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  1. Massively-parallel cDNA sequencing (RNA-Seq) is a new technique that holds great promise for cardiovascular genomics. Here, we used RNA-Seq to study the transcriptomes of matched coronary artery disease cases ...

    Authors: Shurjo K Sen, Jennifer J Barb, Praveen F Cherukuri, David S Accame, Abdel G Elkahloun, Larry N Singh, Shih-Queen Lee-Lin, NISC Comparative Sequencing Program, Frank D Kolodgie, Qi Cheng, XiaoQing Zhao, Marcus Y Chen, Andrew E Arai, Eric D Green, James C Mullikin, Peter J Munson…
    Citation: BMC Genomics 2014 15:198
    Content type: Research article Published on:

  3. Western corn rootworm (WCR) is one of the most significant insect pests of maize in North America. WCR has dramatically increased its range in the last century, invading key maize production areas in the US an...

    Authors: Lex E Flagel, Raman Bansal, Randall A Kerstetter, Mao Chen, Matthew Carroll, Ronald Flannagan, Thomas Clark, Barry S Goldman and Andy P Michel
    Citation: BMC Genomics 2014 15:195
    Content type: Research article Published on:

  5. Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more ent...

    Authors: Chunzhao Zhao, Cees Waalwijk, Pierre JGM de Wit, Dingzhong Tang and Theo van der Lee
    Citation: BMC Genomics 2014 15:191
    Content type: Research article Published on:

  6. Tumor models are critical for our understanding of cancer and the development of cancer therapeutics. Here, we present an integrated map of the genome, transcriptome and immunome of an epithelial mouse tumor, ...

    Authors: John C Castle, Martin Loewer, Sebastian Boegel, Jos de Graaf, Christian Bender, Arbel D Tadmor, Valesca Boisguerin, Thomas Bukur, Patrick Sorn, Claudia Paret, Mustafa Diken, Sebastian Kreiter, Özlem Türeci and Ugur Sahin
    Citation: BMC Genomics 2014 15:190
    Content type: Research article Published on:

  7. Reproductive proteins often evolve rapidly and are thought to be subject to strong sexual selection, and thus may play a key role in reproductive isolation and species divergence. However, our knowledge of rep...

    Authors: Nooria Al-Wathiqui, Sara M Lewis and Erik B Dopman
    Citation: BMC Genomics 2014 15:189
    Content type: Research article Published on:

  8. The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular r...

    Authors: Dacotah Melicher, Alex S Torson, Ian Dworkin and Julia H Bowsher
    Citation: BMC Genomics 2014 15:188
    Content type: Research article Published on:

  9. The recent access to a large set of genome sequences, combined with a robust evolutionary scenario of modern monocot (i.e. grasses) and eudicot (i.e. rosids) species from their founder ancestors, offered the oppo...

    Authors: Rongzhi Zhang, Florent Murat, Caroline Pont, Thierry Langin and Jerome Salse
    Citation: BMC Genomics 2014 15:187
    Content type: Research article Published on:

  10. Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diver...

    Authors: Cheng Sun, Grace Wyngaard, D Brian Walton, Holly A Wichman and Rachel Lockridge Mueller
    Citation: BMC Genomics 2014 15:186
    Content type: Research article Published on:

  11. Next generation targeted resequencing is replacing Sanger sequencing at high pace in routine genetic diagnosis. The need for well validated, high quality enrichment platforms to complement the bench-top next g...

    Authors: Bram De Wilde, Steve Lefever, Wes Dong, Jude Dunne, Syed Husain, Stefaan Derveaux, Jan Hellemans and Jo Vandesompele
    Citation: BMC Genomics 2014 15:184
    Content type: Methodology article Published on:

  12. The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain...

    Authors: Yuuki Kodama, Haruo Suzuki, Hideo Dohra, Manabu Sugii, Tatsuya Kitazume, Katsushi Yamaguchi, Shuji Shigenobu and Masahiro Fujishima
    Citation: BMC Genomics 2014 15:183
    Content type: Research article Published on:

  13. Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1CA oncogene specifically in the posterior silk gland (PS...

    Authors: Li Ma, Qian Ma, Xuan Li, Leilei Cheng, Kai Li and Sheng Li
    Citation: BMC Genomics 2014 15:182
    Content type: Research article Published on:

  14. MicroRNAs (miRNAs) can post-transcriptionally regulate gene expression and have been shown to be critical regulators to the fine-tuning of epithelial immune responses. However, the role of miRNAs in bovine res...

    Authors: Weiwu Jin, Eveline M Ibeagha-Awemu, Guanxiang Liang, Frédéric Beaudoin, Xin Zhao and Le Luo Guan
    Citation: BMC Genomics 2014 15:181
    Content type: Research article Published on:

  15. The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Maj...

    Authors: Biao Wang, Robert Ekblom, Ignas Bunikis, Heli Siitari and Jacob Höglund
    Citation: BMC Genomics 2014 15:180
    Content type: Research article Published on:

  16. Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilita...

    Authors: Malleswari Gelli, Yongchao Duo, Anji Reddy Konda, Chi Zhang, David Holding and Ismail Dweikat
    Citation: BMC Genomics 2014 15:179
    Content type: Research article Published on:

  17. Deviations in the amount of genomic content that arise during tumorigenesis, called copy number alterations, are structural rearrangements that can critically affect gene expression patterns. Additionally, cop...

    Authors: David Mosen-Ansorena, Naiara Telleria, Silvia Veganzones, Virginia De la Orden, Maria Luisa Maestro and Ana M Aransay
    Citation: BMC Genomics 2014 15:178
    Content type: Software Published on:

  18. Spiders have evolved pharmacologically complex venoms that serve to rapidly subdue prey and deter predators. The major toxic factors in most spider venoms are small, disulfide-rich peptides. While there is abu...

    Authors: Sandy S Pineda, Brianna L Sollod, David Wilson, Aaron Darling, Kartik Sunagar, Eivind A B Undheim, Laurence Kely, Agostinho Antunes, Bryan G Fry and Glenn F King
    Citation: BMC Genomics 2014 15:177
    Content type: Research article Published on:

  19. RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research communi...

    Authors: Tiezheng Yuan, Xiaoyi Huang, Rachel L Dittmar, Meijun Du, Manish Kohli, Lisa Boardman, Stephen N Thibodeau and Liang Wang
    Citation: BMC Genomics 2014 15:176
    Content type: Software Published on:

  20. With the advent of paired-end high throughput sequencing, it is now possible to identify various types of structural variation on a genome-wide scale. Although many methods have been proposed for structural va...

    Authors: Gökhan Yavaş, Mehmet Koyutürk, Meetha P Gould, Sarah McMahon and Thomas LaFramboise
    Citation: BMC Genomics 2014 15:175
    Content type: Methodology article Published on:

  21. Mosquito control programmes using chemical insecticides are increasingly threatened by the development of resistance. Such resistance can be the consequence of changes in proteins targeted by insecticides (tar...

    Authors: Jean-Philippe David, Frédéric Faucon, Alexia Chandor-Proust, Rodolphe Poupardin, Muhammad Asam Riaz, Aurélie Bonin, Vincent Navratil and Stéphane Reynaud
    Citation: BMC Genomics 2014 15:174
    Content type: Research article Published on:

  22. Proteins of the major intrinsic protein (MIP) family, or aquaporins, have been detected in almost all organisms. These proteins are important in cells and organisms because they allow for passive transmembrane...

    Authors: Kirill Vladimirovich Khabudaev, Darya Petrovna Petrova, Mikhail Aleksandrovich Grachev and Yelena Valentinovna Likhoshway
    Citation: BMC Genomics 2014 15:173
    Content type: Research article Published on:

  23. 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:

  24. The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been devel...

    Authors: Christophe Plomion, Emilie Chancerel, Jeffrey Endelman, Jean-Baptiste Lamy, Eric Mandrou, Isabelle Lesur, François Ehrenmann, Fikret Isik, Marco CAM Bink, Joost van Heerwaarden and Laurent Bouffier
    Citation: BMC Genomics 2014 15:171
    Content type: Research article Published on:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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