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  1. The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae. The molecular mechanisms underlying the establishment, maintena...

    Authors: Shinichi Sunagawa, Emily C Wilson, Michael Thaler, Marc L Smith, Carlo Caruso, John R Pringle, Virginia M Weis, Mónica Medina and Jodi A Schwarz
    Citation: BMC Genomics 2009 10:258
    Content type: Research article Published on:

  2. In species with exalbuminous seeds, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid e...

    Authors: Yi Huang, Liang Chen, Liping Wang, Kannan Vijayan, Sieu Phan, Ziying Liu, Lianglu Wan, Andrew Ross, Daoquan Xiang, Raju Datla, Youlian Pan and Jitao Zou
    Citation: BMC Genomics 2009 10:256
    Content type: Research article Published on:

  3. In contrast to the essentially fully assembled genome sequences of the kinetoplastid pathogens Leishmania major and Trypanosoma brucei the assembly of the Trypanosoma cruzi genome has been hindered by its repetit...

    Authors: D Brent Weatherly, Courtney Boehlke and Rick L Tarleton
    Citation: BMC Genomics 2009 10:255
    Content type: Research article Published on:

  5. Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at ...

    Authors: Tristan E Coram, Matthew L Settles and Xianming Chen
    Citation: BMC Genomics 2009 10:253
    Content type: Research article Published on:

  6. The requirements for growth and survival of the intracellular pathogen Trypanosoma cruzi within mammalian host cells are poorly understood. Transcriptional profiling of the host cell response to infection serves ...

    Authors: Jaime A Costales, Johanna P Daily and Barbara A Burleigh
    Citation: BMC Genomics 2009 10:252
    Content type: Research article Published on:

  7. Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequenc...

    Authors: Amy N Bernardo, Peter J Bradbury, Hongxiang Ma, Shengwa Hu, Robert L Bowden, Edward S Buckler and Guihua Bai
    Citation: BMC Genomics 2009 10:251
    Content type: Research article Published on:

  8. The subtelomeric regions of human chromosomes exhibit an extraordinary plasticity. To date, due to the high GC content and to the presence of telomeric repeats, the subtelomeric sequences are underrepresented ...

    Authors: Valerio Costa, Amelia Casamassimi, Roberta Roberto, Fernando Gianfrancesco, Maria R Matarazzo, Michele D'Urso, Maurizio D'Esposito, Mariano Rocchi and Alfredo Ciccodicola
    Citation: BMC Genomics 2009 10:250
    Content type: Research article Published on:

  9. The ability to localise or follow endogenous proteins in real time in vivo is of tremendous utility for cell biology or systems biology studies. Protein trap screens utilise the random genomic insertion of a tran...

    Authors: Jelena Aleksic, Ranko Lazic, Ilka Müller, Steven R Russell and Boris Adryan
    Citation: BMC Genomics 2009 10:249
    Content type: Methodology article Published on:

  10. We have performed Quantitative Trait Loci (QTL) analysis of an F2 intercross between two chicken lines divergently selected for juvenile body-weight. In a previous study 13 identified loci with effects on body-we...

    Authors: Per Wahlberg, Örjan Carlborg, Mario Foglio, Xavier Tordoir, Ann-Christine Syvänen, Mark Lathrop, Ivo G Gut, Paul B Siegel and Leif Andersson
    Citation: BMC Genomics 2009 10:248
    Content type: Research article Published on:

  11. Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because ...

    Authors: Zuogang Peng, Navin Elango, Derek E Wildman and Soojin V Yi
    Citation: BMC Genomics 2009 10:247
    Content type: Methodology article Published on:

  12. For more than a decade, microarrays have been a powerful and widely used tool to explore the transcriptome of biological systems. However, the amount of biological material from cell sorting or laser capture m...

    Authors: Mathieu Clément-Ziza, David Gentien, Stanislas Lyonnet, Jean-Paul Thiery, Claude Besmond and Charles Decraene
    Citation: BMC Genomics 2009 10:246
    Content type: Methodology article Published on:

  13. Two-component signal transduction systems (TCSTs), consisting of a histidine kinase (HK) and a response regulator (RR), represent a major paradigm for signal transduction in prokaryotes. TCSTs play critical ro...

    Authors: Youfu Zhao, Dongping Wang, Sridevi Nakka, George W Sundin and Schuyler S Korban
    Citation: BMC Genomics 2009 10:245
    Content type: Research article Published on:

  15. Expressed sequence tag (EST) databases represent a valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. One class of markers der...

    Authors: Maria Domenica Moccia, Christine Oger-Desfeux, Gabriel AB Marais and Alex Widmer
    Citation: BMC Genomics 2009 10:243
    Content type: Research article Published on:

  17. The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp1...

    Authors: Jianzhong Li, Xia Chen, Xuelian Gong, Ying Liu, Hao Feng, Lei Qiu, Zhenlin Hu and Junping Zhang
    Citation: BMC Genomics 2009 10:241
    Content type: Research article Published on:

  18. We have recently identified two large families of extinct transposable elements termed Short Interspersed DEgenerated Retroposons (SIDERs) in the parasitic protozoan Leishmania major. The characterization of SIDE...

    Authors: Martin Smith, Frédéric Bringaud and Barbara Papadopoulou
    Citation: BMC Genomics 2009 10:240
    Content type: Research article Published on:

  19. Chlamydia trachomatis is the most common cause of sexually transmitted infections globally and the leading cause of preventable blindness in the developing world. There are two biovariants of C. trachomatis: 'tra...

    Authors: Helena MB Seth-Smith, Simon R Harris, Kenneth Persson, Pete Marsh, Andrew Barron, Alexandra Bignell, Carina Bjartling, Louise Clark, Lesley T Cutcliffe, Paul R Lambden, Nicola Lennard, Sarah J Lockey, Michael A Quail, Omar Salim, Rachel J Skilton, Yibing Wang…
    Citation: BMC Genomics 2009 10:239
    Content type: Research article Published on:

  20. Dermatophytes are fungi that cause superficial infections of the skin, hair, and nails. They are the most common agents of fungal infections worldwide. Dermatophytic fungi constitute three genera, Trichophyton, E...

    Authors: Yuan Wu, Jian Yang, Fan Yang, Tao Liu, Wenchuan Leng, Yonglie Chu and Qi Jin
    Citation: BMC Genomics 2009 10:238
    Content type: Research article Published on:

  22. Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicat...

    Authors: Benjamin Nota, Mirte Bosse, Bauke Ylstra, Nico M van Straalen and Dick Roelofs
    Citation: BMC Genomics 2009 10:236
    Content type: Research article Published on:

  23. The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of

    Authors: Isabelle Florent, Betina M Porcel, Elodie Guillaume, Corinne Da Silva, François Artiguenave, Eric Maréchal, Laurent Bréhélin, Olivier Gascuel, Sébastien Charneau, Patrick Wincker and Philippe Grellier
    Citation: BMC Genomics 2009 10:235
    Content type: Research article Published on:

  24. Flesh flies in the genus Sarcophaga are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of Sarcophaga flesh flies as models for insec...

    Authors: Daniel A Hahn, Gregory J Ragland, D DeWayne Shoemaker and David L Denlinger
    Citation: BMC Genomics 2009 10:234
    Content type: Research article Published on:

  25. The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome of Itk-def...

    Authors: K Emelie M Blomberg, Nicole Boucheron, Jessica M Lindvall, Liang Yu, Julia Raberger, Anna Berglöf, Wilfried Ellmeier and CI Edvard Smith
    Citation: BMC Genomics 2009 10:233
    Content type: Research article Published on:

  26. The protozoan pathogens Leishmania major, Trypanosoma brucei and Trypanosoma cruzi (the Tritryps) are parasites that produce devastating human diseases. These organisms show very unusual mechanisms of gene expres...

    Authors: Norma E Padilla-Mejía, Luis E Florencio-Martínez, Elisa E Figueroa-Angulo, Rebeca G Manning-Cela, Rosaura Hernández-Rivas, Peter J Myler and Santiago Martínez-Calvillo
    Citation: BMC Genomics 2009 10:232
    Content type: Research article Published on:

  27. Stat5 is a latent transcription factor that regulates essential growth and survival functions in normal cells. Constitutive activity of Stat5 and the involvement of its C-terminally truncated variant have been...

    Authors: Tali Eilon and Itamar Barash
    Citation: BMC Genomics 2009 10:231
    Content type: Research article Published on:

  28. Correction to Dolan J, Walshe K, Alsbury S, Hokamp K, O'Keeffe S, Okafuji T, Miller SF, Tear G, Mitchell KJ: The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary...

    Authors: Jackie Dolan, Karen Walshe, Samantha Alsbury, Karsten Hokamp, Sean O'Keeffe, Tatsuya Okafuji, Suzanne FC Miller, Guy Tear and Kevin J Mitchell
    Citation: BMC Genomics 2009 10:230
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2007 8:320

  29. Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the ph...

    Authors: Shani Tzahor, Dikla Man-Aharonovich, Benjamin C Kirkup, Tali Yogev, Ilana Berman-Frank, Martin F Polz, Oded Béjà and Yael Mandel-Gutfreund
    Citation: BMC Genomics 2009 10:229
    Content type: Research article Published on:

  30. Neuropeptides are cell to cell signalling molecules that regulate many critical biological processes including development, growth and reproduction. These peptides result from the complex processing of prohorm...

    Authors: Bruce R Southey, Sandra L Rodriguez-Zas and Jonathan V Sweedler
    Citation: BMC Genomics 2009 10:228
    Content type: Research article Published on:

  34. Soft-shelled turtle iridovirus (STIV) is the causative agent of severe systemic diseases in cultured soft-shelled turtles (Trionyx sinensis). To our knowledge, the only molecular information available on STIV mai...

    Authors: Youhua Huang, Xiaohong Huang, Hong Liu, Jie Gong, Zhengliang Ouyang, Huachun Cui, Jianhao Cao, Yingtao Zhao, Xiujie Wang, Yulin Jiang and Qiwei Qin
    Citation: BMC Genomics 2009 10:224
    Content type: Research article Published on:

  35. DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of par...

    Authors: Jian Li, Fei Gao, Ning Li, Shengting Li, Guangliang Yin, Geng Tian, Shangang Jia, Kai Wang, Xiuqing Zhang, Huanming Yang, Anders Lade Nielsen and Lars Bolund
    Citation: BMC Genomics 2009 10:223
    Content type: Research article Published on:

  36. Hydrothermal vents and cold seeps represent oases of life in the deep-sea environment, but are also characterized by challenging physical and chemical conditions. The effect of temperature fluctuations on vent...

    Authors: Isabelle Boutet, Didier Jollivet, Bruce Shillito, Dario Moraga and Arnaud Tanguy
    Citation: BMC Genomics 2009 10:222
    Content type: Research article Published on:

  37. High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.

    Authors: Joshua S Bloom, Zia Khan, Leonid Kruglyak, Mona Singh and Amy A Caudy
    Citation: BMC Genomics 2009 10:221
    Content type: Research article Published on:

  39. New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand ...

    Authors: Eli Meyer, Galina V Aglyamova, Shi Wang, Jade Buchanan-Carter, David Abrego, John K Colbourne, Bette L Willis and Mikhail V Matz
    Citation: BMC Genomics 2009 10:219
    Content type: Research article Published on:

  41. Serine proteinase inhibitors (Serpins) are a large superfamily of structurally related, but functionally diverse proteins that control essential proteolytic pathways in most branches of life. Given their impor...

    Authors: Albert Mulenga, Rabuesak Khumthong and Katelyn C Chalaire
    Citation: BMC Genomics 2009 10:217
    Content type: Research article Published on:

  42. Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variatio...

    Authors: Oliver C Jann, Annemarie King, Nestor Lopez Corrales, Susan I Anderson, Kirsty Jensen, Tahar Ait-ali, Haizhou Tang, Chunhua Wu, Noelle E Cockett, Alan L Archibald and Elizabeth J Glass
    Citation: BMC Genomics 2009 10:216
    Content type: Research article Published on:

  43. Wood is the end product of secondary vascular system development, which begins from the cambium. The wood formation process includes four major stages: cell expansion, secondary wall biosynthesis, lignificatio...

    Authors: Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang and Meng-Zhu Lu
    Citation: BMC Genomics 2009 10:215
    Content type: Research article Published on:

  44. MicroRNAs (miRNAs) are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human...

    Authors: You-Jia Hua, Zhong-Yi Tang, Kang Tu, Li Zhu, Yi-Xue Li, Lu Xie and Hua-Sheng Xiao
    Citation: BMC Genomics 2009 10:214
    Content type: Research article Published on:

  45. Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis and entering meiosis, progressi...

    Authors: Xin Wang, Yongjun Zhao, Kim Wong, Peter Ehlers, Yuji Kohara, Steven J Jones, Marco A Marra, Robert A Holt, Donald G Moerman and Dave Hansen
    Citation: BMC Genomics 2009 10:213
    Content type: Research article Published on:

  46. Water deficit has significant effects on grape berry composition resulting in improved wine quality by the enhancement of color, flavors, or aromas. While some pathways or enzymes affected by water deficit hav...

    Authors: Laurent G Deluc, David R Quilici, Alain Decendit, Jérôme Grimplet, Matthew D Wheatley, Karen A Schlauch, Jean-Michel Mérillon, John C Cushman and Grant R Cramer
    Citation: BMC Genomics 2009 10:212
    Content type: Research article Published on:

  47. Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assemb...

    Authors: Jian-Gang Ma, Hiroshi Yasue, Katie E Eyer, Hideki Hiraiwa, Takeshi Shimogiri, Stacey N Meyers, Jonathan E Beever, Lawrence B Schook, Craig W Beattie and Wan-Sheng Liu
    Citation: BMC Genomics 2009 10:211
    Content type: Research article Published on:

  48. The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary met...

    Authors: Alan L Kwan, Linya Li, David C Kulp, Susan K Dutcher and Gary D Stormo
    Citation: BMC Genomics 2009 10:210
    Content type: Research article Published on:

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