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  1. Spore germination of the yeast Saccharomyces cerevisiae is a multi-step developmental path on which dormant spores re-enter the mitotic cell cycle and resume vegetative growth. Upon addition of a fermentable carb...

    Authors: Cecilia Geijer, Ivan Pirkov, Wanwipa Vongsangnak, Abraham Ericsson, Jens Nielsen, Marcus Krantz and Stefan Hohmann
    Citation: BMC Genomics 2012 13:554
    Content type: Research article Published on:

  2. The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicke...

    Authors: Biao Wang, Robert Ekblom, Tanja M Strand, Silvia Portela-Bens and Jacob Höglund
    Citation: BMC Genomics 2012 13:553
    Content type: Research article Published on:

  3. As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was ...

    Authors: Laure Frésard, Sophie Leroux, Patrice Dehais, Bertrand Servin, Hélène Gilbert, Olivier Bouchez, Christophe Klopp, Cédric Cabau, Florence Vignoles, Katia Feve, Amélie Ricros, David Gourichon, Christian Diot, Sabine Richard, Christine Leterrier, Catherine Beaumont…
    Citation: BMC Genomics 2012 13:551
    Content type: Research article Published on:

  4. Small non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria ...

    Authors: Nadja Patenge, André Billion, Peter Raasch, Jana Normann, Aleksandra Wisniewska-Kucper, Julia Retey, Valesca Boisguérin, Thomas Hartsch, Torsten Hain and Bernd Kreikemeyer
    Citation: BMC Genomics 2012 13:550
    Content type: Research article Published on:

  5. Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. Although the general hypothesis of an increased molecular flexibility in the cold is widely ac...

    Authors: Heidrun Sigrid Windisch, Magnus Lucassen and Stephan Frickenhaus
    Citation: BMC Genomics 2012 13:549
    Content type: Research article Published on:

  6. Epinotia aporema (Lepidoptera: Tortricidae) is an important pest of legume crops in South America. Epinotia aporema granulovirus (EpapGV) is a baculovirus that causes a polyorganotropic infection in the host larv...

    Authors: María Leticia Ferrelli, Ricardo Salvador, Marina Elizabeth Biedma, Marcelo Facundo Berretta, Santiago Haase, Alicia Sciocco-Cap, Pablo Daniel Ghiringhelli and Víctor Romanowski
    Citation: BMC Genomics 2012 13:548
    Content type: Research article Published on:

  7. New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pi...

    Authors: Yuliaxis Ramayo-Caldas, Nuria Mach, Anna Esteve-Codina, Jordi Corominas, Anna Castelló, Maria Ballester, Jordi Estellé, Noelia Ibáñez-Escriche, Ana I Fernández, Miguel Pérez-Enciso and Josep M Folch
    Citation: BMC Genomics 2012 13:547
    Content type: Research article Published on:

  8. Coordinated cell growth and development requires that cells regulate the expression of large sets of genes in an appropriate manner, and one of the most complex and metabolically demanding pathways that cells ...

    Authors: James T Arnone, Adam Robbins-Pianka, Jeffrey R Arace, Sara Kass-Gergi and Michael A McAlear
    Citation: BMC Genomics 2012 13:546
    Content type: Research article Published on:

  9. The classical Bordetella subspecies are phylogenetically closely related, yet differ in some of the most interesting and important characteristics of pathogens, such as host range, virulence and persistence. The ...

    Authors: Jihye Park, Ying Zhang, Anne M Buboltz, Xuqing Zhang, Stephan C Schuster, Umesh Ahuja, Minghsun Liu, Jeff F Miller, Mohammed Sebaihia, Stephen D Bentley, Julian Parkhill and Eric T Harvill
    Citation: BMC Genomics 2012 13:545
    Content type: Research article Published on:

  10. The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four...

    Authors: Amit Katiyar, Shuchi Smita, Sangram Keshari Lenka, Ravi Rajwanshi, Viswanathan Chinnusamy and Kailash Chander Bansal
    Citation: BMC Genomics 2012 13:544
    Content type: Research article Published on:

  11. The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strate...

    Authors: Rasmus Froberg Brøndum, Guosheng Su, Mogens Sandø Lund, Philip J Bowman, Michael E Goddard and Benjamin J Hayes
    Citation: BMC Genomics 2012 13:543
    Content type: Methodology article Published on:

  12. The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been...

    Authors: Jason J Gill, Joel D Berry, William K Russell, Lauren Lessor, Diego A Escobar-Garcia, Daniel Hernandez, Ashley Kane, Jennifer Keene, Matthew Maddox, Rebecca Martin, Sheba Mohan, Ashlyn M Thorn, David H Russell and Ry Young
    Citation: BMC Genomics 2012 13:542
    Content type: Research article Published on:

  13. Myostatin, a member of the TGFβ superfamily, is well known as a potent and specific negative regulator of muscle growth. Targeting the myostatin signalling pathway may offer promising therapeutic strategies fo...

    Authors: Olivier Monestier, Caroline Brun, Katy Heu, Bruno Passet, Mélanie Malhouroux, Laetitia Magnol, Jean-Luc Vilotte and Véronique Blanquet
    Citation: BMC Genomics 2012 13:541
    Content type: Research article Published on:

  14. S. aureus is one of the main pathogens responsible for the intra-mammary infection in dairy ruminants. Although much work has been carried out to understand the complex physiological and cellular events that occu...

    Authors: Paola Cremonesi, Rossana Capoferri, Giuliano Pisoni, Marcello Del Corvo, Francesco Strozzi, Rachel Rupp, Hugues Caillat, Paola Modesto, Paolo Moroni, John L Williams, Bianca Castiglioni and Alessandra Stella
    Citation: BMC Genomics 2012 13:540
    Content type: Research article Published on:

  15. Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. ...

    Authors: Liang Zhao, Lv Yuanda, Cai Caiping, Tong Xiangchao, Chen Xiangdong, Zhang Wei, Du Hao, Guo Xiuhua and Guo Wangzhen
    Citation: BMC Genomics 2012 13:539
    Content type: Research article Published on:

  17. Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To fac...

    Authors: Qiong Zhang, Baiquan Ma, Hui Li, Yuansheng Chang, Yuanyuan Han, Jing Li, Guochao Wei, Shuang Zhao, Muhammad Awais Khan, Ying Zhou, Chao Gu, Xingzhong Zhang, Zhenhai Han, Schuyler S Korban, Shaohua Li and Yuepeng Han
    Citation: BMC Genomics 2012 13:537
    Content type: Research article Published on:

  18. Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of strat...

    Authors: Li Ma, George R Wiggans, Shengwen Wang, Tad S Sonstegard, Jing Yang, Brian A Crooker, John B Cole, Curtis P Van Tassell, Thomas J Lawlor and Yang Da
    Citation: BMC Genomics 2012 13:536
    Content type: Research article Published on:

  19. Although many diseases have been well characterized at the molecular level, the underlying mechanisms are often unknown. Nearly half of all human genes remain poorly studied, yet these genes may contribute to ...

    Authors: Sipko van Dam, Rui Cordeiro, Thomas Craig, Jesse van Dam, Shona H Wood and João Pedro de Magalhães
    Citation: BMC Genomics 2012 13:535
    Content type: Research article Published on:

  20. Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-met...

    Authors: Heiko Niewerth, Jörg Schuldes, Katja Parschat, Patrick Kiefer, Julia A Vorholt, Rolf Daniel and Susanne Fetzner
    Citation: BMC Genomics 2012 13:534
    Content type: Research article Published on:

  21. The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. ca...

    Authors: Jeff R Broadbent, Eric C Neeno-Eckwall, Buffy Stahl, Kanokwan Tandee, Hui Cai, Wesley Morovic, Philippe Horvath, Jessie Heidenreich, Nicole T Perna, Rodolphe Barrangou and James L Steele
    Citation: BMC Genomics 2012 13:533
    Content type: Research article Published on:

  22. DNA methylation is a fundamental component of epigenetic modification, which is intimately involved in the regulation of gene expression. One important DNA methylation pathway reduces the abilities of transcri...

    Authors: Weixing Feng, Zengchao Dong, Bo He and Kejun Wang
    Citation: BMC Genomics 2012 13:532
    Content type: Methodology article Published on:

  23. Trypanosoma cruzi marinkellei is a bat-associated parasite of the subgenus Schizotrypanum and it is regarded as a T. cruzi subspecies. Here we report a draft genome sequence of T. c. marinkellei and comparison wi...

    Authors: Oscar Franzén, Carlos Talavera-López, Stephen Ochaya, Claire E Butler, Louisa A Messenger, Michael D Lewis, Martin S Llewellyn, Cornelis J Marinkelle, Kevin M Tyler, Michael A Miles and Björn Andersson
    Citation: BMC Genomics 2012 13:531
    Content type: Research article Published on:

  24. Bluefin tunas are highly prized pelagic fish species representing a significant economic resource to fisheries throughout the world. Atlantic bluefin tuna (Thunnus thynnus) populations have significantly declined...

    Authors: Luke D Gardner, Nishad Jayasundara, Pedro C Castilho and Barbara Block
    Citation: BMC Genomics 2012 13:530
    Content type: Research article Published on:

  25. Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In t...

    Authors: Xiao-Wei Wang, Qiong-Yi Zhao, Jun-Bo Luan, Yu-Jun Wang, Gen-Hong Yan and Shu-Sheng Liu
    Citation: BMC Genomics 2012 13:529
    Content type: Research article Published on:

  26. In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level reg...

    Authors: Flora Picard, Hélène Milhem, Pascal Loubière, Béatrice Laurent, Muriel Cocaign-Bousquet and Laurence Girbal
    Citation: BMC Genomics 2012 13:528
    Content type: Research article Published on:

  27. Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allel...

    Authors: Marina de Miguel, Nuria de Maria, M Ángeles Guevara, Luis Diaz, Enrique Sáez-Laguna, David Sánchez-Gómez, Emilie Chancerel, Ismael Aranda, Carmen Collada, Christophe Plomion, José-Antonio Cabezas and María-Teresa Cervera
    Citation: BMC Genomics 2012 13:527
    Content type: Research article Published on:

  28. The relative contribution of epigenetic mechanisms to carcinogenesis is not well understood, including the extent to which epigenetic dysregulation and somatic mutations target similar genes and pathways. We h...

    Authors: Jung H Kim, Alla Karnovsky, Vasudeva Mahavisno, Terry Weymouth, Manjusha Pande, Dana C Dolinoy, Laura S Rozek and Maureen A Sartor
    Citation: BMC Genomics 2012 13:526
    Content type: Research article Published on:

  29. Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable “CYPomes” ranging from one to more tha...

    Authors: Venkatesh Moktali, Jongsun Park, Natalie D Fedorova-Abrams, Bongsoo Park, Jaeyoung Choi, Yong-Hwan Lee and Seogchan Kang
    Citation: BMC Genomics 2012 13:525
    Content type: Research article Published on:

  30. Assessing the reliability of experimental replicates (or global alterations corresponding to different experimental conditions) is a critical step in analyzing RNA-Seq data. Pearson’s correlation coefficient r ha...

    Authors: Stefan K Schulze, Rahul Kanwar, Meike Gölzenleuchter, Terry M Therneau and Andreas S Beutler
    Citation: BMC Genomics 2012 13:524
    Content type: Methodology article Published on:

  31. Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing tec...

    Authors: Wanxing Wang, Shunmou Huang, Yumei Liu, Zhiyuan Fang, Limei Yang, Wei Hua, Suxia Yuan, Shengyi Liu, Jifeng Sun, Mu Zhuang, Yangyong Zhang and Aisong Zeng
    Citation: BMC Genomics 2012 13:523
    Content type: Research article Published on:

  32. Switchgrass (Panicum virgatum) is a herbaceous crop for the cellulosic biofuel feedstock development in the USA and Europe. As switchgrass is a naturally outcrossing species, accurate identification of selfed pro...

    Authors: Linglong Liu and Yanqi Wu
    Citation: BMC Genomics 2012 13:522
    Content type: Methodology article Published on:

  34. The Guinea pig (Cavia porcellus) is one of the most extensively used animal models to study infectious diseases. However, despite its tremendous contribution towards understanding the establishment, progression a...

    Authors: Ruchi Jain, Bappaditya Dey and Anil K Tyagi
    Citation: BMC Genomics 2012 13:520
    Content type: Research article Published on:

  35. The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immuno-compromised patients. Recently developed high-throughput transcrip...

    Authors: Sebastian Müller, Clara Baldin, Marco Groth, Reinhard Guthke, Olaf Kniemeyer, Axel A Brakhage and Vito Valiante
    Citation: BMC Genomics 2012 13:519
    Content type: Research article Published on:

  36. Early stages of fruit development from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this...

    Authors: Kaori Ando, Kevin M Carr and Rebecca Grumet
    Citation: BMC Genomics 2012 13:518
    Content type: Research article Published on:

  37. Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced ...

    Authors: Oscar Dias, Andreas K Gombert, Eugénio C Ferreira and Isabel Rocha
    Citation: BMC Genomics 2012 13:517
    Content type: Research article Published on:

  38. B-cell non-Hodgkin lymphoma represents a diverse group of hematological malignancies, of which follicular lymphoma (FL) is one of the most common subtypes. Family and epidemiological studies suggest an importa...

    Authors: Christine F Skibola, Lucia Conde, Jia-Nee Foo, Jacques Riby, Keith Humphreys, Fenna CM Sillé, Hatef Darabi, Sylvia Sanchez, Henrik Hjalgrim, Jianjun Liu, Paige M Bracci and Karin E Smedby
    Citation: BMC Genomics 2012 13:516
    Content type: Research article Published on:

  39. Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published...

    Authors: Joanne Purves, Matthew Blades, Yasrab Arafat, Salman A Malik, Christopher D Bayliss and Julie A Morrissey
    Citation: BMC Genomics 2012 13:515
    Content type: Research article Published on:

  40. Guinea pig (Cavia porcellus) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a...

    Authors: Falk Hildebrand, Tine Ebersbach, Henrik Bjørn Nielsen, Xiaoping Li, Si Brask Sonne, Marcelo Bertalan, Peter Dimitrov, Lise Madsen, Junjie Qin, Jun Wang, Jeroen Raes, Karsten Kristiansen and Tine Rask Licht
    Citation: BMC Genomics 2012 13:514
    Content type: Research article Published on:

  41. Owing to the low cost of the high throughput Next Generation Sequencing (NGS) technology, more and more species have been and will be sequenced. However, de novo assemblies of large eukaryotic genomes thus produc...

    Authors: Man Rao, Mireille Morisson, Thomas Faraut, Suzanne Bardes, Katia Fève, Emmanuelle Labarthe, Valérie Fillon, Yinhua Huang, Ning Li and Alain Vignal
    Citation: BMC Genomics 2012 13:513
    Content type: Research article Published on:

  43. During sexual development, filamentous ascomycetes form complex, three-dimensional fruiting bodies for the protection and dispersal of sexual spores. Fruiting bodies contain a number of cell types not found in...

    Authors: Ines Teichert, Gabriele Wolff, Ulrich Kück and Minou Nowrousian
    Citation: BMC Genomics 2012 13:511
    Content type: Research article Published on:

  44. In Gram-negative bacteria, the outer membrane is composed of an asymmetric lipid bilayer of phopspholipids and lipopolysaccharides, and the transmembrane proteins that reside in this membrane are almost exclus...

    Authors: Nagarajan Paramasivam, Michael Habeck and Dirk Linke
    Citation: BMC Genomics 2012 13:510
    Content type: Research article Published on:

  45. The events leading to sepsis start with an invasive infection of a primary organ of the body followed by an overwhelming systemic response. Intra-abdominal infections are the second most common cause of sepsis...

    Authors: Minny Bhatty, Ruping Fan, William M Muir, Stephen B Pruett and Bindu Nanduri
    Citation: BMC Genomics 2012 13:509
    Content type: Research article Published on:

  46. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease...

    Authors: Ryan Tewhey, Christopher R Cannavino, John AD Leake, Vikas Bansal, Eric J Topol, Ali Torkamani, John S Bradley and Nicholas J Schork
    Citation: BMC Genomics 2012 13:508
    Content type: Research article Published on:

  47. Genomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (Anguilla anguilla) stock has been dec...

    Authors: Jose Martin Pujolar, Ilaria AM Marino, Massimo Milan, Alessandro Coppe, Gregory E Maes, Fabrizio Capoccioni, Eleonora Ciccotti, Lieven Bervoets, Adrian Covaci, Claude Belpaire, Gordon Cramb, Tomaso Patarnello, Luca Bargelloni, Stefania Bortoluzzi and Lorenzo Zane
    Citation: BMC Genomics 2012 13:507
    Content type: Research article Published on:

  48. Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as ...

    Authors: Katherine H Fisher, Victoria M Wright, Amy Taylor, Martin P Zeidler and Stephen Brown
    Citation: BMC Genomics 2012 13:506
    Content type: Research article Published on:

  49. Metastasis is characterized by spreading of neoplastic cells to an organ other than where they originated and is the predominant cause of death among cancer patients. This holds true for melanoma, whose incide...

    Authors: Jared J Gartner, Sean Davis, Xiaomu Wei, Jimmy C Lin, Niraj S Trivedi, Jamie K Teer, Paul S Meltzer, Steven A Rosenberg and Yardena Samuels
    Citation: BMC Genomics 2012 13:505
    Content type: Research article Published on:

  50. The function of RNA from the non-coding (the so called “dark matter”) regions of the genome has been a subject of considerable recent debate. Perhaps the most controversy is regarding the function of RNAs foun...

    Authors: Georges St Laurent, Dmitry Shtokalo, Michael R Tackett, Zhaoqing Yang, Tatyana Eremina, Claes Wahlestedt, Silvio Urcuqui-Inchima, Bernd Seilheimer, Timothy A McCaffrey and Philipp Kapranov
    Citation: BMC Genomics 2012 13:504
    Content type: Research article Published on:

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BMC Genomics

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