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  1. Important developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi). Dicers, ...

    Authors: Meenu Kapoor, Rita Arora, Tenisha Lama, Aashima Nijhawan, Jitendra P Khurana, Akhilesh K Tyagi and Sanjay Kapoor
    Citation: BMC Genomics 2008 9:451
  2. SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to...

    Authors: Shaolin Wang, Zhenxia Sha, Tad S Sonstegard, Hong Liu, Peng Xu, Benjaporn Somridhivej, Eric Peatman, Huseyin Kucuktas and Zhanjiang Liu
    Citation: BMC Genomics 2008 9:450
  3. Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and ...

    Authors: Roy Gross, Carlos A Guzman, Mohammed Sebaihia, Vítor AP Martins dos Santos, Dietmar H Pieper, Ralf Koebnik, Melanie Lechner, Daniela Bartels, Jens Buhrmester, Jomuna V Choudhuri, Thomas Ebensen, Lars Gaigalat, Stefanie Herrmann, Amit N Khachane, Christof Larisch, Stefanie Link…
    Citation: BMC Genomics 2008 9:449
  4. Invasion-related genes over-expressed by tumor cells as well as by reacting host cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal ...

    Authors: Obul Reddy Bandapalli, Christoph Kahlert, Victoria Hellstern, Luis Galindo, Peter Schirmacher, Jürgen Weitz and Karsten Brand
    Citation: BMC Genomics 2008 9:448
  5. Bovine tuberculosis (BTB) caused by Mycobacterium bovis continues to cause substantial losses to global agriculture and has significant repercussions for human health. The advent of high throughput genomics has f...

    Authors: Kieran G Meade, Eamonn Gormley, Cliona O'Farrelly, Stephen D Park, Eamon Costello, Joseph Keane, Yingdong Zhao and David E MacHugh
    Citation: BMC Genomics 2008 9:447
  6. Hop (Humulus lupulus L.) is an economically important plant forming organogenic nodules which can be used for genetic transformation and micropropagation. We are interested in the mechanisms underlying reprogramm...

    Authors: Ana M Fortes, Filipa Santos, Young H Choi, Marta S Silva, Andreia Figueiredo, Lisete Sousa, Fernando Pessoa, Bartolomeu A Santos, Mónica Sebastiana, Klaus Palme, Rui Malhó, Rob Verpoorte and Maria S Pais
    Citation: BMC Genomics 2008 9:445
  7. Successful strategies for QTL gene identification benefit from combined experimental and bioinformatic approaches. Unique design aspects of the BXD recombinant inbred line mapping panel allow use of archived g...

    Authors: Lu Lu, Lai Wei, Jeremy L Peirce, Xusheng Wang, Jianhua Zhou, Ramin Homayouni, Robert W Williams and David C Airey
    Citation: BMC Genomics 2008 9:444
  8. Liver plays a profound role in the acute phase response (APR) observed in the early phase of acute bovine mastitis caused by Escherichia coli (E. coli). To gain an insight into the genes and pathways involved in ...

    Authors: Li Jiang, Peter Sørensen, Christine Røntved, Lotte Vels and Klaus L Ingvartsen
    Citation: BMC Genomics 2008 9:443
  9. The ribosome biogenesis (RiBi) genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulati...

    Authors: Seth J Brown, Michael D Cole and Albert J Erives
    Citation: BMC Genomics 2008 9:442
  10. The identification of novel drug targets by assessing gene functions is most conveniently achieved by high-throughput loss-of-function RNA interference screening. There is a growing need to employ primary cell...

    Authors: Angelika Oehmig, Andrea Klotzbücher, Maria Thomas, Frank Weise, Ursula Hagner, Ralf Brundiers, Dirk Waldherr, Andreas Lingnau, Achim Knappik, Michael HG Kubbutat, Thomas O Joos and Hansjürgen Volkmer
    Citation: BMC Genomics 2008 9:441
  11. Ubiquitination is an important post-translational modification involved in diverse biological processes. Therefore, genomewide representation of the ubiquitination system for a species is important.

    Authors: Won-Chul Lee, Minho Lee, Jin Woo Jung, Kwang Pyo Kim and Dongsup Kim
    Citation: BMC Genomics 2008 9:440
  12. Microarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions o...

    Authors: Felipe F Aceituno, Nick Moseyko, Seung Y Rhee and Rodrigo A Gutiérrez
    Citation: BMC Genomics 2008 9:438
  13. Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improve...

    Authors: Yanfang Wang, Oliver P Couture, Long Qu, Jolita J Uthe, Shawn MD Bearson, Daniel Kuhar, Joan K Lunney, Dan Nettleton, Jack CM Dekkers and Christopher K Tuggle
    Citation: BMC Genomics 2008 9:437
  14. The key steps in germ cell survival during ovarian development are the entry into meiosis of oogonies and the formation of primordial follicles, which then determine the reproductive lifespan of the ovary. In ...

    Authors: Adrienne Baillet, Béatrice Mandon-Pépin, Cédric Cabau, Elodie Poumerol, Eric Pailhoux and Corinne Cotinot
    Citation: BMC Genomics 2008 9:436
  15. Authors: Jodi A Schwarz, Peter B Brokstein, Christian Voolstra, Astrid Y Terry, Chitra F Manohar, David J Miller, Alina M Szmant, Mary Alice Coffroth and Mónica Medina
    Citation: BMC Genomics 2008 9:435

    The original article was published in BMC Genomics 2008 9:97

  16. Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to ada...

    Authors: Stephen J Robinson and Isobel AP Parkin
    Citation: BMC Genomics 2008 9:434
  17. Nasal carriage of Staphylococcus aureus is a major risk factor in clinical and community settings due to the range of etiologies caused by the organism. We have identified unique immunological and ultrastructural...

    Authors: Karthikeyan Sivaraman, Nitya Venkataraman, Jennifer Tsai, Scott Dewell and Alexander M Cole
    Citation: BMC Genomics 2008 9:433
  18. Wheat is a major crop in the world, and the high temperature stress can reduce the yield of wheat by as much as 15%. The molecular changes in response to heat stress are poorly understood. Using GeneChip® Wheat G...

    Authors: Dandan Qin, Haiyan Wu, Huiru Peng, Yingyin Yao, Zhongfu Ni, Zhenxing Li, Chunlei Zhou and Qixin Sun
    Citation: BMC Genomics 2008 9:432
  19. With improvements in genotyping technologies, genome-wide association studies with hundreds of thousands of SNPs allow the identification of candidate genetic loci for multifactorial diseases in different popu...

    Authors: Nao Nishida, Asako Koike, Atsushi Tajima, Yuko Ogasawara, Yoshimi Ishibashi, Yasuka Uehara, Ituro Inoue and Katsushi Tokunaga
    Citation: BMC Genomics 2008 9:431
  20. The goldfish (Carassius auratus) uses steroids and prostaglandins as pheromone cues at different stages of the reproductive cycle to facilitate spawning synchronization. Steroid progestin pheromone binding has be...

    Authors: Nikolay N Kolmakov, Michael Kube, Richard Reinhardt and Adelino VM Canario
    Citation: BMC Genomics 2008 9:429
  21. Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium that is the causative agent of furunculosis, a bacterial septicaemia of salmonid fish. While other species of Aeromonas are opportunistic path...

    Authors: Michael E Reith, Rama K Singh, Bruce Curtis, Jessica M Boyd, Anne Bouevitch, Jennifer Kimball, Janet Munholland, Colleen Murphy, Darren Sarty, Jason Williams, John HE Nash, Stewart C Johnson and Laura L Brown
    Citation: BMC Genomics 2008 9:427
  22. The IN hibitor of G rowth (ING) family of type II tumor suppressors (ING1–ING5) is involved in many cellular processes such as cell aging, apoptosis, DNA repair and tumorigenesis. To expand our understanding of t...

    Authors: Paul MK Gordon, Mohamed A Soliman, Pinaki Bose, Quang Trinh, Christoph W Sensen and Karl Riabowol
    Citation: BMC Genomics 2008 9:426
  23. Bursicon is a heterodimer neuropeptide responsible for regulating cuticle sclerotization and wing expansion in several insect species. Recent studies indicate that the action of bursicon is mediated by a speci...

    Authors: Shiheng An, Songjie Wang, Lawrence I Gilbert, Brenda Beerntsen, Mark Ellersieck and Qisheng Song
    Citation: BMC Genomics 2008 9:424
  24. Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-t...

    Authors: Javier Terol, M Angel Naranjo, Patrick Ollitrault and Manuel Talon
    Citation: BMC Genomics 2008 9:423
  25. Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide t...

    Authors: Florian Odronitz, Holger Pillmann, Oliver Keller, Stephan Waack and Martin Kollmar
    Citation: BMC Genomics 2008 9:422
  26. Zinc (Zn) is an essential trace element. However, Zn bioavailability from commonly consumed plants may be reduced due to phytic acid. Zn supplementation has been used to treat diarrheal disease in children, an...

    Authors: Michelle M Martínez-Montemayor, Gretchen M Hill, Nancy E Raney, Valencia D Rilington, Robert J Tempelman, Jane E Link, Christopher P Wilkinson, Antonio M Ramos and Catherine W Ernst
    Citation: BMC Genomics 2008 9:421
  27. Mouse and rat models are mainstays in pharmacology, toxicology and drug development – but differences between strains and between species complicate data interpretation and application to human health. Dioxin-...

    Authors: Paul C Boutros, Rui Yan, Ivy D Moffat, Raimo Pohjanvirta and Allan B Okey
    Citation: BMC Genomics 2008 9:419
  28. "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Para...

    Authors: Lucie Hanriot, Céline Keime, Nadine Gay, Claudine Faure, Carole Dossat, Patrick Wincker, Céline Scoté-Blachon, Christelle Peyron and Olivier Gandrillon
    Citation: BMC Genomics 2008 9:418
  29. Establishment of aspergillosis is depending upon the exit from dormancy and germination of the conidia of Aspergillus fumigatus in the lung. To gain an understanding of the molecular mechanisms underlying the ear...

    Authors: Claude Lamarre, Sergueï Sokol, Jean-Paul Debeaupuis, Christine Henry, Céline Lacroix, Philippe Glaser, Jean-Yves Coppée, Jean-Marie François and Jean-Paul Latgé
    Citation: BMC Genomics 2008 9:417
  30. We have previously shown that using multiple prediction methods improves the accuracy of disorder predictions. It is, however, a time-consuming procedure, since individual outputs of multiple predictions have ...

    Authors: Philippe Lieutaud, Bruno Canard and Sonia Longhi
    Citation: BMC Genomics 2008 9(Suppl 2):S25

    This article is part of a Supplement: Volume 9 Supplement 2

  31. We present a mixture model-based analysis for identifying differences in the distribution of RNA polymerase II (Pol II) in transcribed regions, measured using ChIP-seq (chromatin immunoprecipitation following ...

    Authors: Weixing Feng, Yunlong Liu, Jiejun Wu, Kenneth P Nephew, Tim HM Huang and Lang Li
    Citation: BMC Genomics 2008 9(Suppl 2):S23

    This article is part of a Supplement: Volume 9 Supplement 2

  32. Gene expression profiles based on microarray data are recognized as potential diagnostic indices of cancer. Molecular tumor classifications resulted from these data and learning algorithms have advanced our un...

    Authors: Rattikorn Hewett and Phongphun Kijsanayothin
    Citation: BMC Genomics 2008 9(Suppl 2):S21

    This article is part of a Supplement: Volume 9 Supplement 2

  33. Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable det...

    Authors: Heng Huang, Nha Nguyen, Soontorn Oraintara and An Vo
    Citation: BMC Genomics 2008 9(Suppl 2):S17

    This article is part of a Supplement: Volume 9 Supplement 2

  34. Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become ...

    Authors: Feng Yue, Meng Zhang and Jijun Tang
    Citation: BMC Genomics 2008 9(Suppl 2):S15

    This article is part of a Supplement: Volume 9 Supplement 2

  35. As studies of molecular biology system attempt to achieve a comprehensive understanding of a particular system, Type 1 errors may be a significant problem. However, few investigators are inclined to accept the...

    Authors: Jian Wu, Nataliya I Lenchik and Ivan C Gerling
    Citation: BMC Genomics 2008 9(Suppl 2):S12

    This article is part of a Supplement: Volume 9 Supplement 2

  36. Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistic...

    Authors: Mehdi Pirooznia, Ping Gong, Jack Y Yang, Mary Qu Yang, Edward J Perkins and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):S11

    This article is part of a Supplement: Volume 9 Supplement 2

  37. BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time co...

    Authors: Mehdi Pirooznia, Edward J Perkins and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):S10

    This article is part of a Supplement: Volume 9 Supplement 2

  38. Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors up...

    Authors: Jack Y Yang, Andrzej Niemierko, Mary Qu Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 2):S9

    This article is part of a Supplement: Volume 9 Supplement 2

  39. The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always...

    Authors: Cole Harris and Noushin Ghaffari
    Citation: BMC Genomics 2008 9(Suppl 2):S7

    This article is part of a Supplement: Volume 9 Supplement 2

  40. Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results u...

    Authors: Yunfeng Yang, Mengxia Zhu, Liyou Wu and Jizhong Zhou
    Citation: BMC Genomics 2008 9(Suppl 2):S5

    This article is part of a Supplement: Volume 9 Supplement 2

  41. Bidirectional promoters lie between adjacent genes, which are transcribed from opposite strands of DNA. The functional mechanisms underlying the activation of bidirectional promoters are currently uncharacteri...

    Authors: Mary Qu Yang and Laura L Elnitski
    Citation: BMC Genomics 2008 9(Suppl 2):S3

    This article is part of a Supplement: Volume 9 Supplement 2

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