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  1. Understanding how pathogens respond to antimicrobial peptides, and how this compares to currently available antibiotics, is crucial for optimizing antimicrobial therapy. Staphylococcus aureus has several known re...

    Authors: Milla Pietiäinen, Patrice François, Hanne-Leena Hyyryläinen, Manuela Tangomo, Vera Sass, Hans-Georg Sahl, Jacques Schrenzel and Vesa P Kontinen
    Citation: BMC Genomics 2009 10:429
    Content type: Research article Published on:

  2. Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40%...

    Authors: M Carmen Marques, Hugo Alonso-Cantabrana, Javier Forment, Raquel Arribas, Santiago Alamar, Vicente Conejero and Miguel A Perez-Amador
    Citation: BMC Genomics 2009 10:428
    Content type: Research article Published on:

  3. Trypanosomes undergo extensive developmental changes during their complex life cycle. Crucial among these is the transition between slender and stumpy bloodstream forms and, thereafter, the differentiation fro...

    Authors: Sarah Kabani, Katelyn Fenn, Alan Ross, Al Ivens, Terry K Smith, Peter Ghazal and Keith Matthews
    Citation: BMC Genomics 2009 10:427
    Content type: Research article Published on:

  4. The use of microarray technology for describing changes in mRNA expression to address ecological and evolutionary questions is becoming increasingly popular. Since three-spine stickleback are an important ecol...

    Authors: Erica H Leder, Juha Merilä and Craig R Primmer
    Citation: BMC Genomics 2009 10:426
    Content type: Methodology article Published on:

  5. Lactobacillus plantarum is a normal, potentially probiotic, inhabitant of the human gastrointestinal (GI) tract. The bacterium has great potential as food-grade cell factory and for in situ delivery of biomolecul...

    Authors: Geir Mathiesen, Anita Sveen, May Bente Brurberg, Lasse Fredriksen, Lars Axelsson and Vincent GH Eijsink
    Citation: BMC Genomics 2009 10:425
    Content type: Research article Published on:

  6. Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims...

    Authors: Jérôme Toussaint, Anieta M Sieuwerts, Benjamin Haibe-Kains, Christine Desmedt, Ghizlane Rouas, Adrian L Harris, Denis Larsimont, Martine Piccart, John A Foekens, Virginie Durbecq and Christos Sotiriou
    Citation: BMC Genomics 2009 10:424
    Content type: Methodology article Published on:

  7. Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders suc...

    Authors: Paula Vizoso, Lee A Meisel, Andrés Tittarelli, Mariano Latorre, Juan Saba, Rodrigo Caroca, Jonathan Maldonado, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana and Herman Silva
    Citation: BMC Genomics 2009 10:423
    Content type: Research article Published on:

  8. Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans regulatory variation. Understanding the source of expression variation has important implications for disease susceptib...

    Authors: Bradley J Main, Ryan D Bickel, Lauren M McIntyre, Rita M Graze, Peter P Calabrese and Sergey V Nuzhdin
    Citation: BMC Genomics 2009 10:422
    Content type: Methodology article Published on:

  9. Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develo...

    Authors: Mannu Jayakanthan, Jayaraman Muthukumaran, Sanniyasi Chandrasekar, Konika Chawla, Ankita Punetha and Durai Sundar
    Citation: BMC Genomics 2009 10:421
    Content type: Database Published on:

  10. Alterations in brain-derived neurotrophic factor (BDNF) gene expression contribute to serious pathologies such as depression, epilepsy, cancer, Alzheimer's, Huntington and Parkinson's disease. Therefore, explorin...

    Authors: Tamara Aid-Pavlidis, Pavlos Pavlidis and Tõnis Timmusk
    Citation: BMC Genomics 2009 10:420
    Content type: Research article Published on:

  12. Tol2, a member of the hAT family of transposons, has become a useful tool for genetic manipulation of model animals, but information about its interactions with vertebrate genomes is still limited. Furthermore, p...

    Authors: Igor Kondrychyn, Marta Garcia-Lecea, Alexander Emelyanov, Sergey Parinov and Vladimir Korzh
    Citation: BMC Genomics 2009 10:418
    Content type: Research article Published on:

  13. The general population is constantly exposed to low levels of radiation through natural, occupational or medical irradiation. Even if the biological effects of low-level radiation have been intensely debated a...

    Authors: Florian Bonin, Manuella Molina, Claude Malet, Chantal Ginestet, Odile Berthier-Vergnes, Michèle T Martin and Jérôme Lamartine
    Citation: BMC Genomics 2009 10:417
    Content type: Research article Published on:

  14. WNT4 is a critical signalling molecule in embryogenesis and homeostasis, but the elements that control its transcriptional regulation are largely unknown. This study uses comparative cross species sequence and...

    Authors: Hongshi Yu, Andrew J Pask, Geoffrey Shaw and Marilyn B Renfree
    Citation: BMC Genomics 2009 10:416
    Content type: Research article Published on:

  15. The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evo...

    Authors: Nasheeman Ashraf, Deepali Ghai, Pranjan Barman, Swaraj Basu, Nagaraju Gangisetty, Mihir K Mandal, Niranjan Chakraborty, Asis Datta and Subhra Chakraborty
    Citation: BMC Genomics 2009 10:415
    Content type: Research article Published on:

  16. Telomeric and subtelomeric regions are essential for genome stability and regular chromosome replication. In this work, we have characterized the wheat BAC (bacterial artificial chromosome) clones containing S...

    Authors: Elena A Salina, Ekaterina M Sergeeva, Irina G Adonina, Andrey B Shcherban, Dmitry A Afonnikov, Harry Belcram, Cecile Huneau and Boulos Chalhoub
    Citation: BMC Genomics 2009 10:414
    Content type: Research article Published on:

  17. During microRNA (miRNA) maturation in humans and flies, Drosha and Dicer cut the precursor transcript, thereby producing a short RNA duplex. One strand of this duplex becomes a functional component of the RNA-...

    Authors: Hai Yang Hu, Zheng Yan, Ying Xu, Hao Hu, Corinna Menzel, Yan Hong Zhou, Wei Chen and Philipp Khaitovich
    Citation: BMC Genomics 2009 10:413
    Content type: Research article Published on:

  18. Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbe...

    Authors: Thomas Ohnesorg, Stefanie Eggers, Wouter N Leonhard, Andrew H Sinclair and Stefan J White
    Citation: BMC Genomics 2009 10:412
    Content type: Methodology article Published on:

  19. DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which...

    Authors: Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto and Yasushi Okuno
    Citation: BMC Genomics 2009 10:411
    Content type: Software Published on:

  20. The marine model organism Rhodopirellula baltica SH1T was the first Planctomycete to have its genome completely sequenced. The genome analysis predicted a complex lifestyle and a variety of genetic opportunities ...

    Authors: Patricia Wecker, Christine Klockow, Andreas Ellrott, Christian Quast, Philipp Langhammer, Jens Harder and Frank Oliver Glöckner
    Citation: BMC Genomics 2009 10:410
    Content type: Research article Published on:

  22. Microarray analysis still is a powerful tool to identify new components of the transcriptosome. It helps to increase the knowledge of targets triggered by stress conditions such as hypoxia and nitric oxide. Ho...

    Authors: Emeka I Igwe, Silke Essler, Natalie Al-Furoukh, Nathalie Dehne and Bernhard Brüne
    Citation: BMC Genomics 2009 10:408
    Content type: Research article Published on:

  23. MicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease process...

    Authors: Yongxin Chen, Jonathan AL Gelfond, Linda M McManus and Paula K Shireman
    Citation: BMC Genomics 2009 10:407
    Content type: Methodology article Published on:

  24. Sodium tungstate is known to be an effective anti-diabetic agent, able to increase beta cell mass in animal models of diabetes, although the molecular mechanisms of this treatment and the genes that control pa...

    Authors: Jordi Altirriba, Albert Barbera, Héctor Del Zotto, Belen Nadal, Sandra Piquer, Alex Sánchez-Pla, Juan J Gagliardino and Ramon Gomis
    Citation: BMC Genomics 2009 10:406
    Content type: Research article Published on:

  25. Amyotrophic Lateral Sclerosis (ALS) is a lethal disorder characterized by progressive degeneration of motor neurons in the brain and spinal cord. Diagnosis is mainly based on clinical symptoms, and there is cu...

    Authors: Christiaan GJ Saris, Steve Horvath, Paul WJ van Vught, Michael A van Es, Hylke M Blauw, Tova F Fuller, Peter Langfelder, Joseph DeYoung, John HJ Wokke, Jan H Veldink, Leonard H van den Berg and Roel A Ophoff
    Citation: BMC Genomics 2009 10:405
    Content type: Research article Published on:

  26. We employed DNA microarray technology to investigate the host response to Streptococcus pneumoniae in a mouse model of asymptomatic carriage. Over a period of six weeks, we profiled transcript abundance and compl...

    Authors: Elizabeth A Joyce, Stephen J Popper and Stanley Falkow
    Citation: BMC Genomics 2009 10:404
    Content type: Research article Published on:

  27. Human peripheral blood monocytes (Mo) consist of subsets distinguished by expression of CD16 (FCγRIII) and chemokine receptors. Classical CD16- Mo express CCR2 and migrate in response to CCL2, while a minor CD16+

    Authors: Petronela Ancuta, Kuang-Yu Liu, Vikas Misra, Vanessa Sue Wacleche, Annie Gosselin, Xiaobo Zhou and Dana Gabuzda
    Citation: BMC Genomics 2009 10:403
    Content type: Research article Published on:

  28. Porcine enteropathogenic Escherichia coli (PEPEC) strains of serogroup O45 cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most O45 PEPEC strains possess the locus of ...

    Authors: Guillaume Bruant, Yongxiang Zhang, Philippe Garneau, Justin Wong, Chad Laing, John M Fairbrother, Victor PJ Gannon and Josée Harel
    Citation: BMC Genomics 2009 10:402
    Content type: Research article Published on:

  29. Array comparative genomic hybridization (aCGH) is a popular technique for detection of genomic copy number imbalances. These play a critical role in the onset of various types of cancer. In the analysis of aCG...

    Authors: Bart PP van Houte, Thomas W Binsl, Hannes Hettling, Walter Pirovano and Jaap Heringa
    Citation: BMC Genomics 2009 10:401
    Content type: Research article Published on:

  30. New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though ...

    Authors: Carol Soderlund, Eric Johnson, Matthew Bomhoff and Anne Descour
    Citation: BMC Genomics 2009 10:400
    Content type: Software Published on:

  31. Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and ...

    Authors: Fiammetta Alagna, Nunzio D'Agostino, Laura Torchia, Maurizio Servili, Rosa Rao, Marco Pietrella, Giovanni Giuliano, Maria Luisa Chiusano, Luciana Baldoni and Gaetano Perrotta
    Citation: BMC Genomics 2009 10:399
    Content type: Research article Published on:

  32. Rice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a compar...

    Authors: Harkamal Walia, Clyde Wilson, Abdelbagi M Ismail, Timothy J Close and Xinping Cui
    Citation: BMC Genomics 2009 10:398
    Content type: Research article Published on:

  33. The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and trans...

    Authors: Diana L Williams, Richard A Slayden, Amol Amin, Alejandra N Martinez, Tana L Pittman, Alex Mira, Anirban Mitra, Valakunja Nagaraja, Norman E Morrison, Milton Moraes and Thomas P Gillis
    Citation: BMC Genomics 2009 10:397
    Content type: Research article Published on:

  34. Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well describ...

    Authors: Trine B Rounge, Thomas Rohrlack, Alexander J Nederbragt, Tom Kristensen and Kjetill S Jakobsen
    Citation: BMC Genomics 2009 10:396
    Content type: Research article Published on:

  35. Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion sy...

    Authors: David J Studholme, Selena Gimenez Ibanez, Daniel MacLean, Jeffery L Dangl, Jeff H Chang and John P Rathjen
    Citation: BMC Genomics 2009 10:395
    Content type: Research article Published on:

  36. Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iro...

    Authors: Raquel Quatrini, Corinne Appia-Ayme, Yann Denis, Eugenia Jedlicki, David S Holmes and Violaine Bonnefoy
    Citation: BMC Genomics 2009 10:394
    Content type: Research article Published on:

  38. Recent transcriptomic analyses in mammals have uncovered the widespread occurrence of endogenous antisense transcripts, termed natural antisense transcripts (NATs). NATs are transcribed from the opposite stran...

    Authors: Koji Numata, Yuko Osada, Yuki Okada, Rintaro Saito, Noriko Hiraiwa, Hajime Nakaoka, Naoyuki Yamamoto, Kazufumi Watanabe, Kazue Okubo, Chihiro Kohama, Akio Kanai, Kuniya Abe and Hidenori Kiyosawa
    Citation: BMC Genomics 2009 10:392
    Content type: Research article Published on:

  39. During evolution selection forces such as changing environments shape the architecture of genomes. The distribution of genes along chromosomes and the length of intragenic regions are basic genomic features kn...

    Authors: Tamir Tuller, Eytan Ruppin and Martin Kupiec
    Citation: BMC Genomics 2009 10:391
    Content type: Research article Published on:

  41. Bombyx mori, the domesticated silkworm, is a well-studied model insect with great economic and scientific significance. Although more than 400 mutations have been described in silkworms, most have not been identi...

    Authors: Shuai Zhan, Jianhua Huang, Qiuhong Guo, Yunpo Zhao, Weihua Li, Xuexia Miao, Marian R Goldsmith, Muwang Li and Yongping Huang
    Citation: BMC Genomics 2009 10:389
    Content type: Research article Published on:

  42. Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinica...

    Authors: Simona Granata, Gianluigi Zaza, Simona Simone, Gaetano Villani, Dominga Latorre, Paola Pontrelli, Massimo Carella, Francesco Paolo Schena, Giuseppe Grandaliano and Giovanni Pertosa
    Citation: BMC Genomics 2009 10:388
    Content type: Research article Published on:

  43. There is a major paradox in our understanding of honey bee immunity: the high population density in a bee colony implies a high rate of disease transmission among individuals, yet bees are predicted to express...

    Authors: Queenie WT Chan, Andony P Melathopoulos, Stephen F Pernal and Leonard J Foster
    Citation: BMC Genomics 2009 10:387
    Content type: Research article Published on:

  44. Malaria is a tropical disease caused by protozoan parasite, Plasmodium, which is transmitted to humans by various species of female anopheline mosquitoes. Anopheles stephensi is one such major malaria vector in u...

    Authors: Deepak P Patil, Santosh Atanur, Dhiraj P Dhotre, D Anantharam, Vineet S Mahajan, Sandeep A Walujkar, Rakesh K Chandode, Girish J Kulkarni, Pankaj S Ghate, Abhishek Srivastav, Kannayakanahalli M Dayananda, Neha Gupta, Bhakti Bhagwat, Rajendra R Joshi, Devendra T Mourya, Milind S Patole…
    Citation: BMC Genomics 2009 10:386
    Content type: Research article Published on:

  45. The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these qua...

    Authors: Lars Snipen, Trygve Almøy and David W Ussery
    Citation: BMC Genomics 2009 10:385
    Content type: Methodology article Published on:

  46. Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of...

    Authors: Tadeja Režen, Viola Tamasi, Anita Lövgren-Sandblom, Ingemar Björkhem, Urs A Meyer and Damjana Rozman
    Citation: BMC Genomics 2009 10:384
    Content type: Research article Published on:

  47. Oral squamous cell carcinoma (OSCC) is one of the most common forms of cancer associated with the presence of precancerous oral leukoplakia. Given the poor prognosis associated with oral leukoplakia, and the d...

    Authors: Zhi Wang, Xiaodong Feng, Xinyu Liu, Lu Jiang, Xin Zeng, Ning Ji, Jing Li, Longjiang Li and Qianming Chen
    Citation: BMC Genomics 2009 10:383
    Content type: Research article Published on:

  48. The declining cost of DNA sequencing is making genome sequencing a feasible option for more organisms, including many of interest to ecologists and evolutionary biologists. While obtaining high-depth, complete...

    Authors: David A Rasmussen and Mohamed AF Noor
    Citation: BMC Genomics 2009 10:382
    Content type: Research article Published on:

  49. To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanis...

    Authors: Fabio Parisi, Bernhard Sonderegger, Pratyaksha Wirapati, Mauro Delorenzi and Felix Naef
    Citation: BMC Genomics 2009 10:381
    Content type: Research article Published on:

  50. The human microflora is known to be extremely complex, yet most pathogenesis research is conducted in mono-species models of infection. Consequently, it remains unclear whether the level of complexity of a hos...

    Authors: Jeffrey J Mans, Kate von Lackum, Cassandra Dorsey, Shaun Willis, Shannon M Wallet, Henry V Baker, Richard J Lamont and Martin Handfield
    Citation: BMC Genomics 2009 10:380
    Content type: Research article Published on:

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BMC Genomics

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