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  1. We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinic...

    Authors: Shaleen K Botting, Jerome P Trzeciakowski, Michelle F Benoit, Salama A Salama and Concepcion R Diaz-Arrastia
    Citation: BMC Bioinformatics 2009 10:66
  2. An algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, referred to as the Inverse Langmuir Method (ILM), estimates the binding of transcripts to complementary probes using DNA/RNA ...

    Authors: Geert CWM Mulders, Gerard T Barkema and Enrico Carlon
    Citation: BMC Bioinformatics 2009 10:64
  3. Genome-wide association studies with single nucleotide polymorphisms (SNPs) show great promise to identify genetic determinants of complex human traits. In current analyses, genotype calling and imputation of ...

    Authors: Zhaoxia Yu, Chad Garner, Argyrios Ziogas, Hoda Anton-Culver and Daniel J Schaid
    Citation: BMC Bioinformatics 2009 10:63
  4. Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that al...

    Authors: Vasyl Pihur, Susmita Datta and Somnath Datta
    Citation: BMC Bioinformatics 2009 10:62
  5. Various normalisation techniques have been developed in the context of microarray analysis to try to correct expression measurements for experimental bias and random fluctuations. Major techniques include: tot...

    Authors: Monica Chiogna, Maria Sofia Massa, Davide Risso and Chiara Romualdi
    Citation: BMC Bioinformatics 2009 10:61
  6. Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn b...

    Authors: Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, Ruedi Aebersold and Ernst Hafen
    Citation: BMC Bioinformatics 2009 10:59
  7. Development of a fast and accurate scoring function in virtual screening remains a hot issue in current computer-aided drug research. Different scoring functions focus on diverse aspects of ligand binding, and...

    Authors: Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang and Hualiang Jiang
    Citation: BMC Bioinformatics 2009 10:58
  8. Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offer...

    Authors: Naryttza N Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus and Tim W Nattkemper
    Citation: BMC Bioinformatics 2009 10:56
  9. Computational enzyme design is far from being applicable for the general case. Due to computational complexity and limited knowledge of the structure-function interplay, heuristic methods have to be used.

    Authors: André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner and Rainer Merkl
    Citation: BMC Bioinformatics 2009 10:54
  10. Information extraction from microarrays has not yet been widely used in diagnostic or prognostic decision-support systems, due to the diversity of results produced by the available techniques, their instabilit...

    Authors: Michalis Zervakis, Michalis E Blazadonakis, Georgia Tsiliki, Vasiliki Danilatou, Manolis Tsiknakis and Dimitris Kafetzopoulos
    Citation: BMC Bioinformatics 2009 10:53
  11. In the fields of life sciences, so-called designed studies are used for studying complex biological systems. The data derived from these studies comply with a study design aimed at generating relevant informat...

    Authors: Uwe Thissen, Suzan Wopereis, Sjoerd AA van den Berg, Ivana Bobeldijk, Robert Kleemann, Teake Kooistra, Ko Willems van Dijk, Ben van Ommen and Age K Smilde
    Citation: BMC Bioinformatics 2009 10:52
  12. Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phyloge...

    Authors: José C Clemente, Kazuho Ikeo, Gabriel Valiente and Takashi Gojobori
    Citation: BMC Bioinformatics 2009 10:51
  13. Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the M...

    Authors: Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler…
    Citation: BMC Bioinformatics 2009 10:50
  14. Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest ef...

    Authors: Yueyi I Liu, Paul H Wise and Atul J Butte
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S14

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

  15. Statistical interactions between disease-associated loci of complex genetic diseases suggest that genes from these regions are involved in a common mechanism impacting, or impacted by, the disease. The computa...

    Authors: Benjamin J Keller and Richard C McEachin
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S13

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

  16. In response to the frequently overwhelming output of high-throughput microarray experiments, we propose a methodology to facilitate interpretation of biological data in the context of existing knowledge. Throu...

    Authors: Hannah J Tipney, Sonia M Leach, Weiguo Feng, Richard Spritz, Trevor Williams and Lawrence Hunter
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S12

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

  17. To address the limitations of traditional virus and pathogen detection methodologies in clinical diagnosis, scientists have developed high-throughput oligonucleotide microarrays to rapidly identify infectious ...

    Authors: Yang Liu, Lee Sam, Jianrong Li and Yves A Lussier
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S11

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

  18. This paper proposes a novel framework for bioinformatics assisted biosurveillance and early warning to address the inefficiencies in traditional surveillance as well as the need for more timely and comprehensi...

    Authors: Vitali Sintchenko, Blanca Gallego, Grace Chung and Enrico Coiera
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S10

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

  19. 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

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

  20. The evolving complexity of genome-scale experiments has increasingly centralized the role of a highly computable, accurate, and comprehensive resource spanning multiple biological scales and viewpoints. To pro...

    Authors: Lee T Sam, Eneida A Mendonça, Jianrong Li, Judith Blake, Carol Friedman and Yves A Lussier
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S8

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

  21. Bayesian networks are powerful instruments to learn genetic models from association studies data. They are able to derive the existing correlation between genetic markers and phenotypic traits and, at the same...

    Authors: Alberto Malovini, Angelo Nuzzo, Fulvia Ferrazzi, Annibale A Puca and Riccardo Bellazzi
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S7

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

  22. Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes. The field is rapidly gaining importance: it promises drugs targeted to particular subpopulatio...

    Authors: Yael Garten and Russ B Altman
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S6

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

  23. Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarker...

    Authors: Jianji Yang, Aaron Cohen and William Hersh
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S5

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

  24. 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

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

  25. A critical challenge in neuroscience is organizing, managing, and accessing the explosion in neuroscientific knowledge, particularly anatomic knowledge. We believe that explicit knowledge-based approaches to m...

    Authors: Daniel L Rubin, Ion-Florin Talos, Michael Halle, Mark A Musen and Ron Kikinis
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S3

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

  26. 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

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

  27. 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

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

  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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

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

  34. 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

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

  35. 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

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

  36. 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

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

  37. 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

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

  38. 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

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

  39. 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
  40. 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

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

  41. 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

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

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