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  1. Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-mot...

    Authors: Yuanfang Guan, Victoria Yao, Kyle Tsui, Marinella Gebbia, Maitreya J Dunham, Corey Nislow and Olga G Troyanskaya
    Citation: BMC Genomics 2011 12:466
  2. The creation of lymphoblastoid cell lines (LCLs) through Epstein-Barr virus (EBV) transformation of B-lymphocytes can result in a valuable biomaterial for cell biology research and a renewable source of DNA. W...

    Authors: Eric R Londin, Margaret A Keller, Michael R D'Andrea, Kathleen Delgrosso, Adam Ertel, Saul Surrey and Paolo Fortina
    Citation: BMC Genomics 2011 12:464
  3. Photoperiod-sensitive genic male sterile (PGMS) rice, Nongken 58S, was discovered in 1973. It has been widely used for the production of hybrid rice, and great achievements have been made in improving rice yie...

    Authors: Wei Wang, Zhenwei Liu, Zhibin Guo, Gaoyuan Song, Qin Cheng, Daiming Jiang, Yingguo Zhu and Daichang Yang
    Citation: BMC Genomics 2011 12:462
  4. Adipogenesis is the developmental process by which mesenchymal stem cells (MSC) differentiate into pre-adipocytes and adipocytes. The aim of the study was to analyze the developmental strategies of human bone ...

    Authors: Adriane Menssen, Thomas Häupl, Michael Sittinger, Bruno Delorme, Pierre Charbord and Jochen Ringe
    Citation: BMC Genomics 2011 12:461
  5. A central aim for studying runs of homozygosity (ROHs) in genome-wide SNP data is to detect the effects of autozygosity (stretches of the two homologous chromosomes within the same individual that are identica...

    Authors: Daniel P Howrigan, Matthew A Simonson and Matthew C Keller
    Citation: BMC Genomics 2011 12:460
  6. Cardiomyopathy syndrome (CMS) is a disease associated with severe myocarditis primarily in adult farmed Atlantic salmon (Salmo salar L.), caused by a double-stranded RNA virus named piscine myocarditis virus (PMC...

    Authors: Gerrit Timmerhaus, Aleksei Krasnov, Pål Nilsen, Marta Alarcon, Sergey Afanasyev, Marit Rode, Harald Takle and Sven Martin Jørgensen
    Citation: BMC Genomics 2011 12:459
  7. Invasive species are valuable model systems for examining the evolutionary processes and molecular mechanisms associated with their specific characteristics by comparison with closely related species. Over the...

    Authors: Xiao-Wei Wang, Jun-Bo Luan, Jun-Min Li, Yun-Lin Su, Jun Xia and Shu-Sheng Liu
    Citation: BMC Genomics 2011 12:458
  8. Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across g...

    Authors: Upeka Samarakoon, Joseph M Gonzales, Jigar J Patel, Asako Tan, Lisa Checkley and Michael T Ferdig
    Citation: BMC Genomics 2011 12:457
  9. Comparative Genomic Hybridization (CGH) with DNA microarrays has many biological applications including surveys of copy number changes in tumorogenesis, species detection and identification, and functional gen...

    Authors: Luz B Gilbert, Lee Chae, Takao Kasuga and John W Taylor
    Citation: BMC Genomics 2011 12:456
  10. Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a vari...

    Authors: Luke D Gardner, David Mills, Aaron Wiegand, David Leavesley and Abigail Elizur
    Citation: BMC Genomics 2011 12:455
  11. Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes ...

    Authors: Shaogui Guo, Jingan Liu, Yi Zheng, Mingyun Huang, Haiying Zhang, Guoyi Gong, Hongju He, Yi Ren, Silin Zhong, Zhangjun Fei and Yong Xu
    Citation: BMC Genomics 2011 12:454
  12. Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution has been likened to lactation in mammals, ...

    Authors: Meagan J Gillespie, Volker R Haring, Kenneth A McColl, Paul Monaghan, John A Donald, Kevin R Nicholas, Robert J Moore and Tamsyn M Crowley
    Citation: BMC Genomics 2011 12:452
  13. Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In add...

    Authors: Wenliang Wei, Xiaoqiong Qi, Linhai Wang, Yanxin Zhang, Wei Hua, Donghua Li, Haixia Lv and Xiurong Zhang
    Citation: BMC Genomics 2011 12:451
  14. As scientists continue to pursue various 'omics-based research, there is a need for high quality data for the most fundamental 'omics of all: genomics. The bacterium Paenibacillus larvae is the causative agent of...

    Authors: Queenie WT Chan, R Scott Cornman, Inanc Birol, Nancy Y Liao, Simon K Chan, T Roderick Docking, Shaun D Jackman, Greg A Taylor, Steven JM Jones, Dirk C de Graaf, Jay D Evans and Leonard J Foster
    Citation: BMC Genomics 2011 12:450
  15. Gene expression assays have been shown to yield high quality genome-wide data from partially degraded RNA samples. However, these methods have not yet been applied to postmortem human brain tissue, despite the...

    Authors: Maggie L Chow, Hai-Ri Li, Mary E Winn, Craig April, Cynthia C Barnes, Anthony Wynshaw-Boris, Jian-Bing Fan, Xiang-Dong Fu, Eric Courchesne and Nicholas J Schork
    Citation: BMC Genomics 2011 12:449
  16. Elucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth.

    Authors: Congying Chen, Huashui Ai, Jun Ren, Wanbo Li, Pinghua Li, Ruimin Qiao, Jing Ouyang, Ming Yang, Junwu Ma and Lusheng Huang
    Citation: BMC Genomics 2011 12:448
  17. A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-...

    Authors: Yang Zhang, Xiaojun Zhang, Thomas H O'Hare, William S Payne, Jennifer J Dong, Chantel F Scheuring, Meiping Zhang, James J Huang, Mi-Kyung Lee, Mary E Delany, Hong-Bin Zhang and Jerry B Dodgson
    Citation: BMC Genomics 2011 12:447
  18. Parasitoid insects manipulate their hosts' physiology by injecting various factors into their host upon parasitization. Transcriptomic approaches provide a powerful approach to study insect host-parasitoid int...

    Authors: Kayvan Etebari, Robin W Palfreyman, David Schlipalius, Lars K Nielsen, Richard V Glatz and Sassan Asgari
    Citation: BMC Genomics 2011 12:446
  19. Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation be...

    Authors: Doug J Hinchliffe, Rickie B Turley, Marina Naoumkina, Hee Jin Kim, Yuhong Tang, Kathleen M Yeater, Ping Li and David D Fang
    Citation: BMC Genomics 2011 12:445
  20. Copy neutral loss of heterozygosity (CN-LOH) refers to a special case of LOH occurring without any resulting loss in copy number. These alterations is sometimes seen in tumors as a way to inactivate a tumor su...

    Authors: Hanna Kryh, Helena Carén, Jennie Erichsen, Rose-Marie Sjöberg, Jonas Abrahamsson, Per Kogner and Tommy Martinsson
    Citation: BMC Genomics 2011 12:443
  21. Doubly Uniparental Inheritance (DUI) is a fascinating exception to matrilinear inheritance of mitochondrial DNA (mtDNA). Species with DUI are characterized by two distinct mtDNAs that are inherited either thro...

    Authors: Marco Passamonti, Andrea Ricci, Liliana Milani and Fabrizio Ghiselli
    Citation: BMC Genomics 2011 12:442
  22. The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic

    Authors: Rathi D Thiagarajan, Nicole Cloonan, Brooke B Gardiner, Tim R Mercer, Gabriel Kolle, Ehsan Nourbakhsh, Shivangi Wani, Dave Tang, Keerthana Krishnan, Kylie M Georgas, Bree A Rumballe, Han S Chiu, Jason A Steen, John S Mattick, Melissa H Little and Sean M Grimmond
    Citation: BMC Genomics 2011 12:441
  23. Piwi-associated RNAs (piRNAs) bind transcripts from retrotransposable elements (RTE) in mouse germline cells and seemingly act as guides for genomic methylation, thereby repressing the activity of RTEs. It is ...

    Authors: Tobias Mourier
    Citation: BMC Genomics 2011 12:440
  24. To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue.

    Authors: Pei-Ing Hwang, Huan-Bin Wu, Chin-Di Wang, Bai-Ling Lin, Cheng-Tao Chen, Shinsheng Yuan, Guani Wu and Ker-Chau Li
    Citation: BMC Genomics 2011 12:439
  25. Our previously published reports have described an effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA sequence and several regulator genes share homologous sequences with those of P. aeruginosa,...

    Authors: Da-Qiang Wu, Jing Ye, Hong-Yu Ou, Xue Wei, Xianqing Huang, Ya-Wen He and Yuquan Xu
    Citation: BMC Genomics 2011 12:438
  26. The genome of Pseudomonas aeruginosa contains at least three genes encoding eukaryotic-type Ser/Thr protein kinases, one of which, ppkA, has been implicated in P. aeruginosa virulence. Together with the adjacent

    Authors: Jana Goldová, Aleš Ulrych, Kamil Hercík and Pavel Branny
    Citation: BMC Genomics 2011 12:437
  27. Segmental duplications (SDs) are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as ot...

    Authors: Giuliana Giannuzzi, Pietro D'Addabbo, Marica Gasparro, Maurizio Martinelli, Francesco N Carelli, Donato Antonacci and Mario Ventura
    Citation: BMC Genomics 2011 12:436
  28. microRNAs (miRNA) are short, endogenous transcripts that negatively regulate the expression of specific mRNA targets. miRNAs are found both in tissues and body fluids such as plasma. A major perspective for th...

    Authors: Steffen G Jensen, Philippe Lamy, Mads H Rasmussen, Marie S Ostenfeld, Lars Dyrskjøt, Torben F Ørntoft and Claus L Andersen
    Citation: BMC Genomics 2011 12:435
  29. Meiotic recombination ensures that each child inherits distinct genetic materials from each parent, but the distribution of crossovers along meiotic chromosomes remains difficult to identify. In this study, we...

    Authors: Yun-Shien Lee, Angel Chao, Chun-Houh Chen, Tina Chou, Shih-Yee Mimi Wang and Tzu-Hao Wang
    Citation: BMC Genomics 2011 12:434
  30. Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. However, determining protein-coding genes for most new genomes is almost completely performed ...

    Authors: Charles Ansong, Nikola Tolić, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith, Scott N Peterson, Fred Heffron, Michael McClelland and Joshua N Adkins
    Citation: BMC Genomics 2011 12:433
  31. Plant phenolics are important nutritional antioxidants which could aid in overcoming chronic diseases such as cardiovascular disease and cancer, two leading causes of death in the world. The oil palm (Elaeis guin...

    Authors: Soon-Sen Leow, Shamala Devi Sekaran, Kalyana Sundram, YewAi Tan and Ravigadevi Sambanthamurthi
    Citation: BMC Genomics 2011 12:432
  32. The highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to unde...

    Authors: William Hintz, Michael Pinchback, Paul de la Bastide, Steven Burgess, Volker Jacobi, Richard Hamelin, Colette Breuil and Louis Bernier
    Citation: BMC Genomics 2011 12:431
  33. The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed the...

    Authors: Timothy R Schmidt, Edgar J Scott II and David W Dyer
    Citation: BMC Genomics 2011 12:430
  34. We introduce Glaucoma Discovery Platform (GDP), an online environment for facile visualization and interrogation of complex transcription profiling datasets for glaucoma. We also report the availability of Dat...

    Authors: Gareth R Howell, David O Walton, Benjamin L King, Richard T Libby and Simon WM John
    Citation: BMC Genomics 2011 12:429
  35. In Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we anal...

    Authors: Atsuko Shinhara, Motomu Matsui, Kiriko Hiraoka, Wataru Nomura, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori and Akio Kanai
    Citation: BMC Genomics 2011 12:428
  36. There are two selenophosphate synthetases (SPSs) in higher eukaryotes, SPS1 and SPS2. Of these two isotypes, only SPS2 catalyzes selenophosphate synthesis. Although SPS1 does not contain selenophosphate synthe...

    Authors: Kwang Hee Lee, Myoung Sup Shim, Jin Young Kim, Hee Kyoung Jung, Eunji Lee, Bradley A Carlson, Xue-Ming Xu, Jin Mo Park, Dolph L Hatfield, Taesung Park and Byeong Jae Lee
    Citation: BMC Genomics 2011 12:426
  37. Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evid...

    Authors: Henk C den Bakker, Andrea I Moreno Switt, Gregory Govoni, Craig A Cummings, Matthew L Ranieri, Lovorka Degoricija, Karin Hoelzer, Lorraine D Rodriguez-Rivera, Stephanie Brown, Elena Bolchacova, Manohar R Furtado and Martin Wiedmann
    Citation: BMC Genomics 2011 12:425
  38. The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and g...

    Authors: Luis Rodríguez-Moreno, Víctor M González, Andrej Benjak, M Carmen Martí, Pere Puigdomènech, Miguel A Aranda and Jordi Garcia-Mas
    Citation: BMC Genomics 2011 12:424
  39. Phloem-feeding aphids deprive plants of assimilates, but mostly manage to avoid causing the mechanical tissue damage inflicted by chewing insects. Nevertheless, jasmonate signalling that is induced by infestat...

    Authors: Anna Kuśnierczyk, Diem HT Tran, Per Winge, Tommy S Jørstad, John C Reese, Joanna Troczyńska and Atle M Bones
    Citation: BMC Genomics 2011 12:423
  40. The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it ...

    Authors: Chenwei Wang, Janine E Deakin, Willem Rens, Kyall R Zenger, Katherine Belov, Jennifer A Marshall Graves and Frank W Nicholas
    Citation: BMC Genomics 2011 12:422
  41. The major histocompatibility complex (MHC) is a group of genes with a variety of roles in the innate and adaptive immune responses. MHC genes form a genetically linked cluster in eutherian mammals, an organiza...

    Authors: Hannah V Siddle, Janine E Deakin, Penny Coggill, Laurens G Wilming, Jennifer Harrow, Jim Kaufman, Stephan Beck and Katherine Belov
    Citation: BMC Genomics 2011 12:421
  42. The thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have mult...

    Authors: Emily SW Wong, Anthony T Papenfuss, Andreas Heger, Arthur L Hsu, Chris P Ponting, Robert D Miller, Jane C Fenelon, Marilyn B Renfree, Richard A Gibbs and Katherine Belov
    Citation: BMC Genomics 2011 12:420
  43. Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challen...

    Authors: Danielle Carpenter, Susan Walker, Natalie Prescott, Joost Schalkwijk and John AL Armour
    Citation: BMC Genomics 2011 12:418
  44. Successful achievement of early folliculogenesis is crucial for female reproductive function. The process is finely regulated by cell-cell interactions and by the coordinated expression of genes in both the oo...

    Authors: Agnes Bonnet, Claudia Bevilacqua, Francis Benne, Loys Bodin, Corinne Cotinot, Laurence Liaubet, Magali Sancristobal, Julien Sarry, Elena Terenina, Patrice Martin, Gwenola Tosser-Klopp and Beatrice Mandon-Pepin
    Citation: BMC Genomics 2011 12:417
  45. Transcription promoters are fundamental genomic cis-elements controlling gene expression. They can be classified into two types by the degree of imprecision of their transcription start sites: peak promoters, whi...

    Authors: Tadasu Nozaki, Nozomu Yachie, Ryu Ogawa, Anton Kratz, Rintaro Saito and Masaru Tomita
    Citation: BMC Genomics 2011 12:416

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