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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  23. 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:

  24. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not...

    Authors: Nicole AR Walter, Daniel Bottomly, Ted Laderas, Michael A Mooney, Priscila Darakjian, Robert P Searles, Christina A Harrington, Shannon K McWeeney, Robert Hitzemann and Kari J Buck
    Citation: BMC Genomics 2009 10:379
    Content type: Research article Published on:

  37. Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in...

    Authors: Bhupendra Chaudhary, Ran Hovav, Lex Flagel, Ron Mittler and Jonathan F Wendel
    Citation: BMC Genomics 2009 10:378
    Content type: Research article Published on:

  38. The hard clam, Mercenaria mercenaria, has been affected by severe mortality episodes associated with the protistan parasite QPX (Quahog Parasite Unknown) for several years. Despite the commercial importance of ha...

    Authors: Mickael Perrigault, Arnaud Tanguy and Bassem Allam
    Citation: BMC Genomics 2009 10:377
    Content type: Research article Published on:

  39. Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on s...

    Authors: Jamie A O'Rourke, Rex T Nelson, David Grant, Jeremy Schmutz, Jane Grimwood, Steven Cannon, Carroll P Vance, Michelle A Graham and Randy C Shoemaker
    Citation: BMC Genomics 2009 10:376
    Content type: Research article Published on:

  40. Venomous animals incapacitate their prey using complex venoms that can contain hundreds of unique protein toxins. The realisation that many of these toxins may have pharmaceutical and insecticidal potential du...

    Authors: David LA Wood, Tomas Miljenović, Shuzhi Cai, Robert J Raven, Quentin Kaas, Pierre Escoubas, Volker Herzig, David Wilson and Glenn F King
    Citation: BMC Genomics 2009 10:375
    Content type: Database Published on:

  41. Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore, in the framework of the Inter...

    Authors: Andreia J Amaral, Hendrik-Jan Megens, Hindrik HD Kerstens, Henri CM Heuven, Bert Dibbits, Richard PMA Crooijmans, Johan T den Dunnen and Martien AM Groenen
    Citation: BMC Genomics 2009 10:374
    Content type: Methodology article Published on:

  42. Hepatitis C virus (HCV) is a major cause of chronic liver disease by infecting over 170 million people worldwide. Recent studies have shown that microRNAs (miRNAs), a class of small non-coding regulatory RNAs,...

    Authors: Xinxia Peng, Yu Li, Kathie-Anne Walters, Elizabeth R Rosenzweig, Sharon L Lederer, Lauri D Aicher, Sean Proll and Michael G Katze
    Citation: BMC Genomics 2009 10:373
    Content type: Research article Published on:

  43. Interferons (IFNs) are potent antiviral cytokines capable of reprogramming the macrophage phenotype through the induction of interferon-stimulated genes (ISGs). Here we have used targeted RNA interference to s...

    Authors: Paul Lacaze, Sobia Raza, Garwin Sing, David Page, Thorsten Forster, Petter Storm, Marie Craigon, Tarif Awad, Peter Ghazal and Tom C Freeman
    Citation: BMC Genomics 2009 10:372
    Content type: Research article Published on:

  44. Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced b...

    Authors: Qingyi Yu, Eric Tong, Rachel L Skelton, John E Bowers, Meghan R Jones, Jan E Murray, Shaobin Hou, Peizhu Guan, Ricelle A Acob, Ming-Cheng Luo, Paul H Moore, Maqsudul Alam, Andrew H Paterson and Ray Ming
    Citation: BMC Genomics 2009 10:371
    Content type: Research article Published on:

  45. Chronic chagasic cardiomyopathy is a debilitating and frequently fatal outcome of human infection with the protozoan parasite, Trypanosoma cruzi. Microarray analysis of gene expression during the T. cruzi life-cy...

    Authors: Todd A Minning, D Brent Weatherly, James Atwood III, Ron Orlando and Rick L Tarleton
    Citation: BMC Genomics 2009 10:370
    Content type: Research article Published on:

  46. Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have acquired a specialized and distinct morphology, they are immotile and infertile. It is only after...

    Authors: Benoît Guyonnet, Guillemette Marot, Jean-Louis Dacheux, Marie-José Mercat, Sandrine Schwob, Florence Jaffrézic and Jean-Luc Gatti
    Citation: BMC Genomics 2009 10:369
    Content type: Research article Published on:

  47. Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar) farming worldwide. The disease causes large mortalities at both the fry- an...

    Authors: Thomas Moen, Matthew Baranski, Anna K Sonesson and Sissel Kjøglum
    Citation: BMC Genomics 2009 10:368
    Content type: Research article Published on:

  48. The relationship between the parasitic fungus Pneumocystis carinii and its host, the laboratory rat, presumably involves features that allow the fungus to circumvent attacks by the immune system. It is hypothesiz...

    Authors: Scott P Keely and James R Stringer
    Citation: BMC Genomics 2009 10:367
    Content type: Research article Published on:

  50. The Central Dogma of biology holds, in famously simplified terms, that DNA makes RNA makes proteins, but there is considerable uncertainty regarding the general, genome-wide correlation between levels of RNA a...

    Authors: Marcus Gry, Rebecca Rimini, Sara Strömberg, Anna Asplund, Fredrik Pontén, Mathias Uhlén and Peter Nilsson
    Citation: BMC Genomics 2009 10:365
    Content type: Research article Published on:

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BMC Genomics

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