:471
    Content type: Research article Published on:

  49. A fundamental question in molecular neurobiology is how genes that determine basic neuronal properties shape the functional organization of brain circuits underlying complex learned behaviors. Given the growin...

    Authors: Peter V Lovell, Julia B Carleton and Claudio V Mello
    Citation: BMC Genomics 2013 14:470
    Content type: Research article Published on:

  50. Biopsies taken from individual tumours exhibit extensive differences in their cellular composition due to the inherent heterogeneity of cancers and vagaries of sample collection. As a result genes expressed in...

    Authors: Tamasin N Doig, David A Hume, Thanasis Theocharidis, John R Goodlad, Christopher D Gregory and Tom C Freeman
    Citation: BMC Genomics 2013 14:469
    Content type: Research article Published on:

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BMC Genomics

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