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  1. Although more than 246 loci/genes are associated with inherited retinal diseases, the mechanistic events that link genetic mutations to photoreceptor cell death are poorly understood. miRNAs play a relevant ro...

    Authors: Sem Genini, Karina E Guziewicz, William A Beltran and Gustavo D Aguirre
    Citation: BMC Genomics 2014 15:172
    Content type: Research article Published on:

  2. Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host’s health status. In this s...

    Authors: Francesca Bottacini, Mary O’Connell Motherway, Justin Kuczynski, Kerry Joan O’Connell, Fausta Serafini, Sabrina Duranti, Christian Milani, Francesca Turroni, Gabriele Andrea Lugli, Aldert Zomer, Daria Zhurina, Christian Riedel, Marco Ventura and Douwe van Sinderen
    Citation: BMC Genomics 2014 15:170
    Content type: Research article Published on:

  3. A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The ...

    Authors: Katrine L Whiteson, David Hernandez, Vladimir Lazarevic, Nadia Gaia, Laurent Farinelli, Patrice François, Paola Pilo, Joachim Frey and Jacques Schrenzel
    Citation: BMC Genomics 2014 15:169
    Content type: Research article Published on:

  4. Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified...

    Authors: Xuan Ma, Yingjie Zhu, Chunfang Li, Peng Xue, Yanmei Zhao, Shilin Chen, Fuquan Yang and Long Miao
    Citation: BMC Genomics 2014 15:168
    Content type: Research article Published on:

  5. Social dominance is important for the reproductive success of males in many species. In the black-faced blenny (Tripterygion delaisi) during the reproductive season, some males change color and invest in nest mak...

    Authors: Celia Schunter, Steven V Vollmer, Enrique Macpherson and Marta Pascual
    Citation: BMC Genomics 2014 15:167
    Content type: Research article Published on:

  6. Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associa...

    Authors: Serap Gonen, Natalie R Lowe, Timothé Cezard, Karim Gharbi, Stephen C Bishop and Ross D Houston
    Citation: BMC Genomics 2014 15:166
    Content type: Research article Published on:

  7. Yellowtail (Seriola quinqueradiata) are an economically important species in Japan. However, there are currently no methods for captive breeding and early rearing for yellowtail. Thus, the commercial cultivation ...

    Authors: Jun-ya Aoki, Wataru Kai, Yumi Kawabata, Akiyuki Ozaki, Kazunori Yoshida, Tatsuo Tsuzaki, Kanako Fuji, Takashi Koyama, Takashi Sakamoto and Kazuo Araki
    Citation: BMC Genomics 2014 15:165
    Content type: Research article Published on:

  8. The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important p...

    Authors: Lyndel W Meinhardt, Gustavo Gilson Lacerda Costa, Daniela PT Thomazella, Paulo José PL Teixeira, Marcelo Falsarella Carazzolle, Stephan C Schuster, John E Carlson, Mark J Guiltinan, Piotr Mieczkowski, Andrew Farmer, Thiruvarangan Ramaraj, Jayne Crozier, Robert E Davis, Jonathan Shao, Rachel L Melnick, Gonçalo AG Pereira…
    Citation: BMC Genomics 2014 15:164
    Content type: Research article Published on:

  9. The Type VI secretion system (T6SS) has been identified in several different bacteria, including the plant pathogenPantoea ananatis. Previous in silico analyses described three different T6SS loci present in the ...

    Authors: Divine Yufetar Shyntum, Stephanus Nicolaas Venter, Lucy Novungayo Moleleki, Ian Toth and Teresa Ann Coutinho
    Citation: BMC Genomics 2014 15:163
    Content type: Research article Published on:

  11. Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of ...

    Authors: Heather E Machado, Ginger Jui, Domino A Joyce, Christian RL Reilly III, David H Lunt and Suzy CP Renn
    Citation: BMC Genomics 2014 15:161
    Content type: Research article Published on:

  12. Clostridium difficile is an anaerobic, Gram-positive bacterium that can reside as a commensal within the intestinal microbiota of healthy individuals or cause life-threatening antibiotic-associated diarrhea in im...

    Authors: Laura J Pettit, Hilary P Browne, Lu Yu, Wiep Klaas Smits, Robert P Fagan, Lars Barquist, Melissa J Martin, David Goulding, Sylvia H Duncan, Harry J Flint, Gordon Dougan, Jyoti S Choudhary and Trevor D Lawley
    Citation: BMC Genomics 2014 15:160
    Content type: Research article Published on:

  13. The unfolded protein response (UPR) is a network of intracellular signaling pathways that supports the ability of the secretory pathway to maintain a balance between the load of proteins entering the endoplasm...

    Authors: Karthik Krishnan, Zhaowei Ren, Liliana Losada, William C Nierman, Long Jason Lu and David S Askew
    Citation: BMC Genomics 2014 15:159
    Content type: Research article Published on:

  14. Synthetic lethality is an appealing technique for selectively targeting cancer cells which have acquired molecular changes that distinguish them from normal cells. High-throughput RNAi-based screens have been ...

    Authors: Michael Boettcher, Andrew Lawson, Viola Ladenburger, Johannes Fredebohm, Jonas Wolf, Jörg D Hoheisel, Christian Frezza and Tomer Shlomi
    Citation: BMC Genomics 2014 15:158
    Content type: Research article Published on:

  15. Transcriptional activator-like (TAL) effectors, formerly known as the AvrBs3/PthA protein family, are DNA-binding effectors broadly found in Xanthomonas spp. that transactivate host genes upon injection via the b...

    Authors: Andre LA Pereira, Marcelo F Carazzolle, Valeria Y Abe, Maria LP de Oliveira, Mariane N Domingues, Jaqueline C Silva, Raul A Cernadas and Celso E Benedetti
    Citation: BMC Genomics 2014 15:157
    Content type: Research article Published on:

  16. Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endomet...

    Authors: Ting Gu, Meng-jin Zhu, Martine Schroyen, Long Qu, Dan Nettleton, Dan Kuhar, Joan K Lunney, Jason W Ross, Shu-hong Zhao and Christopher K Tuggle
    Citation: BMC Genomics 2014 15:156
    Content type: Research article Published on:

  17. Defining cell type-specific transcriptomes in mammals can be challenging, especially for unannotated regions of the genome. We have developed an analytical pipeline called groHMM for annotating primary transcr...

    Authors: Xin Luo, Minho Chae, Raga Krishnakumar, Charles G Danko and W Lee Kraus
    Citation: BMC Genomics 2014 15:155
    Content type: Research article Published on:

  18. High-throughput sequencing is gradually replacing microarrays as the preferred method for studying mRNA expression levels, providing nucleotide resolution and accurately measuring absolute expression levels of...

    Authors: Jeremy A Miller, Vilas Menon, Jeff Goldy, Ajamete Kaykas, Chang-Kyu Lee, Kimberly A Smith, Elaine H Shen, John W Phillips, Ed S Lein and Mike J Hawrylycz
    Citation: BMC Genomics 2014 15:154
    Content type: Methodology article Published on:

  19. Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition...

    Authors: Claudia T Guimaraes, Christiano C Simoes, Maria Marta Pastina, Lyza G Maron, Jurandir V Magalhaes, Renato CC Vasconcellos, Lauro JM Guimaraes, Ubiraci GP Lana, Carlos FS Tinoco, Roberto W Noda, Silvia N Jardim-Belicuas, Leon V Kochian, Vera MC Alves and Sidney N Parentoni
    Citation: BMC Genomics 2014 15:153
    Content type: Research article Published on:

  20. Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids betw...

    Authors: Karen S Aitken, Meredith D McNeil, Scott Hermann, Peter C Bundock, Andrzej Kilian, Katarzyna Heller-Uszynska, Robert J Henry and Jingchuan Li
    Citation: BMC Genomics 2014 15:152
    Content type: Research article Published on:

  21. Regular smoking is associated with a wide variety of syndromes with prominent inflammatory components such as cancer, obesity and type 2 diabetes. Heavy regular smoking is also associated with changes in the D...

    Authors: Meeshanthini V Dogan, Bridget Shields, Carolyn Cutrona, Long Gao, Frederick X Gibbons, Ronald Simons, Martha Monick, Gene H Brody, Kai Tan, Steven RH Beach and Robert A Philibert
    Citation: BMC Genomics 2014 15:151
    Content type: Research article Published on:

  22. Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of organisms, where these transcripts have been shown to p...

    Authors: T Nicolai Siegel, Chung-Chau Hon, Qinfeng Zhang, Jose-Juan Lopez-Rubio, Christine Scheidig-Benatar, Rafael M Martins, Odile Sismeiro, Jean-Yves Coppée and Artur Scherf
    Citation: BMC Genomics 2014 15:150
    Content type: Research article Published on:

  23. Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (S...

    Authors: Nur Kholilatul Izzah, Jonghoon Lee, Murukarthick Jayakodi, Sampath Perumal, Mina Jin, Beom-Seok Park, Kyounggu Ahn and Tae-Jin Yang
    Citation: BMC Genomics 2014 15:149
    Content type: Research article Published on:

  24. The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biot...

    Authors: Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi and Shifra Ben-Dor
    Citation: BMC Genomics 2014 15:148
    Content type: Methodology article Published on:

  25. Thoroughbred racehorses are subject to non-traumatic distal limb bone fractures that occur during racing and exercise. Susceptibility to fracture may be due to underlying disturbances in bone metabolism which ...

    Authors: Sarah C Blott, June E Swinburne, Charlene Sibbons, Laura Y Fox-Clipsham, Maud Helwegen, Lynn Hillyer, Tim DH Parkin, J Richard Newton and Mark Vaudin
    Citation: BMC Genomics 2014 15:147
    Content type: Research article Published on:

  26. microRNAs (miRNAs) are endogenous, noncoding, small RNAs that have essential regulatory functions in plant growth, development, and stress response processes. However, limited information is available about th...

    Authors: Jianxia Jiang, Meiling Lv, Ying Liang, Zhiming Ma and Jiashu Cao
    Citation: BMC Genomics 2014 15:146
    Content type: Research article Published on:

  27. Individual genotypes at specific loci can result in different patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) influence methylation across extended genomic regions and may under...

    Authors: Alicia K Smith, Varun Kilaru, Mehmet Kocak, Lynn M Almli, Kristina B Mercer, Kerry J Ressler, Frances A Tylavsky and Karen N Conneely
    Citation: BMC Genomics 2014 15:145
    Content type: Research article Published on:

  28. Penicillium chrysogenum has been used in producing penicillin and derived β-lactam antibiotics for many years. Although the genome of the mutant strain P. chrysogenum Wisconsin 54-1255 has already been sequenced,...

    Authors: Qin Peng, Yihui Yuan, Meiying Gao, Xupeng Chen, Biao Liu, Pengming Liu, Yan Wu and Dandan Wu
    Citation: BMC Genomics 2014 15:144
    Content type: Research article Published on:

  29. The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we...

    Authors: Luis A Martínez-López, Neftalí Ochoa-Alejo and Octavio Martínez
    Citation: BMC Genomics 2014 15:143
    Content type: Research article Published on:

  30. Even in the age of next-generation sequencing (NGS), it has been unclear whether or not cells within a single organism have systematically distinctive genomes. Resolving this question, one of the most basic biolo...

    Authors: Deepti Diwan, Shun Komazaki, Miho Suzuki, Naoto Nemoto, Takuyo Aita, Akiko Satake and Koichi Nishigaki
    Citation: BMC Genomics 2014 15:142
    Content type: Methodology article Published on:

  31. In teleosts such as Atlantic salmon (Salmo salar L.), segmentation and subsequent mineralisation of the notochord during embryonic stages are essential for normal vertebrae formation. However, the molecular mecha...

    Authors: Shou Wang, Tomasz Furmanek, Harald Kryvi, Christel Krossøy, Geir K Totland, Sindre Grotmol and Anna Wargelius
    Citation: BMC Genomics 2014 15:141
    Content type: Research article Published on:

  32. Arabidopsis thaliana, a member of the Brassicaceae family is the dominant genetic model plant. However, while the flowers within the Brassicaceae members are rather uniform, mainly radially symmetrical, mostly wh...

    Authors: Amey Bhide, Simon Schliesky, Marlis Reich, Andreas PM Weber and Annette Becker
    Citation: BMC Genomics 2014 15:140
    Content type: Research article Published on:

  33. Aneuploidy, a karyotype deviating from multiples of a haploid chromosome set, affects the physiology of eukaryotes. In humans, aneuploidy is linked to pathological defects such as developmental abnormalities, ...

    Authors: Milena Dürrbaum, Anastasia Yurievna Kuznetsova, Verena Passerini, Silvia Stingele, Gabriele Stoehr and Zuzana Storchová
    Citation: BMC Genomics 2014 15:139
    Content type: Research article Published on:

  34. Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Ca...

    Authors: Maria Raffaella Ercolano, Adriana Sacco, Francesca Ferriello, Raffaella D’Alessandro, Paola Tononi, Alessandra Traini, Amalia Barone, Elisa Zago, Maria Luisa Chiusano, Genny Buson, Massimo Delledonne and Luigi Frusciante
    Citation: BMC Genomics 2014 15:138
    Content type: Research article Published on:

  36. Saccharomyces cerevisiae strains isolated from natural settings form structured biofilm colonies that are equipped with intricate protective mechanisms. These wild strains are able to reprogram themselves with a ...

    Authors: Vratislav Šťovíček, Libuše Váchová, Markéta Begany, Derek Wilkinson and Zdena Palková
    Citation: BMC Genomics 2014 15:136
    Content type: Research article Published on:

  37. Royal jelly (RJ) is a proteinaceous secretion produced from the hypopharyngeal and mandibular glands of nurse bees. It plays vital roles in honeybee biology and in the improvement of human health. However, som...

    Authors: Lan Zhang, Bin Han, Rongli Li, Xiaoshan Lu, Aiying Nie, Lihai Guo, Yu Fang, Mao Feng and Jianke Li
    Citation: BMC Genomics 2014 15:135
    Content type: Research article Published on:

  38. Honey bees (Apis mellifera) contribute substantially to the worldwide economy and ecosystem health as pollinators. Pollen is essential to the bee’s diet, providing protein, lipids, and micronutrients. The dramati...

    Authors: Vanessa Corby-Harris, Beryl M Jones, Alexander Walton, Melissa R Schwan and Kirk E Anderson
    Citation: BMC Genomics 2014 15:134
    Content type: Research article Published on:

  39. Insects are the most important epidemiological factors for plant virus disease spread, with >75% of viruses being dependent on insects for transmission to new hosts. The black-faced leafhopper (Graminella nigrifr...

    Authors: Bryan J Cassone, Saranga Wijeratne, Andrew P Michel, Lucy R Stewart, Yuting Chen, Pearlly Yan and Margaret G Redinbaugh
    Citation: BMC Genomics 2014 15:133
    Content type: Research article Published on:

  40. Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describ...

    Authors: Marius Gheorghe, Marc Snoeck, Michael Emmerich, Thomas Bäck, Jelle J Goeman and Vered Raz
    Citation: BMC Genomics 2014 15:132
    Content type: Methodology article Published on:

  41. Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of...

    Authors: Pankaj Chopra, Ligia A Papale, Andrew T J White, Andrea Hatch, Ryan M Brown, Mark A Garthwaite, Patrick H Roseboom, Thaddeus G Golos, Stephen T Warren and Reid S Alisch
    Citation: BMC Genomics 2014 15:131
    Content type: Methodology article Published on:

  42. Dinoroseobacter shibae, a member of the Roseobacter clade abundant in marine environments, maintains morphological heterogeneity throughout growth, with small cells dividing by binary fission and large cells divi...

    Authors: Hui Wang, Lisa Ziesche, Oliver Frank, Victoria Michael, Madeleine Martin, Jörn Petersen, Stefan Schulz, Irene Wagner-Döbler and Jürgen Tomasch
    Citation: BMC Genomics 2014 15:130
    Content type: Research article Published on:

  43. Campylobacter jejuni and C. coli share a multitude of risk factors associated with human gastrointestinal disease, yet their phylogeny differs significantly. C. jejuni is scattered into several lineages, with no ...

    Authors: Caroline PA Skarp-de Haan, Alejandra Culebro, Thomas Schott, Joana Revez, Elke KH Schweda, Marja-Liisa Hänninen and Mirko Rossi
    Citation: BMC Genomics 2014 15:129
    Content type: Research article Published on:

  44. Cathelicidins comprise a major group of host-defence peptides. Conserved across a wide range of species, they have several functions related to host defence. Only one cathelicidin has been found in humans but ...

    Authors: Cormac J Whelehan, Anne Barry-Reidy, Kieran G Meade, P David Eckersall, Aspinas Chapwanya, Fernando Narciandi, Andrew T Lloyd and Cliona O’Farrelly
    Citation: BMC Genomics 2014 15:128
    Content type: Research article Published on:

  46. Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and us...

    Authors: Jorge Duarte, Nathalie Rivière, Alain Baranger, Grégoire Aubert, Judith Burstin, Laurent Cornet, Clément Lavaud, Isabelle Lejeune-Hénaut, Jean-Pierre Martinant, Jean-Philippe Pichon, Marie-Laure Pilet-Nayel and Gilles Boutet
    Citation: BMC Genomics 2014 15:126
    Content type: Research article Published on:

  47. Leaf pigment content is an important trait involved in environmental interactions. In order to determine its impact on drought tolerance in wheat, we characterized a pale-green durum wheat mutant (Triticum turgid...

    Authors: Ariadna Peremarti, Caterina Marè, Alessio Aprile, Enrica Roncaglia, Luigi Cattivelli, Dolors Villegas and Conxita Royo
    Citation: BMC Genomics 2014 15:125
    Content type: Research article Published on:

  48. Paracoccus aminophilus JCM 7686 is a methylotrophic α-Proteobacterium capable of utilizing reduced one-carbon compounds as sole carbon and energy source for growth, including toxic N,N-dimethylformamide, formamid...

    Authors: Lukasz Dziewit, Jakub Czarnecki, Daniel Wibberg, Monika Radlinska, Paulina Mrozek, Michal Szymczak, Andreas Schlüter, Alfred Pühler and Dariusz Bartosik
    Citation: BMC Genomics 2014 15:124
    Content type: Research article Published on:

  49. Currently, six commercial whole-genome SNP chips are available for cattle genotyping, produced by two different genotyping platforms. Technical issues need to be addressed to combine data that originates from ...

    Authors: Ezequiel Luis Nicolazzi, Matteo Picciolini, Francesco Strozzi, Robert David Schnabel, Cindy Lawley, Ali Pirani, Fiona Brew and Alessandra Stella
    Citation: BMC Genomics 2014 15:123
    Content type: Database Published on:

  50. The alveolates include a large number of important lineages of protists and algae, among which are three major eukaryotic groups: ciliates, apicomplexans and dinoflagellates. Collectively alveolates are presen...

    Authors: Renny Lee, Hugo Lai, Shehre Banoo Malik, Juan F Saldarriaga, Patrick J Keeling and Claudio H Slamovits
    Citation: BMC Genomics 2014 15:122
    Content type: Research article Published on:

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BMC Genomics

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