Skip to main content

Articles

Page 194 of 251

  1. BioProspecting is a novel approach that enabled our team to mine data related to genetic markers from the New England Journal of Medicine (NEJM) utilizing SNOMED CT and the Human Gene Onotology (HUGO). The Bio...

    Authors: Peter L Elkin, Mark S Tuttle, Brett E Trusko and Steven H Brown
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  2. This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facil...

    Authors: Isaac Kunz, Ming-Chin Lin and Lewis Frey
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  3. Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Cl...

    Authors: Parsa Mirhaji, Min Zhu, Mattew Vagnoni, Elmer V Bernstam, Jiajie Zhang and Jack W Smith
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  4. The volume of publicly available genomic scale data is increasing. Genomic datasets in public repositories are annotated with free-text fields describing the pathological state of the studied sample. These ann...

    Authors: Nigam H Shah, Clement Jonquet, Annie P Chiang, Atul J Butte, Rong Chen and Mark A Musen
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  5. The volume of data available on genetic variations has increased considerably with the recent development of high-density, single-nucleotide polymorphism (SNP) arrays. Several software programs have been devel...

    Authors: Sergio Barlati, Sergio Chiesa and Chiara Magri
    Citation: BMC Bioinformatics 2009 10:49
    Content type: Software Published on:

  6. Since the inception of the GO annotation project, a variety of tools have been developed that support exploring and searching the GO database. In particular, a variety of tools that perform GO enrichment analy...

    Authors: Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson and Zohar Yakhini
    Citation: BMC Bioinformatics 2009 10:48
    Content type: Software Published on:

  7. Analysis of microarray and other high-throughput data on the basis of gene sets, rather than individual genes, is becoming more important in genomic studies. Correspondingly, a large number of statistical appr...

    Authors: Marit Ackermann and Korbinian Strimmer
    Citation: BMC Bioinformatics 2009 10:47
    Content type: Methodology article Published on:

  11. Many studies have provided algorithms or methods to assess a statistical significance in quantitative proteomics when multiple replicates for a protein sample and a LC/MS analysis are available. But, confidenc...

    Authors: Qingbo Li and Bryan AP Roxas
    Citation: BMC Bioinformatics 2009 10:43
    Content type: Methodology article Published on:

  12. Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expressio...

    Authors: Vlad Popovici, Darlene R Goldstein, Janine Antonov, Rolf Jaggi, Mauro Delorenzi and Pratyaksha Wirapati
    Citation: BMC Bioinformatics 2009 10:42
    Content type: Methodology article Published on:

  13. In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very...

    Authors: Quan Long, Qingrun Zhang and Jurg Ott
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S75
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  14. Identifying the genetic components of common diseases has long been an important area of research. Recently, genotyping technology has reached the level where it is cost effective to genotype single nucleotide...

    Authors: Søren Besenbacher, Christian NS Pedersen and Thomas Mailund
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S74
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  15. Gene copy number and gene expression values play important roles in cancer initiation and progression. Both can be measured with high-throughput microarrays and some methodologies to integrate and analyze thes...

    Authors: Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi and Jaakko Astola
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S70
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  16. Genome-wide association studies prove to be a powerful approach to identify the genetic basis of different human diseases. We studied the relationship between seven diseases characterized in a previous genome-...

    Authors: Wenhui Huang, Pengyuan Wang, Zhen Liu and Liqing Zhang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S68
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  17. Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy. Some gene deletion studies on in silico organism models at genome-scale have been made, but most of them w...

    Authors: Zixiang Xu, Xiao Sun and Shihai Yu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S62
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  18. Protein-Protein Interactions (PPIs) play important roles in many biological functions. Protein domains, which are defined as independently folding structural blocks of proteins, physically interact with each o...

    Authors: Kelvin X Zhang and BF Francis Ouellette
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S60
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  19. Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotyp...

    Authors: Yanping Xi, Yi-Ping Phoebe Chen, Ming Cao, Weirong Wang and Fei Wang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S58
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  20. Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative inte...

    Authors: Jisu Kim, De-Shuang Huang and Kyungsook Han
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S57
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  21. Genes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc....

    Authors: Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong and Yixue Li
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S56
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  22. The gene shaving algorithm and many other clustering algorithms identify gene clusters showing high variation across samples. However, gene expression in many signaling pathways show only modest and concordant...

    Authors: Dongxiao Zhu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S54
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  23. The Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway is one of the most important targets for myeloproliferative disorder (MPD). Although several efforts toward modeling the pat...

    Authors: Hong-Hee Won, Inho Park, Eunjung Lee, Jong-Won Kim and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S53
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  24. Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each ...

    Authors: Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori and Jun Sese
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S52
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  25. Spectra resulting from Surface-Enhanced Laser Desorption/Ionisation (SELDI) mass spectrometry measurements are constructed by combining sub-spectra, each of which are the result of a single firing of the laser...

    Authors: Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Lodewyk FA Wessels and Marcel JT Reinders
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S51
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  26. Peptide identification via tandem mass spectrometry is the basic task of current proteomics research. Due to the complexity of mass spectra, the majority of mass spectra cannot be interpreted at present. The e...

    Authors: Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian and Si-Min He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S50
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  27. SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Underst...

    Authors: Krongsakda Phakthanakanok, Khanok Ratanakhanokchai, Khin Lay Kyu, Pornthep Sompornpisut, Aaron Watts and Surapong Pinitglang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S48
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  28. Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midn...

    Authors: Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang and Leonidas N Carayannopoulos
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S46
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  29. The studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism. The folding/unfolding behaviors of proteins which have similar topolog...

    Authors: Liling Zhao, Jihua Wang, Xianghua Dou and Zanxia Cao
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S44
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  30. Intrinsically unstructured or disordered proteins are common and functionally important. Prediction of disordered regions in proteins can provide useful information for understanding protein function and for h...

    Authors: Pengfei Han, Xiuzhen Zhang and Zhi-Ping Feng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S42
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  31. Microsatellites (MSs) are DNA markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput...

    Authors: Lars Kraemer, Bánk Beszteri, Steffi Gäbler-Schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann and Stephan Frickenhaus
    Citation: BMC Bioinformatics 2009 10:41
    Content type: Software Published on:

  32. Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6...

    Authors: Weitao Sun and Jing He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S40
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  33. RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, an...

    Authors: Unyanee Poolsap, Yuki Kato and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S38
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  34. Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using til...

    Authors: Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen and Tao Jiang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S36
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  35. RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNA...

    Authors: Chi Yu Chan, C Steven Carmack, Dang D Long, Anil Maliyekkel, Yu Shao, Igor B Roninson and Ye Ding
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S33
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  36. MicroRNA (miRNA) target prediction is an important component in understanding gene regulation. One approach is computational: searching nucleotide sequences for miRNA complementary base pairing. An alternative...

    Authors: Brian J Parker and Jiayu Wen
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S32
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  37. Clustering analysis is a common statistical tool for knowledge discovery. It is mainly conducted when a project still is in the exploratory phase without any priori hypotheses. However, the statistical signifi...

    Authors: Wensheng Zhang, Hong-Bin Fang and Jiuzhou Song
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S26
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  38. Different microarray data sets can be collected for studying the same or similar diseases. We expect to achieve a more efficient analysis of differential expression if an efficient statistical method can be de...

    Authors: Yinglei Lai, Sarah E Eckenrode and Jin-Xiong She
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S23
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  39. The importance of network-based approach to identifying biological markers for diagnostic classification and prognostic assessment in the context of microarray data has been increasingly recognized. To our kno...

    Authors: Yanni Zhu, Xiaotong Shen and Wei Pan
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  40. Microarray gene expression profiling has provided extensive datasets that can describe characteristics of cancer patients. An important challenge for this type of data is the discovery of gene sets which can b...

    Authors: Md Rafiul Hassan, M Maruf Hossain, James Bailey, Geoff Macintyre, Joshua WK Ho and Kotagiri Ramamohanarao
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  41. The emerging next-generation sequencing method based on PCR technology boosts genome sequencing speed considerably, the expense is also get decreased. It has been utilized to address a broad range of bioinform...

    Authors: Wendi Wang, Peiheng Zhang and Xinchun Liu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  42. DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DN...

    Authors: Francis YL Chin, Henry CM Leung, Wei-Lin Li and Siu-Ming Yiu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  44. Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as ...

    Authors: Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch and Stephan C Schuster
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  45. A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstr...

    Authors: Feng Yue, Jian Shi and Jijun Tang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  46. Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While mod...

    Authors: Krister M Swenson and Bernard ME Moret
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  47. With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite...

    Authors: Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty and Dong Xu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  48. Generating sequence alignments from superimposed structures is an important part of many structure comparison programs. The accuracy of the alignment affects structure recognition, classification and possibly ...

    Authors: Chin-Hsien Tai, James J Vincent, Changhoon Kim and Byungkook Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  49. Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living...

    Authors: GX Yu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 2.9
    5-year Journal Impact Factor: 3.6
    Source Normalized Impact per Paper (SNIP): 0.821
    SCImago Journal Rank (SJR): 1.005

    Speed 2023
    Submission to first editorial decision (median days): 12
    Submission to acceptance (median days): 146

    Usage 2023
    Downloads: 5,987,678
    Altmetric mentions: 4,858

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us