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  1. As the only truly flying mammals, bats use their unique wing - consisting of four elongated digits (digits II-V) connected by membranes - to power their flight. In addition to the elongated digits II-V, the fo...

    Authors: Zhe Wang, Dong Dong, Binghua Ru, Rebecca L Young, Naijian Han, Tingting Guo and Shuyi Zhang
    Citation: BMC Genomics 2010 11:619
    Content type: Research article Published on:

  2. Although melon (Cucumis melo L.) is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,02...

    Authors: Víctor M González, Luis Rodríguez-Moreno, Emilio Centeno, Andrej Benjak, Jordi Garcia-Mas, Pere Puigdomènech and Miguel A Aranda
    Citation: BMC Genomics 2010 11:618
    Content type: Research article Published on:

  3. In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translationa...

    Authors: Conrad von Mandach and Rainer Merkl
    Citation: BMC Genomics 2010 11:617
    Content type: Research article Published on:

  4. The chicken karyotype is composed of 39 chromosome pairs, of which 9 still remain totally absent from the current genome sequence assembly, despite international efforts towards complete coverage. Some others ...

    Authors: Romain Solinhac, Sophie Leroux, Svetlana Galkina, Olympe Chazara, Katia Feve, Florence Vignoles, Mireille Morisson, Svetlana Derjusheva, Bertrand Bed'hom, Alain Vignal, Valérie Fillon and Frédérique Pitel
    Citation: BMC Genomics 2010 11:616
    Content type: Research article Published on:

  5. Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA) transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular reg...

    Authors: Tirza Doniger, Rodolfo Katz, Chaim Wachtel, Shulamit Michaeli and Ron Unger
    Citation: BMC Genomics 2010 11:615
    Content type: Research article Published on:

  6. Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression...

    Authors: Björn Reinius, Chengxi Shi, Liu Hengshuo, Kuljeet Singh Sandhu, Katarzyna J Radomska, Glenn D Rosen, Lu Lu, Klas Kullander, Robert W Williams and Elena Jazin
    Citation: BMC Genomics 2010 11:614
    Content type: Research article Published on:

  7. Microarray gene expression data are accumulating in public databases. The expression profiles contain valuable information for understanding human gene expression patterns. However, the effective use of public...

    Authors: Liangjiang Wang, Anand K Srivastava and Charles E Schwartz
    Citation: BMC Genomics 2010 11(Suppl 2):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  8. Long branch attraction (LBA) is a problem that afflicts both the parsimony and maximum likelihood phylogenetic analysis techniques. Research has shown that parsimony is particularly vulnerable to inferring the...

    Authors: Timothy O’Connor, Kenneth Sundberg, Hyrum Carroll, Mark Clement and Quinn Snell
    Citation: BMC Genomics 2010 11(Suppl 2):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  9. Starches are the main storage polysaccharides in plants and are distributed widely throughout plants including seeds, roots, tubers, leaves, stems and so on. Currently, microscopic observation is one of the mo...

    Authors: Shengwen Guo, Jinshan Tang, Youping Deng and Qun Xia
    Citation: BMC Genomics 2010 11(Suppl 2):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  10. Breast cancer is worldwide the second most common type of cancer after lung cancer. Plasma proteome profiling may have a higher chance to identify protein changes between plasma samples such as normal and brea...

    Authors: Fan Zhang and Jake Y Chen
    Citation: BMC Genomics 2010 11(Suppl 2):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  11. A large amount of functional genomic data have provided enough knowledge in predicting gene function computationally, which uses known functional annotations and relationship between unknown genes and known on...

    Authors: Yiming Chen, Zhoujun Li, Xiaofeng Wang, Jiali Feng and Xiaohua Hu
    Citation: BMC Genomics 2010 11(Suppl 2):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  12. Identification of protein complexes in large interaction networks is crucial to understand principles of cellular organization and predict protein functions, which is one of the most important issues in the po...

    Authors: Jianxin Wang, Binbin Liu, Min Li and Yi Pan
    Citation: BMC Genomics 2010 11(Suppl 2):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  13. Ultrasound imaging technology has wide applications in cattle reproduction and has been used to monitor individual follicles and determine the patterns of follicular development. However, the speckles in ultra...

    Authors: Jinshan Tang, Shengwen Guo, Qingling Sun, Youping Deng and Dongfeng Zhou
    Citation: BMC Genomics 2010 11(Suppl 2):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  14. Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to ge...

    Authors: Viktor Martyanov and Robert H Gross
    Citation: BMC Genomics 2010 11(Suppl 2):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  15. Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few research...

    Authors: Chen Zhao, Hui Liu, Jiang Li, Youping Deng and Tieliu Shi
    Citation: BMC Genomics 2010 11(Suppl 2):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  16. Modern approaches to treating genetic disorders, cancers and even epidemics rely on a detailed understanding of the underlying gene signaling network. Previous work has used time series microarray data to infe...

    Authors: David Oviatt, Mark Clement, Quinn Snell, Kenneth Sundberg, Chun Wan J Lai, Jared Allen and Randall Roper
    Citation: BMC Genomics 2010 11(Suppl 2):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  17. Protein destabilization is a common mechanism by which amino acid substitutions cause human diseases. Although several machine learning methods have been reported for predicting protein stability changes upon ...

    Authors: Shaolei Teng, Anand K Srivastava and Liangjiang Wang
    Citation: BMC Genomics 2010 11(Suppl 2):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  19. Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a s...

    Authors: Jianjun Hu and Jia Xu
    Citation: BMC Genomics 2010 11(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  20. Many essential cellular processes, such as cellular metabolism, transport, cellular metabolism and most regulatory mechanisms, rely on physical interactions between proteins. Genome-wide protein interactome ne...

    Authors: Feng Xu, Guang Li, Chen Zhao, Yuhua Li, Peng Li, Jian Cui, Youping Deng and Tieliu Shi
    Citation: BMC Genomics 2010 11(Suppl 2):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  21. Genomic islands (GIs) are clusters of alien genes in some bacterial genomes, but not be seen in the genomes of other strains within the same genus. The detection of GIs is extremely important to the medical an...

    Authors: Dongsheng Che, Cory Hockenbury, Robert Marmelstein and Khaled Rasheed
    Citation: BMC Genomics 2010 11(Suppl 2):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  22. The shell of the pearl-producing bivalve Pinctada margaritifera is composed of an organic cell-free matrix that plays a key role in the dynamic process of biologically-controlled biomineralization. In order to in...

    Authors: Caroline Joubert, David Piquemal, Benjamin Marie, Laurent Manchon, Fabien Pierrat, Isabelle Zanella-Cléon, Nathalie Cochennec-Laureau, Yannick Gueguen and Caroline Montagnani
    Citation: BMC Genomics 2010 11:613
    Content type: Research article Published on:

  23. Several Echinacea species have been used as nutraceuticals or botanical drugs for "immunostimulation", but scientific evidence supporting their therapeutic use is still controversial. In this study, a phytocompou...

    Authors: Shu-Yi Yin, Wen-Hsin Wang, Pei-Hsueh Wang, Kandan Aravindaram, Pei-Ing Hwang, Han-Ming Wu and Ning-Sun Yang
    Citation: BMC Genomics 2010 11:612
    Content type: Research article Published on:

  24. Apoptosis is regulated in an orderly fashion by a series of genes, and has a crucial role in important physiological processes such as growth development, immunological response and so on. Recently, substantia...

    Authors: Jin-Ye Zhang, Min-Hui Pan, Zhi-Ya Sun, Shu-Jing Huang, Zi-Shu Yu, Di Liu, Dan-Hong Zhao and Cheng Lu
    Citation: BMC Genomics 2010 11:611
    Content type: Research article Published on:

  25. Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for ne...

    Authors: Priscila VSZ Capriles, Ana CR Guimarães, Thomas D Otto, Antonio B Miranda, Laurent E Dardenne and Wim M Degrave
    Citation: BMC Genomics 2010 11:610
    Content type: Research article Published on:

  26. Dysregulated expression of microRNAs (miRNAs) has been previously observed in human cancer tissues and shown promise in defining tumor status. However, there is little information as to if or when expression c...

    Authors: Zhiguang Li, William S Branham, Stacey L Dial, Yexun Wang, Lei Guo, Leming Shi and Tao Chen
    Citation: BMC Genomics 2010 11:609
    Content type: Research article Published on:

  27. Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consisten...

    Authors: Shoshana Greenberger, Erez Y Levanon, Nurit Paz-Yaacov, Aviv Barzilai, Michal Safran, Sivan Osenberg, Ninette Amariglio, Gideon Rechavi and Eli Eisenberg
    Citation: BMC Genomics 2010 11:608
    Content type: Research article Published on:

  29. Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as...

    Authors: Purushothaman Natarajan, Deepa Kanagasabapathy, Gnanasekaran Gunadayalan, Jasintha Panchalingam, Noopur shree, Priyanka Annabel Sugantham, Kavita Kumari Singh and Parani Madasamy
    Citation: BMC Genomics 2010 11:606
    Content type: Research article Published on:

  30. The genus Bothrops is widespread throughout Central and South America and is the principal cause of snakebite in these regions. Transcriptomic and proteomic studies have examined the venom composition of several ...

    Authors: Kiara C Cardoso, Márcio J Da Silva, Gustavo GL Costa, Tatiana T Torres, Luiz Eduardo V Del Bem, Ramon O Vidal, Marcelo Menossi and Stephen Hyslop
    Citation: BMC Genomics 2010 11:605
    Content type: Research article Published on:

  31. Sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpota...

    Authors: Roland Schafleitner, Luz R Tincopa, Omar Palomino, Genoveva Rossel, Ronald F Robles, Rocio Alagon, Carlos Rivera, Cynthia Quispe, Luis Rojas, Jaime A Pacheco, Julio Solis, Diogenes Cerna, Ji Young Kim, Jack Hou and Reinhard Simon
    Citation: BMC Genomics 2010 11:604
    Content type: Research article Published on:

  32. Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, alt...

    Authors: Amit Bahl, Paul H Davis, Michael Behnke, Florence Dzierszinski, Manjunatha Jagalur, Feng Chen, Dhanasekaran Shanmugam, Michael W White, David Kulp and David S Roos
    Citation: BMC Genomics 2010 11:603
    Content type: Research article Published on:

  33. The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understan...

    Authors: R Scott Cornman, Michael C Schatz, J Spencer Johnston, Yan-Ping Chen, Jeff Pettis, Greg Hunt, Lanie Bourgeois, Chris Elsik, Denis Anderson, Christina M Grozinger and Jay D Evans
    Citation: BMC Genomics 2010 11:602
    Content type: Research article Published on:

  35. Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea t...

    Authors: Ludmila Tyler, Jennifer N Bragg, Jiajie Wu, Xiaohan Yang, Gerald A Tuskan and John P Vogel
    Citation: BMC Genomics 2010 11:600
    Content type: Research article Published on:

  37. Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundanc...

    Authors: Philippe Castagnone-Sereno, Etienne GJ Danchin, Emeline Deleury, Thomas Guillemaud, Thibaut Malausa and Pierre Abad
    Citation: BMC Genomics 2010 11:598
    Content type: Research article Published on:

  38. The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has...

    Authors: Ming-Long Yuan, Dan-Dan Wei, Bao-Jun Wang, Wei Dou and Jin-Jun Wang
    Citation: BMC Genomics 2010 11:597
    Content type: Research article Published on:

  39. Anabolic steroids, such as nandrolone, slow muscle atrophy, but the mechanisms responsible for this effect are largely unknown. Their effects on muscle size and gene expression depend upon time, and the cause ...

    Authors: Weiping Qin, Jiangping Pan, William A Bauman and Christopher P Cardozo
    Citation: BMC Genomics 2010 11:596
    Content type: Research article Published on:

  40. Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time ...

    Authors: Moreno Colaiacovo, Annalisa Subacchi, Paolo Bagnaresi, Antonella Lamontanara, Luigi Cattivelli and Primetta Faccioli
    Citation: BMC Genomics 2010 11:595
    Content type: Research article Published on:

  41. The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassi...

    Authors: Jinsong Xu, Xiaoju Qian, Xiaofeng Wang, Ruiyuan Li, Xiaomao Cheng, Yuan Yang, Jie Fu, Shunchang Zhang, Graham J King, Jiangsheng Wu and Kede Liu
    Citation: BMC Genomics 2010 11:594
    Content type: Research article Published on:

  42. Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to id...

    Authors: Yuliaxis Ramayo-Caldas, Anna Castelló, Romi N Pena, Estefania Alves, Anna Mercadé, Carla A Souza, Ana I Fernández, Miguel Perez-Enciso and Josep M Folch
    Citation: BMC Genomics 2010 11:593
    Content type: Research article Published on:

  43. Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellu...

    Authors: Stéphane Fenart, Yves-Placide Assoumou Ndong, Jorge Duarte, Nathalie Rivière, Jeroen Wilmer, Olivier van Wuytswinkel, Anca Lucau, Emmanuelle Cariou, Godfrey Neutelings, Laurent Gutierrez, Brigitte Chabbert, Xavier Guillot, Reynald Tavernier, Simon Hawkins and Brigitte Thomasset
    Citation: BMC Genomics 2010 11:592
    Content type: Research article Published on:

  44. The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interfere...

    Authors: Torben Friedrich, Sven Rahmann, Wilfried Weigel, Wolfgang Rabsch, Angelika Fruth, Eliora Ron, Florian Gunzer, Thomas Dandekar, Jörg Hacker, Tobias Müller and Ulrich Dobrindt
    Citation: BMC Genomics 2010 11:591
    Content type: Research article Published on:

  45. Peroxide turnover and signalling are involved in many biological phenomena relevant to human diseases. Yet, all the players and mechanisms involved in peroxide perception are not known. Elucidating very remote...

    Authors: Krzysztof Pawłowski, Anna Muszewska, Anna Lenart, Teresa Szczepińska, Adam Godzik and Marcin Grynberg
    Citation: BMC Genomics 2010 11:590
    Content type: Research article Published on:

  46. Since human brain tissue is often unavailable for transcriptional profiling studies, blood expression data is frequently used as a substitute. The underlying hypothesis in such studies is that genes expressed ...

    Authors: Chaochao Cai, Peter Langfelder, Tova F Fuller, Michael C Oldham, Rui Luo, Leonard H van den Berg, Roel A Ophoff and Steve Horvath
    Citation: BMC Genomics 2010 11:589
    Content type: Research article Published on:

  47. Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralog...

    Authors: Marit S Bratlie, Jostein Johansen, Brad T Sherman, Da Wei Huang, Richard A Lempicki and Finn Drabløs
    Citation: BMC Genomics 2010 11:588
    Content type: Research article Published on:

  48. The bacterium Pseudomonas aeruginosa is capable of three types of motilities: swimming, twitching and swarming. The latter is characterized by a fast and coordinated group movement over a semi-solid surface resul...

    Authors: Julien Tremblay and Eric Déziel
    Citation: BMC Genomics 2010 11:587
    Content type: Research article Published on:

  49. A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus s...

    Authors: India Leclercq, Nicolas Berthet, Christophe Batéjat, Claudine Rousseaux, Philip Dickinson, Iain G Old, Katherine Kong, Giulia C Kennedy, Stewart T Cole and Jean-Claude Manuguerra
    Citation: BMC Genomics 2010 11:586
    Content type: Methodology article Published on:

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BMC Genomics

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