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  1. Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissu...

    Authors: Joseph I Hoffman, Michael AS Thorne, Philip N Trathan and Jaume Forcada
    Citation: BMC Genomics 2013 14:52
    Content type: Research article Published on:

  3. The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-a...

    Authors: Walter L Eckalbar, Elizabeth D Hutchins, Glenn J Markov, April N Allen, Jason J Corneveaux, Kerstin Lindblad-Toh, Federica Di Palma, Jessica Alföldi, Matthew J Huentelman and Kenro Kusumi
    Citation: BMC Genomics 2013 14:49
    Content type: Research article Published on:

  4. Select retrotransposons in the long terminal repeat (LTR) class exhibit interindividual variation in DNA methylation that is altered by developmental environmental exposures. Yet, neither the full extent of va...

    Authors: Christopher Faulk, Amanda Barks and Dana C Dolinoy
    Citation: BMC Genomics 2013 14:48
    Content type: Research article Published on:

  5. Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of su...

    Authors: Carsten Kuenne, André Billion, Mobarak Abu Mraheil, Axel Strittmatter, Rolf Daniel, Alexander Goesmann, Sukhadeo Barbuddhe, Torsten Hain and Trinad Chakraborty
    Citation: BMC Genomics 2013 14:47
    Content type: Research article Published on:

  6. Network biology (systems biology) approaches are useful tools for elucidating the host infection processes that often accompany complex immune networks. Although many studies have recently focused on Haemophilus ...

    Authors: Ming Zhao, Xiang-dong Liu, Xin-yun Li, Hong-bo Chen, Hui Jin, Rui Zhou, Meng-jin Zhu and Shu-hong Zhao
    Citation: BMC Genomics 2013 14:46
    Content type: Research article Published on:

  7. Erhualian pigs, one of Chinese Taihu pig breeds, are known to have the largest recorded litter size in the world. A lower prenatal death rate is the major contributing factor to the prolificacy of Taihu pigs. ...

    Authors: Hao Zhang, Shouqi Wang, Manqing Liu, Ailing Zhang, Zhenfang Wu, Zhe Zhang and Jiaqi Li
    Citation: BMC Genomics 2013 14:45
    Content type: Research article Published on:

  8. ADA2 proteins, together with ADA3, SGF29 and GCN5 form the acetyltransferase module of GNAT-type histone acetyltransferase complexes. ADA2b is present in the SAGA complex, which plays roles in various chromati...

    Authors: Tibor Pankotai, Nóra Zsindely, Edith E Vamos, Orbán Komonyi, László Bodai and Imre M Boros
    Citation: BMC Genomics 2013 14:44
    Content type: Research article Published on:

  9. Gene duplication, followed by functional evolution of duplicate genes, is a primary engine of evolutionary innovation. In turn, gene expression evolution is a critical component of overall functional evolution...

    Authors: Jia Zeng and Sridhar Hannenhalli
    Citation: BMC Genomics 2013 14(Suppl 1):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  10. One challenge in applying bioinformatic tools to clinical or biological data is high number of features that might be provided to the learning algorithm without any prior knowledge on which ones should be used...

    Authors: Habil Zare, Gholamreza Haffari, Arvind Gupta and Ryan R Brinkman
    Citation: BMC Genomics 2013 14(Suppl 1):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  11. With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next...

    Authors: Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu and Can Alkan
    Citation: BMC Genomics 2013 14(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  12. Structural variations in human genomes, such as deletions, play an important role in cancer development. Next-Generation Sequencing technologies have been central in providing ways to detect such variations. M...

    Authors: Roland Wittler
    Citation: BMC Genomics 2013 14(Suppl 1):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

    The Erratum to this article has been published in BMC Genomics 2013 14:S16

  13. Identifying the genetic variants that contribute to disease susceptibilities is important both for developing methodologies and for studying complex diseases in molecular biology. It has been demonstrated that...

    Authors: Jiayin Wang, Zhongmeng Zhao, Zhi Cao, Aiyuan Yang and Jin Zhang
    Citation: BMC Genomics 2013 14(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  14. Reconstructability of population history, from genetic information of extant individuals, is studied under a simulation setting. We do not address the issue of accuracy of the reconstruction algorithms: we ass...

    Authors: Filippo Utro, Marc Pybus and Laxmi Parida
    Citation: BMC Genomics 2013 14(Suppl 1):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  15. The cost of RNA-Seq has been decreasing over the last few years. Despite this, experiments with four or less biological replicates are still quite common. Estimating the variances of gene expression estimates ...

    Authors: Ellis Patrick, Michael Buckley, David Ming Lin and Yee Hwa Yang
    Citation: BMC Genomics 2013 14(Suppl 1):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  16. Recent studies in genomics have highlighted the significance of structural variation in determining individual variation. Current methods for identifying structural variation, however, are predominantly focuse...

    Authors: Nathaniel Parrish, Benjamin Sudakov and Eleazar Eskin
    Citation: BMC Genomics 2013 14(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  17. Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (mul...

    Authors: Sergey I Nikolenko, Anton I Korobeynikov and Max A Alekseyev
    Citation: BMC Genomics 2013 14(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  18. Yeast deletion-mutant collections have been successfully used to infer the mode-of-action of drugs especially by profiling chemical-genetic and genetic-genetic interactions on a genome-wide scale. Although ten...

    Authors: Minho Lee, Sangjo Han, Hyeshik Chang, Youn-Sig Kwak, David M Weller and Dongsup Kim
    Citation: BMC Genomics 2013 14(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  19. Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild so...

    Authors: Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu and Henry T Nguyen
    Citation: BMC Genomics 2013 14(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  20. Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previ...

    Authors: Zhen Gao, Ruizhe Zhao and Jianhua Ruan
    Citation: BMC Genomics 2013 14(Suppl 1):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  21. Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic i...

    Authors: W Evan Durno, Niels W Hanson, Kishori M Konwar and Steven J Hallam
    Citation: BMC Genomics 2013 14(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  22. MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount ...

    Authors: Chih-Hung Chou, Feng-Mao Lin, Min-Te Chou, Sheng-Da Hsu, Tzu-Hao Chang, Shun-Long Weng, Sirjana Shrestha, Chiung-Chih Hsiao, Jui-Hung Hung and Hsien-Da Huang
    Citation: BMC Genomics 2013 14(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  23. Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic varian...

    Authors: Quan Chen and Fengzhu Sun
    Citation: BMC Genomics 2013 14(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  24. Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiati...

    Authors: Sarika, Vasu Arora, Mir Asif Iquebal, Anil Rai and Dinesh Kumar
    Citation: BMC Genomics 2013 14:43
    Content type: Database Published on:

  25. MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Recently, a large number of miRNAs and their ...

    Authors: Jiajie Sun, Mijie Li, Zhuanjian Li, Jing Xue, Xianyong Lan, Chunlei Zhang, Chuzhao Lei and Hong Chen
    Citation: BMC Genomics 2013 14:42
    Content type: Research article Published on:

  26. Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to dis...

    Authors: Luca Venturini, Alberto Ferrarini, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Silvia Dal Santo, Andrea Minio, Genny Buson, Paola Tononi, Elisa Debora Zago, Gianpiero Zamperin, Diana Bellin, Mario Pezzotti and Massimo Delledonne
    Citation: BMC Genomics 2013 14:41
    Content type: Research article Published on:

  27. The outer cell wall of the pollen grain (exine) is an extremely resistant structure containing sporopollenin, a mixed polymer made up of fatty acids and phenolic compounds. The synthesis of sporopollenin in th...

    Authors: Gabino Ríos, Francisco R Tadeo, Carmen Leida and María L Badenes
    Citation: BMC Genomics 2013 14:40
    Content type: Research article Published on:

  28. The C. elegans cell fate map, in which the lineage of its approximately 1000 cells is visibly charted beginning from the zygote, represents a developmental biology milestone. Nematode development is invariant fro...

    Authors: Wenyu Zhou, Yunbing Tan, Donovan J Anderson, Eva M Crist, Hannele Ruohola-Baker, Stephen J Salipante and Marshall S Horwitz
    Citation: BMC Genomics 2013 14:39
    Content type: Research article Published on:

  29. Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, locali...

    Authors: Paolo Margaria, Simona Abbà and Sabrina Palmano
    Citation: BMC Genomics 2013 14:38
    Content type: Research article Published on:

  31. Proteomics Signature Profiling (PSP) is a novel hit-rate based method that proved useful in resolving consistency and coverage issues in proteomics. As a follow-up study, several points need to be addressed: 1...

    Authors: Wilson Wen Bin Goh, Mengyuan Fan, Hong Sang Low, Marek Sergot and Limsoon Wong
    Citation: BMC Genomics 2013 14:35
    Content type: Research article Published on:

  32. Comparative genomics brings insight into sequence evolution, but even more may be learned by coupling sequence analyses with experimental tests of gene function and regulation. However, the reliability of such...

    Authors: Yuanfang Guan, Maitreya J Dunham, Olga G Troyanskaya and Amy A Caudy
    Citation: BMC Genomics 2013 14:33
    Content type: Research article Published on:

  33. Microarray technology is widely utilized for monitoring the expression changes of thousands of genes simultaneously. However, the requirement of relatively large amount of RNA for labeling and hybridization ma...

    Authors: Fugui Wang, Rui Chen, Dong Ji, Shunong Bai, Minping Qian and Minghua Deng
    Citation: BMC Genomics 2013 14:31
    Content type: Research article Published on:

  34. Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous recretohalophyte has unique morphological characteristics that allow it to tolerate the stress impos...

    Authors: Zhen-hua Dang, Lin-lin Zheng, Jia Wang, Zhe Gao, Shu-biao Wu, Zhi Qi and Ying-chun Wang
    Citation: BMC Genomics 2013 14:29
    Content type: Research article Published on:

  35. Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousa...

    Authors: Zhi-Liang Zheng and Yihong Zhao
    Citation: BMC Genomics 2013 14:27
    Content type: Research article Published on:

  36. Both large deletions in genome and heat shock stress would lead to alterations in the gene expression profile; however, whether there is any potential linkage between these disturbances to the transcriptome ha...

    Authors: Bei-Wen Ying, Shigeto Seno, Fuyuro Kaneko, Hideo Matsuda and Tetsuya Yomo
    Citation: BMC Genomics 2013 14:25
    Content type: Research article Published on:

  37. Apoptosis is a critical process in endothelial cell (EC) biology and pathology, which has been extensively studied at protein level. Numerous gene expression studies of EC apoptosis have also been performed, h...

    Authors: Muna Affara, Debbie Sanders, Hiromitsu Araki, Yoshinori Tamada, Benjamin J Dunmore, Sally Humphreys, Seiya Imoto, Christopher Savoie, Satoru Miyano, Satoru Kuhara, David Jeffries, Cristin Print and D Stephen Charnock-Jones
    Citation: BMC Genomics 2013 14:23
    Content type: Research article Published on:

  38. The genome of Fusarium graminearum has been sequenced and annotated previously, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA ...

    Authors: Chunzhao Zhao, Cees Waalwijk, Pierre J G M de Wit, Dingzhong Tang and Theo van der Lee
    Citation: BMC Genomics 2013 14:21
    Content type: Research article Published on:

  39. The endosymbiont Wolbachia pipientis causes diverse and sometimes dramatic phenotypes in its invertebrate hosts. Four Wolbachia strains sequenced to date indicate that the constitution of the genome is dynamic, b...

    Authors: Anne Duplouy, Iñaki Iturbe-Ormaetxe, Scott A Beatson, Jan M Szubert, Jeremy C Brownlie, Conor J McMeniman, Elizabeth A McGraw, Gregory D D Hurst, Sylvain Charlat, Scott L O’Neill and Megan Woolfit
    Citation: BMC Genomics 2013 14:20
    Content type: Research article Published on:

  40. Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focuse...

    Authors: Rongrong Zhai, Yue Feng, Huimin Wang, Xiaodeng Zhan, Xihong Shen, Weiming Wu, Yingxin Zhang, Daibo Chen, Gaoxing Dai, Zhanlie Yang, Liyong Cao and Shihua Cheng
    Citation: BMC Genomics 2013 14:19
    Content type: Research article Published on:

  41. Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breedin...

    Authors: Pedro IT Silva, Alexandre M Martins, Ediene G Gouvea, Marco Pessoa-Filho and Márcio E Ferreira
    Citation: BMC Genomics 2013 14:17
    Content type: Research article Published on:

  42. This study is aimed at the analysis of genetic and physiological effects of myostatin on economically relevant meat quality traits in a genetic background of high muscularity. For this purpose, we generated G3 po...

    Authors: Stefan Kärst, Eva M Strucken, Armin O Schmitt, Alexandra Weyrich, Fernando PM de Villena, Hyuna Yang and Gudrun A Brockmann
    Citation: BMC Genomics 2013 14:16
    Content type: Research article Published on:

  44. New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technolog...

    Authors: Mikhail Ozerov, Anti Vasemägi, Vidar Wennevik, Eero Niemelä, Sergey Prusov, Matthew Kent and Juha-Pekka Vähä
    Citation: BMC Genomics 2013 14:12
    Content type: Methodology article Published on:

  45. A reciprocal recurrent selection program has been under way for the Coffea canephora coffee tree for approximately thirty years in the Ivory Coast. Association genetics would help to speed up this program by more...

    Authors: Philippe Cubry, Fabien de Bellis, Komlan Avia, Sophie Bouchet, David Pot, Magali Dufour, Hyacinthe Legnate and Thierry Leroy
    Citation: BMC Genomics 2013 14:10
    Content type: Research article Published on:

  46. Regulatory network of cytoplasmic male sterility (CMS) occurrence is still largely unknown in plants, although numerous researches have been attempted to isolate genes involved in CMS. Here, we employed high-t...

    Authors: Jinghua Yang, Xunyan Liu, Baochen Xu, Na Zhao, Xiaodong Yang and Mingfang Zhang
    Citation: BMC Genomics 2013 14:9
    Content type: Research article Published on:

  47. Sequencing technologies have different biases, in single-genome sequencing and metagenomic sequencing; these can significantly affect ORFs recovery and the population distribution of a metagenome. In this pape...

    Authors: Fabio Gori, Susannah G Tringe, Gianluigi Folino, Sacha AFT van Hijum, Huub JM Op den Camp, Mike SM Jetten and Elena Marchiori
    Citation: BMC Genomics 2013 14:7
    Content type: Research article Published on:

  49. Water and nitrogen are two of the most critical inputs required to achieve the high yield potential of modern corn varieties. Under most agricultural settings however they are often scarce and costly. Fortunat...

    Authors: Sabrina Humbert, Sanjeena Subedi, Jonathan Cohn, Bin Zeng, Yong-Mei Bi, Xi Chen, Tong Zhu, Paul D McNicholas and Steven J Rothstein
    Citation: BMC Genomics 2013 14:3
    Content type: Research article Published on:

  50. Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provi...

    Authors: Paul F Bray, Steven E McKenzie, Leonard C Edelstein, Srikanth Nagalla, Kathleen Delgrosso, Adam Ertel, Joan Kupper, Yi Jing, Eric Londin, Phillipe Loher, Huang-Wen Chen, Paolo Fortina and Isidore Rigoutsos
    Citation: BMC Genomics 2013 14:1
    Content type: Research article Published on:

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BMC Genomics

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