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  1. Housekeeping genes (HKG) are constitutively expressed in all tissues while tissue-enriched genes (TEG) are expressed at a much higher level in a single tissue type than in others. HKGs serve as valuable experi...

    Authors: Xinwei She, Carol A Rohl, John C Castle, Amit V Kulkarni, Jason M Johnson and Ronghua Chen
    Citation: BMC Genomics 2009 10:269
  2. Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversi...

    Authors: Michelle M Meyer, Tyler D Ames, Daniel P Smith, Zasha Weinberg, Michael S Schwalbach, Stephen J Giovannoni and Ronald R Breaker
    Citation: BMC Genomics 2009 10:268
  3. Filarial nematode parasites cause serious diseases such as elephantiasis and river blindness in humans, and heartworm infections in dogs. Third stage filarial larvae (L3) are a critical stage in the life cycle...

    Authors: Ben-Wen Li, Amy C Rush, Makedonka Mitreva, Yong Yin, David Spiro, Elodie Ghedin and Gary J Weil
    Citation: BMC Genomics 2009 10:267
  4. The deleterious effect of a mutation can be reverted by a second-site interacting residue. This is an epistatic compensatory process explaining why mutations that are deleterious in some species are tolerated ...

    Authors: Luísa Azevedo, João Carneiro, Barbara van Asch, Ana Moleirinho, Filipe Pereira and António Amorim
    Citation: BMC Genomics 2009 10:266
  5. Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of t...

    Authors: Paxton Payton, Kameswara Rao Kottapalli, Diane Rowland, Wilson Faircloth, Baozhu Guo, Mark Burow, Naveen Puppala and Maria Gallo
    Citation: BMC Genomics 2009 10:265
  6. Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising t...

    Authors: Shrinivasrao P Mane, Clive Evans, Kristal L Cooper, Oswald R Crasta, Otto Folkerts, Stephen K Hutchison, Timothy T Harkins, Danielle Thierry-Mieg, Jean Thierry-Mieg and Roderick V Jensen
    Citation: BMC Genomics 2009 10:264
  7. Among deuterostomes, the regenerative potential is maximally expressed in echinoderms, animals that can quickly replace most injured organs. In particular, sea cucumbers are excellent models for studying organ...

    Authors: Pablo A Ortiz-Pineda, Francisco Ramírez-Gómez, Judit Pérez-Ortiz, Sebastián González-Díaz, Francisco Santiago-De Jesús, Josue Hernández-Pasos, Cristina Del Valle-Avila, Carmencita Rojas-Cartagena, Edna C Suárez-Castillo, Karen Tossas, Ana T Méndez-Merced, José L Roig-López, Humberto Ortiz-Zuazaga and José E García-Arrarás
    Citation: BMC Genomics 2009 10:262
  8. The molecular mechanisms of cell cycle exit are poorly understood. Studies on lymphocytes at cell cycle exit after growth factor deprivation have predominantly focused on the initiation of apoptosis. We aimed ...

    Authors: Magdalena Chechlinska, Jan Konrad Siwicki, Monika Gos, Malgorzata Oczko-Wojciechowska, Michal Jarzab, Aleksandra Pfeifer, Barbara Jarzab and Jan Steffen
    Citation: BMC Genomics 2009 10:261
  9. Clostridium perfringens (Cp) is a Gram-positive anaerobic bacterium that causes necrotic enteritis (NE) in poultry when it overgrows in the small intestine. NE disease has previously been controlled through the u...

    Authors: Aimie J Sarson, Ying Wang, Zhumei Kang, Scot E Dowd, Yang Lu, Hai Yu, Yanming Han, Huaijun Zhou and Joshua Gong
    Citation: BMC Genomics 2009 10:260
  10. Homology-based comparisons of the genes involved in innate immunity across many insect taxa with fully sequenced genomes has revealed a striking pattern of gene gain and loss, particularly among genes that enc...

    Authors: Timothy B Sackton and Andrew G Clark
    Citation: BMC Genomics 2009 10:259
  11. 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
  12. The mosquito Anopheles gambiae is a major vector of human malaria. Increasing evidence indicates that blood cells (hemocytes) comprise an essential arm of the mosquito innate immune response against both bacteria...

    Authors: Luke A Baton, Anne Robertson, Emma Warr, Michael R Strand and George Dimopoulos
    Citation: BMC Genomics 2009 10:257
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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

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

  36. 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
  37. 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
  38. 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
  39. 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
  40. 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

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