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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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

  12. 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
  13. 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
  14. Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important...

    Authors: Timothy G Lilburn, Jianying Gu, Hong Cai and Yufeng Wang
    Citation: BMC Genomics 2010 11:369
  15. elicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the...

    Authors: Jean-Michel Thiberge, Caroline Boursaux-Eude, Philippe Lehours, Marie-Agnès Dillies, Sophie Creno, Jean-Yves Coppée, Zoé Rouy, Aurélie Lajus, Laurence Ma, Christophe Burucoa, Anne Ruskoné-Foumestraux, Anne Courillon-Mallet, Hilde De Reuse, Ivo Gomperts Boneca, Dominique Lamarque, Francis Mégraud…
    Citation: BMC Genomics 2010 11:368
  16. The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and...

    Authors: Eskeatnaf Mulugeta Achame, Evelyne Wassenaar, Jos W Hoogerbrugge, Esther Sleddens-Linkels, Marja Ooms, Zu-Wen Sun, Wilfred FJ van IJcken, J Anton Grootegoed and Willy M Baarends
    Citation: BMC Genomics 2010 11:367
  17. Dinophysis is exceptional among dinoflagellates, possessing plastids derived from cryptophyte algae. Although Dinophysis can be maintained in pure culture for several months, the genus is mixotrophic and needs to...

    Authors: Jennifer H Wisecaver and Jeremiah D Hackett
    Citation: BMC Genomics 2010 11:366
  18. Spinal cord injury leads to neurological dysfunctions affecting the motor, sensory as well as the autonomic systems. Increased excitability of motor neurons has been implicated in injury-induced spasticity, wh...

    Authors: Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn and Ole Kiehn
    Citation: BMC Genomics 2010 11:365
  19. Cell functions depend on molecules organized in the cellular society. Two basic components are mRNA molecules and proteins. The interactions within and between those two components are crucial for carrying out...

    Authors: Haiyun Wang, Qi Wang, Utz J Pape, Bairong Shen, Jianhua Huang, Bin Wu and Xia Li
    Citation: BMC Genomics 2010 11:364
  20. Ticks secrete a cement cone composed of many salivary proteins, some of which are rich in the amino acid glycine in order to attach to their hosts' skin. Glycine-rich proteins (GRPs) are a large family of hete...

    Authors: Sandra R Maruyama, Elen Anatriello, Jennifer M Anderson, José M Ribeiro, Lucinda G Brandão, Jesus G Valenzuela, Beatriz R Ferreira, Gustavo R Garcia, Matias PJ Szabó, Sonal Patel, Richard Bishop and Isabel KF de Miranda-Santos
    Citation: BMC Genomics 2010 11:363
  21. The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentin...

    Authors: Melody S Clark, Michael AS Thorne, Florbela A Vieira, João CR Cardoso, Deborah M Power and Lloyd S Peck
    Citation: BMC Genomics 2010 11:362
  22. Differences in gene expression may be caused by nearby DNA polymorphisms (cis regulation) or by interactions of gene control regions with polymorphic transcription factors (trans regulation). Trans acting loci ar...

    Authors: Harry A Noyes, Morris Agaba, Susan Anderson, Alan L Archibald, Andy Brass, John Gibson, Laurence Hall, Helen Hulme, Sung Jong Oh and Stephen Kemp
    Citation: BMC Genomics 2010 11:361
  23. Increases during aging in extracellular levels of glutamate (Glu), the major excitatory neurotransmitter in the brain, may be linked to chronic neurodegenerative diseases. Little is known about the molecular r...

    Authors: Xinkun Wang, Xiaodong Bao, Ranu Pal, Abdulbaki Agbas and Elias K Michaelis
    Citation: BMC Genomics 2010 11:360
  24. Glucocorticoids (GCs) control expression of a large number of genes via binding to the GC receptor (GR). Transcription may be regulated either by binding of the GR dimer to DNA regulatory elements or by protei...

    Authors: Raoul Frijters, Wilco Fleuren, Erik JM Toonen, Jan P Tuckermann, Holger M Reichardt, Hans van der Maaden, Andrea van Elsas, Marie-Jose van Lierop, Wim Dokter, Jacob de Vlieg and Wynand Alkema
    Citation: BMC Genomics 2010 11:359
  25. Aspergillus fumigatus (A. fumigatus) is a ubiquitous fungus which reproduces asexually by releasing abundant airborne conidia (spores), which are easily respirable. In allergic and immunocompromised individuals A...

    Authors: Pol Gomez, Tillie L Hackett, Margo M Moore, Darryl A Knight and Scott J Tebbutt
    Citation: BMC Genomics 2010 11:358
  26. The human genome displays extensive copy-number variation (CNV). Recent discoveries have shown that large segments of DNA, ranging in size from hundreds to thousands of nucleotides, are either deleted or dupli...

    Authors: Krishna R Kalari, Scott J Hebbring, High Seng Chai, Liang Li, Jean-Pierre A Kocher, Liewei Wang and Richard M Weinshilboum
    Citation: BMC Genomics 2010 11:357
  27. Different approaches have been developed to dissect the interplay between transcription factors (TFs) and their cis-acting sequences on DNA in order to identify TF target genes. Here we used a combination of c...

    Authors: Francesca Orso, Davide Corà, Benedetta Ubezio, Paolo Provero, Michele Caselle and Daniela Taverna
    Citation: BMC Genomics 2010 11:355
  28. The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying producti...

    Authors: Serena Ferraresso, Massimo Milan, Caterina Pellizzari, Nicola Vitulo, Richard Reinhardt, Adelino VM Canario, Tomaso Patarnello and Luca Bargelloni
    Citation: BMC Genomics 2010 11:354
  29. Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a nov...

    Authors: Ruben Pio, David Blanco, Maria Jose Pajares, Elena Aibar, Olga Durany, Teresa Ezponda, Jackeline Agorreta, Javier Gomez-Roman, Miguel Angel Anton, Angel Rubio, Maria D Lozano, Jose M López-Picazo, Francesc Subirada, Tamara Maes and Luis M Montuenga
    Citation: BMC Genomics 2010 11:352
  30. Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory elements. Compelling eviden...

    Authors: Xiaofei Wang, Samuel Nahashon, Tromondae K Feaster, Ann Bohannon-Stewart and Nathaniel Adefope
    Citation: BMC Genomics 2010 11:351
  31. The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studi...

    Authors: Ranjit Kumar, Pratik Shah, Edwin Swiatlo, Shane C Burgess, Mark L Lawrence and Bindu Nanduri
    Citation: BMC Genomics 2010 11:350
  32. Normalization of microarrays is a standard practice to account for and minimize effects which are not due to the controlled factors in an experiment. There is an overwhelming number of different methods that c...

    Authors: Ramona Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel-Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich and Karsten Quast
    Citation: BMC Genomics 2010 11:349
  33. The importance of in silico predictions for understanding cellular processes is now widely accepted, and a variety of algorithms useful for studying different biological features have been designed. In particular...

    Authors: Christian Hödar, Rodrigo Assar, Marcela Colombres, Andrés Aravena, Leonardo Pavez, Mauricio González, Servet Martínez, Nibaldo C Inestrosa and Alejandro Maass
    Citation: BMC Genomics 2010 11:348
  34. Drosophila females commit tremendous resources to egg production and males produce some of the longest sperm in the animal kingdom. We know little about the coordinated regulation of gene expression patterns in d...

    Authors: Michael J Parisi, Vaijayanti Gupta, David Sturgill, James T Warren, Jean-Marc Jallon, John H Malone, Yu Zhang, Lawrence I Gilbert and Brian Oliver
    Citation: BMC Genomics 2010 11:346
  35. Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disorder caused by mutations in the dystrophin gene. DMD has a complex and as yet incompletely defined molecular pathophysiology hindering developmen...

    Authors: Mohammad M Ghahramani Seno, Capucine Trollet, Takis Athanasopoulos, Ian R Graham, Pingzhao Hu and George Dickson
    Citation: BMC Genomics 2010 11:345
  36. Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for ...

    Authors: Cyril Degletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, Paul Chuchana, Pierre Jouventin, Christian Gautier and Claude Duchamp
    Citation: BMC Genomics 2010 11:344
  37. Changes in cellular phenotype result from underlying changes in mRNA transcription and translation. Endothelin-1 stimulates cardiomyocyte hypertrophy with associated changes in mRNA/protein expression and an i...

    Authors: Thomais Markou, Andrew K Marshall, Timothy E Cullingford, El L Tham, Peter H Sugden and Angela Clerk
    Citation: BMC Genomics 2010 11:343
  38. In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distrib...

    Authors: Manoj Bhasin, Lei Yuan, Derin B Keskin, Hasan H Otu, Towia A Libermann and Peter Oettgen
    Citation: BMC Genomics 2010 11:342
  39. There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight...

    Authors: Heather A Amthauer and Costas Tsatsoulis
    Citation: BMC Genomics 2010 11:340
  40. Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high intra-specific genetic variation, morphologic diversity an...

    Authors: Víctor M González, Jordi Garcia-Mas, Pere Arús and Pere Puigdomènech
    Citation: BMC Genomics 2010 11:339
  41. Pollen development from the microspore involves a series of coordinated cellular events, and the resulting mature pollen has a specialized function to quickly germinate, produce a polar-growth pollen tube deri...

    Authors: Li Q Wei, Wen Y Xu, Zhu Y Deng, Zhen Su, Yongbiao Xue and Tai Wang
    Citation: BMC Genomics 2010 11:338
  42. Osteopetrosis is a skeletal disorder of humans and animals characterized by the formation of overly dense bones, resulting from a deficiency in the number and/or function of bone-resorbing osteoclast cells. In...

    Authors: Stacey N Meyers, Tara G McDaneld, Shannon L Swist, Brandy M Marron, David J Steffen, Donal O'Toole, Jeffrey R O'Connell, Jonathan E Beever, Tad S Sonstegard and Timothy PL Smith
    Citation: BMC Genomics 2010 11:337

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