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  1. Inappropriate activation of AKT signaling is a relatively common occurrence in human tumors, and can be caused by activation of components of, or by loss or decreased activity of inhibitors of, this signaling ...

    Authors: Rakesh Kumar, Stephen J Blakemore, Catherine E Ellis, Emanuel F Petricoin III, Dexter Pratt, Michael Macoritto, Andrea L Matthews, Joseph J Loureiro and Keith Elliston
    Citation: BMC Genomics 2010 11:419
  2. The immune response is an energy demanding process, which has effects in many physiological pathways in the body including protein and lipid metabolism. During an inflammatory response the liver is required to...

    Authors: Samuel AM Martin, Alex Douglas, Dominic F Houlihan and Christopher J Secombes
    Citation: BMC Genomics 2010 11:418
  3. Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels ...

    Authors: Guanjie Chen, Daniel Shriner, Jie Zhou, Ayo Doumatey, Hanxia Huang, Norman P Gerry, Alan Herbert, Michael F Christman, Yuanxiu Chen, Georgia M Dunston, Mezbah U Faruque, Charles N Rotimi and Adebowale Adeyemo
    Citation: BMC Genomics 2010 11:417
  4. Allele frequency is one of the most important population indices and has been broadly applied to genetic/genomic studies. Estimation of allele frequency using genotypes is convenient but may lose data informat...

    Authors: Hsin-Chou Yang, Hsin-Chi Lin, Mei-Chu Huang, Ling-Hui Li, Wen-Harn Pan, Jer-Yuarn Wu and Yuan-Tsong Chen
    Citation: BMC Genomics 2010 11:415
  5. The method of chromatin immunoprecipitation combined with microarrays (ChIP-Chip) is a powerful tool for genome-wide analysis of protein binding. However, a high background signal is a common phenomenon.

    Authors: Torsten Waldminghaus and Kirsten Skarstad
    Citation: BMC Genomics 2010 11:414
  6. The template switching PCR (TS-PCR) method of cDNA synthesis represents one of the most straightforward approaches to generating full length cDNA for sequencing efforts. However, when applied to very small RNA...

    Authors: Jeremy Kapteyn, Ruifeng He, Eric T McDowell and David R Gang
    Citation: BMC Genomics 2010 11:413
  7. With the wealth of genomic data available it has become increasingly important to assign putative protein function through functional transfer between orthologs. Therefore, correct elucidation of the evolution...

    Authors: Anna Henricson, Kristoffer Forslund and Erik LL Sonnhammer
    Citation: BMC Genomics 2010 11:412
  8. Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosi...

    Authors: Diego Mauricio Riaño-Pachón, Sabrina Kleessen, Jost Neigenfind, Pawel Durek, Elke Weber, Wolfgang R Engelsberger, Dirk Walther, Joachim Selbig, Waltraud X Schulze and Birgit Kersten
    Citation: BMC Genomics 2010 11:411
  9. Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and subst...

    Authors: David J Witherspoon, Jinchuan Xing, Yuhua Zhang, W Scott Watkins, Mark A Batzer and Lynn B Jorde
    Citation: BMC Genomics 2010 11:410
  10. MicroRNA (miRNA) play an important role in gene expression regulation. At present, the number of annotated miRNA continues to grow rapidly, in part due to advances of high-throughput sequencing techniques. Her...

    Authors: Ning-Yi Shao, Hai Yang Hu, Zheng Yan, Ying Xu, Hao Hu, Corinna Menzel, Na Li, Wei Chen and Philipp Khaitovich
    Citation: BMC Genomics 2010 11:409
  11. More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppress...

    Authors: Dario Cantu, Leonardo S Vanzetti, Adam Sumner, Martin Dubcovsky, Marta Matvienko, Assaf Distelfeld, Richard W Michelmore and Jorge Dubcovsky
    Citation: BMC Genomics 2010 11:408
  12. The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently appr...

    Authors: Eduardo R Macagno, Terry Gaasterland, Lee Edsall, Vineet Bafna, Marcelo B Soares, Todd Scheetz, Thomas Casavant, Corinne Da Silva, Patrick Wincker, Aurélie Tasiemski and Michel Salzet
    Citation: BMC Genomics 2010 11:407
  13. The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- ...

    Authors: James C Mullikin, Nancy F Hansen, Lei Shen, Heather Ebling, William F Donahue, Wei Tao, David J Saranga, Adrianne Brand, Marc J Rubenfield, Alice C Young, Pedro Cruz, Carlos Driscoll, Victor David, Samer WK Al-Murrani, Mary F Locniskar, Mitchell S Abrahamsen…
    Citation: BMC Genomics 2010 11:406
  14. Serine proteases (SPs) and serine proteases homologs (SPHs) are a large group of proteolytic enzymes, with important roles in a variety of physiological processes, such as cell signalling, defense and developm...

    Authors: Ping Zhao, Gen-Hong Wang, Zhao-Ming Dong, Jun Duan, Ping-Zhen Xu, Ting-Cai Cheng, Zhong-Huai Xiang and Qing-You Xia
    Citation: BMC Genomics 2010 11:405
  15. Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream att...

    Authors: Mercedes Moreno-Paz, Manuel J Gómez, Aida Arcas and Víctor Parro
    Citation: BMC Genomics 2010 11:404
  16. Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically de...

    Authors: Shao-Ke Lou, Ka-Lok Wong, Ming Li, Paul Pui-Hay But, Stephen Kwok-Wing Tsui and Pang-Chui Shaw
    Citation: BMC Genomics 2010 11:402
  17. About 10% of cases of male infertility are due to the presence of microdeletions within the long arm of the Y chromosome (Yq). Despite the large literature covering this critical issue, very little is known ab...

    Authors: Valentina Gatta, Florina Raicu, Alberto Ferlin, Ivana Antonucci, Anna Paola Scioletti, Andrea Garolla, Giandomenico Palka, Carlo Foresta and Liborio Stuppia
    Citation: BMC Genomics 2010 11:401
  18. Whitefly (Bemisia tabaci) causes extensive crop damage throughout the world by feeding directly on plants and by vectoring hundreds of species of begomoviruses. Yet little is understood about its genes involved i...

    Authors: Xiao-Wei Wang, Jun-Bo Luan, Jun-Min Li, Yan-Yuan Bao, Chuan-Xi Zhang and Shu-Sheng Liu
    Citation: BMC Genomics 2010 11:400
  19. Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of al...

    Authors: Timothée Revil, Daniel Gaffney, Christel Dias, Jacek Majewski and Loydie A Jerome-Majewska
    Citation: BMC Genomics 2010 11:399
  20. Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month...

    Authors: Beatrice A McGivney, Paul A McGettigan, John A Browne, Alexander CO Evans, Rita G Fonseca, Brendan J Loftus, Amanda Lohan, David E MacHugh, Barbara A Murphy, Lisa M Katz and Emmeline W Hill
    Citation: BMC Genomics 2010 11:398
  21. Carbonic anhydrases (CAs) are a family of enzymes that regulate pH homeostasis in various tissues. CA IX is an exceptional member of this family because in addition to the basic CA function, it has been implic...

    Authors: Heini Kallio, Mika Hilvo, Alejandra Rodriguez, Eeva-Helena Lappalainen, Anna-Maria Lappalainen and Seppo Parkkila
    Citation: BMC Genomics 2010 11:397
  22. Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. ba...

    Authors: Lifeng Lin, Gary J Pierce, John E Bowers, James C Estill, Rosana O Compton, Lisa K Rainville, Changsoo Kim, Cornelia Lemke, Junkang Rong, Haibao Tang, Xiyin Wang, Michele Braidotti, Amy H Chen, Kristen Chicola, Kristi Collura, Ethan Epps…
    Citation: BMC Genomics 2010 11:395
  23. Trypanosomosis is the most economically important disease constraint to livestock productivity in Africa. A number of trypanotolerant cattle breeds are found in West Africa, and identification of the genes con...

    Authors: Joseph K Nganga, Morris Soller and Fuad A Iraqi
    Citation: BMC Genomics 2010 11:394
  24. The genus Erwinia includes plant-associated pathogenic and non-pathogenic Enterobacteria. Important pathogens such as Erwinia amylovora, the causative agent of fire blight and E. pyrifoliae causing bacterial shoo...

    Authors: Michael Kube, Alexander M Migdoll, Isabel Gehring, Katja Heitmann, Yvonne Mayer, Heiner Kuhl, Florian Knaust, Klaus Geider and Richard Reinhardt
    Citation: BMC Genomics 2010 11:393
  25. The zebrafish intestine is a simple tapered tube that is folded into three sections. However, whether the intestine is functionally similar along its length remains unknown. Thus, a systematic structural and f...

    Authors: Zhengyuan Wang, Jianguo Du, Siew Hong Lam, Sinnakarupan Mathavan, Paul Matsudaira and Zhiyuan Gong
    Citation: BMC Genomics 2010 11:392
  26. Understanding the genetic basis of adaptive changes has been a major goal of evolutionary biology. In complex organisms without sequenced genomes, de novo transcriptome assembly using a longer read sequencing ...

    Authors: Wiesław Babik, Michał Stuglik, Weihong Qi, Marzanna Kuenzli, Katarzyna Kuduk, Paweł Koteja and Jacek Radwan
    Citation: BMC Genomics 2010 11:390
  27. Clostridium difficile is a Gram-positive, anaerobic, spore-forming bacterium that is responsible for C. difficile associated disease in humans and is currently the most common cause of nosocomial diarrhoea in the...

    Authors: Gemma L Marsden, Ian J Davis, Victoria J Wright, Mohammed Sebaihia, Ed J Kuijper and Nigel P Minton
    Citation: BMC Genomics 2010 11:389
  28. Circulating CD34+ progenitor cells have the potential to differentiate into a variety of cells, including endothelial cells. Knowledge is still scarce about the transcriptional programs used by CD34+ cells fro...

    Authors: Tineke CTM van der Pouw Kraan, Stephan H Schirmer, Joost O Fledderus, Perry D Moerland, Josefien M Baggen, Thomas A Leyen, Anja M van der Laan, Jan J Piek, Niels van Royen and Anton JG Horrevoets
    Citation: BMC Genomics 2010 11:388
  29. Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a nov...

    Authors: Julien Portela, Christoph Grunau, Céline Cosseau, Sophie Beltran, Christelle Dantec, Hugues Parrinello and Jérôme Boissier
    Citation: BMC Genomics 2010 11:387
  30. Chromatin in the nucleus of all eukaryotes is organized into a system of loops and domains. These loops remain fastened at their bases to the fundamental framework of the nucleus, the matrix or the scaffold. T...

    Authors: Sushma S Padmaja, Jagannathan Lakshmanan, Ravi Gupta, Santanu Banerjee, Pennathur Gautam and Sulagna Banerjee
    Citation: BMC Genomics 2010 11:386
  31. Cucumber, Cucumis sativus L., is an economically and nutritionally important crop of the Cucurbitaceae family and has long served as a primary model system for sex determination studies. Recently, the sequencing ...

    Authors: Shaogui Guo, Yi Zheng, Je-Gun Joung, Shiqiang Liu, Zhonghua Zhang, Oswald R Crasta, Bruno W Sobral, Yong Xu, Sanwen Huang and Zhangjun Fei
    Citation: BMC Genomics 2010 11:384
  32. Tiling arrays have been the tool of choice for probing an organism's transcriptome without prior assumptions about the transcribed regions, but RNA-Seq is becoming a viable alternative as the costs of sequenci...

    Authors: Ashish Agarwal, David Koppstein, Joel Rozowsky, Andrea Sboner, Lukas Habegger, LaDeana W Hillier, Rajkumar Sasidharan, Valerie Reinke, Robert H Waterston and Mark Gerstein
    Citation: BMC Genomics 2010 11:383
  33. Physical maps employing libraries of bacterial artificial chromosome (BAC) clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread whea...

    Authors: Delphine Fleury, Ming-Cheng Luo, Jan Dvorak, Luke Ramsay, Bikram S Gill, Olin D Anderson, Frank M You, Zahra Shoaei, Karin R Deal and Peter Langridge
    Citation: BMC Genomics 2010 11:382
  34. Biological processes occur on a vast range of time scales, and many of them occur concurrently. As a result, system-wide measurements of gene expression have the potential to capture many of these processes si...

    Authors: David A Orlando, Siobhan M Brady, Thomas MA Fink, Philip N Benfey and Sebastian E Ahnert
    Citation: BMC Genomics 2010 11:381
  35. The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, w...

    Authors: Benoît Remenant, Bénédicte Coupat-Goutaland, Alice Guidot, Gilles Cellier, Emmanuel Wicker, Caitilyn Allen, Mark Fegan, Olivier Pruvost, Mounira Elbaz, Alexandra Calteau, Gregory Salvignol, Damien Mornico, Sophie Mangenot, Valérie Barbe, Claudine Médigue and Philippe Prior
    Citation: BMC Genomics 2010 11:379
  36. The developmental transition between the late fetus and a newborn animal is associated with profound changes in skeletal muscle function as it adapts to the new physiological demands of locomotion and postural...

    Authors: Keren Byrne, Tony Vuocolo, Cedric Gondro, Jason D White, Noelle E Cockett, Tracy Hadfield, Christopher A Bidwell, Jolena N Waddell and Ross L Tellam
    Citation: BMC Genomics 2010 11:378
  37. Recently, a new livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) Sequence Type 398 (ST398) isolate has emerged worldwide. Although there have been reports of invasive disease in humans, MRS...

    Authors: Maarten J Schijffelen, CH Edwin Boel, Jos AG van Strijp and Ad C Fluit
    Citation: BMC Genomics 2010 11:376
  38. Worldwide, bacterial vaginosis (BV) is the most common vaginal disorder. It is associated with risk for preterm birth and HIV infection. The etiology of the condition has been debated for nearly half a century...

    Authors: Michael D Harwich Jr, Joao M Alves, Gregory A Buck, Jerome F Strauss III, Jennifer L Patterson, Aminat T Oki, Philippe H Girerd and Kimberly K Jefferson
    Citation: BMC Genomics 2010 11:375
  39. The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome,...

    Authors: Felix D Guerrero, Paula Moolhuijzen, Daniel G Peterson, Shelby Bidwell, Elisabet Caler, Matthew Bellgard, Vishvanath M Nene and Appolinaire Djikeng
    Citation: BMC Genomics 2010 11:374
  40. Authors: Ying Wang, Vinayak Brahmakshatriya, Huifeng Zhu, Blanca Lupiani, Sanjay M Reddy, Byung-Jun Yoon, Preethi H Gunaratne, Jong Hwan Kim, Rui Chen, Ashley L Benham, Junjun Wang and Huaijun Zhou
    Citation: BMC Genomics 2010 11:373

    The original article was published in BMC Genomics 2009 10:512

  41. Animal mitochondrial genomes are potential models for molecular evolution and markers for phylogenetic and population studies. Previous research has shown interesting features in hymenopteran mitochondrial gen...

    Authors: Shu-jun Wei, Min Shi, Michael J Sharkey, Cornelis van Achterberg and Xue-xin Chen
    Citation: BMC Genomics 2010 11:371
  42. Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although...

    Authors: Maxy Mariasegaram, Antonio Reverter, Wes Barris, Sigrid A Lehnert, Brian Dalrymple and Kishore Prayaga
    Citation: BMC Genomics 2010 11:370

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