Skip to main content

Articles

Page 195 of 248

  2. The customary medicinal plant knowledge possessed by the Australian Aboriginal people is a significant resource. Published information on it is scattered throughout the literature, in heterogeneous data format...

    Authors: Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen and Shoba Ranganathan
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S25
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  3. Initiation and regulation of immune responses in humans involves recognition of peptides presented by human leukocyte antigen class II (HLA-II) molecules. These peptides (HLA-II T-cell epitopes) are increasing...

    Authors: Hong Huang Lin, Guang Lan Zhang, Songsak Tongchusak, Ellis L Reinherz and Vladimir Brusic
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S22
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  4. In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functi...

    Authors: Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, Yixue Li and Zhiwei Cao
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  5. Semantic role labeling (SRL) is an important text analysis technique. In SRL, sentences are represented by one or more predicate-argument structures (PAS). Each PAS is composed of a predicate (verb) and severa...

    Authors: Richard Tzong-Han Tsai, Hong-Jie Dai, Chi-Hsin Huang and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  6. A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differ...

    Authors: Wu Hsiung Wu, Feng Sheng Wang and Maw Shang Chang
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  7. The import of most intraperoxisomal proteins is mediated by peroxisome targeting signals at their C-termini (PTS1) or N-terminal regions (PTS2). Both signals have been integrated in subcellular location predic...

    Authors: Yumi Mizuno, Igor V Kurochkin, Marlis Herberth, Yasushi Okazaki and Christian Schönbach
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  8. Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical...

    Authors: Khar Heng Choo and Shoba Ranganathan
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  9. Prediction of protein solvent accessibility, also called accessible surface area (ASA) prediction, is an important step for tertiary structure prediction directly from one-dimensional sequences. Traditionally,...

    Authors: Darby Tien-Hao Chang, Hsuan-Yu Huang, Yu-Tang Syu and Chih-Peng Wu
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  10. The rapid growth of protein-protein interaction (PPI) data has led to the emergence of PPI network analysis. Despite advances in high-throughput techniques, the interactomes of several model organisms are stil...

    Authors: Sheng-An Lee, Cheng-hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao and Chi-Ying F Huang
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  11. With the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Function...

    Authors: Chuan-Kun Liu, Yan-Hau Chen, Cheng-Yang Tang, Shu-Chuan Chang, Yi-Jung Lin, Ming-Fang Tsai, Yuan-Tsong Chen and Adam Yao
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  12. Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs ass...

    Authors: Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunchai Assawamakin, Ekachai Jenwitheesuk and Sissades Tongsima
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  13. Accurate identification of splice sites in DNA sequences plays a key role in the prediction of gene structure in eukaryotes. Already many computational methods have been proposed for the detection of splice si...

    Authors: AKMA Baten, SK Halgamuge and BCH Chang
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  14. Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used...

    Authors: Chung-Chin Lu, Wei-Hao Yuan and Te-Ming Chen
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  15. RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. Identification of RNA-binding ...

    Authors: Cheng-Wei Cheng, Emily Chia-Yu Su, Jenn-Kang Hwang, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  16. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules (20–24 nt), which are believed to participate in repression of gene expression. They play important roles in several biological processes (e.g. ...

    Authors: Dang Hung Tran, Kenji Satou and Tu Bao Ho
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  17. MicroRNAs (miRNAs) are a set of small non-coding RNAs serving as important negative gene regulators. In animals, miRNAs turn down protein translation by binding to the 3' UTR regions of target genes with imper...

    Authors: Yuchen Yang, Yu-Ping Wang and Kuo-Bin Li
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  18. MicroRNAs are small non-coding RNA gene products that play diversified roles from species to species. The explosive growth of microRNA researches in recent years proves the importance of microRNAs in the biolo...

    Authors: Wing-Sze Leung, Marie CM Lin, David W Cheung and SM Yiu
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  19. MicroRNAs (miRNAs) are short non-coding RNA molecules participating in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs) over the years....

    Authors: Darby Tien-Hao Chang, Chih-Ching Wang and Jian-Wei Chen
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  20. The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InC...

    Authors: Shoba Ranganathan, Wen-Lian Hsu, Ueng-Cheng Yang and Tin Wee Tan
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  21. Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specif...

    Authors: Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi and David M Gilbert
    Citation: BMC Bioinformatics 2008 9:530
    Content type: Database Published on:

  22. Mass spectrometry (MS) based label-free protein quantitation has mainly focused on analysis of ion peak heights and peptide spectral counts. Most analyses of tandem mass spectrometry (MS/MS) data begin with an...

    Authors: John C Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M Marcotte, Alan R Rodrigues, Rong Wang, Shih-Ting Huang, Erik S Ferlanti, Alexander I Saeed, Robert D Fleischmann, Scott N Peterson and Rembert Pieper
    Citation: BMC Bioinformatics 2008 9:529
    Content type: Software Published on:

  23. Millions of single nucleotide polymorphisms have been identified as a result of the human genome project and the rapid advance of high throughput genotyping technology. Genetic association studies, such as rec...

    Authors: Wei Yu, Anja Wulf, Tiebin Liu, Muin J Khoury and Marta Gwinn
    Citation: BMC Bioinformatics 2008 9:528
    Content type: Software Published on:

  24. Computational discovery of motifs in biomolecular sequences is an established field, with applications both in the discovery of functional sites in proteins and regulatory sites in DNA. In recent years there h...

    Authors: Geir Kjetil Sandve, Osman Abul and Finn Drabløs
    Citation: BMC Bioinformatics 2008 9:527
    Content type: Methodology article Published on:

  27. The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of...

    Authors: Rain Simons, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton and Joana C Silva
    Citation: BMC Bioinformatics 2008 9:524
    Content type: Software Published on:

  31. Microarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable...

    Authors: Carl R Pelz, Molly Kulesz-Martin, Grover Bagby and Rosalie C Sears
    Citation: BMC Bioinformatics 2008 9:520
    Content type: Methodology article Published on:

  32. Proteomic profiling using mass spectrometry (MS) is one of the most promising methods for the analysis of complex biological samples such as urine, serum and tissue for biomarker discovery. Such experiments ar...

    Authors: David A Cairns, David N Perkins, Anthea J Stanley, Douglas Thompson, Jennifer H Barrett, Peter J Selby and Rosamonde E Banks
    Citation: BMC Bioinformatics 2008 9:519
    Content type: Methodology article Published on:

  33. OMA is a project that aims to identify orthologs within publicly available, complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects of its kind.

    Authors: Alexander CJ Roth, Gaston H Gonnet and Christophe Dessimoz
    Citation: BMC Bioinformatics 2008 9:518
    Content type: Methodology article Published on:

  35. Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a...

    Authors: Martin Bader, Mohamed I Abouelhoda and Enno Ohlebusch
    Citation: BMC Bioinformatics 2008 9:516
    Content type: Methodology article Published on:

  36. Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS) of peptides from complex digests with theor...

    Authors: Allison Gehrke, Shaojun Sun, Lukasz Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar and Krzysztof Cios
    Citation: BMC Bioinformatics 2008 9:515
    Content type: Research article Published on:

  37. Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and fl...

    Authors: Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette and Bjoern Peters
    Citation: BMC Bioinformatics 2008 9:514
    Content type: Software Published on:

  38. The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficu...

    Authors: Shu-Yi Su, Jonathan White, David J Balding and Lachlan JM Coin
    Citation: BMC Bioinformatics 2008 9:513
    Content type: Research article Published on:

  40. The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include coun...

    Authors: Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser and Rob Knight
    Citation: BMC Bioinformatics 2008 9:511
    Content type: Research article Published on:

  41. Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate method...

    Authors: Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong and Xuan Wang
    Citation: BMC Bioinformatics 2008 9:510
    Content type: Research article Published on:

  42. The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microa...

    Authors: Thomas Naiser, Jona Kayser, Timo Mai, Wolfgang Michel and Albrecht Ott
    Citation: BMC Bioinformatics 2008 9:509
    Content type: Research article Published on:

  43. Large biological data sets, such as expression profiles, benefit from reduction of random noise. Principal component (PC) analysis has been used for this purpose, but it tends to remove small features as well ...

    Authors: Joseph W Foley and Fumiaki Katagiri
    Citation: BMC Bioinformatics 2008 9:508
    Content type: Methodology article Published on:

  44. One-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound ident...

    Authors: Jianguo Xia, Trent C Bjorndahl, Peter Tang and David S Wishart
    Citation: BMC Bioinformatics 2008 9:507
    Content type: Research article Published on:

  46. High-throughput microarrays are widely used to study gene expression across tissues and developmental stages. Analysis of gene expression data is challenging in these experiments due to the presence of signifi...

    Authors: Terri T Ni, William J Lemon, Yu Shyr and Tao P Zhong
    Citation: BMC Bioinformatics 2008 9:505
    Content type: Methodology article Published on:

  47. Liquid chromatography coupled to mass spectrometry (LC/MS) is an important analytical technology for e.g. metabolomics experiments. Determining the boundaries, centres and intensities of the two-dimensional si...

    Authors: Ralf Tautenhahn, Christoph Böttcher and Steffen Neumann
    Citation: BMC Bioinformatics 2008 9:504
    Content type: Research article Published on:

  49. There is accumulating evidence that the milieu of repeat elements and other non-genic sequence features at a given chromosomal locus, here defined as the genome environment, can play an important role in regul...

    Authors: Derek Huntley, Y Amy Tang, Tatyana B Nesterova, Sarah Butcher and Neil Brockdorff
    Citation: BMC Bioinformatics 2008 9:501
    Content type: Software Published on:

  50. The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at th...

    Authors: Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit and Meriem El Karoui
    Citation: BMC Bioinformatics 2008 9:498
    Content type: Database Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

    2023 Usage
    5,987,678 downloads
    4,858 Altmetric mentions 

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us