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  1. Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this fiel...

    Authors: Álvaro Cuadros-Inostroza, Camila Caldana, Henning Redestig, Miyako Kusano, Jan Lisec, Hugo Peña-Cortés, Lothar Willmitzer and Matthew A Hannah
    Citation: BMC Bioinformatics 2009 10:428
    Content type: Software Published on:

  2. MicroRNA (miRNA), which is short non-coding RNA, plays a pivotal role in the regulation of many biological processes and affects the stability and/or translation of mRNA. Recently, machine learning algorithms ...

    Authors: Jiamin Xiao, Yizhou Li, Kelong Wang, Zhining Wen, Menglong Li, Lifang Zhang and Xuanmin Guang
    Citation: BMC Bioinformatics 2009 10:427
    Content type: Research article Published on:

  4. Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae fam...

    Authors: Jeroen J Jansen, Nicole M van Dam, Huub CJ Hoefsloot and Age K Smilde
    Citation: BMC Bioinformatics 2009 10:425
    Content type: Methodology article Published on:

  5. Genomic alterations frequently occur in many cancer patients and play important mechanistic roles in the pathogenesis of cancer. Furthermore, they can modify the expression level of genes due to altered copy n...

    Authors: Mikyung Lee and Yangseok Kim
    Citation: BMC Bioinformatics 2009 10:424
    Content type: Software Published on:

  7. Multiple gene expression signatures derived from microarray experiments have been published in the field of leukemia research. A comparison of these signatures with results from new experiments is useful for v...

    Authors: Hans-Ulrich Klein, Christian Ruckert, Alexander Kohlmann, Lars Bullinger, Christian Thiede, Torsten Haferlach and Martin Dugas
    Citation: BMC Bioinformatics 2009 10:422
    Content type: Research article Published on:

  8. Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST so...

    Authors: Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer and Thomas L Madden
    Citation: BMC Bioinformatics 2009 10:421
    Content type: Software Published on:

  9. Widespread use of high-throughput techniques such as microarrays to monitor gene expression levels has resulted in an explosive growth of data sets in public domains. Integration and exploration of these compl...

    Authors: Jun Wu, Qingchao Qiu, Lu Xie, Joseph Fullerton, Jian Yu, Yu Shyr, Alfred L George Jr and Yajun Yi
    Citation: BMC Bioinformatics 2009 10:420
    Content type: Software Published on:

  11. Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still requir...

    Authors: Haiquan Li, Vagner A Benedito, Michael K Udvardi and Patrick Xuechun Zhao
    Citation: BMC Bioinformatics 2009 10:418
    Content type: Research article Published on:

  12. A wide variety of biological data can be modeled as network structures, including experimental results (e.g. protein-protein interactions), computational predictions (e.g. functional interaction networks), or ...

    Authors: Curtis Huttenhower, Sajid O Mehmood and Olga G Troyanskaya
    Citation: BMC Bioinformatics 2009 10:417
    Content type: Software Published on:

  13. Machine learning-based methods have been proven to be powerful in developing new fold recognition tools. In our previous work [Zhang, Kochhar and Grigorov (2005) Protein Science, 14: 431-444], a machine learning-...

    Authors: Ren-Xiang Yan, Jing-Na Si, Chuan Wang and Ziding Zhang
    Citation: BMC Bioinformatics 2009 10:416
    Content type: Methodology article Published on:

  15. Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chai...

    Authors: Marcin J Mizianty and Lukasz Kurgan
    Citation: BMC Bioinformatics 2009 10:414
    Content type: Methodology article Published on:

  19. In high density arrays, the identification of relevant genes for disease classification is complicated by not only the curse of dimensionality but also the highly correlated nature of the array data. In this p...

    Authors: Amira Djebbari and Aurélie Labbe
    Citation: BMC Bioinformatics 2009 10:410
    Content type: Research article Published on:

  20. Microarray gene expression time-course experiments provide the opportunity to observe the evolution of transcriptional programs that cells use to respond to internal and external stimuli. Most commonly used me...

    Authors: Martin J Aryee, José A Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti and John Quackenbush
    Citation: BMC Bioinformatics 2009 10:409
    Content type: Research article Published on:

  21. microRNAs (miRNAs) regulate target gene expression by controlling their mRNAs post-transcriptionally. Increasing evidence demonstrates that miRNAs play important roles in various biological processes. However,...

    Authors: Bing Liu, Jiuyong Li, Anna Tsykin, Lin Liu, Arti B Gaur and Gregory J Goodall
    Citation: BMC Bioinformatics 2009 10:408
    Content type: Methodology article Published on:

  22. Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understandin...

    Authors: Vishwesh Venkatraman, Yifeng D Yang, Lee Sael and Daisuke Kihara
    Citation: BMC Bioinformatics 2009 10:407
    Content type: Research article Published on:

  25. DNA methylation plays an important role in the process of tumorigenesis. Identifying differentially methylated genes or CpG islands (CGIs) associated with genes between two tumor subtypes is thus an important ...

    Authors: Shuying Sun, Pearlly S Yan, Tim HM Huang and Shili Lin
    Citation: BMC Bioinformatics 2009 10:404
    Content type: Research article Published on:

  26. The number of corpora, collections of structured texts, has been increasing, as a result of the growing interest in the application of natural language processing methods to biological texts. Many named entity...

    Authors: Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2009 10:403
    Content type: Research article Published on:

  32. Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet ...

    Authors: Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain Torrance, Johannes Wagener, Egon L Willighagen, Christoph Steinbeck and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2009 10:397
    Content type: Software Published on:

  33. The rapid advancement of computer and information technology in recent years has resulted in the rise of e-learning technologies to enhance and complement traditional classroom teaching in many fields, includi...

    Authors: Shen Jean Lim, Asif Mohammad Khan, Mark De Silva, Kuan Siong Lim, Yongli Hu, Chay Hoon Tan and Tin Wee Tan
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  34. The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the info...

    Authors: In-Hwan Paik, Jeongheui Lim, Byung-Sun Chun, Seon-Duck Jin, Jae-Pyoung Yu, Joon-Woo Lee, Jong Bhak and Woon-Kee Paek
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  35. The current approach to screen for drug-like molecules is to sieve for molecules with biochemical properties suitable for desirable pharmacokinetics and reduced toxicity, using predominantly biophysical proper...

    Authors: Varun Khanna and Shoba Ranganathan
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  36. The genetic factors leading to hypertension have been extensively studied, and large numbers of research papers have been published on the subject. One of hypertension researchers' primary research tasks is to...

    Authors: Richard Tzong-Han Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  37. The study of protein subcellular localization (PSL) is important for elucidating protein functions involved in various cellular processes. However, determining the localization sites of a protein through wet-l...

    Authors: Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  38. To automatically process large quantities of biological literature for knowledge discovery and information curation, text mining tools are becoming essential. Abbreviation recognition is related to NER and can...

    Authors: Cheng-Ju Kuo, Maurice HT Ling, Kuan-Ting Lin and Chun-Nan Hsu
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  39. The tumor suppressor protein p53 is regulated by the ubiquitin ligase MDM2 which down-regulates p53. In tumours with overexpressed MDM2, the p53-MDM2 interaction can be interrupted by a peptide or small molecu...

    Authors: Shubhra Ghosh Dastidar, David P Lane and Chandra S Verma
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  41. High content screening techniques are increasingly used to understand the regulation and progression of cell motility. The demand of new platforms, coupled with availability of terabytes of data has challenged...

    Authors: Merlin Veronika, James Evans, Paul Matsudaira, Roy Welsch and Jagath Rajapakse
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  42. The first Korean individual diploid genome sequence data (KOREF) was publicized in December 2008.

    Authors: Woo-Yeon Kim, Sang-Yoon Kim, Tae-Hyung Kim, Sung-Min Ahn, Ha Na Byun, Deokhoon Kim, Dae-Soo Kim, Yong Seok Lee, Ho Ghang, Daeui Park, Byoung-Chul Kim, Chulhong Kim, Sunghoon Lee, Seong-Jin Kim and Jong Bhak
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  43. Amino-terminal signal peptides (SPs) are short regions that guide the targeting of secretory proteins to the correct subcellular compartments in the cell. They are cleaved off upon the passenger protein reachi...

    Authors: Khar Heng Choo, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  44. The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), ...

    Authors: Shoba Ranganathan
    Citation: BMC Bioinformatics 2009 10(Suppl 15):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 15

  47. Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an experimental context. Our aim is ...

    Authors: Yohan Kim, John Sidney, Clemencia Pinilla, Alessandro Sette and Bjoern Peters
    Citation: BMC Bioinformatics 2009 10:394
    Content type: Research article Published on:

  48. The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data ...

    Authors: Janusz Dutkowski and Jerzy Tiuryn
    Citation: BMC Bioinformatics 2009 10:393
    Content type: Research article Published on:

  49. RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring per...

    Authors: Yuki Naito, Jun Yoshimura, Shinichi Morishita and Kumiko Ui-Tei
    Citation: BMC Bioinformatics 2009 10:392
    Content type: Software Published on:

  50. ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without s...

    Authors: Chunguang Liang, Alexander Schmid, María José López-Sánchez, Andres Moya, Roy Gross, Jörg Bernhardt and Thomas Dandekar
    Citation: BMC Bioinformatics 2009 10:391
    Content type: Software Published on:

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