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  1. Mucins are large glycoproteins implicated in protection of all mucosal surfaces. In humans and rodents, the mucin gene family has been well described and previous studies have investigated the distribution and...

    Authors: Prisca R Hoorens, Manuela Rinaldi, Robert W Li, Bruno Goddeeris, Edwin Claerebout, Jozef Vercruysse and Peter Geldhof
    Citation: BMC Genomics 2011 12:140
  2. Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordi...

    Authors: Todd A Minning, D Brent Weatherly, Stephane Flibotte and Rick L Tarleton
    Citation: BMC Genomics 2011 12:139
  3. MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an imp...

    Authors: Vivek Jayaswal, Mark Lutherborrow, David DF Ma and Yee H Yang
    Citation: BMC Genomics 2011 12:138
  4. Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding pr...

    Authors: Jorge AP Paiva, Elisa Prat, Sonia Vautrin, Mauro D Santos, Hélène San-Clemente, Sérgio Brommonschenkel, Paulo GS Fonseca, Dario Grattapaglia, Xiang Song, Jetty SS Ammiraju, David Kudrna, Rod A Wing, Ana T Freitas, Hélène Bergès and Jacqueline Grima-Pettenati
    Citation: BMC Genomics 2011 12:137
  5. Ticks--vectors of medical and veterinary importance--are themselves also significant pests. Tick salivary proteins are the result of adaptation to blood feeding and contain inhibitors of blood clotting, platel...

    Authors: José MC Ribeiro, Jennifer M Anderson, Nicholas C Manoukis, Zhaojing Meng and Ivo MB Francischetti
    Citation: BMC Genomics 2011 12:136
  6. Surface proteins are a key to a deeper understanding of the behaviour of Gram-positive bacteria interacting with the human gastro-intestinal tract. Such proteins contribute to cell wall synthesis and maintenan...

    Authors: Liv Anette Bøhle, Tahira Riaz, Wolfgang Egge-Jacobsen, Morten Skaugen, Øyvind L Busk, Vincent GH Eijsink and Geir Mathiesen
    Citation: BMC Genomics 2011 12:135
  7. Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription fac...

    Authors: Joshua WK Ho, Eric Bishop, Peter V Karchenko, Nicolas Nègre, Kevin P White and Peter J Park
    Citation: BMC Genomics 2011 12:134
  8. In recent years, planaria have emerged as an important model system for research into stem cells and regeneration. Attention is focused on their unique stem cells, the neoblasts, which can differentiate into a...

    Authors: Enrique Fernández-Taboada, Gustavo Rodríguez-Esteban, Emili Saló and Josep F Abril
    Citation: BMC Genomics 2011 12:133
  9. Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been descr...

    Authors: Goran Bozinovic, Tim L Sit, David E Hinton and Marjorie F Oleksiak
    Citation: BMC Genomics 2011 12:132
  10. Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little genomic inform...

    Authors: Cheng-Ying Shi, Hua Yang, Chao-Ling Wei, Oliver Yu, Zheng-Zhu Zhang, Chang-Jun Jiang, Jun Sun, Ye-Yun Li, Qi Chen, Tao Xia and Xiao-Chun Wan
    Citation: BMC Genomics 2011 12:131
  11. Bovine mastitis is one of the most costly and prevalent diseases affecting dairy cows worldwide. In order to develop new strategies to prevent Escherichia coli-induced mastitis, a detailed understanding of the mo...

    Authors: Bart Buitenhuis, Christine M Røntved, Stefan M Edwards, Klaus L Ingvartsen and Peter Sørensen
    Citation: BMC Genomics 2011 12:130
  12. MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced g...

    Authors: Andreas W Schreiber, Bu-Jun Shi, Chun-Yuan Huang, Peter Langridge and Ute Baumann
    Citation: BMC Genomics 2011 12:129
  13. Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human ...

    Authors: Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard and Curt P Van Tassell
    Citation: BMC Genomics 2011 12:127
  14. Iron acquisition systems are important virulence factors in pathogenic bacteria. To identify these systems in Acinetobacter baumannii, the transcriptomic response of the completely sequenced strain ATCC 17978 und...

    Authors: Bart A Eijkelkamp, Karl A Hassan, Ian T Paulsen and Melissa H Brown
    Citation: BMC Genomics 2011 12:126
  15. Evolutionary divergence in the position of the translational start site among orthologous genes can have significant functional impacts. Divergence can alter the translation rate, degradation rate, subcellular...

    Authors: John Dunbar, Judith D Cohn and Michael E Wall
    Citation: BMC Genomics 2011 12:125
  16. We have previously demonstrated that alcohol exposure at early neurulation induces growth retardation, neural tube abnormalities, and alteration of DNA methylation. To explore the global gene expression change...

    Authors: Feng C Zhou, Qianqian Zhao, Yunlong Liu, Charles R Goodlett, Tiebing Liang, Jeanette N McClintick, Howard J Edenberg and Lang Li
    Citation: BMC Genomics 2011 12:124
  17. Mucosal infections elicit inflammatory responses via regulated signaling pathways. Infection outcome depends strongly on early events occurring immediately when bacteria start interacting with cells in the muc...

    Authors: Jorrit Boekel, Örjan Källskog, Monica Rydén-Aulin, Mikael Rhen and Agneta Richter-Dahlfors
    Citation: BMC Genomics 2011 12:123
  18. Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by inf...

    Authors: Sara Sestili, Annalisa Polverari, Laura Luongo, Alberto Ferrarini, Michele Scotton, Jamshaid Hussain, Massimo Delledonne, Nadia Ficcadenti and Alessandra Belisario
    Citation: BMC Genomics 2011 12:122
  19. Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene ...

    Authors: Luca Lenzi, Federica Facchin, Francesco Piva, Matteo Giulietti, Maria Chiara Pelleri, Flavia Frabetti, Lorenza Vitale, Raffaella Casadei, Silvia Canaider, Stefania Bortoluzzi, Alessandro Coppe, Gian Antonio Danieli, Giovanni Principato, Sergio Ferrari and Pierluigi Strippoli
    Citation: BMC Genomics 2011 12:121
  20. Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal comme...

    Authors: Nicholas J Croucher, Georgios S Vernikos, Julian Parkhill and Stephen D Bentley
    Citation: BMC Genomics 2011 12:120
  21. Many parasites use multicopy protein families to avoid their host's immune system through a strategy called antigenic variation. RIFIN and STEVOR proteins are variable surface antigens uniquely found in the ma...

    Authors: Nicolas Joannin, Yvonne Kallberg, Mats Wahlgren and Bengt Persson
    Citation: BMC Genomics 2011 12:119
  22. Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the lo...

    Authors: Rashmi Gaur, Niroj K Sethy, Shalu Choudhary, Bhumika Shokeen, Varsha Gupta and Sabhyata Bhatia
    Citation: BMC Genomics 2011 12:117
  23. Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenge...

    Authors: Upeka Samarakoon, Allison Regier, Asako Tan, Brian A Desany, Brendan Collins, John C Tan, Scott J Emrich and Michael T Ferdig
    Citation: BMC Genomics 2011 12:116
  24. Current methods of measuring transcription in high-throughput have led to significant improvements in our knowledge of transcriptional regulation and Systems Biology. However, endpoint measurements obtained fr...

    Authors: Saravanan Rajan, Haig Djambazian, Huan Chu Pham Dang, Rob Sladek and Thomas J Hudson
    Citation: BMC Genomics 2011 12:115
  25. The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagio...

    Authors: Francois Thiaucourt, Lucia Manso-Silvan, Woubit Salah, Valérie Barbe, Benoit Vacherie, Daniel Jacob, Marc Breton, Virginie Dupuy, Anne Marie Lomenech, Alain Blanchard and Pascal Sirand-Pugnet
    Citation: BMC Genomics 2011 12:114
  26. DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid...

    Authors: Daniel Baron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péréon, Reiner Veitia, Frédérique Savagner, Gérard Ramstein and Rémi Houlgatte
    Citation: BMC Genomics 2011 12:113
  27. The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related...

    Authors: Vonick Sibut, Christelle Hennequet-Antier, Elisabeth Le Bihan-Duval, Sylvain Marthey, Michel J Duclos and Cécile Berri
    Citation: BMC Genomics 2011 12:112
  28. The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation...

    Authors: Xiaojie Sun, Shuqi Mei, Hu Tao, Guodong Wang, Lina Su, Siwen Jiang, Changyan Deng, Yuanzhu Xiong and Fenge Li
    Citation: BMC Genomics 2011 12:111
  29. C57BL/6J mice possess a single intelectin (Itln) gene on chromosome 1. The function of intelectins is not well understood, but roles have been postulated in insulin sensitivity, bacterial recognition, intestinal ...

    Authors: Zen H Lu, Alex di Domenico, Steven H Wright, Pamela A Knight, C Bruce A Whitelaw and Alan D Pemberton
    Citation: BMC Genomics 2011 12:110
  30. Chlamydiae are obligate intracellular bacteria that multiply in a vacuolar compartment, the inclusion. Several chlamydial proteins containing a bilobal hydrophobic domain are translocated by a type III secretion ...

    Authors: Pierre Dehoux, Rhonda Flores, Catherine Dauga, Guangming Zhong and Agathe Subtil
    Citation: BMC Genomics 2011 12:109
  31. Several tools are available to identify miRNAs from deep-sequencing data, however, only a few of them, like miRDeep, can identify novel miRNAs and are also available as a standalone application. Given the diff...

    Authors: Vivek Thakur, Samart Wanchana, Mercedes Xu, Richard Bruskiewich, William Paul Quick, Axel Mosig and Xin-Guang Zhu
    Citation: BMC Genomics 2011 12:108
  32. Mannoproteins construct the outer cover of the fungal cell wall. The covalently linked cell wall protein Ccw12p is an abundant mannoprotein. It is considered as crucial structural cell wall component since in ...

    Authors: Enrico Ragni, Heidi Piberger, Christine Neupert, Jesús García-Cantalejo, Laura Popolo, Javier Arroyo, Markus Aebi and Sabine Strahl
    Citation: BMC Genomics 2011 12:107
  33. Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The reso...

    Authors: Phuong Nguyen, Jing Ma, Deqing Pei, Caroline Obert, Cheng Cheng and Terrence L Geiger
    Citation: BMC Genomics 2011 12:106
  34. The horn fly, Haematobia irritans (Linnaeus, 1758) (Diptera: Muscidae) is one of the most important ectoparasites of pastured cattle. Horn flies infestations reduce cattle weight gain and milk production. Additio...

    Authors: Lorena Torres, Consuelo Almazán, Nieves Ayllón, Ruth C Galindo, Rodrigo Rosario-Cruz, Héctor Quiroz-Romero and José de la Fuente
    Citation: BMC Genomics 2011 12:105
  35. Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat ...

    Authors: José Blanca, Joaquín Cañizares, Cristina Roig, Pello Ziarsolo, Fernando Nuez and Belén Picó
    Citation: BMC Genomics 2011 12:104
  36. Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations ...

    Authors: Ryouka Kawahara-Miki, Kaoru Tsuda, Yuh Shiwa, Yuko Arai-Kichise, Takashi Matsumoto, Yu Kanesaki, Sen-ichi Oda, Shizufumi Ebihara, Shunsuke Yajima, Hirofumi Yoshikawa and Tomohiro Kono
    Citation: BMC Genomics 2011 12:103
  37. In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but al...

    Authors: Alexei A Sharov, Akira Nishiyama, Yulan Piao, Lina S Correa-Cerro, Tomokazu Amano, Marshall Thomas, Samir Mehta and Minoru SH Ko
    Citation: BMC Genomics 2011 12:102
  38. The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing map...

    Authors: Jun Wang, Derek J Lydiate, Isobel AP Parkin, Cyril Falentin, Régine Delourme, Pierre WC Carion and Graham J King
    Citation: BMC Genomics 2011 12:101
  39. Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular ...

    Authors: Satya S Narina, Ramesh Buyyarapu, Kameswara Rao Kottapalli, Alieu M Sartie, Mohamed I Ali, Asiedu Robert, Mignouna JD Hodeba, Brian L Sayre and Brian E Scheffler
    Citation: BMC Genomics 2011 12:100
  40. Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in f...

    Authors: Joshua P Der, Michael S Barker, Norman J Wickett, Claude W dePamphilis and Paul G Wolf
    Citation: BMC Genomics 2011 12:99
  41. Many human diseases and phenotypes are related to RNA expression, levels of which are influenced by a wide spectrum of genetic and exposure-related factors. In a large genome-wide study of muscle tissue expres...

    Authors: Clinton C Mason, Robert L Hanson, Vicky Ossowski, Li Bian, Leslie J Baier, Jonathan Krakoff and Clifton Bogardus
    Citation: BMC Genomics 2011 12:98
  42. Several approaches have been developed for miRNA target prediction, including methods that incorporate expression profiling. However the methods are still in need of improvements due to a high false discovery ...

    Authors: Claus H Bang-Berthelsen, Lykke Pedersen, Tina Fløyel, Peter H Hagedorn, Titus Gylvin and Flemming Pociot
    Citation: BMC Genomics 2011 12:97
  43. Divergently selected Lean and Fat mouse lines represent unique models for a polygenic form of resistance and susceptibility to obesity development. Previous research on these lines focused mainly on obesity-su...

    Authors: Matjaž Simončič, Tadeja Režen, Peter Juvan, Damjana Rozman, Gregor Fazarinc, Catherine Fievet, Bart Staels and Simon Horvat
    Citation: BMC Genomics 2011 12:96
  44. Lactation increases energy demands four- to five-fold, leading to a two- to three-fold increase in food consumption, requiring a proportional adjustment in the ability of the lactating dam to absorb nutrients ...

    Authors: Antony Athippozhy, Liping Huang, Clavia Ruth Wooton-Kee, Tianyong Zhao, Paiboon Jungsuwadee, Arnold J Stromberg and Mary Vore
    Citation: BMC Genomics 2011 12:95
  45. Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more compl...

    Authors: Hindrik HD Kerstens, Richard PMA Crooijmans, Bert W Dibbits, Addie Vereijken, Ron Okimoto and Martien AM Groenen
    Citation: BMC Genomics 2011 12:94
  46. Clostridium acetobutylicum, a gram-positive and spore-forming anaerobe, is a major strain for the fermentative production of acetone, butanol and ethanol. But a previously isolated hyper-butanol producing strain

    Authors: Shiyuan Hu, Huajun Zheng, Yang Gu, Jingbo Zhao, Weiwen Zhang, Yunliu Yang, Shengyue Wang, Guoping Zhao, Sheng Yang and Weihong Jiang
    Citation: BMC Genomics 2011 12:93
  47. Genome-wide association studies (GWAS) of common diseases have had a tremendous impact on genetic research over the last five years; the field is now moving from microarray-based technology towards next-genera...

    Authors: Benjamin Lehne, Cathryn M Lewis and Thomas Schlitt
    Citation: BMC Genomics 2011 12:92

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