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1640 result(s) for 'natural language processing' within BMC Bioinformatics

Page 25 of 33

  1. Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of the...

    Authors: Feng Li, Maoyu Li, Zhiqiang Xiao, Pengfei Zhang, Jianling Li and Zhuchu Chen
    Citation: BMC Bioinformatics 2006 7:13
    Content type: Research article Published on:

  2. Graphs are mathematical structures widely used for expressing relationships among elements when representing biomedical and biological information. On top of these representations, several analyses are perform...

    Authors: Nicola Licheri, Vincenzo Bonnici, Marco Beccuti and Rosalba Giugno
    Citation: BMC Bioinformatics 2021 22:209
    Content type: Methodology article Published on:

  3. In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge...

    Authors: Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2004 5:163
    Content type: Software Published on:

  4. This report summarizes the scientific content and activities of the first edition of the Latin American Symposium organized by the Student Council of the International Society for Computational Biology (ISCB),...

    Authors: R Gonzalo Parra, Franco L Simonetti, Marcia A Hasenahuer, Gabriel J Olguin-Orellana and Avinash K Shanmugam
    Citation: BMC Bioinformatics 2015 16(Suppl 8):A1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  5. A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region bet...

    Authors: Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian and Minghua Deng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S29
    Content type: Research Published on:

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

  8. Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. Howe...

    Authors: Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao and Yunping Zhu
    Citation: BMC Bioinformatics 2017 18:452
    Content type: Database Published on:

  10. The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant ...

    Authors: Pedro Seoane, Marina Espigares, Rosario Carmona, Álvaro Polonio, Julia Quintana, Enrico Cretazzo, Josefina Bota, Alejandro Pérez-García, Juan de Dios Alché, Luis Gómez and M. Gonzalo Claros
    Citation: BMC Bioinformatics 2018 19(Suppl 14):416
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  11. As a gold-standard quantitative technique based on mass spectrometry, multiple reaction monitoring (MRM) has been widely used in proteomics and metabolomics. In the analysis of MRM data, as no peak picking alg...

    Authors: Ruimin Wang, Hengxuan Jiang, Miaoshan Lu, Junjie Tong, Shaowei An, Jinyin Wang and Changbin Yu
    Citation: BMC Bioinformatics 2024 25:60
    Content type: Software Published on:

  13. S-sulphenylation is a ubiquitous protein post-translational modification (PTM) where an S-hydroxyl (−SOH) bond is formed via the reversible oxidation on the Sulfhydryl group of cysteine (C). Recent experimenta...

    Authors: Xiaochuan Wang, Chen Li, Fuyi Li, Varun S. Sharma, Jiangning Song and Geoffrey I. Webb
    Citation: BMC Bioinformatics 2019 20:602
    Content type: Software Published on:

  14. The advent of high-throughput experimental techniques paved the way to genome-wide computational analysis and predictive annotation studies. When considering the joint annotation of a large set of related enti...

    Authors: Stefano Teso, Luca Masera, Michelangelo Diligenti and Andrea Passerini
    Citation: BMC Bioinformatics 2019 20:338
    Content type: Software Published on:

  15. The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of clinically relevant biomarkers. As...

    Authors: Mohammed Dakna, Keith Harris, Alexandros Kalousis, Sebastien Carpentier, Walter Kolch, Joost P Schanstra, Marion Haubitz, Antonia Vlahou, Harald Mischak and Mark Girolami
    Citation: BMC Bioinformatics 2010 11:594
    Content type: Research article Published on:

  16. Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distr...

    Authors: Paolo Romano, Peter Dawyndt, Francesca Piersigilli and Jean Swings
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S23
    Content type: Research article Published on:

    This article is part of a Supplement: Volume 6 Supplement 4

  17. Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping...

    Authors: Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg and Anita Brandstätter
    Citation: BMC Bioinformatics 2010 11:122
    Content type: Database Published on:

  18. With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i

    Authors: Julien Gagneur, Markus C Elze and Achim Tresch
    Citation: BMC Bioinformatics 2011 12:406
    Content type: Research article Published on:

  19. Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as therapeutic candidates is gaining relevance due to their effectivene...

    Authors: Jorge F. Beltrán, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda and Stefania Short
    Citation: BMC Bioinformatics 2024 25:148
    Content type: Software Published on:

  20. Identifying associations among biological variables is a major challenge in modern quantitative biological research, particularly given the systemic and statistical noise endemic to biological systems. Drug se...

    Authors: Petr Smirnov, Ian Smith, Zhaleh Safikhani, Wail Ba-alawi, Farnoosh Khodakarami, Eva Lin, Yihong Yu, Scott Martin, Janosch Ortmann, Tero Aittokallio, Marc Hafner and Benjamin Haibe-Kains
    Citation: BMC Bioinformatics 2022 23:188
    Content type: Research Published on:

  21. Predicting disease-associated genes is helpful for understanding the molecular mechanisms during the disease progression. Since the pathological mechanisms of neurodegenerative diseases are very complex, tradi...

    Authors: Xue Jiang, Han Zhang, Feng Duan and Xiongwen Quan
    Citation: BMC Bioinformatics 2017 18:447
    Content type: Research Article Published on:

  22. With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and th...

    Authors: Peisen Zhang, Jinghui Zhang, Huitao Sheng, James J Russo, Brian Osborne and Kenneth Buetow
    Citation: BMC Bioinformatics 2006 7:135
    Content type: Methodology article Published on:

  23. Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annota...

    Authors: Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel and Ulf Leser
    Citation: BMC Bioinformatics 2005 6:81
    Content type: Database Published on:

  25. The rapid identification of Bacillus spores and bacterial identification are paramount because of their implications in food poisoning, pathogenesis and their use as potential biowarfare agents. Many automated an...

    Authors: Elon Correa and Royston Goodacre
    Citation: BMC Bioinformatics 2011 12:33
    Content type: Methodology article Published on:

  26. An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analy...

    Authors: Ricardo ZN Vêncio, Helena Brentani, Diogo FC Patrão and Carlos AB Pereira
    Citation: BMC Bioinformatics 2004 5:119
    Content type: Methodology article Published on:

  29. The ab initio approaches to protein structure prediction usually employ the Monte Carlo technique to search the structural conformation that has the lowest energy. However, the widely-used energy functions are us...

    Authors: Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu
    Citation: BMC Bioinformatics 2019 20(Suppl 3):135
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  30. Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography ...

    Authors: Thomas L Rodgers, David Burnell, Phil D Townsend, Ehmke Pohl, Martin J Cann, Mark R Wilson and Tom CB McLeish
    Citation: BMC Bioinformatics 2013 14:183
    Content type: Software Published on:

  34. The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerate...

    Authors: Julie Hurel, Sophie Schbath, Stéphanie Bougeard, Mathieu Rolland, Mauro Petrillo and Fabrice Touzain
    Citation: BMC Bioinformatics 2020 21:284
    Content type: Methodology article Published on:

  35. ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a...

    Authors: Yomtov Almozlino, Nir Atias, Dana Silverbush and Roded Sharan
    Citation: BMC Bioinformatics 2017 18:495
    Content type: Software Published on:

  38. Gene Ontology (GO) has been widely used in biological databases, annotation projects, and computational analyses. Although the three GO categories are structured as independent ontologies, the biological relat...

    Authors: Jiajie Peng, Jin Chen and Yadong Wang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  39. Methods of weakening and attenuating pathogens’ abilities to infect and propagate in a host, thus allowing the natural immune system to more easily decimate invaders, have gained attention as alternatives to b...

    Authors: Eithon Cadag, Peter Tarczy-Hornoch and Peter J Myler
    Citation: BMC Bioinformatics 2012 13:321
    Content type: Methodology article Published on:

  40. A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins ...

    Authors: Christopher K Hobbs, Michelle Leung, Herbert H Tsang and H Alexander Ebhardt
    Citation: BMC Bioinformatics 2014 15:344
    Content type: Software Published on:

  41. Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial co...

    Authors: Theodor Sperlea, Stefan Füser, Jens Boenigk and Dominik Heider
    Citation: BMC Bioinformatics 2018 19(Suppl 15):440
    Content type: Software Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  42. Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...

    Authors: Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján, Eri Kibukawa, David R Powel, Pjotr Prins, Jacqueline Quinn…
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  44. Generally, SNPs are abundant in the genome; however, they display low power in linkage analysis because of their limited heterozygosity. Haplotype markers, on the other hand, which are composed of many SNPs, g...

    Authors: Feng Cheng, Xianglong Zhang, Yinan Zhang, Chaohua Li and Changqing Zeng
    Citation: BMC Bioinformatics 2011 12:350
    Content type: Software Published on:

  45. With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the ...

    Authors: Holger Fröhlich, Nora Speer, Annemarie Poustka and Tim Beißbarth
    Citation: BMC Bioinformatics 2007 8:166
    Content type: Software Published on:

  46. The increasing abundance of neuromorphological data provides both the opportunity and the challenge to compare massive numbers of neurons from a wide diversity of sources efficiently and effectively. We implem...

    Authors: Todd A Gillette, Parsa Hosseini and Giorgio A Ascoli
    Citation: BMC Bioinformatics 2015 16:209
    Content type: Research article Published on:

  47. Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mi...

    Authors: Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown and Josh D Neufeld
    Citation: BMC Bioinformatics 2012 13:31
    Content type: Software Published on:

  48. Consanguinity is an important risk factor for autosomal recessive (AR) disorders. Extended genomic regions identical by descent (IBD) in the offspring of consanguineous parents give rise to recessive disorders wi...

    Authors: Federico Andrea Santoni, Periklis Makrythanasis and Stylianos E. Antonarakis
    Citation: BMC Bioinformatics 2015 16:310
    Content type: Software Published on:

  50. Accurately predicting drug-target binding affinity (DTA) in silico plays an important role in drug discovery. Most of the computational methods developed for predicting DTA use machine learning models, especia...

    Authors: Shaofu Lin, Chengyu Shi and Jianhui Chen
    Citation: BMC Bioinformatics 2022 23:367
    Content type: Research Published on:

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