Skip to main content

Articles

Page 305 of 332

  1. A key problem in the sequence-based reconstruction of regulatory networks in bacteria is the lack of specificity in operator predictions. The problem is especially prominent in the identification of transcript...

    Authors: Christof Francke, Robert Kerkhoven, Michiel Wels and Roland J Siezen
    Citation: BMC Genomics 2008 9:145
    Content type: Research article Published on:

  2. The oomycete Plasmopara viticola (Berk. and Curt.) Berl. and de Toni causes downy mildew in grapevine (Vitis vinifera L.). This pathogen is strictly biotrophic, thus completely dependent on living host cells for ...

    Authors: Marianna Polesani, Filomena Desario, Alberto Ferrarini, Anita Zamboni, Mario Pezzotti, Andreas Kortekamp and Annalisa Polverari
    Citation: BMC Genomics 2008 9:142
    Content type: Research article Published on:

  3. The response of the trout, O. mykiss, head kidney to bacterial lipopolysaccharide (LPS) or active and attenuated infectious hematopoietic necrosis virus (IHNV and attINHV respectively) intraperitoneal challenge, ...

    Authors: Simon MacKenzie, Joan C Balasch, Beatriz Novoa, Laia Ribas, Nerea Roher, Aleksei Krasnov and Antonio Figueras
    Citation: BMC Genomics 2008 9:141
    Content type: Research article Published on:

  5. Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for spec...

    Authors: Chun Ming Wang, Loong Chueng Lo, Felicia Feng, Ping Gong, Jian Li, Ze Yuan Zhu, Grace Lin and Gen Hua Yue
    Citation: BMC Genomics 2008 9:139
    Content type: Research article Published on:

  6. Sequence closure often represents the end-point of a genome project, without a system in place for subsequent improvement and refinement. Building on the genome project of Vibrio fischeri ES114, we used a compara...

    Authors: Mark J Mandel, Eric V Stabb and Edward G Ruby
    Citation: BMC Genomics 2008 9:138
    Content type: Research article Published on:

  9. Mycobacterium avium (M. avium) subspecies vary widely in both pathogenicity and host specificity, but the genetic features contributing to this diversity remain unclear.

    Authors: Michael L Paustian, Xiaochun Zhu, Srinand Sreevatsan, Suelee Robbe-Austerman, Vivek Kapur and John P Bannantine
    Citation: BMC Genomics 2008 9:135
    Content type: Research article Published on:

  10. Identifying consistent changes in cellular function that occur in multiple types of cancer could revolutionize the way cancer is treated. Previous work has produced promising results such as the identification...

    Authors: Leszek A Rybaczyk, Meredith J Bashaw, Dorothy R Pathak and Kun Huang
    Citation: BMC Genomics 2008 9:134
    Content type: Research article Published on:

  12. Simple sequence repeats (SSRs) of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in th...

    Authors: Jyoti Srivastava, Sanjay Premi, Sudhir Kumar and Sher Ali
    Citation: BMC Genomics 2008 9:132
    Content type: Research article Published on:

  13. Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular met...

    Authors: Feng Yue, Liying Cui, Claude W dePamphilis, Bernard ME Moret and Jijun Tang
    Citation: BMC Genomics 2008 9(Suppl 1):S25
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  15. The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical analysis that a number of antig...

    Authors: Jack Y Yang, Mary Qu Yang, Zuojie Luo, Yan Ma, Jianling Li, Youping Deng and Xudong Huang
    Citation: BMC Genomics 2008 9(Suppl 1):S23
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  16. Temperature and salt concentration are very helpful experimental conditions for a probe to hybridize uniquely to its intended target. In large families of closely related target sequences, the high degree of s...

    Authors: Ping Deng, My T Thai, Qingkai Ma and Weili Wu
    Citation: BMC Genomics 2008 9(Suppl 1):S22
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  19. This is a first report, using our MotifModeler informatics program, to simultaneously identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray data. Based on the assum...

    Authors: Guohua Wang, Xin Wang, Yadong Wang, Jack Y Yang, Lang Li, Kenneth P Nephew, Howard J Edenberg, Feng C Zhou and Yunlong Liu
    Citation: BMC Genomics 2008 9(Suppl 1):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  20. Transcription factors (TFs) have multiple combinatorial forms to regulate the transcription of a target gene. For example, one TF can help another TF to stabilize onto regulatory DNA sequence and the other TF ...

    Authors: Chieh-Chun Chen, Xin-Guang Zhu and Sheng Zhong
    Citation: BMC Genomics 2008 9(Suppl 1):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  21. Massively parallel pyrosequencing is a high-throughput technology that can sequence hundreds of thousands of DNA/RNA fragments in a single experiment. Combining it with immunoprecipitation-based biochemical as...

    Authors: Xin Wang, Guohua Wang, Changyu Shen, Lang Li, Xinguo Wang, Sean D Mooney, Howard J Edenberg, Jeremy R Sanford and Yunlong Liu
    Citation: BMC Genomics 2008 9(Suppl 1):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  22. Occurrence of protein in the cell is an important step in understanding its function. It is highly desirable to predict a protein's subcellular locations automatically from its sequence. Most studied methods f...

    Authors: Tanwir Habib, Chaoyang Zhang, Jack Y Yang, Mary Qu Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  23. Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological ...

    Authors: Ping Gong, Xin Guan, Laura S Inouye, Youping Deng, Mehdi Pirooznia and Edward J Perkins
    Citation: BMC Genomics 2008 9(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  24. The budding yeast Saccharomyces cerevisiae is a eukaryotic organism with extensive genetic redundancy. Large-scale gene deletion analysis has shown that over 80% of the ~6200 predicted genes are nonessential and ...

    Authors: Jinghe Mao, Tanwir Habib, Ming Shenwu, Baobin Kang, Wilbur Allen, LaShonda Robertson, Jack Y Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  25. Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neur...

    Authors: Mehdi Pirooznia, Jack Y Yang, Mary Qu Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  26. The most common application of microarray technology in disease research is to identify genes differentially expressed in disease versus normal tissues. However, it is known that, in complex diseases, phenotyp...

    Authors: Min Xu, Ming-Chih J Kao, Juan Nunez-Iglesias, Joseph R Nevins, Mike West and Xianghong Jasmine Zhou
    Citation: BMC Genomics 2008 9(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  27. Iron homeostasis is a key metabolism for most organisms. In many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a Fur gene. Fur also plays roles in virulence, ac...

    Authors: Yunfeng Yang, Daniel P Harris, Feng Luo, Liyou Wu, Andrea B Parsons, Anthony V Palumbo and Jizhong Zhou
    Citation: BMC Genomics 2008 9(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  28. The technological advances in the past decade have lead to massive progress in the field of biotechnology. The documentation of the progress made exists in the form of research articles. The PubMed is the curr...

    Authors: Bhanu C Vanteru, Jahangheer S Shaik and Mohammed Yeasin
    Citation: BMC Genomics 2008 9(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  29. Many protein regions and some entire proteins have no definite tertiary structure, existing instead as dynamic, disorder ensembles under different physiochemical circumstances. Identification of these protein ...

    Authors: Joshua Hecker, Jack Y Yang and Jianlin Cheng
    Citation: BMC Genomics 2008 9(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  31. An important subfamily of membrane proteins are the transmembrane α-helical proteins, in which the membrane-spanning regions are made up of α-helices. Given the obvious biological and medical significance of t...

    Authors: Jack Y Yang, Mary Qu Yang, A Keith Dunker, Youping Deng and Xudong Huang
    Citation: BMC Genomics 2008 9(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  32. Comprehensive evaluation of common genetic variations through association of single nucleotide polymorphisms (SNPs) with complex human diseases on the genome-wide scale is an active area in human genome resear...

    Authors: Qingzhong Liu, Jack Yang, Zhongxue Chen, Mary Qu Yang, Andrew H Sung and Xudong Huang
    Citation: BMC Genomics 2008 9(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  33. The advance in high-throughput genomic technologies including microarrays has demonstrated the potential of generating a tremendous amount of gene expression data for the entire genome. Deciphering transcripti...

    Authors: Mengxia Michelle Zhu and Qishi Wu
    Citation: BMC Genomics 2008 9(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  34. Biclustering of gene expression data searches for local patterns of gene expression. A bicluster (or a two-way cluster) is defined as a set of genes whose expression profiles are mutually similar within a subs...

    Authors: Jiajun Gu and Jun S Liu
    Citation: BMC Genomics 2008 9(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  35. Since the high dimensionality of gene expression microarray data sets degrades the generalization performance of classifiers, feature selection, which selects relevant features and discards irrelevant and redu...

    Authors: Jack Y Yang, Guo-Zheng Li, Hao-Hua Meng, Mary Qu Yang and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  36. Machine learning approaches are emerging as a way to discriminate various classes of functional elements. Previous attempts to create Regulatory Potential (RP) scores to discriminate functional DNA from nonfun...

    Authors: Mary Qu Yang and Laura L Elnitski
    Citation: BMC Genomics 2008 9(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  37. Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind...

    Authors: Christopher J Oldfield, Jingwei Meng, Jack Y Yang, Mary Qu Yang, Vladimir N Uversky and A Keith Dunker
    Citation: BMC Genomics 2008 9(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  38. Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, compar...

    Authors: Jack Y Yang, Mary Qu Yang, Mengxia Michelle Zhu, Hamid R Arabnia and Youping Deng
    Citation: BMC Genomics 2008 9(Suppl 1):I1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  39. Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources wi...

    Authors: Kirstin Replogle, Arthur P Arnold, Gregory F Ball, Mark Band, Staffan Bensch, Eliot A Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M George, George Gong, Dennis Hasselquist, Alvaro G Hernandez, Ryan Kim, Harris A Lewin, Lei Liu…
    Citation: BMC Genomics 2008 9:131
    Content type: Research article Published on:

  41. The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since ...

    Authors: Marine Douaud, Katia Fève, Marie Gerus, Valérie Fillon, Suzanne Bardes, David Gourichon, Deborah A Dawson, Olivier Hanotte, Terry Burke, Florence Vignoles, Mireille Morisson, Michèle Tixier-Boichard, Alain Vignal and Frédérique Pitel
    Citation: BMC Genomics 2008 9:129
    Content type: Research article Published on:

  42. In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative studies that focus on a group of c...

    Authors: Abel D González Pérez, Evelyn González González, Vladimir Espinosa Angarica, Ana Tereza R Vasconcelos and Julio Collado-Vides
    Citation: BMC Genomics 2008 9:128
    Content type: Research article Published on:

  43. The Hedgehog (Hh) signaling pathway plays important roles in human and animal development as well as in carcinogenesis. Hh molecules have been found in both protostomes and deuterostomes, but curiously the nem...

    Authors: Thomas R Bürglin
    Citation: BMC Genomics 2008 9:127
    Content type: Research article Published on:

  44. Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proporti...

    Authors: Christiane Eichner, Petter Frost, Bjarte Dysvik, Inge Jonassen, Bjørn Kristiansen and Frank Nilsen
    Citation: BMC Genomics 2008 9:126
    Content type: Research article Published on:

  45. The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as...

    Authors: Alessandra Riva, Anne-Sophie Carpentier, Frédérique Barloy-Hubler, Angélique Chéron and Alain Hénaut
    Citation: BMC Genomics 2008 9:125
    Content type: Research article Published on:

  46. The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expresse...

    Authors: Paola Pedotti, Peter AC 't Hoen, Erno Vreugdenhil, Geert J Schenk, Rolf HAM Vossen, Yavuz Ariyurek, Mattias de Hollander, Rowan Kuiper, Gertjan JB van Ommen, Johan T den Dunnen, Judith M Boer and Renée X de Menezes
    Citation: BMC Genomics 2008 9:124
    Content type: Research article Published on:

  47. Transcriptomic approaches are relevant for studying virus-host cell dialogues to better understand the physiopathology of infection and the immune response at the cellular level. Pseudorabies virus (PrV), a po...

    Authors: Laurence Flori, Claire Rogel-Gaillard, Marielle Cochet, Gaetan Lemonnier, Karine Hugot, Patrick Chardon, Stéphane Robin and François Lefèvre
    Citation: BMC Genomics 2008 9:123
    Content type: Research article Published on:

  48. Exceptionally, a single nucleotide sequence can be translated in vivo in two different frames to yield distinct proteins. In the case of the G-protein alpha subunit XL-alpha-s transcript, a frameshifted open read...

    Authors: Sebastien Ribrioux, Adrian Brüngger, Birgit Baumgarten, Klaus Seuwen and Markus R John
    Citation: BMC Genomics 2008 9:122
    Content type: Research article Published on:

  49. Hexaploid wheat is one of the most important cereal crops for human nutrition. Molecular understanding of the biology of the developing grain will assist the improvement of yield and quality traits for differe...

    Authors: Yongfang Wan, Rebecca L Poole, Alison K Huttly, Claudia Toscano-Underwood, Kevin Feeney, Sue Welham, Mike J Gooding, Clare Mills, Keith J Edwards, Peter R Shewry and Rowan AC Mitchell
    Citation: BMC Genomics 2008 9:121
    Content type: Research article Published on:

  50. Hepcidin/LEAP-1 is an iron regulatory hormone originally identified as an antimicrobial peptide. As part of a systematic analysis of the evolution of host defense peptides in primates, we have sequenced the or...

    Authors: Ludovica Segat, Alessandra Pontillo, Michele Milanese, Alessandro Tossi and Sergio Crovella
    Citation: BMC Genomics 2008 9:120
    Content type: Research article Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • 2022 Citation Impact
    4.4 - 2-year Impact Factor
    4.7 - 5-year Impact Factor
    1.189 - SNIP (Source Normalized Impact per Paper)
    1.107 - SJR (SCImago Journal Rank)

    2023 Speed
    23 days submission to first editorial decision for all manuscripts (Median)
    137 days submission to accept (Median)

    2023 Usage
    7,167,242 downloads
    4,454 Altmetric mentions

Follow

Sign up for article alerts and news from this journal

BMC Genomics

ISSN: 1471-2164

Contact us